\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTags", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagType", - "in": "query", - "description": "scope of the tag (optional)", - "required": false, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Tag definitions.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagDefinition" - } - } - } - } - } - } - }, + "/api/projects/{projectId}/aligned-features/delete": { "put": { "tags": [ - "Tags" + "Features" ], - "summary": "[EXPERIMENTAL] Add tags to the project", - "description": "[EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "createTags", + "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "deleteAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to add to.", + "description": "project-space to delete from.", "required": true, "schema": { "type": "string" @@ -325,13 +266,12 @@ } ], "requestBody": { - "description": "the tag definitions to be created", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/TagDefinitionImport" + "type": "string" } } } @@ -340,124 +280,72 @@ }, "responses": { "200": { - "description": "the definitions of the tags that have been created", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagDefinition" - } - } - } - } + "description": "OK" } } } }, - "/api/projects/{projectId}/runs/tags/{runId}": { - "put": { + "/api/databases/{databaseId}": { + "get": { "tags": [ - "Runs" + "Searchable Databases" ], - "summary": "[EXPERIMENTAL] Add tags to a run in the project", - "description": "[EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToRunExperimental", + "operationId": "getDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to add to.", "required": true, "schema": { "type": "string" } }, { - "name": "runId", - "in": "path", - "description": "run to add tags to.", - "required": true, + "name": "includeStats", + "in": "query", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true } } ], - "requestBody": { - "description": "tags to add.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - }, - "required": true - }, "responses": { "200": { - "description": "the tags that have been added", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } - }, - "/api/projects/{projectId}/runs/blanksubtract/compute": { + }, "put": { "tags": [ - "Runs" + "Searchable Databases" ], - "summary": "**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter", - "description": "**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter.\n\n
This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
", - "operationId": "computeFoldChangeForBlankSubtraction", + "operationId": "updateDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to compute the fold change in.", "required": true, "schema": { "type": "string" } - }, - { - "name": "optFields", - "in": "query", - "description": "job opt fields.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/JobOptField" - }, - "default": [ - "progress" - ] - } } ], "requestBody": { - "description": "request with lists of run IDs that are sample, blank, and control runs", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SampleTypeFoldChangeRequest" + "$ref": "#/components/schemas/SearchableDatabaseParameters" } } - }, - "required": true + } }, "responses": { "200": { @@ -465,150 +353,107 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } - }, - "/api/projects/{projectId}/compounds/tags/{compoundId}": { - "put": { + }, + "post": { "tags": [ - "Compounds" + "Searchable Databases" ], - "summary": "[EXPERIMENTAL] Tags with the same name will be overwritten", - "description": "[EXPERIMENTAL] Tags with the same name will be overwritten.\n\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToCompoundExperimental", + "operationId": "createDatabase", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to add to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "compoundId", + "name": "databaseId", "in": "path", - "description": "compound (group of ion identities) to add tags to.", "required": true, "schema": { + "pattern": "^[a-zA-Z0-9-_]+$", "type": "string" } } ], "requestBody": { - "description": "tags to add.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/SearchableDatabaseParameters" } } - }, - "required": true + } }, "responses": { "200": { - "description": "the tags that have been added", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } - }, - "/api/projects/{projectId}/compounds/statistics/foldchange/compute": { - "put": { + }, + "delete": { "tags": [ - "Compound Statistics" + "Searchable Databases" ], - "summary": "[EXPERIMENTAL] Compute the fold change between two groups of runs", - "description": "[EXPERIMENTAL] Compute the fold change between two groups of runs.\n
\n The runs need to be tagged and grouped.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "computeCompoundFoldChangesExperimental", + "operationId": "removeDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to compute the fold change in.", "required": true, "schema": { "type": "string" } }, { - "name": "leftGroupName", + "name": "delete", "in": "query", - "description": "name of the left tag group.", - "required": true, + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } - }, + } + ], + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/account/subscriptions/select-active": { + "put": { + "tags": [ + "Login and Account" + ], + "summary": "Select a subscription as active subscription to be used for computations.", + "description": "Select a subscription as active subscription to be used for computations.", + "operationId": "selectSubscription", + "parameters": [ { - "name": "rightGroupName", + "name": "sid", "in": "query", - "description": "name of the right tag group.", "required": true, "schema": { "type": "string" } - }, - { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/AggregationType" - } - }, - { - "name": "quantification", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" - } - }, - { - "name": "optFields", - "in": "query", - "description": "job opt fields.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/JobOptField" - }, - "default": [ - "progress" - ] - } } ], "responses": { "200": { - "description": "OK", + "description": "Account information with updated active subscription", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "$ref": "#/components/schemas/AccountInfo" } } } @@ -616,28 +461,19 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures": { + "/api/projects/{projectId}/jobs": { "get": { "tags": [ - "Features" + "Jobs" ], - "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidates", + "summary": "Get List of all available jobs with information such as current state and progress (if available).", + "description": "Get List of all available jobs with information such as current state and progress (if available).", + "operationId": "getJobs", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" @@ -651,7 +487,7 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" + "$ref": "#/components/schemas/JobOptField" }, "default": [ "none" @@ -661,13 +497,13 @@ ], "responses": { "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", + "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" + "$ref": "#/components/schemas/Job" } } } @@ -675,177 +511,149 @@ } } }, - "put": { + "post": { "tags": [ - "Features" + "Jobs" ], - "summary": "[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.", - "description": "[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list.", - "operationId": "addDeNovoStructureCandidate", + "summary": "Start computation for given compounds and with given parameters.", + "description": "Start computation for given compounds and with given parameters.", + "operationId": "startJob", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "smiles", + "name": "optFields", "in": "query", - "description": "smiles", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "string", - "default": "none" + "type": "array", + "items": { + "$ref": "#/components/schemas/JobOptField" + }, + "default": [ + "command", + "progress" + ] } } ], + "requestBody": { + "description": "configuration of the job that will be submitted of the job to be returned", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/JobSubmission" + } + } + }, + "required": true + }, "responses": { - "200": { - "description": "StructureCandidate of this feature candidate with specified optional fields.", + "202": { + "description": "Accepted", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" - } + "$ref": "#/components/schemas/Job" } } } } } - } - }, - "/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}": { - "put": { + }, + "delete": { "tags": [ - "Features" + "Jobs" ], - "summary": "[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project", - "description": "[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToAlignedFeatureExperimental", + "summary": "* Delete ALL jobs.", + "description": "* Delete ALL jobs. Specify how to behave for running jobs.", + "operationId": "deleteJobs", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to add to.", + "description": "project-space to delete jobs from", "required": true, "schema": { "type": "string" } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "run to add tags to.", - "required": true, + "name": "cancelIfRunning", + "in": "query", + "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true + } + }, + { + "name": "awaitDeletion", + "in": "query", + "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", + "required": false, + "schema": { + "type": "boolean", + "default": true } } ], - "requestBody": { - "description": "tags to add.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - }, - "required": true - }, "responses": { - "200": { - "description": "the tags that have been added", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - } + "202": { + "description": "Accepted" } } } }, - "/api/projects/{projectId}/aligned-features/statistics/foldchange/compute": { - "put": { + "/api/projects/{projectId}/jobs/from-config": { + "post": { "tags": [ - "Feature Statistics" + "Jobs" ], - "summary": "[EXPERIMENTAL] Compute the fold change between two groups of runs", - "description": "[EXPERIMENTAL] Compute the fold change between two groups of runs.\n
\n The runs need to be tagged and grouped.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "computeAlignedFeatureFoldChangesExperimental", + "summary": "Start computation for given compounds and with parameters from a stored job-config.", + "description": "Start computation for given compounds and with parameters from a stored job-config.", + "operationId": "startJobFromConfig", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to compute the fold change in.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left tag group.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "rightGroupName", + "name": "jobConfigName", "in": "query", - "description": "name of the right tag group.", + "description": "name if the config to be used", "required": true, "schema": { "type": "string" } }, { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/AggregationType" - } - }, - { - "name": "quantification", + "name": "recompute", "in": "query", - "description": "quantification type.", + "description": "enable or disable recompute. If null the stored value will be used.", "required": false, "schema": { - "$ref": "#/components/schemas/QuantMeasure" + "type": "boolean" } }, { "name": "optFields", "in": "query", - "description": "job opt fields.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -853,45 +661,14 @@ "$ref": "#/components/schemas/JobOptField" }, "default": [ + "command", "progress" ] } } ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Job" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/delete": { - "put": { - "tags": [ - "Features" - ], - "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "deleteAlignedFeatures", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - } - ], "requestBody": { + "description": "List of alignedFeatureIds to be computed", "content": { "application/json": { "schema": { @@ -905,70 +682,74 @@ "required": true }, "responses": { - "200": { - "description": "OK" + "202": { + "description": "Accepted", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/Job" + } + } + } } } } }, - "/api/databases/{databaseId}": { - "get": { + "/api/projects/{projectId}/import/preprocessed-data-files": { + "post": { "tags": [ - "Searchable Databases" + "Projects" ], - "operationId": "getDatabase", + "summary": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", + "description": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", + "operationId": "importPreprocessedData", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "includeStats", + "name": "ignoreFormulas", "in": "query", "required": false, "schema": { "type": "boolean", - "default": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } + "default": false } - } - } - }, - "put": { - "tags": [ - "Searchable Databases" - ], - "operationId": "updateDatabase", - "parameters": [ + }, { - "name": "databaseId", - "in": "path", - "required": true, + "name": "allowMs1Only", + "in": "query", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true } } ], "requestBody": { "content": { - "application/json": { + "multipart/form-data": { "schema": { - "$ref": "#/components/schemas/SearchableDatabaseParameters" + "required": [ + "inputFiles" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + } + } } } } @@ -979,107 +760,95 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SearchableDatabase" + "$ref": "#/components/schemas/ImportResult" } } } } } - }, + } + }, + "/api/projects/{projectId}/import/preprocessed-data-files-job": { "post": { "tags": [ - "Searchable Databases" + "Projects" ], - "operationId": "createDatabase", + "summary": "Import ms/ms data from the given format into the specified project-space as background job.", + "description": "Import ms/ms data from the given format into the specified project-space as background job.\n Possible formats (ms, mgf, cef, msp)", + "operationId": "importPreprocessedDataAsJob", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", + "description": "project-space to import into.", "required": true, "schema": { - "pattern": "^[a-zA-Z0-9-_]+$", "type": "string" } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabaseParameters" - } - } - } - }, - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - }, - "delete": { - "tags": [ - "Searchable Databases" - ], - "operationId": "removeDatabase", - "parameters": [ + }, { - "name": "databaseId", - "in": "path", - "required": true, + "name": "ignoreFormulas", + "in": "query", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "delete", + "name": "allowMs1Only", "in": "query", "required": false, "schema": { "type": "boolean", - "default": false + "default": true } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/subscriptions/select-active": { - "put": { - "tags": [ - "Login and Account" - ], - "summary": "Select a subscription as active subscription to be used for computations.", - "description": "Select a subscription as active subscription to be used for computations.", - "operationId": "selectSubscription", - "parameters": [ + }, { - "name": "sid", + "name": "optFields", "in": "query", - "required": true, + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, "schema": { - "type": "string" + "type": "array", + "items": { + "$ref": "#/components/schemas/JobOptField" + }, + "default": [ + "progress" + ] } } ], + "requestBody": { + "content": { + "multipart/form-data": { + "schema": { + "required": [ + "inputFiles" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + } + } + } + } + } + }, "responses": { "200": { - "description": "Account information with updated active subscription", + "description": "the import job.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AccountInfo" + "$ref": "#/components/schemas/Job" } } } @@ -1087,68 +856,86 @@ } } }, - "/api/projects/{projectId}/jobs": { - "get": { + "/api/projects/{projectId}/import/ms-data-files": { + "post": { "tags": [ - "Jobs" + "Projects" ], - "summary": "Get List of all available jobs with information such as current state and progress (if available).", - "description": "Get List of all available jobs with information such as current state and progress (if available).", - "operationId": "getJobs", + "summary": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", + "description": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", + "operationId": "importMsRunData", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "Project-space to import into.", "required": true, "schema": { "type": "string" } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/JobOptField" + } + ], + "requestBody": { + "content": { + "multipart/form-data": { + "schema": { + "required": [ + "inputFiles", + "parameters" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + }, + "parameters": { + "$ref": "#/components/schemas/LcmsSubmissionParameters" + } + } }, - "default": [ - "none" - ] + "encoding": { + "parameters": { + "contentType": "application/json" + }, + "inputFiles": { + "contentType": "application/octet-stream" + } + } } } - ], + }, "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Job" - } + "$ref": "#/components/schemas/ImportResult" } } } } } - }, + } + }, + "/api/projects/{projectId}/import/ms-data-files-job": { "post": { "tags": [ - "Jobs" + "Projects" ], - "summary": "Start computation for given compounds and with given parameters.", - "description": "Start computation for given compounds and with given parameters.", - "operationId": "startJob", + "summary": "Import and Align full MS-Runs from various formats into the specified project as background job.", + "description": "Import and Align full MS-Runs from various formats into the specified project as background job.\n Possible formats (mzML, mzXML)", + "operationId": "importMsRunDataAsJob", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "Project-space to import into.", "required": true, "schema": { "type": "string" @@ -1157,7 +944,7 @@ { "name": "optFields", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "Set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -1165,26 +952,48 @@ "$ref": "#/components/schemas/JobOptField" }, "default": [ - "command", "progress" ] } } ], "requestBody": { - "description": "configuration of the job that will be submitted of the job to be returned", "content": { - "application/json": { + "multipart/form-data": { "schema": { - "$ref": "#/components/schemas/JobSubmission" + "required": [ + "inputFiles", + "parameters" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + }, + "parameters": { + "$ref": "#/components/schemas/LcmsSubmissionParameters" + } + } + }, + "encoding": { + "parameters": { + "contentType": "application/json" + }, + "inputFiles": { + "contentType": "application/octet-stream" + } } } - }, - "required": true + } }, "responses": { - "202": { - "description": "Accepted", + "200": { + "description": "the import job.", "content": { "application/json": { "schema": { @@ -1194,141 +1003,154 @@ } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/gui": { + "post": { "tags": [ - "Jobs" + "Gui" ], - "summary": "* Delete ALL jobs.", - "description": "* Delete ALL jobs. Specify how to behave for running jobs.", - "operationId": "deleteJobs", + "summary": "Open GUI instance on specified project-space and bring the GUI window to foreground.", + "description": "Open GUI instance on specified project-space and bring the GUI window to foreground.", + "operationId": "openGui", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete jobs from", + "description": "of project-space the GUI instance will connect to.", "required": true, "schema": { "type": "string" } - }, + } + ], + "responses": { + "201": { + "description": "Created" + } + } + }, + "delete": { + "tags": [ + "Gui" + ], + "summary": "Close GUI instance of given project-space if available.", + "description": "Close GUI instance of given project-space if available.", + "operationId": "closeGui", + "parameters": [ { - "name": "cancelIfRunning", - "in": "query", - "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", - "required": false, + "name": "projectId", + "in": "path", + "description": "if project-space the GUI instance is connected to.", + "required": true, "schema": { - "type": "boolean", - "default": true + "type": "string" } }, { - "name": "awaitDeletion", + "name": "closeProject", "in": "query", - "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", "required": false, "schema": { - "type": "boolean", - "default": true + "type": "boolean" } } ], "responses": { - "202": { - "description": "Accepted" + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "boolean" + } + } + } } } } }, - "/api/projects/{projectId}/jobs/from-config": { - "post": { + "/api/projects/{projectId}/compounds": { + "get": { "tags": [ - "Jobs" + "Compounds" ], - "summary": "Start computation for given compounds and with parameters from a stored job-config.", - "description": "Start computation for given compounds and with parameters from a stored job-config.", - "operationId": "startJobFromConfig", + "summary": "List of all available compounds (group of ion identities) in the given project-space.", + "description": "List of all available compounds (group of ion identities) in the given project-space.", + "operationId": "getCompounds", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "jobConfigName", + "name": "msDataSearchPrepared", "in": "query", - "description": "name if the config to be used", - "required": true, + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "recompute", + "name": "optFields", "in": "query", - "description": "enable or disable recompute. If null the stored value will be used.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean" + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundOptField" + }, + "default": [ + "none" + ] } }, { - "name": "optFields", + "name": "optFieldsFeatures", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/JobOptField" + "$ref": "#/components/schemas/AlignedFeatureOptField" }, "default": [ - "command", - "progress" + "none" ] } } ], - "requestBody": { - "description": "List of alignedFeatureIds to be computed", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "required": true - }, "responses": { - "202": { - "description": "Accepted", + "200": { + "description": "Compounds with additional optional fields (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/Compound" + } } } } } } - } - }, - "/api/projects/{projectId}/import/preprocessed-data-files": { + }, "post": { "tags": [ - "Projects" + "Compounds" ], - "summary": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", - "description": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", - "operationId": "importPreprocessedData", + "summary": "Import Compounds and its contained features.", + "description": "Import Compounds and its contained features. Compounds and Features must not exist in the project.\n Otherwise, they will exist twice.", + "operationId": "addCompounds", "parameters": [ { "name": "projectId", @@ -1340,53 +1162,69 @@ } }, { - "name": "ignoreFormulas", + "name": "profile", "in": "query", + "description": "profile describing the instrument used to measure the data. Used to merge spectra.", "required": false, "schema": { - "type": "boolean", - "default": false + "$ref": "#/components/schemas/InstrumentProfile" } }, { - "name": "allowMs1Only", + "name": "optFields", "in": "query", + "description": "set of optional fields to be included. Use 'none' to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": true + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundOptField" + }, + "default": [ + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", + "description": "set of optional fields of the nested features to be included. Use 'none' to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeatureOptField" + }, + "default": [ + "none" + ] } } ], "requestBody": { + "description": "the compound data to be imported", "content": { - "multipart/form-data": { + "application/json": { "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "files to import into project", - "items": { - "type": "string", - "format": "binary" - } - } + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundImport" } } } - } + }, + "required": true }, "responses": { "200": { - "description": "OK", + "description": "the Compounds that have been imported with specified optional fields", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ImportResult" + "type": "array", + "items": { + "$ref": "#/components/schemas/Compound" + } } } } @@ -1394,42 +1232,34 @@ } } }, - "/api/projects/{projectId}/import/preprocessed-data-files-job": { - "post": { + "/api/projects/{projectId}/aligned-features": { + "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Import ms/ms data from the given format into the specified project-space as background job.", - "description": "Import ms/ms data from the given format into the specified project-space as background job.\n Possible formats (ms, mgf, cef, msp)", - "operationId": "importPreprocessedDataAsJob", + "summary": "Get all available features (aligned over runs) in the given project-space.", + "description": "Get all available features (aligned over runs) in the given project-space.", + "operationId": "getAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to import into.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "ignoreFormulas", + "name": "msDataSearchPrepared", "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", "default": false } }, - { - "name": "allowMs1Only", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - }, { "name": "optFields", "in": "query", @@ -1438,191 +1268,96 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/JobOptField" + "$ref": "#/components/schemas/AlignedFeatureOptField" }, "default": [ - "progress" + "none" ] } } ], - "requestBody": { - "content": { - "multipart/form-data": { - "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "items": { - "type": "string", - "format": "binary" - } - } - } - } - } - } - }, "responses": { "200": { - "description": "the import job.", + "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeature" + } } } } } } - } - }, - "/api/projects/{projectId}/import/ms-data-files": { + }, "post": { "tags": [ - "Projects" + "Features" ], - "summary": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", - "description": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", - "operationId": "importMsRunData", + "summary": "Import (aligned) features into the project.", + "description": "Import (aligned) features into the project. Features must not exist in the project.\n Otherwise, they will exist twice.", + "operationId": "addAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "Project-space to import into.", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } - } - ], - "requestBody": { - "content": { - "multipart/form-data": { - "schema": { - "required": [ - "inputFiles", - "parameters" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "Files to import into project.", - "items": { - "type": "string", - "format": "binary" - } - }, - "parameters": { - "$ref": "#/components/schemas/LcmsSubmissionParameters" - } - } - }, - "encoding": { - "parameters": { - "contentType": "application/json" - }, - "inputFiles": { - "contentType": "application/octet-stream" - } - } - } - } - }, - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ImportResult" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/import/ms-data-files-job": { - "post": { - "tags": [ - "Projects" - ], - "summary": "Import and Align full MS-Runs from various formats into the specified project as background job.", - "description": "Import and Align full MS-Runs from various formats into the specified project as background job.\n Possible formats (mzML, mzXML)", - "operationId": "importMsRunDataAsJob", - "parameters": [ + }, { - "name": "projectId", - "in": "path", - "description": "Project-space to import into.", - "required": true, + "name": "profile", + "in": "query", + "description": "profile describing the instrument used to measure the data. Used to merge spectra.", + "required": false, "schema": { - "type": "string" + "$ref": "#/components/schemas/InstrumentProfile" } }, { "name": "optFields", "in": "query", - "description": "Set of optional fields to be included. Use 'none' only to override defaults.", + "description": "set of optional fields to be included. Use 'none' to override defaults.", "required": false, "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/JobOptField" + "$ref": "#/components/schemas/AlignedFeatureOptField" }, "default": [ - "progress" + "none" ] } } ], "requestBody": { + "description": "the feature data to be imported", "content": { - "multipart/form-data": { + "application/json": { "schema": { - "required": [ - "inputFiles", - "parameters" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "Files to import into project.", - "items": { - "type": "string", - "format": "binary" - } - }, - "parameters": { - "$ref": "#/components/schemas/LcmsSubmissionParameters" - } - } - }, - "encoding": { - "parameters": { - "contentType": "application/json" - }, - "inputFiles": { - "contentType": "application/octet-stream" + "type": "array", + "items": { + "$ref": "#/components/schemas/FeatureImport" } } } - } + }, + "required": true }, "responses": { "200": { - "description": "the import job.", + "description": "the Features that have been imported with specified optional fields", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeature" + } } } } @@ -1630,106 +1365,42 @@ } } }, - "/api/projects/{projectId}/gui": { - "post": { - "tags": [ - "Gui" - ], - "summary": "Open GUI instance on specified project-space and bring the GUI window to foreground.", - "description": "Open GUI instance on specified project-space and bring the GUI window to foreground.", - "operationId": "openGui", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "of project-space the GUI instance will connect to.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "201": { - "description": "Created" - } - } - }, - "delete": { + "/api/job-configs/{name}": { + "get": { "tags": [ - "Gui" + "Jobs" ], - "summary": "Close GUI instance of given project-space if available.", - "description": "Close GUI instance of given project-space if available.", - "operationId": "closeGui", + "summary": "Request job configuration with given name.", + "description": "Request job configuration with given name.", + "operationId": "getJobConfig", "parameters": [ { - "name": "projectId", + "name": "name", "in": "path", - "description": "if project-space the GUI instance is connected to.", + "description": "name of the job-config to return", "required": true, "schema": { "type": "string" } }, { - "name": "closeProject", + "name": "moveParametersToConfigMap", "in": "query", + "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", "required": false, "schema": { - "type": "boolean" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "boolean" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/groups/{groupName}": { - "get": { - "tags": [ - "Tags" - ], - "summary": "[EXPERIMENTAL] Get tag group by name in the given project-space", - "description": "[EXPERIMENTAL] Get tag group by name in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getGroupByName", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "groupName", - "in": "path", - "description": "name of the group", - "required": true, - "schema": { - "type": "string" + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Tag group.", + "description": "{@link JobSubmission JobSubmission} for given name.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TagGroup" + "$ref": "#/components/schemas/StoredJobSubmission" } } } @@ -1738,56 +1409,59 @@ }, "post": { "tags": [ - "Tags" + "Jobs" ], - "summary": "[EXPERIMENTAL] Group tags in the project", - "description": "[EXPERIMENTAL] Group tags in the project. The group name must not exist in the project.\n\n
\n See /tagged for filter syntax.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteGroup", + "summary": "Delete job configuration with given name.", + "description": "Delete job configuration with given name.", + "operationId": "deleteJobConfig", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "groupName", + "name": "name", "in": "path", - "description": "name of group to delete.", + "description": "name of the job-config to delete", "required": true, "schema": { "type": "string" @@ -1822,34 +1487,57 @@ } ], "responses": { - "200": { - "description": "OK" + "202": { + "description": "Accepted" } } } }, - "/api/projects/{projectId}/compounds": { - "get": { + "/api/job-configs/get-command": { + "post": { "tags": [ - "Compounds" + "Jobs" ], - "summary": "List of all available compounds (group of ion identities) in the given project-space.", - "description": "List of all available compounds (group of ion identities) in the given project-space.", - "operationId": "getCompounds", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" + "summary": "Get a CLI command for the given job configuration.", + "description": "Get a CLI command for the given job configuration.", + "operationId": "getCommand", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/JobSubmission" + } } }, + "required": true + }, + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "string" + } + } + } + } + } + } + } + }, + "/api/databases": { + "get": { + "tags": [ + "Searchable Databases" + ], + "operationId": "getDatabases", + "parameters": [ { - "name": "msDataSearchPrepared", + "name": "includeStats", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", @@ -1857,44 +1545,24 @@ } }, { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/CompoundOptField" - }, - "default": [ - "none" - ] - } - }, - { - "name": "optFieldsFeatures", + "name": "includeWithErrors", "in": "query", "required": false, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [ - "none" - ] + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/Compound" + "$ref": "#/components/schemas/SearchableDatabase" } } } @@ -1904,69 +1572,17 @@ }, "post": { "tags": [ - "Compounds" - ], - "summary": "Import Compounds and its contained features.", - "description": "Import Compounds and its contained features. Compounds and Features must not exist in the project.\n Otherwise, they will exist twice.", - "operationId": "addCompounds", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to import into.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "profile", - "in": "query", - "description": "profile describing the instrument used to measure the data. Used to merge spectra.", - "required": false, - "schema": { - "$ref": "#/components/schemas/InstrumentProfile" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/CompoundOptField" - }, - "default": [ - "none" - ] - } - }, - { - "name": "optFieldsFeatures", - "in": "query", - "description": "set of optional fields of the nested features to be included. Use 'none' to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [ - "none" - ] - } - } + "Searchable Databases" ], + "summary": "[DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API.", + "operationId": "addDatabases", "requestBody": { - "description": "the compound data to be imported", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/CompoundImport" + "type": "string" } } } @@ -1975,132 +1591,157 @@ }, "responses": { "200": { - "description": "the Compounds that have been imported with specified optional fields", + "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/Compound" + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } + }, + "deprecated": true } }, - "/api/projects/{projectId}/aligned-features": { - "get": { + "/api/databases/{databaseId}/import/from-files": { + "post": { "tags": [ - "Features" + "Searchable Databases" ], - "summary": "Get all available features (aligned over runs) in the given project-space.", - "description": "Get all available features (aligned over runs) in the given project-space.", - "operationId": "getAlignedFeatures", + "summary": "Start import of structure and spectra files into the specified database.", + "description": "Start import of structure and spectra files into the specified database.", + "operationId": "importIntoDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to read from.", + "description": "database to import into", "required": true, "schema": { "type": "string" } }, { - "name": "msDataSearchPrepared", + "name": "bufferSize", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "integer", + "format": "int32", + "default": 1000 } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" + } + ], + "requestBody": { + "content": { + "multipart/form-data": { + "schema": { + "required": [ + "inputFiles" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + }, + "bioTransformerParameters": { + "$ref": "#/components/schemas/BioTransformerParameters" + } + } }, - "default": [ - "none" - ] + "encoding": { + "bioTransformerParameters": { + "contentType": "application/json" + }, + "inputFiles": { + "contentType": "application/octet-stream" + } + } } } - ], + }, "responses": { "200": { - "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", + "description": "Meta-Information of the affected database after the import has been performed.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeature" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - }, + } + }, + "/api/account/logout": { "post": { "tags": [ - "Features" + "Login and Account" ], - "summary": "Import (aligned) features into the project.", - "description": "Import (aligned) features into the project. Features must not exist in the project.\n Otherwise, they will exist twice.", - "operationId": "addAlignedFeatures", + "summary": "Logout from SIRIUS web services.", + "description": "Logout from SIRIUS web services.", + "operationId": "logout", + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/account/login": { + "post": { + "tags": [ + "Login and Account" + ], + "summary": "Login into SIRIUS web services and activate default subscription if available.", + "description": "Login into SIRIUS web services and activate default subscription if available.", + "operationId": "login", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to import into.", + "name": "acceptTerms", + "in": "query", "required": true, "schema": { - "type": "string" + "type": "boolean" } }, { - "name": "profile", + "name": "failWhenLoggedIn", "in": "query", - "description": "profile describing the instrument used to measure the data. Used to merge spectra.", + "description": "if true request fails if an active login already exists.", "required": false, "schema": { - "$ref": "#/components/schemas/InstrumentProfile" + "type": "boolean", + "default": false } }, { - "name": "optFields", + "name": "includeSubs", "in": "query", - "description": "set of optional fields to be included. Use 'none' to override defaults.", + "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", "required": false, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [ - "none" - ] + "type": "boolean", + "default": false } } ], "requestBody": { - "description": "the feature data to be imported", + "description": "used to log in.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FeatureImport" - } + "$ref": "#/components/schemas/AccountCredentials" } } }, @@ -2108,13 +1749,52 @@ }, "responses": { "200": { - "description": "the Features that have been imported with specified optional fields", + "description": "Basic information about the account that has been logged in and its subscriptions.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/AccountInfo" + } + } + } + } + } + } + }, + "/actuator/shutdown": { + "post": { + "tags": [ + "Actuator" + ], + "summary": "Actuator web endpoint 'shutdown'", + "operationId": "shutdown", + "responses": { + "204": { + "description": "No Content" + }, + "400": { + "description": "Bad Request" + } + } + } + }, + "/api/projects": { + "get": { + "tags": [ + "Projects" + ], + "summary": "List opened project spaces.", + "description": "List opened project spaces.", + "operationId": "getProjects", + "responses": { + "200": { + "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/AlignedFeature" + "$ref": "#/components/schemas/ProjectInfo" } } } @@ -2123,103 +1803,101 @@ } } }, - "/api/job-configs/{name}": { + "/api/projects/{projectId}/npc-data": { "get": { "tags": [ - "Jobs" + "Projects" ], - "summary": "Request job configuration with given name.", - "description": "Request job configuration with given name.", - "operationId": "getJobConfig", + "summary": "Get CANOPUS prediction vector definition for NPC classes", + "operationId": "getCanopusNpcData", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to return", "required": true, "schema": { "type": "string" } }, { - "name": "moveParametersToConfigMap", + "name": "charge", "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", - "required": false, + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "integer", + "format": "int32" } } ], "responses": { "200": { - "description": "{@link JobSubmission JobSubmission} for given name.", + "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "$ref": "#/components/schemas/StoredJobSubmission" + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } } } - }, - "post": { + } + }, + "/api/projects/{projectId}/jobs/{jobId}": { + "get": { "tags": [ "Jobs" ], - "summary": "Add new job configuration with given name.", - "description": "Add new job configuration with given name.", - "operationId": "saveJobConfig", + "summary": "Get job information and its current state and progress (if available).", + "description": "Get job information and its current state and progress (if available).", + "operationId": "getJob", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to add", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "overrideExisting", - "in": "query", - "required": false, + "name": "jobId", + "in": "path", + "description": "of the job to be returned", + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "string" } }, { - "name": "moveParametersToConfigMap", + "name": "optFields", "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters in the return object", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "array", + "items": { + "$ref": "#/components/schemas/JobOptField" + }, + "default": [ + "progress" + ] } } ], - "requestBody": { - "description": "to add", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } - } - }, - "required": true - }, "responses": { "200": { - "description": "StoredJobSubmission that contains the JobSubmission and the probably modified name of the config (to ensure path compatibility).", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/StoredJobSubmission" + "$ref": "#/components/schemas/Job" } } } @@ -2230,18 +1908,47 @@ "tags": [ "Jobs" ], - "summary": "Delete job configuration with given name.", - "description": "Delete job configuration with given name.", - "operationId": "deleteJobConfig", + "summary": "Delete job.", + "description": "Delete job. Specify how to behave for running jobs.", + "operationId": "deleteJob", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to delete", + "description": "project-space to delete job from", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "jobId", + "in": "path", + "description": "of the job to be deleted", "required": true, "schema": { "type": "string" } + }, + { + "name": "cancelIfRunning", + "in": "query", + "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", + "required": false, + "schema": { + "type": "boolean", + "default": true + } + }, + { + "name": "awaitDeletion", + "in": "query", + "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", + "required": false, + "schema": { + "type": "boolean", + "default": true + } } ], "responses": { @@ -2251,189 +1958,120 @@ } } }, - "/api/job-configs/get-command": { - "post": { + "/api/projects/{projectId}/jobs/page": { + "get": { "tags": [ "Jobs" ], - "summary": "Get a CLI command for the given job configuration.", - "description": "Get a CLI command for the given job configuration.", - "operationId": "getCommand", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } + "summary": "Get Page of jobs with information such as current state and progress (if available).", + "description": "Get Page of jobs with information such as current state and progress (if available).", + "operationId": "getJobsPaged", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to run jobs on", + "required": true, + "schema": { + "type": "string" } }, - "required": true - }, - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - } - } - } - } - }, - "/api/databases": { - "get": { - "tags": [ - "Searchable Databases" - ], - "operationId": "getDatabases", - "parameters": [ { - "name": "includeStats", + "name": "page", "in": "query", + "description": "Zero-based page index (0..N)", "required": false, "schema": { - "type": "boolean", - "default": false + "minimum": 0, + "type": "integer", + "default": 0 } }, { - "name": "includeWithErrors", + "name": "size", "in": "query", + "description": "The size of the page to be returned", "required": false, "schema": { - "type": "boolean", - "default": false + "minimum": 1, + "type": "integer", + "default": 20 } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } + }, + { + "name": "sort", + "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string" } } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/JobOptField" + }, + "default": [ + "none" + ] + } } - } - }, - "post": { - "tags": [ - "Searchable Databases" ], - "summary": "DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API.", - "operationId": "addDatabases", - "requestBody": { - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "required": true - }, "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } + "$ref": "#/components/schemas/PagedModelJob" } } } } - }, - "deprecated": true + } } }, - "/api/databases/{databaseId}/import/from-files": { - "post": { + "/api/projects/{projectId}/has-jobs": { + "get": { "tags": [ - "Searchable Databases" + "Jobs" ], - "summary": "Start import of structure and spectra files into the specified database.", - "description": "Start import of structure and spectra files into the specified database.", - "operationId": "importIntoDatabase", + "operationId": "hasJobs", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", - "description": "database to import into", "required": true, "schema": { "type": "string" } }, { - "name": "bufferSize", + "name": "includeFinished", "in": "query", "required": false, "schema": { - "type": "integer", - "format": "int32", - "default": 1000 + "type": "boolean", + "default": false } } ], - "requestBody": { - "content": { - "multipart/form-data": { - "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "files to be imported", - "items": { - "type": "string", - "format": "binary" - } - }, - "bioTransformerParameters": { - "$ref": "#/components/schemas/BioTransformerParameters" - } - } - }, - "encoding": { - "bioTransformerParameters": { - "contentType": "application/json" - }, - "inputFiles": { - "contentType": "application/octet-stream" - } - } - } - } - }, "responses": { "200": { - "description": "Meta-Information of the affected database after the import has been performed.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SearchableDatabase" + "type": "boolean" } } } @@ -2441,77 +2079,44 @@ } } }, - "/api/account/logout": { - "post": { - "tags": [ - "Login and Account" - ], - "summary": "Logout from SIRIUS web services.", - "description": "Logout from SIRIUS web services.", - "operationId": "logout", - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/login": { - "post": { + "/api/projects/{projectId}/fingerid-data": { + "get": { "tags": [ - "Login and Account" + "Projects" ], - "summary": "Login into SIRIUS web services and activate default subscription if available.", - "description": "Login into SIRIUS web services and activate default subscription if available.", - "operationId": "login", + "summary": "Get CSI:FingerID fingerprint (prediction vector) definition", + "operationId": "getFingerIdData", "parameters": [ { - "name": "acceptTerms", - "in": "query", + "name": "projectId", + "in": "path", "required": true, "schema": { - "type": "boolean" - } - }, - { - "name": "failWhenLoggedIn", - "in": "query", - "description": "if true request fails if an active login already exists.", - "required": false, - "schema": { - "type": "boolean", - "default": false + "type": "string" } }, { - "name": "includeSubs", + "name": "charge", "in": "query", - "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", - "required": false, + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "integer", + "format": "int32" } } ], - "requestBody": { - "description": "used to log in.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AccountCredentials" - } - } - }, - "required": true - }, "responses": { "200": { - "description": "Basic information about the account that has been logged in and its subscriptions.", + "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "$ref": "#/components/schemas/AccountInfo" + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } @@ -2519,31 +2124,14 @@ } } }, - "/actuator/shutdown": { - "post": { - "tags": [ - "Actuator" - ], - "summary": "Actuator web endpoint 'shutdown'", - "operationId": "shutdown", - "responses": { - "204": { - "description": "No Content" - }, - "400": { - "description": "Bad Request" - } - } - } - }, - "/api/projects/{projectId}/tags/{tagName}": { + "/api/projects/{projectId}/compounds/{compoundId}": { "get": { "tags": [ - "Tags" + "Compounds" ], - "summary": "[EXPERIMENTAL] Get tag definition by its name in the given project-space", - "description": "[EXPERIMENTAL] Get tag definition by its name in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTag", + "summary": "Get compound (group of ion identities) with the given identifier from the specified project-space.", + "description": "Get compound (group of ion identities) with the given identifier from the specified project-space.", + "operationId": "getCompound", "parameters": [ { "name": "projectId", @@ -2555,22 +2143,61 @@ } }, { - "name": "tagName", + "name": "compoundId", "in": "path", - "description": "name of the tag", + "description": "identifier of the compound (group of ion identities) to access.", "required": true, "schema": { "type": "string" } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundOptField" + }, + "default": [ + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeatureOptField" + }, + "default": [ + "none" + ] + } } ], "responses": { "200": { - "description": "Tag definition.", + "description": "Compounds with additional optional fields (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TagDefinition" + "$ref": "#/components/schemas/Compound" } } } @@ -2579,13 +2206,13 @@ }, "delete": { "tags": [ - "Tags" + "Compounds" ], - "summary": "[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space", - "description": "[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space.\n
\n This will also remove all tags belonging to this definition from every tagged entity.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteTag", - "parameters": [ - { + "summary": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", + "description": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", + "operationId": "deleteCompound", + "parameters": [ + { "name": "projectId", "in": "path", "description": "project-space to delete from.", @@ -2595,9 +2222,9 @@ } }, { - "name": "tagName", + "name": "compoundId", "in": "path", - "description": "name of the tag definition to delete.", + "description": "identifier of the compound to delete.", "required": true, "schema": { "type": "string" @@ -2609,54 +2236,107 @@ "description": "OK" } } - }, - "patch": { + } + }, + "/api/projects/{projectId}/compounds/page": { + "get": { "tags": [ - "Tags" + "Compounds" ], - "summary": "[EXPERIMENTAL] Add a possible value to the tag definition in the project", - "description": "[EXPERIMENTAL] Add a possible value to the tag definition in the project.\n\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addPossibleValuesToTagDefinition", + "summary": "Page of available compounds (group of ion identities) in the given project-space.", + "description": "Page of available compounds (group of ion identities) in the given project-space.", + "operationId": "getCompoundsPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to add to.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "tagName", - "in": "path", - "description": "the tag definition to add the values to", - "required": true, + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, "schema": { - "type": "string" + "minimum": 0, + "type": "integer", + "default": 0 } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "object" - } + }, + { + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, + "schema": { + "minimum": 1, + "type": "integer", + "default": 20 + } + }, + { + "name": "sort", + "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string" } } }, - "required": true - }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundOptField" + }, + "default": [ + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeatureOptField" + }, + "default": [ + "none" + ] + } + } + ], "responses": { "200": { - "description": "the definitions of the tags that have been added", + "description": "Compounds with additional optional fields (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TagDefinition" + "$ref": "#/components/schemas/PagedModelCompound" } } } @@ -2664,24 +2344,44 @@ } } }, - "/api/projects": { + "/api/projects/{projectId}/cf-data": { "get": { "tags": [ "Projects" ], - "summary": "List opened project spaces.", - "description": "List opened project spaces.", - "operationId": "getProjects", + "summary": "Get CANOPUS prediction vector definition for ClassyFire classes", + "operationId": "getCanopusClassyFireData", + "parameters": [ + { + "name": "projectId", + "in": "path", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "charge", + "in": "query", + "required": true, + "schema": { + "type": "integer", + "format": "int32" + } + } + ], "responses": { "200": { "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/ProjectInfo" - } + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } @@ -2689,14 +2389,14 @@ } } }, - "/api/projects/{projectId}/runs/{runId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get run with the given identifier from the specified project-space", - "description": "[EXPERIMENTAL] Get run with the given identifier from the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunExperimental", + "summary": "Get feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Get feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "getAlignedFeature", "parameters": [ { "name": "projectId", @@ -2708,14 +2408,24 @@ } }, { - "name": "runId", + "name": "alignedFeatureId", "in": "path", - "description": "identifier of run to access.", + "description": "identifier of feature (aligned over runs) to access.", "required": true, "schema": { "type": "string" } }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, { "name": "optFields", "in": "query", @@ -2724,48 +2434,48 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/RunOptField" + "$ref": "#/components/schemas/AlignedFeatureOptField" }, - "default": [] + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "Run with tags (if specified).", + "description": "AlignedFeature with additional annotations and MS/MS data (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Run" + "$ref": "#/components/schemas/AlignedFeature" } } } } } - } - }, - "/api/projects/{projectId}/runs/tags/{objectId}": { - "get": { + }, + "delete": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Run", - "description": "[EXPERIMENTAL] Get all tags associated with this Run", - "operationId": "getTagsForRunExperimental", + "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "deleteAlignedFeature", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to get from.", + "description": "project-space to delete from.", "required": true, "schema": { "type": "string" } }, { - "name": "objectId", + "name": "alignedFeatureId", "in": "path", - "description": "RunId to get tags for.", + "description": "identifier of feature (aligned over runs) to delete.", "required": true, "schema": { "type": "string" @@ -2774,104 +2484,92 @@ ], "responses": { "200": { - "description": "the tags of the requested object", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - } + "description": "OK" } } } }, - "/api/projects/{projectId}/runs/tagged": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get runs by tag", - "description": "[EXPERIMENTAL] Get runs by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunPageExperimental", + "summary": "Spectral library match for the given 'alignedFeatureId'.", + "description": "Spectral library match for the given 'alignedFeatureId'.", + "operationId": "getSpectralLibraryMatch", "parameters": [ { "name": "projectId", @@ -2898,60 +2596,119 @@ } }, { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, "schema": { - "minimum": 0, - "type": "integer", - "default": 0 + "type": "string" } }, { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, + "name": "matchId", + "in": "path", + "description": "id of the library match to be returned.", + "required": true, "schema": { - "minimum": 1, - "type": "integer", - "default": 20 + "type": "string" } }, { - "name": "sort", + "name": "optFields", "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/SpectralLibraryMatchOptField" + }, + "default": [ + "none" + ] + } + } + ], + "responses": { + "200": { + "description": "Spectral library match with requested mathcId.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/SpectralLibraryMatch" + } } } + } + } + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary": { + "get": { + "tags": [ + "Features" + ], + "summary": "Summarize matched reference spectra for the given 'alignedFeatureId'.", + "description": "Summarize matched reference spectra for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key.", + "operationId": "getSpectralLibraryMatchesSummary", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" + } }, { - "name": "optFields", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "minSharedPeaks", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "min threshold of shared peaks.", "required": false, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/RunOptField" - }, - "default": [] + "type": "integer", + "format": "int32", + "default": 1 + } + }, + { + "name": "minSimilarity", + "in": "query", + "description": "min spectral similarity threshold.", + "required": false, + "schema": { + "type": "number", + "format": "double", + "default": 0.2 + } + }, + { + "name": "inchiKey", + "in": "query", + "description": "2D inchi key of the compound in the structure database.", + "required": false, + "schema": { + "type": "string", + "default": "" } } ], "responses": { "200": { - "description": "Runs with tags (if specified).", + "description": "Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelRun" + "$ref": "#/components/schemas/SpectralLibraryMatchSummary" } } } @@ -2959,28 +2716,28 @@ } } }, - "/api/projects/{projectId}/runs/grouped": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get runs by tag group", - "description": "[EXPERIMENTAL] Get runs by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunsByGroupExperimental", + "summary": "Page of spectral library matches for the given 'alignedFeatureId'.", + "description": "Page of spectral library matches for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key.", + "operationId": "getSpectralLibraryMatchesPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "groupName", - "in": "query", - "description": "tag group name.", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", "required": true, "schema": { "type": "string" @@ -3020,15 +2777,43 @@ } } }, + { + "name": "minSharedPeaks", + "in": "query", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": 1 + } + }, + { + "name": "minSimilarity", + "in": "query", + "required": false, + "schema": { + "type": "number", + "format": "double", + "default": 0.2 + } + }, + { + "name": "inchiKey", + "in": "query", + "required": false, + "schema": { + "type": "string", + "default": "" + } + }, { "name": "optFields", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/RunOptField" + "$ref": "#/components/schemas/SpectralLibraryMatchOptField" }, "default": [ "none" @@ -3038,11 +2823,11 @@ ], "responses": { "200": { - "description": "tagged runs", + "description": "Spectral library matches of this feature (aligned over runs).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelRun" + "$ref": "#/components/schemas/PagedModelSpectralLibraryMatch" } } } @@ -3050,44 +2835,51 @@ } } }, - "/api/projects/{projectId}/npc-data": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data": { "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Get CANOPUS prediction vector definition for NPC classes", - "operationId": "getCanopusNpcData", + "summary": "Mass Spec data (input data) for the given 'alignedFeatureId' .", + "description": "Mass Spec data (input data) for the given 'alignedFeatureId' .", + "operationId": "getMsData", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "charge", - "in": "query", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the Mass Spec data belongs to.", "required": true, "schema": { - "type": "integer", - "format": "int32" + "type": "string" + } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "OK", + "description": "Mass Spec data of this feature (aligned over runs).", "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { + "application/json": { "schema": { - "type": "string" + "$ref": "#/components/schemas/MsData" } } } @@ -3095,33 +2887,43 @@ } } }, - "/api/projects/{projectId}/jobs/{jobId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas": { "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Get job information and its current state and progress (if available).", - "description": "Get job information and its current state and progress (if available).", - "operationId": "getJob", + "summary": "List of FormulaResultContainers available for this feature with minimal information.", + "description": "List of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", + "operationId": "getFormulaCandidates", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "jobId", + "name": "alignedFeatureId", "in": "path", - "description": "of the job to be returned", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, { "name": "optFields", "in": "query", @@ -3130,156 +2932,151 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/JobOptField" + "$ref": "#/components/schemas/FormulaCandidateOptField" }, "default": [ - "progress" + "none" ] } } ], "responses": { "200": { - "description": "OK", + "description": "All FormulaCandidate of this feature with.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/FormulaCandidate" + } } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}": { + "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Delete job.", - "description": "Delete job. Specify how to behave for running jobs.", - "operationId": "deleteJob", + "summary": "FormulaResultContainers for the given 'formulaId' with minimal information.", + "description": "FormulaResultContainers for the given 'formulaId' with minimal information.\n Can be enriched with an optional results overview and formula candidate information.", + "operationId": "getFormulaCandidate", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete job from", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "jobId", + "name": "alignedFeatureId", "in": "path", - "description": "of the job to be deleted", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "cancelIfRunning", + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "msDataSearchPrepared", "in": "query", - "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", - "default": true + "default": false } }, { - "name": "awaitDeletion", + "name": "optFields", "in": "query", - "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": true - } - } - ], - "responses": { - "202": { - "description": "Accepted" + "type": "array", + "items": { + "$ref": "#/components/schemas/FormulaCandidateOptField" + }, + "default": [ + "none" + ] + } + } + ], + "responses": { + "200": { + "description": "FormulaCandidate of this feature (aligned over runs) with.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/FormulaCandidate" + } + } + } } } } }, - "/api/projects/{projectId}/jobs/page": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation": { "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Get Page of jobs with information such as current state and progress (if available).", - "description": "Get Page of jobs with information such as current state and progress (if available).", - "operationId": "getJobsPaged", + "summary": "Returns Lipid annotation (ElGordo) for the given formulaId", + "description": "Returns Lipid annotation (ElGordo) for the given formulaId.\n
\n ElGordo lipid annotation runs as part of the SIRIUS formula identification step.", + "operationId": "getLipidAnnotation", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "type": "array", - "items": { - "type": "string" - } + "type": "string" } }, { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/JobOptField" - }, - "default": [ - "none" - ] + "type": "string" } } ], "responses": { "200": { - "description": "OK", + "description": "LipidAnnotation", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelJob" + "$ref": "#/components/schemas/LipidAnnotation" } } } @@ -3287,38 +3084,50 @@ } } }, - "/api/projects/{projectId}/has-jobs": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern": { "get": { "tags": [ - "Jobs" + "Features" ], - "operationId": "hasJobs", + "summary": "Returns Isotope pattern information for given formulaId\n ", + "description": "Returns Isotope pattern information for given formulaId\n
\n Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting)\n for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore).", + "operationId": "getIsotopePatternAnnotation", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "includeFinished", - "in": "query", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, + "schema": { + "type": "string" } } ], "responses": { "200": { - "description": "OK", + "description": "Isotope pattern information", "content": { "application/json": { "schema": { - "type": "boolean" + "$ref": "#/components/schemas/IsotopePatternAnnotation" } } } @@ -3326,14 +3135,14 @@ } } }, - "/api/projects/{projectId}/groups": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree": { "get": { "tags": [ - "Tags" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tag based groups in the given project-space", - "description": "[EXPERIMENTAL] Get all tag based groups in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getGroups", + "summary": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n ", + "description": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n
\n This tree is used to rank formula candidates (treeScore).", + "operationId": "getFragTree", "parameters": [ { "name": "projectId", @@ -3345,10 +3154,19 @@ } }, { - "name": "groupType", - "in": "query", - "description": "type of the group", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { "type": "string" } @@ -3356,14 +3174,11 @@ ], "responses": { "200": { - "description": "Groups.", + "description": "Fragmentation Tree", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagGroup" - } + "$ref": "#/components/schemas/FragmentationTree" } } } @@ -3371,44 +3186,54 @@ } } }, - "/api/projects/{projectId}/fingerid-data": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint": { "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Get CSI:FingerID fingerprint (prediction vector) definition", - "operationId": "getFingerIdData", + "summary": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n ", + "description": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n
\n This fingerprint is used to perform structure database search and predict compound classes.", + "operationId": "getFingerprintPrediction", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "charge", - "in": "query", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { - "type": "integer", - "format": "int32" + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, + "schema": { + "type": "string" } } ], "responses": { "200": { - "description": "OK", + "description": "probabilistic fingerprint predicted by CSI:FingerID", "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { + "application/json": { "schema": { - "type": "string" + "type": "array", + "items": { + "type": "number", + "format": "double" + } } } } @@ -3416,14 +3241,14 @@ } } }, - "/api/projects/{projectId}/compounds/{compoundId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "Get compound (group of ion identities) with the given identifier from the specified project-space.", - "description": "Get compound (group of ion identities) with the given identifier from the specified project-space.", - "operationId": "getCompound", + "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesByFormula", "parameters": [ { "name": "projectId", @@ -3435,22 +3260,21 @@ } }, { - "name": "compoundId", + "name": "alignedFeatureId", "in": "path", - "description": "identifier of the compound (group of ion identities) to access.", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "string" } }, { @@ -3461,21 +3285,7 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/CompoundOptField" - }, - "default": [ - "none" - ] - } - }, - { - "name": "optFieldsFeatures", - "in": "query", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" + "$ref": "#/components/schemas/StructureCandidateOptField" }, "default": [ "none" @@ -3485,95 +3295,114 @@ ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Compound" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateScored" + } } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page": { + "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", - "description": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", - "operationId": "deleteCompound", + "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesByFormulaPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "compoundId", + "name": "alignedFeatureId", "in": "path", - "description": "identifier of the compound to delete.", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds/{compoundId}/traces": { - "get": { - "tags": [ - "Compounds" - ], - "summary": "[EXPERIMENTAL] Returns the traces of the given compound", - "description": "[EXPERIMENTAL] Returns the traces of the given compound.\n
\n A trace consists of m/z and intensity values over the retention\n time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,\n but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.\n However, this also means that all traces can be directly compared against each other, as they all lie in the same\n retention time axis.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundTracesExperimental", - "parameters": [ + }, { - "name": "projectId", + "name": "formulaId", "in": "path", - "description": "project-space to read from.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, { - "name": "compoundId", - "in": "path", - "description": "compound which intensities should be read out", - "required": true, + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, "schema": { - "type": "string" + "minimum": 0, + "type": "integer", + "default": 0 + } + }, + { + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, + "schema": { + "minimum": 1, + "type": "integer", + "default": 20 } }, { - "name": "featureId", + "name": "sort", "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { - "type": "string", - "default": "" + "type": "array", + "items": { + "type": "string" + } + } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateOptField" + }, + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "Traces of the given compound.", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" + "$ref": "#/components/schemas/PagedModelStructureCandidateScored" } } } @@ -3581,14 +3410,14 @@ } } }, - "/api/projects/{projectId}/compounds/{compoundId}/quant-table-row": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Returns a single quantification table row for the given compound", - "description": "[EXPERIMENTAL] Returns a single quantification table row for the given compound.\n
\n The quantification table contains a quantification of the feature within all\n samples it is contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundQuantTableRowExperimental", + "summary": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", + "description": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesByFormula", "parameters": [ { "name": "projectId", @@ -3600,31 +3429,49 @@ } }, { - "name": "compoundId", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", "in": "path", - "description": "compound which should be read out", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, { - "name": "type", + "name": "optFields", "in": "query", - "description": "quantification type.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "$ref": "#/components/schemas/QuantMeasure" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateOptField" + }, + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "OK", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateScored" + } } } } @@ -3632,79 +3479,42 @@ } } }, - "/api/projects/{projectId}/compounds/tags/{objectId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Compound", - "description": "[EXPERIMENTAL] Get all tags associated with this Compound", - "operationId": "getTagsForCompoundExperimental", + "summary": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", + "description": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesByFormulaPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to get from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "objectId", + "name": "alignedFeatureId", "in": "path", - "description": "CompoundId to get tags for.", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } - } - ], - "responses": { - "200": { - "description": "the tags of the requested Compound", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/compounds/tagged": { - "get": { - "tags": [ - "Compounds" - ], - "summary": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag", - "description": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFoldChangesByCompoundExperimental", + "summary": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", + "description": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", + "operationId": "getCanopusPrediction", "parameters": [ { "name": "projectId", @@ -3786,9 +3598,18 @@ } }, { - "name": "objectId", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", "in": "path", - "description": "id of the object the fold changes are assigned to.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" @@ -3797,14 +3618,11 @@ ], "responses": { "200": { - "description": "fold changes", + "description": "Predicted compound classes", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FoldChange" - } + "$ref": "#/components/schemas/CanopusPrediction" } } } @@ -3812,14 +3630,14 @@ } } }, - "/api/projects/{projectId}/compounds/statistics/foldchanges/stats-table": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes": { "get": { "tags": [ - "Compound Statistics" + "Features" ], - "summary": "[EXPERIMENTAL] Get table of all fold changes in the project space", - "description": "[EXPERIMENTAL] Get table of all fold changes in the project space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getCompoundFoldChangeTableExperimental", + "summary": "Return Best matching compound classes for given formulaId", + "description": "Return Best matching compound classes for given formulaId.\n
\n Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology,", + "operationId": "getBestMatchingCompoundClasses", "parameters": [ { "name": "projectId", @@ -3831,31 +3649,31 @@ } }, { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "$ref": "#/components/schemas/AggregationType" + "type": "string" } }, { - "name": "quantification", - "in": "query", - "description": "quantification type.", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "$ref": "#/components/schemas/QuantMeasure" + "type": "string" } } ], "responses": { "200": { - "description": "table of fold changes.", + "description": "Best matching Predicted compound classes", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/StatisticsTable" + "$ref": "#/components/schemas/CompoundClasses" } } } @@ -3863,14 +3681,14 @@ } } }, - "/api/projects/{projectId}/compounds/quant-table": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Returns the full quantification table of compounds", - "description": "[EXPERIMENTAL] Returns the full quantification table of compounds.\n
\n The quantification table contains a quantification of the features within all\n runs they are contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundQuantTableExperimental", + "summary": "Returns a fragmentation spectrum (e", + "description": "Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier\n
\n These annotations are only available if a fragmentation tree is available.", + "operationId": "getFormulaAnnotatedSpectrum", "parameters": [ { "name": "projectId", @@ -3882,22 +3700,52 @@ } }, { - "name": "type", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "spectrumIndex", + "in": "query", + "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": -1 + } + }, + { + "name": "searchPrepared", "in": "query", - "description": "quantification type.", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { - "$ref": "#/components/schemas/QuantMeasure" + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "OK", + "description": "Fragmentation spectrum annotated with fragment formulas and losses.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "$ref": "#/components/schemas/AnnotatedSpectrum" } } } @@ -3905,14 +3753,14 @@ } } }, - "/api/projects/{projectId}/compounds/page": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "Page of available compounds (group of ion identities) in the given project-space.", - "description": "Page of available compounds (group of ion identities) in the given project-space.", - "operationId": "getCompoundsPaged", + "summary": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId", + "description": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.\n
\n Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses\n for the given formula result identifier\n These annotations are only available if a fragmentation tree and the structure candidate are available.", + "operationId": "getFormulaAnnotatedMsMsData", "parameters": [ { "name": "projectId", @@ -3924,14 +3772,84 @@ } }, { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "minimum": 0, - "type": "integer", - "default": 0 + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + } + ], + "responses": { + "200": { + "description": "Fragmentation spectra annotated with fragment formulas and losses.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/AnnotatedMsMsData" + } + } + } + } + } + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page": { + "get": { + "tags": [ + "Features" + ], + "summary": "Page of FormulaResultContainers available for this feature with minimal information.", + "description": "Page of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", + "operationId": "getFormulaCandidatesPaged", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, + "schema": { + "minimum": 0, + "type": "integer", + "default": 0 } }, { @@ -3975,21 +3893,7 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/CompoundOptField" - }, - "default": [ - "none" - ] - } - }, - { - "name": "optFieldsFeatures", - "in": "query", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" + "$ref": "#/components/schemas/FormulaCandidateOptField" }, "default": [ "none" @@ -3999,11 +3903,11 @@ ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "All FormulaCandidate of this feature with.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelCompound" + "$ref": "#/components/schemas/PagedModelFormulaCandidate" } } } @@ -4011,28 +3915,28 @@ } } }, - "/api/projects/{projectId}/compounds/grouped": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag group", - "description": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getCompoundsByGroupExperimental", + "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "groupName", - "in": "query", - "description": "tag group name.", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", "required": true, "schema": { "type": "string" @@ -4080,7 +3984,7 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/CompoundOptField" + "$ref": "#/components/schemas/StructureCandidateOptField" }, "default": [ "none" @@ -4090,11 +3994,11 @@ ], "responses": { "200": { - "description": "tagged compounds (group of ion identities)", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelCompound" + "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" } } } @@ -4102,44 +4006,59 @@ } } }, - "/api/projects/{projectId}/cf-data": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures": { "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Get CANOPUS prediction vector definition for ClassyFire classes", - "operationId": "getCanopusClassyFireData", + "summary": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", + "description": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidates", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "charge", - "in": "query", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", "required": true, "schema": { - "type": "integer", - "format": "int32" + "type": "string" + } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateOptField" + }, + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "OK", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { + "application/json": { "schema": { - "type": "string" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateFormula" + } } } } @@ -4147,14 +4066,14 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page": { "get": { "tags": [ "Features" ], - "summary": "Get feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Get feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "getAlignedFeature", + "summary": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", + "description": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesPaged", "parameters": [ { "name": "projectId", @@ -4168,20 +4087,44 @@ { "name": "alignedFeatureId", "in": "path", - "description": "identifier of feature (aligned over runs) to access.", + "description": "feature (aligned over runs) the structure candidates belong to.", "required": true, "schema": { "type": "string" } }, { - "name": "msDataSearchPrepared", + "name": "page", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "description": "Zero-based page index (0..N)", "required": false, "schema": { - "type": "boolean", - "default": false + "minimum": 0, + "type": "integer", + "default": 0 + } + }, + { + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, + "schema": { + "minimum": 1, + "type": "integer", + "default": 20 + } + }, + { + "name": "sort", + "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string" + } } }, { @@ -4192,7 +4135,7 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" + "$ref": "#/components/schemas/StructureCandidateOptField" }, "default": [ "none" @@ -4202,59 +4145,26 @@ ], "responses": { "200": { - "description": "AlignedFeature with additional annotations and MS/MS data (if specified).", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AlignedFeature" + "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" } } } } } - }, - "delete": { - "tags": [ - "Features" - ], - "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "deleteAlignedFeature", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "identifier of feature (aligned over runs) to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces": { + "/api/projects/{projectId}/aligned-features/page": { "get": { "tags": [ "Features" ], - "summary": "[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId).\n
\n Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention\n time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,\n but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.\n However, this also means that all traces can be directly compared against each other, as they all lie in the same\n retention time axis.\n By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set,\n it also includes samples in which the same trace appears in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTracesExperimental", + "summary": "Get all available features (aligned over runs) in the given project-space.", + "description": "Get all available features (aligned over runs) in the given project-space.", + "operationId": "getAlignedFeaturesPaged", "parameters": [ { "name": "projectId", @@ -4266,103 +4176,58 @@ } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "feature which intensities should be read out", - "required": true, + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, "schema": { - "type": "string" + "minimum": 0, + "type": "integer", + "default": 0 } }, { - "name": "includeAll", - "in": "query", - "description": "when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Traces of the given feature.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of spectral library matches for the given 'alignedFeatureId'.", - "description": "List of spectral library matches for the given 'alignedFeatureId'.", - "operationId": "getSpectralLibraryMatches", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "minSharedPeaks", + "name": "size", "in": "query", + "description": "The size of the page to be returned", "required": false, "schema": { + "minimum": 1, "type": "integer", - "format": "int32", - "default": 1 + "default": 20 } }, { - "name": "minSimilarity", + "name": "sort", "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { - "type": "number", - "format": "double", - "default": 0.2 + "type": "array", + "items": { + "type": "string" + } } }, { - "name": "inchiKey", + "name": "msDataSearchPrepared", "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { - "type": "string", - "default": "" + "type": "boolean", + "default": false } }, { "name": "optFields", "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/SpectralLibraryMatchOptField" + "$ref": "#/components/schemas/AlignedFeatureOptField" }, "default": [ "none" @@ -4372,13 +4237,35 @@ ], "responses": { "200": { - "description": "Spectral library matches of this feature (aligned over runs).", + "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/PagedModelAlignedFeature" + } + } + } + } + } + } + }, + "/api/job-configs": { + "get": { + "tags": [ + "Jobs" + ], + "summary": "Request all available job configurations", + "description": "Request all available job configurations", + "operationId": "getJobConfigs", + "responses": { + "200": { + "description": "list of available {@link JobSubmission JobSubmission}s", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "$ref": "#/components/schemas/StoredJobSubmission" } } } @@ -4387,64 +4274,65 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}": { + "/api/job-config-names": { "get": { "tags": [ - "Features" + "Jobs" ], - "summary": "Spectral library match for the given 'alignedFeatureId'.", - "description": "Spectral library match for the given 'alignedFeatureId'.", - "operationId": "getSpectralLibraryMatch", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" + "summary": "[DEPRECATED] Get all (non-default) job configuration names\n ", + "description": "[DEPRECATED] Get all (non-default) job configuration names\n
\n [DEPRECATED] Use /job-configs to get all configs with names. This endpoint is based on local file paths and will likely be removed in future versions of this API.", + "operationId": "getJobConfigNames", + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "string" + } + } + } } - }, + } + }, + "deprecated": true + } + }, + "/api/info": { + "get": { + "tags": [ + "Info" + ], + "operationId": "getInfo", + "parameters": [ { - "name": "matchId", - "in": "path", - "description": "id of the library match to be returned.", - "required": true, + "name": "serverInfo", + "in": "query", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true } }, { - "name": "optFields", + "name": "updateInfo", "in": "query", "required": false, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatchOptField" - }, - "default": [ - "none" - ] + "type": "boolean", + "default": true } } ], "responses": { "200": { - "description": "Spectral library match with requested mathcId.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "$ref": "#/components/schemas/Info" } } } @@ -4452,50 +4340,78 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated": { + "/api/guis": { "get": { "tags": [ - "Features" + "Gui" + ], + "summary": "Get list of currently running gui windows, managed by this SIRIUS instance.", + "description": "Get list of currently running gui windows, managed by this SIRIUS instance.\n Note this will not show any Clients that are connected from a separate process!", + "operationId": "getGuis", + "responses": { + "200": { + "description": "List of GUI windows that are currently managed by this SIRIUS instance.", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/GuiInfo" + } + } + } + } + } + } + } + }, + "/api/default-job-config": { + "get": { + "tags": [ + "Jobs" ], - "summary": "[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations", - "description": "[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedSpectralLibraryMatchExperimental", + "summary": "Request default job configuration", + "description": "Request default job configuration", + "operationId": "getDefaultJobConfig", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, + "name": "includeConfigMap", + "in": "query", + "description": "if true, generic configmap with-defaults will be included", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, + "name": "moveParametersToConfigMap", + "in": "query", + "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "matchId", - "in": "path", - "description": "id of the library match to be returned.", - "required": true, + "name": "includeCustomDbsForStructureSearch", + "in": "query", + "description": "if true, default database selection of structure db search\n spectral library search contains also all available custom DB.\n If No custom dbs are selected, spectral library search is disabled by default.", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Spectral library match with requested mathcId.", + "description": "{@link JobSubmission JobSubmission} with all parameters set to default values.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" + "$ref": "#/components/schemas/JobSubmission" } } } @@ -4503,73 +4419,33 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary": { + "/api/databases/included": { "get": { "tags": [ - "Features" + "Searchable Databases" ], - "summary": "Summarize matched reference spectra for the given 'alignedFeatureId'.", - "description": "Summarize matched reference spectra for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key.", - "operationId": "getSpectralLibraryMatchesSummary", + "operationId": "getIncludedDatabases", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "minSharedPeaks", - "in": "query", - "description": "min threshold of shared peaks.", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1 - } - }, - { - "name": "minSimilarity", - "in": "query", - "description": "min spectral similarity threshold.", - "required": false, - "schema": { - "type": "number", - "format": "double", - "default": 0.2 - } - }, - { - "name": "inchiKey", + "name": "includeStats", "in": "query", - "description": "2D inchi key of the compound in the structure database.", "required": false, "schema": { - "type": "string", - "default": "" + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs).", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SpectralLibraryMatchSummary" + "type": "array", + "items": { + "$ref": "#/components/schemas/SearchableDatabase" + } } } } @@ -4577,118 +4453,42 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page": { + "/api/databases/custom": { "get": { "tags": [ - "Features" + "Searchable Databases" ], - "summary": "Page of spectral library matches for the given 'alignedFeatureId'.", - "description": "Page of spectral library matches for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key.", - "operationId": "getSpectralLibraryMatchesPaged", + "operationId": "getCustomDatabases", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "minSharedPeaks", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1 - } - }, - { - "name": "minSimilarity", - "in": "query", - "required": false, - "schema": { - "type": "number", - "format": "double", - "default": 0.2 - } - }, - { - "name": "inchiKey", + "name": "includeStats", "in": "query", "required": false, "schema": { - "type": "string", - "default": "" + "type": "boolean", + "default": false } }, { - "name": "optFields", + "name": "includeWithErrors", "in": "query", "required": false, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatchOptField" - }, - "default": [ - "none" - ] + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Spectral library matches of this feature (aligned over runs).", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelSpectralLibraryMatch" + "type": "array", + "items": { + "$ref": "#/components/schemas/SearchableDatabase" + } } } } @@ -4696,50 +4496,44 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row": { + "/api/connection-status": { "get": { "tags": [ - "Features" + "Info" ], - "summary": "[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId).\n
\n The quantification table contains a quantity of the feature within all samples it is contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getQuantTableRowExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature which quantity should be read out", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "type", - "in": "query", - "description": "quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" + "operationId": "getConnectionCheck", + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ConnectionCheck" + } + } } } + } + } + }, + "/api/account/subscriptions": { + "get": { + "tags": [ + "Login and Account" ], + "summary": "Get available subscriptions of the account currently logged in.", + "description": "Get available subscriptions of the account currently logged in. Fails if not logged in.", + "operationId": "getSubscriptions", "responses": { "200": { - "description": "Quant table row for this feature", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "type": "array", + "items": { + "$ref": "#/components/schemas/Subscription" + } } } } @@ -4747,41 +4541,43 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report": { + "/api/account/signUp": { "get": { "tags": [ - "Features" + "Login and Account" ], - "summary": "[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)\n ", - "description": "[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)\n
\n Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeatureQualityExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "identifier of feature (aligned over runs) to access.", - "required": true, - "schema": { - "type": "string" + "summary": "Open SignUp window in system browser and return signUp link.", + "description": "Open SignUp window in system browser and return signUp link.", + "operationId": "signUp", + "responses": { + "200": { + "description": "OK", + "content": { + "text/plain;charset=UTF-8": { + "schema": { + "type": "string" + } + } } } + } + } + }, + "/api/account/signUpURL": { + "get": { + "tags": [ + "Login and Account" ], + "summary": "Get SignUp URL (For signUp via web browser)", + "description": "Get SignUp URL (For signUp via web browser)", + "operationId": "getSignUpURL", "responses": { "200": { - "description": "AlignedFeatureQuality quality information of the respective feature.", + "description": "OK", "content": { - "application/json": { + "text/plain;charset=UTF-8": { "schema": { - "$ref": "#/components/schemas/AlignedFeatureQualityExperimental" + "type": "string" } } } @@ -4789,121 +4585,36 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data": { + "/api/account/openPortal": { "get": { "tags": [ - "Features" - ], - "summary": "Mass Spec data (input data) for the given 'alignedFeatureId' .", - "description": "Mass Spec data (input data) for the given 'alignedFeatureId' .", - "operationId": "getMsData", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the Mass Spec data belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } + "Login and Account" ], + "summary": "Open User portal in browser.", + "description": "Open User portal in browser. If user is logged in SIRIUS tries to transfer the login state to the browser.", + "operationId": "openPortal", "responses": { "200": { - "description": "Mass Spec data of this feature (aligned over runs).", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/MsData" - } - } - } + "description": "OK" } } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas": { + "/api/account/isLoggedIn": { "get": { "tags": [ - "Features" - ], - "summary": "List of FormulaResultContainers available for this feature with minimal information.", - "description": "List of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", - "operationId": "getFormulaCandidates", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FormulaCandidateOptField" - }, - "default": [ - "none" - ] - } - } + "Login and Account" ], + "summary": "Check if a user is logged in.", + "description": "Check if a user is logged in.", + "operationId": "isLoggedIn", "responses": { "200": { - "description": "All FormulaCandidate of this feature with.", + "description": "true if the user is logged in", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FormulaCandidate" - } + "type": "boolean" } } } @@ -4911,75 +4622,33 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}": { + "/api/account/": { "get": { "tags": [ - "Features" + "Login and Account" ], - "summary": "FormulaResultContainers for the given 'formulaId' with minimal information.", - "description": "FormulaResultContainers for the given 'formulaId' with minimal information.\n Can be enriched with an optional results overview and formula candidate information.", - "operationId": "getFormulaCandidate", + "summary": "Get information about the account currently logged in.", + "description": "Get information about the account currently logged in. Fails if not logged in.", + "operationId": "getAccountInfo", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", + "name": "includeSubs", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", "required": false, "schema": { "type": "boolean", "default": false } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FormulaCandidateOptField" - }, - "default": [ - "none" - ] - } } ], "responses": { "200": { - "description": "FormulaCandidate of this feature (aligned over runs) with.", + "description": "Basic information about the account that has been logged in and its subscriptions.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/FormulaCandidate" + "$ref": "#/components/schemas/AccountInfo" } } } @@ -4987,3219 +4656,199 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum": { + "/actuator/health": { "get": { "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey\n ", - "description": "[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey\n
\n Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result\n These annotations are only available if a fragmentation tree is available.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedSpectrumExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "inchiKey", - "in": "path", - "description": "2d InChIKey of the structure candidate to be used to annotate the spectrum annotation", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "spectrumIndex", - "in": "query", - "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": -1 - } - }, - { - "name": "searchPrepared", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } + "Actuator" ], + "summary": "Actuator web endpoint 'health'", + "operationId": "health", "responses": { "200": { - "description": "Fragmentation spectrum annotated with fragments and sub-structures.", + "description": "OK", "content": { + "application/vnd.spring-boot.actuator.v3+json": { + "schema": { + "type": "object" + } + }, + "application/vnd.spring-boot.actuator.v2+json": { + "schema": { + "type": "object" + } + }, "application/json": { "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" + "type": "object" } } } } } } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey", - "description": "[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey.\n
\n Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses\n for the given formula result identifier and structure candidate inChIKey.\n These annotations are only available if a fragmentation tree and the structure candidate are available.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedMsDataExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "inchiKey", - "in": "path", - "description": "2d InChIKey of the structure candidate to be used to annotate the spectrum annotation", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectrum annotated with fragments and sub-structures.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedMsMsData" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns Lipid annotation (ElGordo) for the given formulaId", - "description": "Returns Lipid annotation (ElGordo) for the given formulaId.\n
\n ElGordo lipid annotation runs as part of the SIRIUS formula identification step.", - "operationId": "getLipidAnnotation", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "LipidAnnotation", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/LipidAnnotation" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns Isotope pattern information for given formulaId\n ", - "description": "Returns Isotope pattern information for given formulaId\n
\n Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting)\n for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore).", - "operationId": "getIsotopePatternAnnotation", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Isotope pattern information", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/IsotopePatternAnnotation" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n ", - "description": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n
\n This tree is used to rank formula candidates (treeScore).", - "operationId": "getFragTree", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Fragmentation Tree", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/FragmentationTree" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n ", - "description": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n
\n This fingerprint is used to perform structure database search and predict compound classes.", - "operationId": "getFingerprintPrediction", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "probabilistic fingerprint predicted by CSI:FingerID", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesByFormula", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateScored" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesByFormulaPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateScored" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", - "description": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesByFormula", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateScored" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", - "description": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesByFormulaPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateScored" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction": { - "get": { - "tags": [ - "Features" - ], - "summary": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", - "description": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", - "operationId": "getCanopusPrediction", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Predicted compound classes", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CanopusPrediction" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes": { - "get": { - "tags": [ - "Features" - ], - "summary": "Return Best matching compound classes for given formulaId", - "description": "Return Best matching compound classes for given formulaId.\n
\n Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology,", - "operationId": "getBestMatchingCompoundClasses", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Best matching Predicted compound classes", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CompoundClasses" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns a fragmentation spectrum (e", - "description": "Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier\n
\n These annotations are only available if a fragmentation tree is available.", - "operationId": "getFormulaAnnotatedSpectrum", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "spectrumIndex", - "in": "query", - "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": -1 - } - }, - { - "name": "searchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectrum annotated with fragment formulas and losses.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId", - "description": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.\n
\n Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses\n for the given formula result identifier\n These annotations are only available if a fragmentation tree and the structure candidate are available.", - "operationId": "getFormulaAnnotatedMsMsData", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectra annotated with fragment formulas and losses.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedMsMsData" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of FormulaResultContainers available for this feature with minimal information.", - "description": "Page of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", - "operationId": "getFormulaCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FormulaCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "All FormulaCandidate of this feature with.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelFormulaCandidate" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", - "description": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidates", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", - "description": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network", - "description": "[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAdductNetworkWithMergedTracesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "one feature that is considered the main feature of the adduct network", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tags/{objectId}": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Object", - "description": "[EXPERIMENTAL] Get all tags associated with this Object", - "operationId": "getTagsForAlignedFeaturesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to get from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "objectId", - "in": "path", - "description": "object to get tags for.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "the tags of the requested object", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tagged": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get features (aligned over runs) by tag", - "description": "[EXPERIMENTAL] Get features (aligned over runs) by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n
The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeaturesByTagExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project space to get features (aligned over runs) from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "filter", - "in": "query", - "description": "tag filter.", - "required": false, - "schema": { - "type": "string", - "default": "" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [] - } - } - ], - "responses": { - "200": { - "description": "tagged features (aligned over runs)", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId}": { - "get": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] List all fold changes that are associated with an object", - "description": "[EXPERIMENTAL] List all fold changes that are associated with an object.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFoldChangesByAlignedFeatureExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "objectId", - "in": "path", - "description": "id of the object the fold changes are assigned to.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "fold changes", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FoldChange" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table": { - "get": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] Get table of all fold changes in the project space", - "description": "[EXPERIMENTAL] Get table of all fold changes in the project space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeatureFoldChangeTableExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/AggregationType" - } - }, - { - "name": "quantification", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" - } - } - ], - "responses": { - "200": { - "description": "table of fold changes.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/StatisticsTable" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/quant-table": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId).\n
\n Returns the full quantification table. The quantification table contains a quantities of the features within all\n runs they are contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFeatureQuantTableExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "type", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" - } - } - ], - "responses": { - "200": { - "description": "Quant table if akk feature in this project", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Get all available features (aligned over runs) in the given project-space.", - "description": "Get all available features (aligned over runs) in the given project-space.", - "operationId": "getAlignedFeaturesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/grouped": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get features (aligned over runs) by tag group", - "description": "[EXPERIMENTAL] Get features (aligned over runs) by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeaturesByGroupExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "groupName", - "in": "query", - "description": "tag group name.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeatureOptField" - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "tagged features (aligned over runs)", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/job-configs": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Request all available job configurations", - "description": "Request all available job configurations", - "operationId": "getJobConfigs", - "responses": { - "200": { - "description": "list of available {@link JobSubmission JobSubmission}s", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StoredJobSubmission" - } - } - } - } - } - } - } - }, - "/api/job-config-names": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "[DEPRECATED] Get all (non-default) job configuration names\n ", - "description": "[DEPRECATED] Get all (non-default) job configuration names\n
\n [DEPRECATED] Use /job-configs to get all configs with names. This endpoint is based on local file paths and will likely be removed in future versions of this API.", - "operationId": "getJobConfigNames", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - } - } - }, - "deprecated": true - } - }, - "/api/info": { - "get": { - "tags": [ - "Info" - ], - "operationId": "getInfo", - "parameters": [ - { - "name": "serverInfo", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - }, - { - "name": "updateInfo", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Info" - } - } - } - } - } - } - }, - "/api/guis": { - "get": { - "tags": [ - "Gui" - ], - "summary": "Get list of currently running gui windows, managed by this SIRIUS instance.", - "description": "Get list of currently running gui windows, managed by this SIRIUS instance.\n Note this will not show any Clients that are connected from a separate process!", - "operationId": "getGuis", - "responses": { - "200": { - "description": "List of GUI windows that are currently managed by this SIRIUS instance.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/GuiInfo" - } - } - } - } - } - } - } - }, - "/api/default-job-config": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Request default job configuration", - "description": "Request default job configuration", - "operationId": "getDefaultJobConfig", - "parameters": [ - { - "name": "includeConfigMap", - "in": "query", - "description": "if true, generic configmap with-defaults will be included", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "moveParametersToConfigMap", - "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "includeCustomDbsForStructureSearch", - "in": "query", - "description": "if true, default database selection of structure db search\n spectral library search contains also all available custom DB.\n If No custom dbs are selected, spectral library search is disabled by default.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "{@link JobSubmission JobSubmission} with all parameters set to default values.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } - } - } - } - } - } - }, - "/api/databases/included": { - "get": { - "tags": [ - "Searchable Databases" - ], - "operationId": "getIncludedDatabases", - "parameters": [ - { - "name": "includeStats", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - } - } - }, - "/api/databases/custom": { - "get": { - "tags": [ - "Searchable Databases" - ], - "operationId": "getCustomDatabases", - "parameters": [ - { - "name": "includeStats", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "includeWithErrors", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - } - } - }, - "/api/connection-status": { - "get": { - "tags": [ - "Info" - ], - "operationId": "getConnectionCheck", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ConnectionCheck" - } - } - } - } - } - } - }, - "/api/account/subscriptions": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get available subscriptions of the account currently logged in.", - "description": "Get available subscriptions of the account currently logged in. Fails if not logged in.", - "operationId": "getSubscriptions", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Subscription" - } - } - } - } - } - } - } - }, - "/api/account/signUp": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Open SignUp window in system browser and return signUp link.", - "description": "Open SignUp window in system browser and return signUp link.", - "operationId": "signUp", - "responses": { - "200": { - "description": "OK", - "content": { - "text/plain;charset=UTF-8": { - "schema": { - "type": "string" - } - } - } - } - } - } - }, - "/api/account/signUpURL": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get SignUp URL (For signUp via web browser)", - "description": "Get SignUp URL (For signUp via web browser)", - "operationId": "getSignUpURL", - "responses": { - "200": { - "description": "OK", - "content": { - "text/plain;charset=UTF-8": { - "schema": { - "type": "string" - } - } - } - } - } - } - }, - "/api/account/openPortal": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Open User portal in browser.", - "description": "Open User portal in browser. If user is logged in SIRIUS tries to transfer the login state to the browser.", - "operationId": "openPortal", - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/isLoggedIn": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Check if a user is logged in.", - "description": "Check if a user is logged in.", - "operationId": "isLoggedIn", - "responses": { - "200": { - "description": "true if the user is logged in", - "content": { - "application/json": { - "schema": { - "type": "boolean" - } - } - } - } - } - } - }, - "/api/account/": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get information about the account currently logged in.", - "description": "Get information about the account currently logged in. Fails if not logged in.", - "operationId": "getAccountInfo", - "parameters": [ - { - "name": "includeSubs", - "in": "query", - "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Basic information about the account that has been logged in and its subscriptions.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AccountInfo" - } - } - } - } - } - } - }, - "/actuator/health": { - "get": { - "tags": [ - "Actuator" - ], - "summary": "Actuator web endpoint 'health'", - "operationId": "health", - "responses": { - "200": { - "description": "OK", - "content": { - "application/vnd.spring-boot.actuator.v3+json": { - "schema": { - "type": "object" - } - }, - "application/vnd.spring-boot.actuator.v2+json": { - "schema": { - "type": "object" - } - }, - "application/json": { - "schema": { - "type": "object" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/runs/tags/{runId}/{tagName}": { - "delete": { - "tags": [ - "Runs" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromRunExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "runId", - "in": "path", - "description": "run to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds/tags/{compoundId}/{tagName}": { - "delete": { - "tags": [ - "Compounds" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromCompoundExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "compoundId", - "in": "path", - "description": "compound (group of ion identities) to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds/statistics/foldchanges": { - "delete": { - "tags": [ - "Compound Statistics" - ], - "summary": "[EXPERIMENTAL] Delete fold changes", - "description": "[EXPERIMENTAL] Delete fold changes.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteCompoundFoldChangesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "rightGroupName", - "in": "query", - "description": "name of the right group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "required": false, - "schema": { - "$ref": "#/components/schemas/AggregationType" - } - }, - { - "name": "quantification", - "in": "query", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName}": { - "delete": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromAlignedFeatureExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges": { - "delete": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] Delete fold changes", - "description": "[EXPERIMENTAL] Delete fold changes.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteAlignedFeatureFoldChangesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "rightGroupName", - "in": "query", - "description": "name of the right group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "required": false, - "schema": { - "$ref": "#/components/schemas/AggregationType" - } - }, - { - "name": "quantification", - "in": "query", - "required": false, - "schema": { - "$ref": "#/components/schemas/QuantMeasure" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - } - }, - "components": { - "schemas": { - "ProjectChangeEvent": { - "type": "object", - "properties": { - "eventType": { - "$ref": "#/components/schemas/ProjectEventType" - }, - "projectId": { - "type": "string" - }, - "compoundId": { - "type": "string", - "nullable": true - }, - "featuredId": { - "type": "string", - "nullable": true - }, - "formulaId": { - "type": "string", - "nullable": true - }, - "structureInChIKey": { - "type": "string", - "nullable": true - } - } - }, - "DataImportEvent": { - "required": [ - "importedCompoundIds", - "importedFeatureIds" - ], - "type": "object", - "properties": { - "importJobId": { - "type": "string", - "nullable": true - }, - "importedCompoundIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "importedFeatureIds": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "BackgroundComputationsStateEvent": { - "required": [ - "affectedJobs", - "numberOfFinishedJobs", - "numberOfJobs", - "numberOfRunningJobs" - ], - "type": "object", - "properties": { - "affectedJobs": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Job" - } - }, - "numberOfJobs": { - "type": "integer", - "format": "int32" - }, - "numberOfRunningJobs": { - "type": "integer", - "format": "int32" - }, - "numberOfFinishedJobs": { - "type": "integer", - "format": "int32" - } - } - }, - "ProjectEventType": { - "type": "string", - "enum": [ - "PROJECT_OPENED", - "PROJECT_MOVED", - "PROJECT_CLOSED", - "FEATURE_CREATED", - "FEATURE_UPDATED", - "FEATURE_DELETED", - "RESULT_CREATED", - "RESULT_UPDATED", - "RESULT_DELETED" - ] - }, - "ProjectInfoOptField": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "compatibilityInfo", - "sizeInformation" - ] - }, - "ProjectInfo": { - "type": "object", - "properties": { - "projectId": { - "type": "string", - "description": "a user selected unique name of the project for easy access." - }, - "location": { - "type": "string", - "description": "storage location of the project." - }, - "description": { - "type": "string", - "description": "Description of this project.", - "nullable": true - }, - "type": { - "$ref": "#/components/schemas/ProjectType" - }, - "compatible": { - "type": "boolean", - "description": "Indicates whether computed results (e.g. fingerprints, compounds classes) are compatible with the backend.\n If true project is up-to-date and there are no restrictions regarding usage.\n If false project is incompatible and therefore \"read only\" until the incompatible results have been removed. See updateProject endpoint for further information\n If NULL the information has not been requested.", - "nullable": true - }, - "numOfFeatures": { - "type": "integer", - "description": "Number of features (aligned over runs) in this project. If NULL, information has not been requested (See OptField 'sizeInformation').", - "format": "int32", - "nullable": true - }, - "numOfCompounds": { - "type": "integer", - "description": "Number of compounds (group of ion identities) in this project. If NULL, Information has not been requested (See OptField 'sizeInformation') or might be unavailable for this project type.", - "format": "int32", - "nullable": true - }, - "numOfBytes": { - "type": "integer", - "description": "Size in Bytes this project consumes on disk If NULL, Information has not been requested (See OptField 'sizeInformation').", - "format": "int64", - "nullable": true - } - } - }, - "ProjectType": { - "type": "string", - "nullable": true, - "enum": [ - "UNIMPORTED", - "DIRECT_IMPORT", - "PEAKLISTS", - "ALIGNED_RUNS", - "UNALIGNED_RUNS" - ] - }, - "TagDefinitionImport": { - "required": [ - "tagName", - "valueType" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of this tag defined by this definition (key)" - }, - "description": { - "type": "string", - "description": "A human-readable description about the purpose of this tag.", - "nullable": true - }, - "tagType": { - "type": "string", - "description": "A simple string based identifier to specify the type/scope/purpose of this tag.", - "nullable": true - }, - "valueType": { - "$ref": "#/components/schemas/ValueType" - }, - "possibleValues": { - "type": "array", - "nullable": true, - "items": { - "type": "object", - "nullable": true - } - }, - "minValue": { - "type": "object", - "nullable": true - }, - "maxValue": { - "type": "object", - "nullable": true - } - } - }, - "ValueType": { - "type": "string", - "enum": [ - "NONE", - "BOOLEAN", - "INTEGER", - "REAL", - "TEXT", - "DATE", - "TIME" - ] - }, - "TagDefinition": { - "required": [ - "tagName", - "valueType" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of this tag defined by this definition (key)" - }, - "description": { - "type": "string", - "description": "A human-readable description about the purpose of this tag.", - "nullable": true - }, - "tagType": { - "type": "string", - "description": "A simple string based identifier to specify the type/scope/purpose of this tag.", - "nullable": true - }, - "valueType": { - "$ref": "#/components/schemas/ValueType" - }, - "possibleValues": { - "type": "array", - "nullable": true, - "items": { - "type": "object", - "nullable": true - } - }, - "minValue": { - "type": "object", - "nullable": true - }, - "maxValue": { - "type": "object", - "nullable": true - }, - "editable": { - "type": "boolean" - } - } - }, - "Tag": { - "required": [ - "tagName" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of the tag as defined by the corresponding TagDefinition\n Links tag object to their definition." - }, - "value": { - "type": "object", - "description": "Optional value of the tag.\n
\n Generic value of the tag as defined by the corresponding TagDefinition.\n Can be Integer, Double, Boolean and String, whereas String values can represent Text, Date (yyyy-MM-dd) or Time (HH:mm:ss).", - "nullable": true - } - } - }, - "SampleTypeFoldChangeRequest": { - "type": "object", - "properties": { - "sampleRunIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "blankRunIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "controlRunIds": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "JobOptField": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "command", - "progress", - "affectedIds" - ] - }, - "Job": { - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "Unique identifier to access the job via the API" - }, - "command": { - "type": "string", - "description": "Command string of the executed Task", - "nullable": true - }, - "progress": { - "$ref": "#/components/schemas/JobProgress" - }, - "affectedCompoundIds": { - "type": "array", - "description": "List of compoundIds that are affected by this job.\n This lis will also contain compoundIds where not all features of the compound are affected by the job.\n If this job is creating compounds (e.g. data import jobs) this value will be NULL until the jobs has finished", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "affectedAlignedFeatureIds": { - "type": "array", - "description": "List of alignedFeatureIds that are affected by this job.\n If this job is creating features (e.g. data import jobs) this value will be NULL until the jobs has finished", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "jobEffect": { - "$ref": "#/components/schemas/JobEffect" - } - }, - "description": "Identifier created by the SIRIUS Nightsky API for a newly created Job.\n Object can be enriched with Job status/progress information ({@link JobProgress JobProgress}) and/or Job command information.\n This is a return value of the API. So nullable values can also be NOT_REQUIRED to allow for easy removal." - }, - "JobEffect": { - "type": "string", - "nullable": true, - "enum": [ - "IMPORT", - "COMPUTATION", - "DELETION" - ] - }, - "JobProgress": { - "type": "object", - "properties": { - "indeterminate": { - "type": "boolean", - "description": "Is the progress indeterminate or not", - "nullable": true - }, - "state": { - "$ref": "#/components/schemas/JobState" - }, - "currentProgress": { - "type": "integer", - "description": "Current progress value of the job.", - "format": "int64", - "nullable": true - }, - "maxProgress": { - "type": "integer", - "description": "Progress value to reach (might also change during execution)", - "format": "int64", - "nullable": true - }, - "message": { - "type": "string", - "description": "Progress information and warnings.", - "nullable": true - }, - "errorMessage": { - "type": "string", - "description": "Error message if the job did not finish successfully failed.", - "nullable": true - } - }, - "description": "Progress information of a computation job that has already been submitted to SIRIUS.\n if currentProgress == maxProgress job is finished and should change to state done soon.\n if a job is DONE all results can be accessed via the Project-Spaces api.", - "nullable": true - }, - "JobState": { - "type": "string", - "enum": [ - "WAITING", - "READY", - "QUEUED", - "SUBMITTED", - "RUNNING", - "CANCELED", - "FAILED", - "DONE" - ] - }, - "AggregationType": { - "type": "string", - "enum": [ - "AVG", - "MIN", - "MAX" - ] - }, - "QuantMeasure": { - "type": "string", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - }, - "BasicSpectrum": { - "required": [ - "cosineQuery", - "peaks" - ], + } + }, + "components": { + "schemas": { + "ProjectChangeEvent": { "type": "object", "properties": { - "name": { - "type": "string", - "description": "Optional Displayable name of this spectrum.", - "nullable": true - }, - "msLevel": { - "type": "integer", - "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", - "format": "int32", - "nullable": true - }, - "collisionEnergy": { - "type": "string", - "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", - "nullable": true - }, - "instrument": { - "type": "string", - "description": "Instrument information.", - "nullable": true - }, - "precursorMz": { - "type": "number", - "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", - "format": "double", - "nullable": true - }, - "scanNumber": { - "type": "integer", - "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", - "format": "int32", - "nullable": true - }, - "cosineQuery": { - "type": "boolean", - "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", - "default": false - }, - "precursorPeak": { - "$ref": "#/components/schemas/SimplePeak" - }, - "peaks": { - "type": "array", - "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", - "items": { - "$ref": "#/components/schemas/SimplePeak" - } - }, - "absIntensityFactor": { - "type": "number", - "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", - "format": "double", - "nullable": true, - "deprecated": true + "eventType": { + "$ref": "#/components/schemas/ProjectEventType" }, - "maxNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to MAX norm.", - "format": "double", - "nullable": true + "projectId": { + "type": "string" }, - "sumNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to SUM norm.", - "format": "double", + "compoundId": { + "type": "string", "nullable": true }, - "l2NormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", - "format": "double", + "featuredId": { + "type": "string", "nullable": true }, - "firstPeakNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", - "format": "double", + "formulaId": { + "type": "string", "nullable": true - } - }, - "nullable": true - }, - "BinaryFingerprint": { - "type": "object", - "properties": { - "bitsSet": { - "type": "array", - "description": "Array that contains all RELATIVE indices (masked FP) of bits that are set (are 1)", - "items": { - "type": "integer", - "format": "int32" - } - }, - "length": { - "type": "integer", - "description": "Size of the fingerprint (masked fp), e.g. to reconstruct the binary array from the array of set bits", - "format": "int32" - } - }, - "nullable": true - }, - "DBLink": { - "required": [ - "name" - ], - "type": "object", - "properties": { - "name": { - "type": "string" }, - "id": { - "type": "string" + "structureInChIKey": { + "type": "string", + "nullable": true } - }, - "nullable": true + } }, - "PeakPair": { + "DataImportEvent": { "required": [ - "queryPeak", - "referencePeak" + "importedCompoundIds", + "importedFeatureIds" ], "type": "object", "properties": { - "queryPeak": { - "type": "integer", - "format": "int32" + "importJobId": { + "type": "string", + "nullable": true }, - "referencePeak": { - "type": "integer", - "format": "int32" - } - } - }, - "SimplePeak": { - "type": "object", - "properties": { - "mz": { - "type": "number", - "format": "double" + "importedCompoundIds": { + "type": "array", + "items": { + "type": "string" + } }, - "intensity": { - "type": "number", - "format": "double" + "importedFeatureIds": { + "type": "array", + "items": { + "type": "string" + } } } }, - "SpectralLibraryMatch": { + "BackgroundComputationsStateEvent": { "required": [ - "inchiKey", - "querySpectrumIndex", - "similarity", - "uuid" + "affectedJobs", + "numberOfFinishedJobs", + "numberOfJobs", + "numberOfRunningJobs" ], "type": "object", "properties": { - "specMatchId": { - "type": "string" - }, - "rank": { - "type": "integer", - "format": "int32" - }, - "similarity": { - "type": "number", - "description": "Similarity between query and reference spectrum", - "format": "float" - }, - "sharedPeaks": { - "type": "integer", - "description": "Number of shared/matched peaks", - "format": "int32" - }, - "sharedPeakMapping": { + "affectedJobs": { "type": "array", - "description": "List of paired/matched peak indices.\n\n Maps indices of peaks from the query spectrum (mass sorted)\n to indices of matched peaks in the reference spectrum (mass sorted)", "items": { - "$ref": "#/components/schemas/PeakPair" + "$ref": "#/components/schemas/Job" } }, - "querySpectrumIndex": { + "numberOfJobs": { "type": "integer", "format": "int32" }, - "dbName": { - "type": "string" - }, - "dbId": { - "type": "string" - }, - "uuid": { + "numberOfRunningJobs": { "type": "integer", - "format": "int64" - }, - "splash": { - "type": "string" - }, - "molecularFormula": { - "type": "string" - }, - "adduct": { - "type": "string" - }, - "exactMass": { - "type": "number", - "format": "double" - }, - "smiles": { - "type": "string" - }, - "type": { - "$ref": "#/components/schemas/SpectralMatchType" - }, - "inchiKey": { - "type": "string" - }, - "referenceSpectrumType": { - "$ref": "#/components/schemas/SpectrumType" - }, - "referenceSpectrum": { - "$ref": "#/components/schemas/BasicSpectrum" + "format": "int32" }, - "querySpectrumType": { - "$ref": "#/components/schemas/SpectrumType" + "numberOfFinishedJobs": { + "type": "integer", + "format": "int32" } - }, - "nullable": true + } }, - "SpectralMatchType": { + "ProjectEventType": { "type": "string", - "default": "IDENTITY", "enum": [ - "IDENTITY", - "ANALOG" + "PROJECT_OPENED", + "PROJECT_MOVED", + "PROJECT_CLOSED", + "FEATURE_CREATED", + "FEATURE_UPDATED", + "FEATURE_DELETED", + "RESULT_CREATED", + "RESULT_UPDATED", + "RESULT_DELETED" ] }, - "SpectrumType": { + "ProjectInfoOptField": { "type": "string", + "nullable": true, "enum": [ - "SPECTRUM", - "MERGED_SPECTRUM" + "none", + "compatibilityInfo", + "sizeInformation" ] }, - "StructureCandidateFormula": { + "ProjectInfo": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" - }, - "structureName": { + "projectId": { "type": "string", - "nullable": true + "description": "a user selected unique name of the project for easy access." }, - "structureSvg": { + "location": { "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true - }, - "dbLinks": { - "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/DBLink" - } - }, - "spectralLibraryMatches": { - "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" - } - }, - "xlogP": { - "type": "number", - "format": "double", - "nullable": true - }, - "rank": { - "type": "integer", - "description": "the overall rank of this candidate among all candidates of this feature", - "format": "int32" - }, - "csiScore": { - "type": "number", - "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", - "format": "double" - }, - "tanimotoSimilarity": { - "type": "number", - "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", - "format": "double", - "nullable": true + "description": "storage location of the project." }, - "mcesDistToTopHit": { - "type": "number", - "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", - "format": "double", + "description": { + "type": "string", + "description": "Description of this project.", "nullable": true }, - "fingerprint": { - "$ref": "#/components/schemas/BinaryFingerprint" + "type": { + "$ref": "#/components/schemas/ProjectType" }, - "molecularFormula": { - "type": "string", - "description": "Molecular formula of this candidate" + "compatible": { + "type": "boolean", + "description": "Indicates whether computed results (e.g. fingerprints, compounds classes) are compatible with the backend.\n If true project is up-to-date and there are no restrictions regarding usage.\n If false project is incompatible and therefore \"read only\" until the incompatible results have been removed. See updateProject endpoint for further information\n If NULL the information has not been requested.", + "nullable": true }, - "adduct": { - "type": "string", - "description": "Adduct of this candidate" + "numOfFeatures": { + "type": "integer", + "description": "Number of features (aligned over runs) in this project. If NULL, information has not been requested (See OptField 'sizeInformation').", + "format": "int32", + "nullable": true }, - "formulaId": { - "type": "string", - "description": "Id of the corresponding Formula candidate" + "numOfCompounds": { + "type": "integer", + "description": "Number of compounds (group of ion identities) in this project. If NULL, Information has not been requested (See OptField 'sizeInformation') or might be unavailable for this project type.", + "format": "int32", + "nullable": true + }, + "numOfBytes": { + "type": "integer", + "description": "Size in Bytes this project consumes on disk If NULL, Information has not been requested (See OptField 'sizeInformation').", + "format": "int64", + "nullable": true } } }, + "ProjectType": { + "type": "string", + "nullable": true, + "enum": [ + "UNIMPORTED", + "DIRECT_IMPORT", + "PEAKLISTS", + "ALIGNED_RUNS", + "UNALIGNED_RUNS" + ] + }, "SearchableDatabaseParameters": { "type": "object", "properties": { @@ -8936,6 +5585,114 @@ }, "nullable": true }, + "JobOptField": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "command", + "progress", + "affectedIds" + ] + }, + "Job": { + "type": "object", + "properties": { + "id": { + "type": "string", + "description": "Unique identifier to access the job via the API" + }, + "command": { + "type": "string", + "description": "Command string of the executed Task", + "nullable": true + }, + "progress": { + "$ref": "#/components/schemas/JobProgress" + }, + "affectedCompoundIds": { + "type": "array", + "description": "List of compoundIds that are affected by this job.\n This lis will also contain compoundIds where not all features of the compound are affected by the job.\n If this job is creating compounds (e.g. data import jobs) this value will be NULL until the jobs has finished", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } + }, + "affectedAlignedFeatureIds": { + "type": "array", + "description": "List of alignedFeatureIds that are affected by this job.\n If this job is creating features (e.g. data import jobs) this value will be NULL until the jobs has finished", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } + }, + "jobEffect": { + "$ref": "#/components/schemas/JobEffect" + } + }, + "description": "Identifier created by the SIRIUS Nightsky API for a newly created Job.\n Object can be enriched with Job status/progress information ({@link JobProgress JobProgress}) and/or Job command information.\n This is a return value of the API. So nullable values can also be NOT_REQUIRED to allow for easy removal." + }, + "JobEffect": { + "type": "string", + "nullable": true, + "enum": [ + "IMPORT", + "COMPUTATION", + "DELETION" + ] + }, + "JobProgress": { + "type": "object", + "properties": { + "indeterminate": { + "type": "boolean", + "description": "Is the progress indeterminate or not", + "nullable": true + }, + "state": { + "$ref": "#/components/schemas/JobState" + }, + "currentProgress": { + "type": "integer", + "description": "Current progress value of the job.", + "format": "int64", + "nullable": true + }, + "maxProgress": { + "type": "integer", + "description": "Progress value to reach (might also change during execution)", + "format": "int64", + "nullable": true + }, + "message": { + "type": "string", + "description": "Progress information and warnings.", + "nullable": true + }, + "errorMessage": { + "type": "string", + "description": "Error message if the job did not finish successfully failed.", + "nullable": true + } + }, + "description": "Progress information of a computation job that has already been submitted to SIRIUS.\n if currentProgress == maxProgress job is finished and should change to state done soon.\n if a job is DONE all results can be accessed via the Project-Spaces api.", + "nullable": true + }, + "JobState": { + "type": "string", + "enum": [ + "WAITING", + "READY", + "QUEUED", + "SUBMITTED", + "RUNNING", + "CANCELED", + "FAILED", + "DONE" + ] + }, "ImportResult": { "required": [ "affectedAlignedFeatureIds", @@ -9007,21 +5764,94 @@ } } }, - "TagGroup": { + "BasicSpectrum": { + "required": [ + "cosineQuery", + "peaks" + ], "type": "object", "properties": { - "groupName": { + "name": { + "type": "string", + "description": "Optional Displayable name of this spectrum.", + "nullable": true + }, + "msLevel": { + "type": "integer", + "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", + "format": "int32", + "nullable": true + }, + "collisionEnergy": { "type": "string", - "description": "Name of this Grouping query." + "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", + "nullable": true }, - "luceneQuery": { + "instrument": { "type": "string", - "description": "Query used to group the entities in lucene format." + "description": "Instrument information.", + "nullable": true }, - "groupType": { - "type": "string" + "precursorMz": { + "type": "number", + "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", + "format": "double", + "nullable": true + }, + "scanNumber": { + "type": "integer", + "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", + "format": "int32", + "nullable": true + }, + "cosineQuery": { + "type": "boolean", + "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", + "default": false + }, + "precursorPeak": { + "$ref": "#/components/schemas/SimplePeak" + }, + "peaks": { + "type": "array", + "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", + "items": { + "$ref": "#/components/schemas/SimplePeak" + } + }, + "absIntensityFactor": { + "type": "number", + "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", + "format": "double", + "nullable": true, + "deprecated": true + }, + "maxNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to MAX norm.", + "format": "double", + "nullable": true + }, + "sumNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to SUM norm.", + "format": "double", + "nullable": true + }, + "l2NormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", + "format": "double", + "nullable": true + }, + "firstPeakNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", + "format": "double", + "nullable": true } - } + }, + "nullable": true }, "CompoundImport": { "required": [ @@ -9125,8 +5955,21 @@ "$ref": "#/components/schemas/BasicSpectrum" } } - }, - "description": "Represents an (aligned) feature to be imported into a SIRIUS project.\n At least one of the Mass Spec data sources (e.g. mergedMs1, ms1Spectra, ms2Spectra) needs to be given.\n Otherwise, the import will fail." + }, + "description": "Represents an (aligned) feature to be imported into a SIRIUS project.\n At least one of the Mass Spec data sources (e.g. mergedMs1, ms1Spectra, ms2Spectra) needs to be given.\n Otherwise, the import will fail." + }, + "SimplePeak": { + "type": "object", + "properties": { + "mz": { + "type": "number", + "format": "double" + }, + "intensity": { + "type": "number", + "format": "double" + } + } }, "CompoundOptField": { "type": "string", @@ -9351,6 +6194,25 @@ "description": "Spectrum model with peak annotations based on the fragmentation tree and Epimetheus substructure annotations.\n Molecular formula and adduct of the spectrum are identical to the ones of the corresponding molecular formula candidate and FragmentationTree.\n Fragment molecular formulas and adducts correspond to the FragmentationTree's FragmentNodes", "nullable": true }, + "BinaryFingerprint": { + "type": "object", + "properties": { + "bitsSet": { + "type": "array", + "description": "Array that contains all RELATIVE indices (masked FP) of bits that are set (are 1)", + "items": { + "type": "integer", + "format": "int32" + } + }, + "length": { + "type": "integer", + "description": "Size of the fingerprint (masked fp), e.g. to reconstruct the binary array from the array of set bits", + "format": "int32" + } + }, + "nullable": true + }, "CanopusPrediction": { "type": "object", "properties": { @@ -9645,1200 +6507,911 @@ "SINGLETON_FORMULA" ] }, - "FeatureAnnotations": { - "type": "object", - "properties": { - "formulaAnnotation": { - "$ref": "#/components/schemas/FormulaCandidate" - }, - "structureAnnotation": { - "$ref": "#/components/schemas/StructureCandidateScored" - }, - "compoundClassAnnotation": { - "$ref": "#/components/schemas/CompoundClasses" - }, - "confidenceExactMatch": { - "type": "number", - "description": "Confidence Score that represents the confidence whether the top hit is correct.", - "format": "double", - "nullable": true - }, - "confidenceApproxMatch": { - "type": "number", - "description": "Confidence Score that represents the confidence whether the top hit or a very similar hit (estimated by MCES distance) is correct.", - "format": "double", - "nullable": true - }, - "expansiveSearchState": { - "$ref": "#/components/schemas/ConfidenceMode" - }, - "specifiedDatabases": { - "type": "array", - "description": "List of databases that have been specified by for structure db search. Null if no structure db search has been performed.", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "expandedDatabases": { - "type": "array", - "description": "List of databases that have been used to expand search space during expansive search. Null if no structure db search has been performed.", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - } - }, - "description": "Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature.\n The different annotation fields within this summary object are null if the corresponding\n feature does not contain the represented results. If fields are non-null\n the corresponding result has been computed but might still be empty.", - "nullable": true - }, - "FormulaCandidate": { - "type": "object", - "properties": { - "formulaId": { - "type": "string", - "description": "Unique identifier of this formula candidate" - }, - "molecularFormula": { - "type": "string", - "description": "molecular formula of this formula candidate" - }, - "adduct": { - "type": "string", - "description": "Adduct of this formula candidate" - }, - "rank": { - "type": "integer", - "format": "int32" - }, - "siriusScoreNormalized": { - "type": "number", - "description": "Normalized Sirius Score of the formula candidate.\n If NULL result is not available", - "format": "double", - "nullable": true - }, - "siriusScore": { - "type": "number", - "description": "Sirius Score (isotope + tree score) of the formula candidate.\n If NULL result is not available", - "format": "double", - "nullable": true - }, - "isotopeScore": { - "type": "number", - "format": "double", - "nullable": true - }, - "treeScore": { - "type": "number", - "format": "double", - "nullable": true - }, - "zodiacScore": { - "type": "number", - "description": "Zodiac Score of the formula candidate.\n If NULL result is not available", - "format": "double", - "nullable": true - }, - "numOfExplainedPeaks": { - "type": "integer", - "format": "int32", - "nullable": true - }, - "numOfExplainablePeaks": { - "type": "integer", - "format": "int32", - "nullable": true - }, - "totalExplainedIntensity": { - "type": "number", - "format": "double", - "nullable": true - }, - "medianMassDeviation": { - "$ref": "#/components/schemas/Deviation" - }, - "fragmentationTree": { - "$ref": "#/components/schemas/FragmentationTree" - }, - "annotatedSpectrum": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - }, - "isotopePatternAnnotation": { - "$ref": "#/components/schemas/IsotopePatternAnnotation" - }, - "lipidAnnotation": { - "$ref": "#/components/schemas/LipidAnnotation" - }, - "predictedFingerprint": { - "type": "array", - "description": "Probabilistic molecular fingerprint predicted by CSI:FingerID", - "nullable": true, - "items": { - "type": "number", - "format": "double", - "nullable": true - } - }, - "compoundClasses": { - "$ref": "#/components/schemas/CompoundClasses" - }, - "canopusPrediction": { - "$ref": "#/components/schemas/CanopusPrediction" - } - }, - "description": "Molecular formula candidate that holds a unique identifier (molecular formula + adduct).\n It can be extended with optional scoring metrics and the raw results\n such as fragmentation trees and simulated isotope pattern.", - "nullable": true - }, - "FragmentNode": { - "type": "object", - "properties": { - "fragmentId": { - "type": "integer", - "format": "int32" - }, - "molecularFormula": { - "type": "string", - "description": "neutral molecular formula of the fragment without adduct", - "nullable": true - }, - "adduct": { - "type": "string", - "description": "This combines the ionization plus adduct of the fragment. In contrast to the {@link FragmentationTree FragmentationTree}s adduct,\n this adduct may not include any in-source loss.", - "nullable": true - }, - "massDeviationDa": { - "type": "number", - "format": "double", - "nullable": true - }, - "massDeviationPpm": { - "type": "number", - "format": "double", - "nullable": true - }, - "score": { - "type": "number", - "format": "double", - "nullable": true - }, - "intensity": { - "type": "number", - "format": "double", - "nullable": true - }, - "mz": { - "type": "number", - "format": "double", - "nullable": true - } - } - }, - "FragmentationTree": { - "type": "object", - "properties": { - "fragments": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FragmentNode" - } - }, - "losses": { - "type": "array", - "items": { - "$ref": "#/components/schemas/LossEdge" - } - }, - "treeScore": { - "type": "number", - "format": "double" - }, - "molecularFormula": { - "type": "string" - }, - "adduct": { - "type": "string" - } - }, - "description": "Simple and easy serializable fragmentation tree model with annotated fragments/nodes abd losses/edges\n Root fragment has index 0;\n Molecular formula and adduct are identical to the ones of the corresponding molecular formula candidate and SpectrumAnnotation", - "nullable": true - }, - "IsotopePatternAnnotation": { - "type": "object", - "properties": { - "isotopePattern": { - "$ref": "#/components/schemas/BasicSpectrum" - }, - "simulatedPattern": { - "$ref": "#/components/schemas/BasicSpectrum" - } - }, - "nullable": true - }, - "LipidAnnotation": { + "DBLink": { + "required": [ + "name" + ], "type": "object", "properties": { - "lipidSpecies": { - "type": "string", - "description": "Predicted lipid species in LIPID MAPS notation.\n NULL if not classified as lipid.", - "nullable": true - }, - "lipidMapsId": { - "type": "string", - "description": "LIPID MAPS id of the predicted lipid class.", - "nullable": true - }, - "lipidClassName": { - "type": "string", - "description": "Human-readable name of the predicted lipid class.", - "nullable": true - }, - "hypotheticalStructure": { - "type": "string", - "description": "Hypothetical molecular structure of the predicted lipid species as SMILES.\n NULL if hypothetical structure not available.", - "nullable": true + "name": { + "type": "string" }, - "chainsUnknown": { - "type": "boolean", - "description": "True of the formula composition of the chains could not be determined from the MS/MS.", - "nullable": true + "id": { + "type": "string" } }, "nullable": true }, - "LossEdge": { + "FeatureAnnotations": { "type": "object", "properties": { - "sourceFragmentIdx": { - "type": "integer", - "format": "int32" + "formulaAnnotation": { + "$ref": "#/components/schemas/FormulaCandidate" }, - "targetFragmentIdx": { - "type": "integer", - "format": "int32" + "structureAnnotation": { + "$ref": "#/components/schemas/StructureCandidateScored" }, - "molecularFormula": { - "type": "string" + "compoundClassAnnotation": { + "$ref": "#/components/schemas/CompoundClasses" }, - "score": { + "confidenceExactMatch": { "type": "number", - "format": "double" - } - } - }, - "MsData": { - "type": "object", - "properties": { - "isotopePattern": { - "$ref": "#/components/schemas/BasicSpectrum" + "description": "Confidence Score that represents the confidence whether the top hit is correct.", + "format": "double", + "nullable": true }, - "mergedMs1": { - "$ref": "#/components/schemas/BasicSpectrum" + "confidenceApproxMatch": { + "type": "number", + "description": "Confidence Score that represents the confidence whether the top hit or a very similar hit (estimated by MCES distance) is correct.", + "format": "double", + "nullable": true }, - "mergedMs2": { - "$ref": "#/components/schemas/BasicSpectrum" + "expansiveSearchState": { + "$ref": "#/components/schemas/ConfidenceMode" }, - "ms1Spectra": { + "specifiedDatabases": { "type": "array", + "description": "List of databases that have been specified by for structure db search. Null if no structure db search has been performed.", + "nullable": true, "items": { - "$ref": "#/components/schemas/BasicSpectrum" + "type": "string", + "nullable": true } }, - "ms2Spectra": { + "expandedDatabases": { "type": "array", + "description": "List of databases that have been used to expand search space during expansive search. Null if no structure db search has been performed.", + "nullable": true, "items": { - "$ref": "#/components/schemas/BasicSpectrum" + "type": "string", + "nullable": true } } }, - "description": "The MsData wraps all spectral input data belonging to a (aligned) feature. All spectra fields are optional.\n However, at least one Spectrum field needs to be set to create a valid MsData Object.\n The different types of spectra fields can be extended to adapt to other MassSpec measurement techniques not covered yet.\n
\n Each Feature can have:\n - One extracted isotope pattern (optional)\n - One merged MS/MS spectrum (optional)\n - One merged MS spectrum (optional)\n - many MS/MS spectra (optional)\n - many MS spectra (optional)\n
\n Each non-merged spectrum has an index which can be used to access the spectrum.\n
\n In the future we might add some additional information like chromatographic peak or something similar", + "description": "Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature.\n The different annotation fields within this summary object are null if the corresponding\n feature does not contain the represented results. If fields are non-null\n the corresponding result has been computed but might still be empty.", "nullable": true }, - "ParentPeak": { - "required": [ - "lossFormula", - "parentFragmentId", - "parentIdx" - ], + "FormulaCandidate": { "type": "object", "properties": { - "parentIdx": { - "type": "integer", - "description": "Index to the parent peak connected by this loss in this particular spectrum", - "format": "int32" - }, - "parentFragmentId": { - "type": "integer", - "description": "Identifier of the parent fragment connected via this loss. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", - "format": "int32" - }, - "lossFormula": { + "formulaId": { "type": "string", - "description": "Molecular formula of the neutral loss that connects these two peaks." - } - }, - "description": "Link from annotated fragment peak to its parent fragment peak connected by their neutral loss.", - "nullable": true - }, - "PeakAnnotation": { - "required": [ - "fragmentId" - ], - "type": "object", - "properties": { - "fragmentId": { - "type": "integer", - "description": "Identifier of the peak/fragment. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", - "format": "int32" + "description": "Unique identifier of this formula candidate" }, "molecularFormula": { "type": "string", - "description": "Molecular formula that has been annotated to this peak", - "nullable": true + "description": "molecular formula of this formula candidate" }, "adduct": { "type": "string", - "description": "Adduct that has been annotated to this peak", + "description": "Adduct of this formula candidate" + }, + "rank": { + "type": "integer", + "format": "int32" + }, + "siriusScoreNormalized": { + "type": "number", + "description": "Normalized Sirius Score of the formula candidate.\n If NULL result is not available", + "format": "double", "nullable": true }, - "exactMass": { + "siriusScore": { "type": "number", - "description": "Exact mass of the annotated molecular formula and adduct", + "description": "Sirius Score (isotope + tree score) of the formula candidate.\n If NULL result is not available", "format": "double", "nullable": true }, - "massDeviationMz": { + "isotopeScore": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the measured peak mass in mDa", "format": "double", "nullable": true }, - "massDeviationPpm": { + "treeScore": { "type": "number", - "description": "Relative mass deviation of the exact mass to the measured peak mass in ppm", "format": "double", "nullable": true }, - "recalibratedMassDeviationMz": { + "zodiacScore": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the recalibrated peak mass in mDa", + "description": "Zodiac Score of the formula candidate.\n If NULL result is not available", "format": "double", "nullable": true }, - "recalibratedMassDeviationPpm": { + "numOfExplainedPeaks": { + "type": "integer", + "format": "int32", + "nullable": true + }, + "numOfExplainablePeaks": { + "type": "integer", + "format": "int32", + "nullable": true + }, + "totalExplainedIntensity": { "type": "number", - "description": "Relative mass deviation of the exact mass to the recalibrated peak mass in ppm", "format": "double", "nullable": true }, - "parentPeak": { - "$ref": "#/components/schemas/ParentPeak" + "medianMassDeviation": { + "$ref": "#/components/schemas/Deviation" }, - "substructureAtoms": { - "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the atoms of the structure candidate that are part of this fragments substructure\n (highlighted atoms)", - "nullable": true, - "items": { - "type": "integer", - "format": "int32", - "nullable": true - } + "fragmentationTree": { + "$ref": "#/components/schemas/FragmentationTree" }, - "substructureBonds": { - "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that are part of this fragments substructure\n (highlighted bonds)\n\n Null if substructure annotation not available or not requested.", - "nullable": true, - "items": { - "type": "integer", - "format": "int32", - "nullable": true - } + "annotatedSpectrum": { + "$ref": "#/components/schemas/AnnotatedSpectrum" }, - "substructureBondsCut": { + "isotopePatternAnnotation": { + "$ref": "#/components/schemas/IsotopePatternAnnotation" + }, + "lipidAnnotation": { + "$ref": "#/components/schemas/LipidAnnotation" + }, + "predictedFingerprint": { "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that need to be cut to produce this fragments\n substructure (highlighted cutted bonds).\n\n Null if substructure annotation not available or not requested.", + "description": "Probabilistic molecular fingerprint predicted by CSI:FingerID", "nullable": true, "items": { - "type": "integer", - "format": "int32", + "type": "number", + "format": "double", "nullable": true } }, - "substructureScore": { - "type": "number", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n This score roughly reflects the probability of this fragment forming.\n\n This is the score of the path from root to this node which has the maximal score or \"profit\".\n The score of a path is equal to the sum of scores of its contained fragments and edges.\n Note: Refers to 'totalScore' in CombinatorialNode\n\n Null if substructure annotation not available or not requested.", - "format": "float", - "nullable": true + "compoundClasses": { + "$ref": "#/components/schemas/CompoundClasses" }, - "hydrogenRearrangements": { - "type": "integer", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Number of hydrogens rearrangements needed to match the substructure to the fragment formula.\n\n Null if substructure annotation not available or not requested.", - "format": "int32", - "nullable": true + "canopusPrediction": { + "$ref": "#/components/schemas/CanopusPrediction" } }, + "description": "Molecular formula candidate that holds a unique identifier (molecular formula + adduct).\n It can be extended with optional scoring metrics and the raw results\n such as fragmentation trees and simulated isotope pattern.", "nullable": true }, - "SpectrumAnnotation": { + "FragmentNode": { "type": "object", "properties": { + "fragmentId": { + "type": "integer", + "format": "int32" + }, "molecularFormula": { "type": "string", - "description": "Molecular formula that has been annotated to this spectrum", + "description": "neutral molecular formula of the fragment without adduct", "nullable": true }, "adduct": { "type": "string", - "description": "Adduct that has been annotated to this spectrum", + "description": "This combines the ionization plus adduct of the fragment. In contrast to the {@link FragmentationTree FragmentationTree}s adduct,\n this adduct may not include any in-source loss.", "nullable": true }, - "exactMass": { + "massDeviationDa": { "type": "number", - "description": "Exact mass based on the annotated molecular formula and ionization", "format": "double", "nullable": true }, - "massDeviationMz": { + "massDeviationPpm": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in mDa", "format": "double", "nullable": true }, - "massDeviationPpm": { + "score": { "type": "number", - "description": "Relative mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in ppm", "format": "double", "nullable": true }, - "structureAnnotationSmiles": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Smiles of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refer to this specific SMILES.\n If you standardize or canonicalize this SMILES in any way the indices of substructure highlighting might\n not match correctly anymore.\n
\n Null if substructure annotation not available or not requested.", - "nullable": true - }, - "structureAnnotationName": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Name of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation.\n
\n Null if substructure annotation not available or not requested.", - "nullable": true - }, - "structureAnnotationSvg": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n SVG graphics of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refers to this SVG.\n
\n Null if substructure annotation not available or not requested.", + "intensity": { + "type": "number", + "format": "double", "nullable": true }, - "structureAnnotationScore": { + "mz": { "type": "number", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Overall score of all substructure annotations computed for this structure candidate (structureAnnotationSmiles)\n
\n Null if substructure annotation not available or not requested.", "format": "double", "nullable": true } - }, - "nullable": true + } }, - "StructureCandidate": { + "FragmentationTree": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" - }, - "structureName": { - "type": "string", - "nullable": true - }, - "structureSvg": { - "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true - }, - "dbLinks": { + "fragments": { "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, "items": { - "$ref": "#/components/schemas/DBLink" + "$ref": "#/components/schemas/FragmentNode" } }, - "spectralLibraryMatches": { + "losses": { "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "$ref": "#/components/schemas/LossEdge" } }, - "xlogP": { + "treeScore": { "type": "number", - "format": "double", - "nullable": true + "format": "double" + }, + "molecularFormula": { + "type": "string" + }, + "adduct": { + "type": "string" } }, + "description": "Simple and easy serializable fragmentation tree model with annotated fragments/nodes abd losses/edges\n Root fragment has index 0;\n Molecular formula and adduct are identical to the ones of the corresponding molecular formula candidate and SpectrumAnnotation", "nullable": true }, - "StructureCandidateScored": { + "IsotopePatternAnnotation": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" + "isotopePattern": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "structureName": { + "simulatedPattern": { + "$ref": "#/components/schemas/BasicSpectrum" + } + }, + "nullable": true + }, + "LipidAnnotation": { + "type": "object", + "properties": { + "lipidSpecies": { "type": "string", + "description": "Predicted lipid species in LIPID MAPS notation.\n NULL if not classified as lipid.", "nullable": true }, - "structureSvg": { + "lipidMapsId": { "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "description": "LIPID MAPS id of the predicted lipid class.", "nullable": true }, - "dbLinks": { - "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/DBLink" - } - }, - "spectralLibraryMatches": { - "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" - } - }, - "xlogP": { - "type": "number", - "format": "double", + "lipidClassName": { + "type": "string", + "description": "Human-readable name of the predicted lipid class.", "nullable": true }, - "rank": { - "type": "integer", - "description": "the overall rank of this candidate among all candidates of this feature", - "format": "int32" - }, - "csiScore": { - "type": "number", - "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", - "format": "double" - }, - "tanimotoSimilarity": { - "type": "number", - "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", - "format": "double", + "hypotheticalStructure": { + "type": "string", + "description": "Hypothetical molecular structure of the predicted lipid species as SMILES.\n NULL if hypothetical structure not available.", "nullable": true }, - "mcesDistToTopHit": { - "type": "number", - "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", - "format": "double", + "chainsUnknown": { + "type": "boolean", + "description": "True of the formula composition of the chains could not be determined from the MS/MS.", "nullable": true - }, - "fingerprint": { - "$ref": "#/components/schemas/BinaryFingerprint" } }, "nullable": true }, - "StoredJobSubmission": { - "required": [ - "editable", - "jobSubmission", - "name" - ], + "LossEdge": { "type": "object", "properties": { - "name": { - "type": "string", - "description": "Unique name to identify this JobSubmission (job config)." + "sourceFragmentIdx": { + "type": "integer", + "format": "int32" }, - "editable": { - "type": "boolean", - "description": "False for predefined configs which are not editable and not removable." + "targetFragmentIdx": { + "type": "integer", + "format": "int32" }, - "jobSubmission": { - "$ref": "#/components/schemas/JobSubmission" + "molecularFormula": { + "type": "string" + }, + "score": { + "type": "number", + "format": "double" } } }, - "BioTransformerParameters": { - "required": [ - "bioTransformerSequenceSteps", - "cyp450Mode", - "p2Mode" - ], + "MsData": { "type": "object", "properties": { - "cyp450Mode": { - "$ref": "#/components/schemas/Cyp450Mode" + "isotopePattern": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "p2Mode": { - "$ref": "#/components/schemas/P2Mode" + "mergedMs1": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "useDB": { - "type": "boolean", - "description": "\"Specify if you want to enable the retrieving from database (HMDB) feature.\"", - "default": true + "mergedMs2": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "bioTransformerSequenceSteps": { + "ms1Spectra": { "type": "array", - "description": "Specify BioTransformerSequenceSteps to be applied to input structures. MultiStep MetabolicTransformations can\n only be used as singletons (list size of one).", "items": { - "$ref": "#/components/schemas/BioTransformerSequenceStep" + "$ref": "#/components/schemas/BasicSpectrum" + } + }, + "ms2Spectra": { + "type": "array", + "items": { + "$ref": "#/components/schemas/BasicSpectrum" } } - } + }, + "description": "The MsData wraps all spectral input data belonging to a (aligned) feature. All spectra fields are optional.\n However, at least one Spectrum field needs to be set to create a valid MsData Object.\n The different types of spectra fields can be extended to adapt to other MassSpec measurement techniques not covered yet.\n
\n Each Feature can have:\n - One extracted isotope pattern (optional)\n - One merged MS/MS spectrum (optional)\n - One merged MS spectrum (optional)\n - many MS/MS spectra (optional)\n - many MS spectra (optional)\n
\n Each non-merged spectrum has an index which can be used to access the spectrum.\n
\n In the future we might add some additional information like chromatographic peak or something similar", + "nullable": true }, - "BioTransformerSequenceStep": { + "ParentPeak": { + "required": [ + "lossFormula", + "parentFragmentId", + "parentIdx" + ], "type": "object", "properties": { - "metabolicTransformation": { - "$ref": "#/components/schemas/MetabolicTransformation" - }, - "iterations": { + "parentIdx": { "type": "integer", + "description": "Index to the parent peak connected by this loss in this particular spectrum", "format": "int32" - } - } - }, - "Cyp450Mode": { - "type": "string", - "nullable": true, - "default": "COMBINED", - "enum": [ - "RULE_BASED", - "CY_PRODUCT", - "COMBINED" - ] - }, - "MetabolicTransformation": { - "type": "string", - "enum": [ - "PHASE_1_CYP450", - "EC_BASED", - "PHASE_2", - "HUMAN_GUT", - "ALL_HUMAN", - "ABIOTIC", - "HUMAN_CUSTOM_MULTI" - ] - }, - "P2Mode": { - "type": "string", - "nullable": true, - "default": "BT_RULE_BASED", - "enum": [ - "BT_RULE_BASED", - "P2_RULE_ONLY", - "COMBINED_RULES" - ] - }, - "AccountCredentials": { - "type": "object", - "properties": { - "username": { - "type": "string", - "nullable": true }, - "password": { - "type": "string", - "nullable": true + "parentFragmentId": { + "type": "integer", + "description": "Identifier of the parent fragment connected via this loss. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", + "format": "int32" }, - "refreshToken": { + "lossFormula": { "type": "string", - "nullable": true + "description": "Molecular formula of the neutral loss that connects these two peaks." } - }, - "description": "Simple object to hold account credentials, e.g. to perform login operations.\n If refreshToken is given, it is usually preferred over password based authentication.\n But in the end this is up to the respective web service." - }, - "RunOptField": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "tags" - ] + }, + "description": "Link from annotated fragment peak to its parent fragment peak connected by their neutral loss.", + "nullable": true }, - "Run": { + "PeakAnnotation": { + "required": [ + "fragmentId" + ], "type": "object", "properties": { - "runId": { - "type": "string", - "description": "Identifier" + "fragmentId": { + "type": "integer", + "description": "Identifier of the peak/fragment. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", + "format": "int32" }, - "name": { + "molecularFormula": { "type": "string", - "description": "Informative, human-readable name of this run" + "description": "Molecular formula that has been annotated to this peak", + "nullable": true }, - "source": { + "adduct": { "type": "string", - "description": "Source location" + "description": "Adduct that has been annotated to this peak", + "nullable": true }, - "chromatography": { - "type": "string", + "exactMass": { + "type": "number", + "description": "Exact mass of the annotated molecular formula and adduct", + "format": "double", "nullable": true }, - "ionization": { - "type": "string", + "massDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the measured peak mass in mDa", + "format": "double", "nullable": true }, - "fragmentation": { - "type": "string", + "massDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the measured peak mass in ppm", + "format": "double", + "nullable": true + }, + "recalibratedMassDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the recalibrated peak mass in mDa", + "format": "double", "nullable": true }, - "massAnalyzers": { + "recalibratedMassDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the recalibrated peak mass in ppm", + "format": "double", + "nullable": true + }, + "parentPeak": { + "$ref": "#/components/schemas/ParentPeak" + }, + "substructureAtoms": { "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the atoms of the structure candidate that are part of this fragments substructure\n (highlighted atoms)", "nullable": true, "items": { - "type": "string", + "type": "integer", + "format": "int32", "nullable": true } }, - "tags": { - "type": "object", - "additionalProperties": { - "$ref": "#/components/schemas/Tag" - }, - "description": "Key: tagName, value: tag", - "nullable": true - } - } - }, - "PageMetadata": { - "type": "object", - "properties": { - "size": { - "type": "integer", - "format": "int64" - }, - "number": { - "type": "integer", - "format": "int64" - }, - "totalElements": { - "type": "integer", - "format": "int64" + "substructureBonds": { + "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that are part of this fragments substructure\n (highlighted bonds)\n\n Null if substructure annotation not available or not requested.", + "nullable": true, + "items": { + "type": "integer", + "format": "int32", + "nullable": true + } }, - "totalPages": { - "type": "integer", - "format": "int64" - } - } - }, - "PagedModelRun": { - "type": "object", - "properties": { - "content": { + "substructureBondsCut": { "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that need to be cut to produce this fragments\n substructure (highlighted cutted bonds).\n\n Null if substructure annotation not available or not requested.", + "nullable": true, "items": { - "$ref": "#/components/schemas/Run" + "type": "integer", + "format": "int32", + "nullable": true } }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "substructureScore": { + "type": "number", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n This score roughly reflects the probability of this fragment forming.\n\n This is the score of the path from root to this node which has the maximal score or \"profit\".\n The score of a path is equal to the sum of scores of its contained fragments and edges.\n Note: Refers to 'totalScore' in CombinatorialNode\n\n Null if substructure annotation not available or not requested.", + "format": "float", + "nullable": true + }, + "hydrogenRearrangements": { + "type": "integer", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Number of hydrogens rearrangements needed to match the substructure to the fragment formula.\n\n Null if substructure annotation not available or not requested.", + "format": "int32", + "nullable": true } - } + }, + "nullable": true }, - "PagedModelJob": { + "PeakPair": { + "required": [ + "queryPeak", + "referencePeak" + ], "type": "object", "properties": { - "content": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Job" - } + "queryPeak": { + "type": "integer", + "format": "int32" }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "referencePeak": { + "type": "integer", + "format": "int32" } } }, - "AdductEdgeExperimental": { + "SpectralLibraryMatch": { + "required": [ + "inchiKey", + "querySpectrumIndex", + "similarity", + "uuid" + ], "type": "object", "properties": { - "mzDelta": { - "type": "number", - "format": "double" - }, - "annotation": { + "specMatchId": { "type": "string" }, - "from": { - "type": "integer", - "format": "int32" - }, - "to": { + "rank": { "type": "integer", "format": "int32" }, - "mergedCorrelation": { - "type": "number", - "format": "float" - }, - "representativeCorrelation": { - "type": "number", - "format": "float" - }, - "ms2cosine": { + "similarity": { "type": "number", + "description": "Similarity between query and reference spectrum", "format": "float" }, - "pvalue": { - "type": "number", - "format": "float" + "sharedPeaks": { + "type": "integer", + "description": "Number of shared/matched peaks", + "format": "int32" }, - "intensityRatioScore": { - "type": "number", - "format": "float" - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "AdductNetworkExperimental": { - "type": "object", - "properties": { - "nodes": { + "sharedPeakMapping": { "type": "array", + "description": "List of paired/matched peak indices.\n\n Maps indices of peaks from the query spectrum (mass sorted)\n to indices of matched peaks in the reference spectrum (mass sorted)", "items": { - "$ref": "#/components/schemas/AdductNodeExperimental" + "$ref": "#/components/schemas/PeakPair" } }, - "edges": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AdductEdgeExperimental" - } - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "AdductNodeExperimental": { - "type": "object", - "properties": { - "alignedFeatureId": { + "querySpectrumIndex": { + "type": "integer", + "format": "int32" + }, + "dbName": { "type": "string" }, - "mz": { + "dbId": { + "type": "string" + }, + "uuid": { + "type": "integer", + "format": "int64" + }, + "splash": { + "type": "string" + }, + "molecularFormula": { + "type": "string" + }, + "adduct": { + "type": "string" + }, + "exactMass": { "type": "number", "format": "double" }, - "adductAnnotations": { - "type": "object", - "additionalProperties": { - "type": "number", - "format": "double" - } - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "Axes": { - "type": "object", - "properties": { - "scanNumber": { - "type": "array", - "items": { - "type": "integer", - "format": "int32" - } + "smiles": { + "type": "string" }, - "scanIds": { - "type": "array", - "items": { - "type": "string" - } + "type": { + "$ref": "#/components/schemas/SpectralMatchType" }, - "retentionTimeInSeconds": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } + "inchiKey": { + "type": "string" + }, + "referenceSpectrumType": { + "$ref": "#/components/schemas/SpectrumType" + }, + "referenceSpectrum": { + "$ref": "#/components/schemas/BasicSpectrum" + }, + "querySpectrumType": { + "$ref": "#/components/schemas/SpectrumType" } - } + }, + "nullable": true + }, + "SpectralMatchType": { + "type": "string", + "default": "IDENTITY", + "enum": [ + "IDENTITY", + "ANALOG" + ] }, - "TraceAnnotationExperimental": { + "SpectrumAnnotation": { "type": "object", "properties": { - "type": { - "$ref": "#/components/schemas/TraceAnnotationTypeExperimental" + "molecularFormula": { + "type": "string", + "description": "Molecular formula that has been annotated to this spectrum", + "nullable": true }, - "description": { + "adduct": { "type": "string", + "description": "Adduct that has been annotated to this spectrum", "nullable": true }, - "index": { - "type": "integer", - "format": "int32" + "exactMass": { + "type": "number", + "description": "Exact mass based on the annotated molecular formula and ionization", + "format": "double", + "nullable": true }, - "from": { - "type": "integer", - "format": "int32", + "massDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in mDa", + "format": "double", "nullable": true }, - "to": { - "type": "integer", - "format": "int32", + "massDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in ppm", + "format": "double", + "nullable": true + }, + "structureAnnotationSmiles": { + "type": "string", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Smiles of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refer to this specific SMILES.\n If you standardize or canonicalize this SMILES in any way the indices of substructure highlighting might\n not match correctly anymore.\n
\n Null if substructure annotation not available or not requested.", + "nullable": true + }, + "structureAnnotationName": { + "type": "string", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Name of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation.\n
\n Null if substructure annotation not available or not requested.", + "nullable": true + }, + "structureAnnotationSvg": { + "type": "string", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n SVG graphics of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refers to this SVG.\n
\n Null if substructure annotation not available or not requested.", + "nullable": true + }, + "structureAnnotationScore": { + "type": "number", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Overall score of all substructure annotations computed for this structure candidate (structureAnnotationSmiles)\n
\n Null if substructure annotation not available or not requested.", + "format": "double", "nullable": true } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "TraceAnnotationTypeExperimental": { + "SpectrumType": { "type": "string", - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.", "enum": [ - "FEATURE", - "MS2" + "SPECTRUM", + "MERGED_SPECTRUM" ] }, - "TraceExperimental": { + "StructureCandidate": { "type": "object", "properties": { - "id": { + "inchiKey": { + "type": "string" + }, + "smiles": { "type": "string" }, - "sampleId": { + "structureName": { "type": "string", "nullable": true }, - "sampleName": { + "structureSvg": { "type": "string", + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", "nullable": true }, - "label": { + "dbLinks": { + "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, + "items": { + "$ref": "#/components/schemas/DBLink" + } + }, + "spectralLibraryMatches": { + "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, + "items": { + "$ref": "#/components/schemas/SpectralLibraryMatch" + } + }, + "xlogP": { + "type": "number", + "format": "double", + "nullable": true + } + }, + "nullable": true + }, + "StructureCandidateScored": { + "type": "object", + "properties": { + "inchiKey": { "type": "string" }, - "color": { + "smiles": { "type": "string" }, - "intensities": { + "structureName": { + "type": "string", + "nullable": true + }, + "structureSvg": { + "type": "string", + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true + }, + "dbLinks": { "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, "items": { - "type": "number", - "format": "double" + "$ref": "#/components/schemas/DBLink" } }, - "annotations": { + "spectralLibraryMatches": { "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, "items": { - "$ref": "#/components/schemas/TraceAnnotationExperimental" + "$ref": "#/components/schemas/SpectralLibraryMatch" } }, - "mz": { + "xlogP": { "type": "number", - "format": "double" + "format": "double", + "nullable": true }, - "merged": { - "type": "boolean" + "rank": { + "type": "integer", + "description": "the overall rank of this candidate among all candidates of this feature", + "format": "int32" }, - "normalizationFactor": { + "csiScore": { "type": "number", - "description": "Traces are stored with raw intensity values. The normalization factor maps them to relative intensities,\n such that traces from different samples can be compared.", + "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", "format": "double" }, - "noiseLevel": { + "tanimotoSimilarity": { "type": "number", - "description": "The noise level is estimated from the median noise in the surrounding scans. It can be used to\n calculate signal-to-noise ratios.", - "format": "double" + "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", + "format": "double", + "nullable": true + }, + "mcesDistToTopHit": { + "type": "number", + "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", + "format": "double", + "nullable": true + }, + "fingerprint": { + "$ref": "#/components/schemas/BinaryFingerprint" } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "TraceSetExperimental": { + "Tag": { + "required": [ + "tagName" + ], "type": "object", "properties": { - "adductNetwork": { - "$ref": "#/components/schemas/AdductNetworkExperimental" - }, - "sampleId": { - "type": "string" - }, - "sampleName": { - "type": "string" - }, - "axes": { - "$ref": "#/components/schemas/Axes" + "tagName": { + "type": "string", + "description": "Name of the tag as defined by the corresponding TagDefinition\n Links tag object to their definition." }, - "traces": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TraceExperimental" - } + "value": { + "type": "object", + "description": "Optional value of the tag.\n
\n Generic value of the tag as defined by the corresponding TagDefinition.\n Can be Integer, Double, Boolean and String, whereas String values can represent Text, Date (yyyy-MM-dd) or Time (HH:mm:ss).", + "nullable": true } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "QuantRowType": { - "type": "string", - "enum": [ - "FEATURES", - "COMPOUNDS" - ] + "nullable": true }, - "QuantTableExperimental": { + "StoredJobSubmission": { + "required": [ + "editable", + "jobSubmission", + "name" + ], "type": "object", "properties": { - "quantificationMeasure": { - "$ref": "#/components/schemas/QuantMeasure" + "name": { + "type": "string", + "description": "Unique name to identify this JobSubmission (job config)." }, - "rowType": { - "$ref": "#/components/schemas/QuantRowType" + "editable": { + "type": "boolean", + "description": "False for predefined configs which are not editable and not removable." }, - "rowIds": { - "type": "array", - "nullable": true, - "items": { - "type": "integer", - "format": "int64", - "nullable": true - } + "jobSubmission": { + "$ref": "#/components/schemas/JobSubmission" + } + } + }, + "BioTransformerParameters": { + "required": [ + "bioTransformerSequenceSteps", + "cyp450Mode", + "p2Mode" + ], + "type": "object", + "properties": { + "cyp450Mode": { + "$ref": "#/components/schemas/Cyp450Mode" }, - "columnIds": { - "type": "array", - "nullable": true, - "items": { - "type": "integer", - "format": "int64", - "nullable": true - } + "p2Mode": { + "$ref": "#/components/schemas/P2Mode" }, - "rowNames": { - "type": "array", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } + "useDB": { + "type": "boolean", + "description": "\"Specify if you want to enable the retrieving from database (HMDB) feature.\"", + "default": true }, - "columnNames": { + "bioTransformerSequenceSteps": { "type": "array", - "nullable": true, + "description": "Specify BioTransformerSequenceSteps to be applied to input structures. MultiStep MetabolicTransformations can\n only be used as singletons (list size of one).", "items": { - "type": "string", - "nullable": true + "$ref": "#/components/schemas/BioTransformerSequenceStep" } + } + } + }, + "BioTransformerSequenceStep": { + "type": "object", + "properties": { + "metabolicTransformation": { + "$ref": "#/components/schemas/MetabolicTransformation" }, - "values": { - "type": "array", - "items": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } + "iterations": { + "type": "integer", + "format": "int32" } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + } + }, + "Cyp450Mode": { + "type": "string", + "nullable": true, + "default": "COMBINED", + "enum": [ + "RULE_BASED", + "CY_PRODUCT", + "COMBINED" + ] + }, + "MetabolicTransformation": { + "type": "string", + "enum": [ + "PHASE_1_CYP450", + "EC_BASED", + "PHASE_2", + "HUMAN_GUT", + "ALL_HUMAN", + "ABIOTIC", + "HUMAN_CUSTOM_MULTI" + ] }, - "PagedModelCompound": { + "P2Mode": { + "type": "string", + "nullable": true, + "default": "BT_RULE_BASED", + "enum": [ + "BT_RULE_BASED", + "P2_RULE_ONLY", + "COMBINED_RULES" + ] + }, + "AccountCredentials": { "type": "object", "properties": { - "content": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Compound" - } + "username": { + "type": "string", + "nullable": true }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "password": { + "type": "string", + "nullable": true + }, + "refreshToken": { + "type": "string", + "nullable": true } - } + }, + "description": "Simple object to hold account credentials, e.g. to perform login operations.\n If refreshToken is given, it is usually preferred over password based authentication.\n But in the end this is up to the respective web service." }, - "FoldChange": { - "required": [ - "foldChange", - "objectId", - "quantType" - ], + "PageMetadata": { "type": "object", "properties": { - "leftGroup": { - "type": "string" - }, - "rightGroup": { - "type": "string" - }, - "aggregation": { - "$ref": "#/components/schemas/AggregationType" - }, - "quantification": { - "$ref": "#/components/schemas/QuantMeasure" + "size": { + "type": "integer", + "format": "int64" }, - "quantType": { - "$ref": "#/components/schemas/QuantRowType" + "number": { + "type": "integer", + "format": "int64" }, - "objectId": { - "type": "string" + "totalElements": { + "type": "integer", + "format": "int64" }, - "foldChange": { - "type": "number", - "format": "double" + "totalPages": { + "type": "integer", + "format": "int64" } } }, - "StatisticsTable": { + "PagedModelJob": { "type": "object", "properties": { - "statisticsType": { - "$ref": "#/components/schemas/StatisticsType" - }, - "aggregationType": { - "$ref": "#/components/schemas/AggregationType" - }, - "quantificationMeasure": { - "$ref": "#/components/schemas/QuantMeasure" - }, - "rowType": { - "$ref": "#/components/schemas/QuantRowType" - }, - "rowIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "columnNames": { - "type": "array", - "items": { - "type": "string" - } - }, - "columnLeftGroups": { + "content": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/Job" } }, - "columnRightGroups": { + "page": { + "$ref": "#/components/schemas/PageMetadata" + } + } + }, + "PagedModelCompound": { + "type": "object", + "properties": { + "content": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/Compound" } }, - "values": { - "type": "array", - "items": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } + "page": { + "$ref": "#/components/schemas/PageMetadata" } } }, - "StatisticsType": { - "type": "string", - "enum": [ - "FOLD_CHANGE" - ] - }, "SpectralLibraryMatchOptField": { "type": "string", "nullable": true, @@ -10886,70 +7459,6 @@ } } }, - "AlignedFeatureQualityExperimental": { - "required": [ - "alignedFeatureId", - "categories", - "overallQuality" - ], - "type": "object", - "properties": { - "alignedFeatureId": { - "type": "string", - "description": "Id of the feature (aligned over runs) this quality information belongs to." - }, - "overallQuality": { - "$ref": "#/components/schemas/DataQuality" - }, - "categories": { - "type": "object", - "additionalProperties": { - "$ref": "#/components/schemas/Category" - }, - "description": "Contains all pre-computation quality information that belong to\n this feature (aligned over runs), such as information about the quality of the peak shape, MS2 spectrum etc.," - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "Category": { - "type": "object", - "properties": { - "categoryName": { - "type": "string" - }, - "overallQuality": { - "$ref": "#/components/schemas/DataQuality" - }, - "items": { - "type": "array", - "items": { - "$ref": "#/components/schemas/QualityItem" - } - } - } - }, - "QualityItem": { - "type": "object", - "properties": { - "description": { - "type": "string" - }, - "quality": { - "$ref": "#/components/schemas/DataQuality" - }, - "weight": { - "$ref": "#/components/schemas/QualityWeight" - } - } - }, - "QualityWeight": { - "type": "string", - "enum": [ - "MINOR", - "MAJOR", - "CRITICAL" - ] - }, "FormulaCandidateOptField": { "type": "string", "nullable": true, @@ -10965,24 +7474,6 @@ "canopusPredictions" ] }, - "AnnotatedMsMsData": { - "required": [ - "mergedMs2", - "ms2Spectra" - ], - "type": "object", - "properties": { - "mergedMs2": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - }, - "ms2Spectra": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - } - } - } - }, "StructureCandidateOptField": { "type": "string", "nullable": true, @@ -11008,6 +7499,24 @@ } } }, + "AnnotatedMsMsData": { + "required": [ + "mergedMs2", + "ms2Spectra" + ], + "type": "object", + "properties": { + "mergedMs2": { + "$ref": "#/components/schemas/AnnotatedSpectrum" + }, + "ms2Spectra": { + "type": "array", + "items": { + "$ref": "#/components/schemas/AnnotatedSpectrum" + } + } + } + }, "PagedModelFormulaCandidate": { "type": "object", "properties": { @@ -11036,6 +7545,84 @@ } } }, + "StructureCandidateFormula": { + "type": "object", + "properties": { + "inchiKey": { + "type": "string" + }, + "smiles": { + "type": "string" + }, + "structureName": { + "type": "string", + "nullable": true + }, + "structureSvg": { + "type": "string", + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true + }, + "dbLinks": { + "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, + "items": { + "$ref": "#/components/schemas/DBLink" + } + }, + "spectralLibraryMatches": { + "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, + "items": { + "$ref": "#/components/schemas/SpectralLibraryMatch" + } + }, + "xlogP": { + "type": "number", + "format": "double", + "nullable": true + }, + "rank": { + "type": "integer", + "description": "the overall rank of this candidate among all candidates of this feature", + "format": "int32" + }, + "csiScore": { + "type": "number", + "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", + "format": "double" + }, + "tanimotoSimilarity": { + "type": "number", + "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", + "format": "double", + "nullable": true + }, + "mcesDistToTopHit": { + "type": "number", + "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", + "format": "double", + "nullable": true + }, + "fingerprint": { + "$ref": "#/components/schemas/BinaryFingerprint" + }, + "molecularFormula": { + "type": "string", + "description": "Molecular formula of this candidate" + }, + "adduct": { + "type": "string", + "description": "Adduct of this candidate" + }, + "formulaId": { + "type": "string", + "description": "Id of the corresponding Formula candidate" + } + } + }, "PagedModelAlignedFeature": { "type": "object", "properties": { diff --git a/.updater/api/api-docs-strings.json b/.updater/api/api-docs-strings.json index 6ee25d2e..f30b2feb 100644 --- a/.updater/api/api-docs-strings.json +++ b/.updater/api/api-docs-strings.json @@ -16,10 +16,6 @@ "name": "Info", "description": "Status und Information" }, - { - "name": "Feature Statistics", - "description": "[EXPERIMENTAL] This feature based API allows computing and accessing statistics for features (aligned over runs).All endpoints are experimental and not part of the stable API specification. These endpoints can change at any time, even in minor updates." - }, { "name": "Jobs", "description": "Start, monitor and cancel background jobs." @@ -28,26 +24,6 @@ "name": "Compounds", "description": "This compound based API allows to retrieve all AlignedFeatures that belong to the same compound (also known as a group of ion identities). It also provides for each AlignedFeature the corresponding annotation results (which are usually computed on a per-feature basis)" }, - { - "name": "Gui", - "description": "GUI Control: Open, control and close SIRIUS Graphical User Interface (GUI) on specified projects." - }, - { - "name": "Projects", - "description": "Manage SIRIUS projects." - }, - { - "name": "Runs", - "description": "[EXPERIMENTAL] This API allows accessing LC/MS runs. All endpoints are experimental and not part of the stable API specification. These endpoints can change at any time, even in minor updates." - }, - { - "name": "Compound Statistics", - "description": "[EXPERIMENTAL] This compound based API allows allows computing and accessing statistics for compounds (also known as a group of ion identities). All endpoints are experimental and not part of the stable API specification. These endpoints can change at any time, even in minor updates." - }, - { - "name": "Tags", - "description": "[EXPERIMENTAL] This API allows managing tags and tag based data groupings. All endpoints are experimental and not part of the stable API specification. These endpoints can change at any time, even in minor updates." - }, { "name": "Login and Account", "description": "Perform signIn, signOut and signUp. Get tokens and account information." @@ -67,6 +43,14 @@ { "name": "Features", "description": "This feature based API allows access features (aligned over runs) and there Annotations of a specified project-space. This is the entry point to access all raw annotation results an there summaries." + }, + { + "name": "Gui", + "description": "GUI Control: Open, control and close SIRIUS Graphical User Interface (GUI) on specified projects." + }, + { + "name": "Projects", + "description": "Manage SIRIUS projects." } ], "paths": { @@ -280,44 +264,77 @@ } } }, - "/api/projects/{projectId}/tags": { - "get": { + "/api/projects/{projectId}/aligned-features/delete": { + "put": { "tags": [ - "Tags" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tag definitions in the given project-space", - "description": "[EXPERIMENTAL] Get all tag definitions in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTags", + "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "deleteAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", + "description": "project-space to delete from.", + "required": true, + "schema": { + "type": "string" + } + } + ], + "requestBody": { + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "string" + } + } + } + }, + "required": true + }, + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/databases/{databaseId}": { + "get": { + "tags": [ + "Searchable Databases" + ], + "operationId": "getDatabase", + "parameters": [ + { + "name": "databaseId", + "in": "path", "required": true, "schema": { "type": "string" } }, { - "name": "tagType", + "name": "includeStats", "in": "query", - "description": "scope of the tag (optional)", "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true } } ], "responses": { "200": { - "description": "Tag definitions.", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagDefinition" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } @@ -326,16 +343,13 @@ }, "put": { "tags": [ - "Tags" + "Searchable Databases" ], - "summary": "[EXPERIMENTAL] Add tags to the project", - "description": "[EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "createTags", + "operationId": "updateDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to add to.", "required": true, "schema": { "type": "string" @@ -343,213 +357,121 @@ } ], "requestBody": { - "description": "the tag definitions to be created", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagDefinitionImport" - } + "$ref": "#/components/schemas/SearchableDatabaseParameters" } } - }, - "required": true + } }, "responses": { "200": { - "description": "the definitions of the tags that have been created", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TagDefinition" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } - }, - "/api/projects/{projectId}/runs/tags/{runId}": { - "put": { + }, + "post": { "tags": [ - "Runs" + "Searchable Databases" ], - "summary": "[EXPERIMENTAL] Add tags to a run in the project", - "description": "[EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToRunExperimental", + "operationId": "createDatabase", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to add to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "runId", + "name": "databaseId", "in": "path", - "description": "run to add tags to.", "required": true, "schema": { + "pattern": "^[a-zA-Z0-9-_]+$", "type": "string" } } ], "requestBody": { - "description": "tags to add.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/SearchableDatabaseParameters" } } - }, - "required": true + } }, "responses": { "200": { - "description": "the tags that have been added", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/SearchableDatabase" } } } } } - } - }, - "/api/projects/{projectId}/runs/blanksubtract/compute": { - "put": { + }, + "delete": { "tags": [ - "Runs" + "Searchable Databases" ], - "summary": "**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter", - "description": "**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter.\n\n
This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
", - "operationId": "computeFoldChangeForBlankSubtraction", + "operationId": "removeDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "project-space to compute the fold change in.", "required": true, "schema": { "type": "string" } }, { - "name": "optFields", + "name": "delete", "in": "query", - "description": "job opt fields.", "required": false, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "command", - "progress", - "affectedIds" - ] - }, - "default": [ - "progress" - ] + "type": "boolean", + "default": false } } ], - "requestBody": { - "description": "request with lists of run IDs that are sample, blank, and control runs", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SampleTypeFoldChangeRequest" - } - } - }, - "required": true - }, "responses": { "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Job" - } - } - } + "description": "OK" } } } }, - "/api/projects/{projectId}/compounds/tags/{compoundId}": { + "/api/account/subscriptions/select-active": { "put": { "tags": [ - "Compounds" + "Login and Account" ], - "summary": "[EXPERIMENTAL] Tags with the same name will be overwritten", - "description": "[EXPERIMENTAL] Tags with the same name will be overwritten.\n\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToCompoundExperimental", + "summary": "Select a subscription as active subscription to be used for computations.", + "description": "Select a subscription as active subscription to be used for computations.", + "operationId": "selectSubscription", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to add to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "compoundId", - "in": "path", - "description": "compound (group of ion identities) to add tags to.", + "name": "sid", + "in": "query", "required": true, "schema": { "type": "string" } } ], - "requestBody": { - "description": "tags to add.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - }, - "required": true - }, "responses": { "200": { - "description": "the tags that have been added", + "description": "Account information with updated active subscription", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/AccountInfo" } } } @@ -557,75 +479,28 @@ } } }, - "/api/projects/{projectId}/compounds/statistics/foldchange/compute": { - "put": { + "/api/projects/{projectId}/jobs": { + "get": { "tags": [ - "Compound Statistics" + "Jobs" ], - "summary": "[EXPERIMENTAL] Compute the fold change between two groups of runs", - "description": "[EXPERIMENTAL] Compute the fold change between two groups of runs.\n
\n The runs need to be tagged and grouped.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "computeCompoundFoldChangesExperimental", + "summary": "Get List of all available jobs with information such as current state and progress (if available).", + "description": "Get List of all available jobs with information such as current state and progress (if available).", + "operationId": "getJobs", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to compute the fold change in.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left tag group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "rightGroupName", - "in": "query", - "description": "name of the right tag group.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, - { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, - "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] - } - }, - { - "name": "quantification", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - }, { "name": "optFields", "in": "query", - "description": "job opt fields.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -640,7 +515,7 @@ ] }, "default": [ - "progress" + "none" ] } } @@ -651,36 +526,28 @@ "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/Job" + } } } } } } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures": { - "get": { + }, + "post": { "tags": [ - "Features" + "Jobs" ], - "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidates", + "summary": "Start computation for given compounds and with given parameters.", + "description": "Start computation for given compounds and with given parameters.", + "operationId": "startJob", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" @@ -698,124 +565,155 @@ "nullable": true, "enum": [ "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" + "command", + "progress", + "affectedIds" ] }, "default": [ - "none" + "command", + "progress" ] } } ], + "requestBody": { + "description": "configuration of the job that will be submitted of the job to be returned", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/JobSubmission" + } + } + }, + "required": true + }, "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", + "202": { + "description": "Accepted", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" - } + "$ref": "#/components/schemas/Job" } } } } } }, - "put": { + "delete": { "tags": [ - "Features" + "Jobs" ], - "summary": "[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.", - "description": "[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list.", - "operationId": "addDeNovoStructureCandidate", + "summary": "* Delete ALL jobs.", + "description": "* Delete ALL jobs. Specify how to behave for running jobs.", + "operationId": "deleteJobs", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", + "description": "project-space to delete jobs from", "required": true, "schema": { "type": "string" } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, + "name": "cancelIfRunning", + "in": "query", + "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": true } }, { - "name": "smiles", + "name": "awaitDeletion", "in": "query", - "description": "smiles", + "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", "required": false, "schema": { - "type": "string", - "default": "none" + "type": "boolean", + "default": true } } ], "responses": { - "200": { - "description": "StructureCandidate of this feature candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" - } - } - } - } + "202": { + "description": "Accepted" } } } }, - "/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}": { - "put": { + "/api/projects/{projectId}/jobs/from-config": { + "post": { "tags": [ - "Features" + "Jobs" ], - "summary": "[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project", - "description": "[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addTagsToAlignedFeatureExperimental", + "summary": "Start computation for given compounds and with parameters from a stored job-config.", + "description": "Start computation for given compounds and with parameters from a stored job-config.", + "operationId": "startJobFromConfig", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to add to.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "run to add tags to.", + "name": "jobConfigName", + "in": "query", + "description": "name if the config to be used", "required": true, "schema": { "type": "string" } + }, + { + "name": "recompute", + "in": "query", + "description": "enable or disable recompute. If null the stored value will be used.", + "required": false, + "schema": { + "type": "boolean" + } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "command", + "progress", + "affectedIds" + ] + }, + "default": [ + "command", + "progress" + ] + } } ], "requestBody": { - "description": "tags to add.", + "description": "List of alignedFeatureIds to be computed", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/Tag" + "type": "string" } } } @@ -823,15 +721,12 @@ "required": true }, "responses": { - "200": { - "description": "the tags that have been added", + "202": { + "description": "Accepted", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/Job" } } } @@ -839,75 +734,119 @@ } } }, - "/api/projects/{projectId}/aligned-features/statistics/foldchange/compute": { - "put": { + "/api/projects/{projectId}/import/preprocessed-data-files": { + "post": { "tags": [ - "Feature Statistics" + "Projects" ], - "summary": "[EXPERIMENTAL] Compute the fold change between two groups of runs", - "description": "[EXPERIMENTAL] Compute the fold change between two groups of runs.\n
\n The runs need to be tagged and grouped.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "computeAlignedFeatureFoldChangesExperimental", + "summary": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", + "description": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", + "operationId": "importPreprocessedData", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to compute the fold change in.", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "leftGroupName", + "name": "ignoreFormulas", "in": "query", - "description": "name of the left tag group.", - "required": true, + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "rightGroupName", + "name": "allowMs1Only", "in": "query", - "description": "name of the right tag group.", + "required": false, + "schema": { + "type": "boolean", + "default": true + } + } + ], + "requestBody": { + "content": { + "multipart/form-data": { + "schema": { + "required": [ + "inputFiles" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + } + } + } + } + } + }, + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ImportResult" + } + } + } + } + } + } + }, + "/api/projects/{projectId}/import/preprocessed-data-files-job": { + "post": { + "tags": [ + "Projects" + ], + "summary": "Import ms/ms data from the given format into the specified project-space as background job.", + "description": "Import ms/ms data from the given format into the specified project-space as background job.\n Possible formats (ms, mgf, cef, msp)", + "operationId": "importPreprocessedDataAsJob", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "aggregation", + "name": "ignoreFormulas", "in": "query", - "description": "aggregation type.", "required": false, "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] + "type": "boolean", + "default": false } }, { - "name": "quantification", + "name": "allowMs1Only", "in": "query", - "description": "quantification type.", "required": false, "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] + "type": "boolean", + "default": true } }, { "name": "optFields", "in": "query", - "description": "job opt fields.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -927,9 +866,31 @@ } } ], + "requestBody": { + "content": { + "multipart/form-data": { + "schema": { + "required": [ + "inputFiles" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + } + } + } + } + } + }, "responses": { "200": { - "description": "OK", + "description": "the import job.", "content": { "application/json": { "schema": { @@ -941,19 +902,19 @@ } } }, - "/api/projects/{projectId}/aligned-features/delete": { - "put": { + "/api/projects/{projectId}/import/ms-data-files": { + "post": { "tags": [ - "Features" + "Projects" ], - "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "deleteAlignedFeatures", + "summary": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", + "description": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", + "operationId": "importMsRunData", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "Project-space to import into.", "required": true, "schema": { "type": "string" @@ -962,193 +923,199 @@ ], "requestBody": { "content": { - "application/json": { + "multipart/form-data": { "schema": { - "type": "array", - "items": { - "type": "string" + "required": [ + "inputFiles", + "parameters" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + }, + "parameters": { + "$ref": "#/components/schemas/LcmsSubmissionParameters" + } + } + }, + "encoding": { + "parameters": { + "contentType": "application/json" + }, + "inputFiles": { + "contentType": "application/octet-stream" } } } - }, - "required": true + } }, "responses": { "200": { - "description": "OK" + "description": "OK", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ImportResult" + } + } + } } } } }, - "/api/databases/{databaseId}": { - "get": { + "/api/projects/{projectId}/import/ms-data-files-job": { + "post": { "tags": [ - "Searchable Databases" + "Projects" ], - "operationId": "getDatabase", + "summary": "Import and Align full MS-Runs from various formats into the specified project as background job.", + "description": "Import and Align full MS-Runs from various formats into the specified project as background job.\n Possible formats (mzML, mzXML)", + "operationId": "importMsRunDataAsJob", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", + "description": "Project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "includeStats", + "name": "optFields", "in": "query", + "description": "Set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - }, - "put": { - "tags": [ - "Searchable Databases" - ], - "operationId": "updateDatabase", - "parameters": [ - { - "name": "databaseId", - "in": "path", - "required": true, - "schema": { - "type": "string" + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "command", + "progress", + "affectedIds" + ] + }, + "default": [ + "progress" + ] } } ], "requestBody": { "content": { - "application/json": { + "multipart/form-data": { "schema": { - "$ref": "#/components/schemas/SearchableDatabaseParameters" + "required": [ + "inputFiles", + "parameters" + ], + "type": "object", + "properties": { + "inputFiles": { + "type": "array", + "description": "files to import into project", + "items": { + "type": "string", + "format": "binary" + } + }, + "parameters": { + "$ref": "#/components/schemas/LcmsSubmissionParameters" + } + } + }, + "encoding": { + "parameters": { + "contentType": "application/json" + }, + "inputFiles": { + "contentType": "application/octet-stream" + } } } } }, "responses": { "200": { - "description": "OK", + "description": "the import job.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SearchableDatabase" + "$ref": "#/components/schemas/Job" } } } } } - }, + } + }, + "/api/projects/{projectId}/gui": { "post": { "tags": [ - "Searchable Databases" + "Gui" ], - "operationId": "createDatabase", + "summary": "Open GUI instance on specified project-space and bring the GUI window to foreground.", + "description": "Open GUI instance on specified project-space and bring the GUI window to foreground.", + "operationId": "openGui", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", + "description": "of project-space the GUI instance will connect to.", "required": true, "schema": { - "pattern": "^[a-zA-Z0-9-_]+$", "type": "string" } } ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabaseParameters" - } - } - } - }, "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } + "201": { + "description": "Created" } } }, "delete": { "tags": [ - "Searchable Databases" + "Gui" ], - "operationId": "removeDatabase", + "summary": "Close GUI instance of given project-space if available.", + "description": "Close GUI instance of given project-space if available.", + "operationId": "closeGui", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", + "description": "if project-space the GUI instance is connected to.", "required": true, "schema": { "type": "string" } }, { - "name": "delete", + "name": "closeProject", "in": "query", "required": false, "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/subscriptions/select-active": { - "put": { - "tags": [ - "Login and Account" - ], - "summary": "Select a subscription as active subscription to be used for computations.", - "description": "Select a subscription as active subscription to be used for computations.", - "operationId": "selectSubscription", - "parameters": [ - { - "name": "sid", - "in": "query", - "required": true, - "schema": { - "type": "string" + "type": "boolean" } } ], "responses": { "200": { - "description": "Account information with updated active subscription", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AccountInfo" + "type": "boolean" } } } @@ -1156,24 +1123,34 @@ } } }, - "/api/projects/{projectId}/jobs": { + "/api/projects/{projectId}/compounds": { "get": { "tags": [ - "Jobs" + "Compounds" ], - "summary": "Get List of all available jobs with information such as current state and progress (if available).", - "description": "Get List of all available jobs with information such as current state and progress (if available).", - "operationId": "getJobs", + "summary": "List of all available compounds (group of ion identities) in the given project-space.", + "description": "List of all available compounds (group of ion identities) in the given project-space.", + "operationId": "getCompounds", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, { "name": "optFields", "in": "query", @@ -1186,26 +1163,51 @@ "nullable": true, "enum": [ "none", - "command", - "progress", - "affectedIds" + "consensusAnnotations", + "consensusAnnotationsDeNovo", + "customAnnotations", + "tags" ] }, "default": [ "none" ] } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Job" + }, + { + "name": "optFieldsFeatures", + "in": "query", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", + "tags" + ] + }, + "default": [ + "none" + ] + } + } + ], + "responses": { + "200": { + "description": "Compounds with additional optional fields (if specified).", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/Compound" } } } @@ -1215,25 +1217,39 @@ }, "post": { "tags": [ - "Jobs" + "Compounds" ], - "summary": "Start computation for given compounds and with given parameters.", - "description": "Start computation for given compounds and with given parameters.", - "operationId": "startJob", + "summary": "Import Compounds and its contained features.", + "description": "Import Compounds and its contained features. Compounds and Features must not exist in the project.\n Otherwise, they will exist twice.", + "operationId": "addCompounds", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, + { + "name": "profile", + "in": "query", + "description": "profile describing the instrument used to measure the data. Used to merge spectra.", + "required": false, + "schema": { + "type": "string", + "nullable": true, + "enum": [ + "QTOF", + "ORBITRAP" + ] + } + }, { "name": "optFields", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "set of optional fields to be included. Use 'none' to override defaults.", "required": false, "schema": { "type": "array", @@ -1242,127 +1258,179 @@ "nullable": true, "enum": [ "none", - "command", - "progress", - "affectedIds" + "consensusAnnotations", + "consensusAnnotationsDeNovo", + "customAnnotations", + "tags" ] }, "default": [ - "command", - "progress" + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", + "description": "set of optional fields of the nested features to be included. Use 'none' to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", + "tags" + ] + }, + "default": [ + "none" ] } } ], "requestBody": { - "description": "configuration of the job that will be submitted of the job to be returned", + "description": "the compound data to be imported", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/JobSubmission" + "type": "array", + "items": { + "$ref": "#/components/schemas/CompoundImport" + } } } }, "required": true }, "responses": { - "202": { - "description": "Accepted", + "200": { + "description": "the Compounds that have been imported with specified optional fields", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/Compound" + } } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features": { + "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "* Delete ALL jobs.", - "description": "* Delete ALL jobs. Specify how to behave for running jobs.", - "operationId": "deleteJobs", + "summary": "Get all available features (aligned over runs) in the given project-space.", + "description": "Get all available features (aligned over runs) in the given project-space.", + "operationId": "getAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete jobs from", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "cancelIfRunning", + "name": "msDataSearchPrepared", "in": "query", - "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", - "default": true + "default": false } }, { - "name": "awaitDeletion", + "name": "optFields", "in": "query", - "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": true + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", + "tags" + ] + }, + "default": [ + "none" + ] } } ], "responses": { - "202": { - "description": "Accepted" + "200": { + "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeature" + } + } + } + } } } - } - }, - "/api/projects/{projectId}/jobs/from-config": { + }, "post": { "tags": [ - "Jobs" + "Features" ], - "summary": "Start computation for given compounds and with parameters from a stored job-config.", - "description": "Start computation for given compounds and with parameters from a stored job-config.", - "operationId": "startJobFromConfig", + "summary": "Import (aligned) features into the project.", + "description": "Import (aligned) features into the project. Features must not exist in the project.\n Otherwise, they will exist twice.", + "operationId": "addAlignedFeatures", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to run jobs on", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "jobConfigName", - "in": "query", - "description": "name if the config to be used", + "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "recompute", + "name": "profile", "in": "query", - "description": "enable or disable recompute. If null the stored value will be used.", + "description": "profile describing the instrument used to measure the data. Used to merge spectra.", "required": false, "schema": { - "type": "boolean" + "type": "string", + "nullable": true, + "enum": [ + "QTOF", + "ORBITRAP" + ] } }, { "name": "optFields", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "set of optional fields to be included. Use 'none' to override defaults.", "required": false, "schema": { "type": "array", @@ -1371,26 +1439,28 @@ "nullable": true, "enum": [ "none", - "command", - "progress", - "affectedIds" + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", + "tags" ] }, "default": [ - "command", - "progress" + "none" ] } } ], "requestBody": { - "description": "List of alignedFeatureIds to be computed", + "description": "the feature data to be imported", "content": { "application/json": { "schema": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/FeatureImport" } } } @@ -1398,12 +1468,15 @@ "required": true }, "responses": { - "202": { - "description": "Accepted", + "200": { + "description": "the Features that have been imported with specified optional fields", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/AlignedFeature" + } } } } @@ -1411,99 +1484,178 @@ } } }, - "/api/projects/{projectId}/import/preprocessed-data-files": { - "post": { + "/api/job-configs/{name}": { + "get": { "tags": [ - "Projects" + "Jobs" ], - "summary": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", - "description": "Import already preprocessed ms/ms data from various formats into the specified project\n Possible formats (ms, mgf, cef, msp)", - "operationId": "importPreprocessedData", + "summary": "Request job configuration with given name.", + "description": "Request job configuration with given name.", + "operationId": "getJobConfig", "parameters": [ { - "name": "projectId", + "name": "name", "in": "path", - "description": "project-space to import into.", + "description": "name of the job-config to return", "required": true, "schema": { "type": "string" } }, { - "name": "ignoreFormulas", + "name": "moveParametersToConfigMap", "in": "query", + "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", "required": false, "schema": { "type": "boolean", "default": false } - }, - { - "name": "allowMs1Only", - "in": "query", + } + ], + "responses": { + "200": { + "description": "{@link JobSubmission JobSubmission} for given name.", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/StoredJobSubmission" + } + } + } + } + } + }, + "post": { + "tags": [ + "Jobs" + ], + "summary": "Add new job configuration with given name.", + "description": "Add new job configuration with given name.", + "operationId": "saveJobConfig", + "parameters": [ + { + "name": "name", + "in": "path", + "description": "name of the job-config to add", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "overrideExisting", + "in": "query", "required": false, "schema": { "type": "boolean", - "default": true + "default": false + } + }, + { + "name": "moveParametersToConfigMap", + "in": "query", + "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters in the return object", + "required": false, + "schema": { + "type": "boolean", + "default": false } } ], "requestBody": { + "description": "to add", "content": { - "multipart/form-data": { + "application/json": { "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "files to import into project", - "items": { - "type": "string", - "format": "binary" - } - } - } + "$ref": "#/components/schemas/JobSubmission" } } - } + }, + "required": true }, "responses": { "200": { - "description": "OK", + "description": "StoredJobSubmission that contains the JobSubmission and the probably modified name of the config (to ensure path compatibility).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ImportResult" + "$ref": "#/components/schemas/StoredJobSubmission" } } } } } - } - }, - "/api/projects/{projectId}/import/preprocessed-data-files-job": { - "post": { + }, + "delete": { "tags": [ - "Projects" + "Jobs" ], - "summary": "Import ms/ms data from the given format into the specified project-space as background job.", - "description": "Import ms/ms data from the given format into the specified project-space as background job.\n Possible formats (ms, mgf, cef, msp)", - "operationId": "importPreprocessedDataAsJob", + "summary": "Delete job configuration with given name.", + "description": "Delete job configuration with given name.", + "operationId": "deleteJobConfig", "parameters": [ { - "name": "projectId", + "name": "name", "in": "path", - "description": "project-space to import into.", + "description": "name of the job-config to delete", "required": true, "schema": { "type": "string" } + } + ], + "responses": { + "202": { + "description": "Accepted" + } + } + } + }, + "/api/job-configs/get-command": { + "post": { + "tags": [ + "Jobs" + ], + "summary": "Get a CLI command for the given job configuration.", + "description": "Get a CLI command for the given job configuration.", + "operationId": "getCommand", + "requestBody": { + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/JobSubmission" + } + } }, + "required": true + }, + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "type": "string" + } + } + } + } + } + } + } + }, + "/api/databases": { + "get": { + "tags": [ + "Searchable Databases" + ], + "operationId": "getDatabases", + "parameters": [ { - "name": "ignoreFormulas", + "name": "includeStats", "in": "query", "required": false, "schema": { @@ -1512,89 +1664,95 @@ } }, { - "name": "allowMs1Only", + "name": "includeWithErrors", "in": "query", "required": false, "schema": { "type": "boolean", - "default": true + "default": false } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "command", - "progress", - "affectedIds" - ] - }, - "default": [ - "progress" - ] + } + ], + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/SearchableDatabase" + } + } + } } } + } + }, + "post": { + "tags": [ + "Searchable Databases" ], + "summary": "[DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API.", + "operationId": "addDatabases", "requestBody": { "content": { - "multipart/form-data": { + "application/json": { "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "items": { - "type": "string", - "format": "binary" - } - } + "type": "array", + "items": { + "type": "string" } } } - } + }, + "required": true }, "responses": { "200": { - "description": "the import job.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/SearchableDatabase" + } } } } } - } + }, + "deprecated": true } }, - "/api/projects/{projectId}/import/ms-data-files": { + "/api/databases/{databaseId}/import/from-files": { "post": { "tags": [ - "Projects" + "Searchable Databases" ], - "summary": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", - "description": "Import and Align full MS-Runs from various formats into the specified project\n Possible formats (mzML, mzXML)", - "operationId": "importMsRunData", + "summary": "Start import of structure and spectra files into the specified database.", + "description": "Start import of structure and spectra files into the specified database.", + "operationId": "importIntoDatabase", "parameters": [ { - "name": "projectId", + "name": "databaseId", "in": "path", - "description": "Project-space to import into.", + "description": "database to import into", "required": true, "schema": { "type": "string" } + }, + { + "name": "bufferSize", + "in": "query", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": 1000 + } } ], "requestBody": { @@ -1602,26 +1760,25 @@ "multipart/form-data": { "schema": { "required": [ - "inputFiles", - "parameters" + "inputFiles" ], "type": "object", "properties": { "inputFiles": { "type": "array", - "description": "Files to import into project.", + "description": "files to import into project", "items": { "type": "string", "format": "binary" } }, - "parameters": { - "$ref": "#/components/schemas/LcmsSubmissionParameters" + "bioTransformerParameters": { + "$ref": "#/components/schemas/BioTransformerParameters" } } }, "encoding": { - "parameters": { + "bioTransformerParameters": { "contentType": "application/json" }, "inputFiles": { @@ -1633,11 +1790,11 @@ }, "responses": { "200": { - "description": "OK", + "description": "Meta-Information of the affected database after the import has been performed.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/ImportResult" + "$ref": "#/components/schemas/SearchableDatabase" } } } @@ -1645,88 +1802,77 @@ } } }, - "/api/projects/{projectId}/import/ms-data-files-job": { + "/api/account/logout": { "post": { "tags": [ - "Projects" + "Login and Account" ], - "summary": "Import and Align full MS-Runs from various formats into the specified project as background job.", - "description": "Import and Align full MS-Runs from various formats into the specified project as background job.\n Possible formats (mzML, mzXML)", - "operationId": "importMsRunDataAsJob", + "summary": "Logout from SIRIUS web services.", + "description": "Logout from SIRIUS web services.", + "operationId": "logout", + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/account/login": { + "post": { + "tags": [ + "Login and Account" + ], + "summary": "Login into SIRIUS web services and activate default subscription if available.", + "description": "Login into SIRIUS web services and activate default subscription if available.", + "operationId": "login", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "Project-space to import into.", + "name": "acceptTerms", + "in": "query", "required": true, "schema": { - "type": "string" + "type": "boolean" } }, { - "name": "optFields", + "name": "failWhenLoggedIn", "in": "query", - "description": "Set of optional fields to be included. Use 'none' only to override defaults.", + "description": "if true request fails if an active login already exists.", "required": false, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "command", - "progress", - "affectedIds" - ] - }, - "default": [ - "progress" - ] + "type": "boolean", + "default": false + } + }, + { + "name": "includeSubs", + "in": "query", + "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", + "required": false, + "schema": { + "type": "boolean", + "default": false } } ], "requestBody": { + "description": "used to log in.", "content": { - "multipart/form-data": { + "application/json": { "schema": { - "required": [ - "inputFiles", - "parameters" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "Files to import into project.", - "items": { - "type": "string", - "format": "binary" - } - }, - "parameters": { - "$ref": "#/components/schemas/LcmsSubmissionParameters" - } - } - }, - "encoding": { - "parameters": { - "contentType": "application/json" - }, - "inputFiles": { - "contentType": "application/octet-stream" - } + "$ref": "#/components/schemas/AccountCredentials" } } - } + }, + "required": true }, "responses": { "200": { - "description": "the import job.", + "description": "Basic information about the account that has been logged in and its subscriptions.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "$ref": "#/components/schemas/AccountInfo" } } } @@ -1734,54 +1880,71 @@ } } }, - "/api/projects/{projectId}/gui": { + "/actuator/shutdown": { "post": { "tags": [ - "Gui" + "Actuator" ], - "summary": "Open GUI instance on specified project-space and bring the GUI window to foreground.", - "description": "Open GUI instance on specified project-space and bring the GUI window to foreground.", - "operationId": "openGui", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "of project-space the GUI instance will connect to.", - "required": true, - "schema": { - "type": "string" - } + "summary": "Actuator web endpoint 'shutdown'", + "operationId": "shutdown", + "responses": { + "204": { + "description": "No Content" + }, + "400": { + "description": "Bad Request" } + } + } + }, + "/api/projects": { + "get": { + "tags": [ + "Projects" ], + "summary": "List opened project spaces.", + "description": "List opened project spaces.", + "operationId": "getProjects", "responses": { - "201": { - "description": "Created" + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/ProjectInfo" + } + } + } + } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/npc-data": { + "get": { "tags": [ - "Gui" + "Projects" ], - "summary": "Close GUI instance of given project-space if available.", - "description": "Close GUI instance of given project-space if available.", - "operationId": "closeGui", + "summary": "Get CANOPUS prediction vector definition for NPC classes", + "operationId": "getCanopusNpcData", "parameters": [ { "name": "projectId", "in": "path", - "description": "if project-space the GUI instance is connected to.", "required": true, "schema": { "type": "string" } }, { - "name": "closeProject", + "name": "charge", "in": "query", - "required": false, + "required": true, "schema": { - "type": "boolean" + "type": "integer", + "format": "int32" } } ], @@ -1789,9 +1952,14 @@ "200": { "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "type": "boolean" + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } @@ -1799,193 +1967,179 @@ } } }, - "/api/projects/{projectId}/groups/{groupName}": { + "/api/projects/{projectId}/jobs/{jobId}": { "get": { "tags": [ - "Tags" + "Jobs" ], - "summary": "[EXPERIMENTAL] Get tag group by name in the given project-space", - "description": "[EXPERIMENTAL] Get tag group by name in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getGroupByName", + "summary": "Get job information and its current state and progress (if available).", + "description": "Get job information and its current state and progress (if available).", + "operationId": "getJob", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to read from.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "groupName", + "name": "jobId", "in": "path", - "description": "name of the group", + "description": "of the job to be returned", "required": true, "schema": { "type": "string" } + }, + { + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "command", + "progress", + "affectedIds" + ] + }, + "default": [ + "progress" + ] + } } ], "responses": { "200": { - "description": "Tag group.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TagGroup" + "$ref": "#/components/schemas/Job" } } } } } }, - "post": { + "delete": { "tags": [ - "Tags" + "Jobs" ], - "summary": "[EXPERIMENTAL] Group tags in the project", - "description": "[EXPERIMENTAL] Group tags in the project. The group name must not exist in the project.\n\n
\n See /tagged for filter syntax.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteGroup", + "summary": "Get Page of jobs with information such as current state and progress (if available).", + "description": "Get Page of jobs with information such as current state and progress (if available).", + "operationId": "getJobsPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to run jobs on", "required": true, "schema": { "type": "string" } }, { - "name": "groupName", - "in": "path", - "description": "name of group to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds": { - "get": { - "tags": [ - "Compounds" - ], - "summary": "List of all available compounds (group of ion identities) in the given project-space.", - "description": "List of all available compounds (group of ion identities) in the given project-space.", - "operationId": "getCompounds", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, "schema": { - "type": "string" + "minimum": 0, + "type": "integer", + "default": 0 } }, { - "name": "msDataSearchPrepared", + "name": "size", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "description": "The size of the page to be returned", "required": false, "schema": { - "type": "boolean", - "default": false + "minimum": 1, + "type": "integer", + "default": 20 } }, { - "name": "optFields", + "name": "sort", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { "type": "array", "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "consensusAnnotations", - "consensusAnnotationsDeNovo", - "customAnnotations", - "tags" - ] - }, - "default": [ - "none" - ] + "type": "string" + } } }, { - "name": "optFieldsFeatures", + "name": "optFields", "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -1994,12 +2148,9 @@ "nullable": true, "enum": [ "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" + "command", + "progress", + "affectedIds" ] }, "default": [ @@ -2010,124 +2161,95 @@ ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "OK", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Compound" - } + "$ref": "#/components/schemas/PagedModelJob" } } } } } - }, - "post": { + } + }, + "/api/projects/{projectId}/has-jobs": { + "get": { "tags": [ - "Compounds" + "Jobs" ], - "summary": "Import Compounds and its contained features.", - "description": "Import Compounds and its contained features. Compounds and Features must not exist in the project.\n Otherwise, they will exist twice.", - "operationId": "addCompounds", + "operationId": "hasJobs", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to import into.", "required": true, "schema": { "type": "string" } }, { - "name": "profile", + "name": "includeFinished", "in": "query", - "description": "profile describing the instrument used to measure the data. Used to merge spectra.", "required": false, "schema": { - "type": "string", - "nullable": true, - "enum": [ - "QTOF", - "ORBITRAP" - ] + "type": "boolean", + "default": false } - }, + } + ], + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "type": "boolean" + } + } + } + } + } + } + }, + "/api/projects/{projectId}/fingerid-data": { + "get": { + "tags": [ + "Projects" + ], + "summary": "Get CSI:FingerID fingerprint (prediction vector) definition", + "operationId": "getFingerIdData", + "parameters": [ { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' to override defaults.", - "required": false, + "name": "projectId", + "in": "path", + "required": true, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "consensusAnnotations", - "consensusAnnotationsDeNovo", - "customAnnotations", - "tags" - ] - }, - "default": [ - "none" - ] + "type": "string" } }, { - "name": "optFieldsFeatures", + "name": "charge", "in": "query", - "description": "set of optional fields of the nested features to be included. Use 'none' to override defaults.", - "required": false, + "required": true, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" - ] - }, - "default": [ - "none" - ] + "type": "integer", + "format": "int32" } } ], - "requestBody": { - "description": "the compound data to be imported", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/CompoundImport" - } - } - } - }, - "required": true - }, "responses": { "200": { - "description": "the Compounds that have been imported with specified optional fields", + "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Compound" - } + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } @@ -2135,14 +2257,14 @@ } } }, - "/api/projects/{projectId}/aligned-features": { + "/api/projects/{projectId}/compounds/{compoundId}": { "get": { "tags": [ - "Features" + "Compounds" ], - "summary": "Get all available features (aligned over runs) in the given project-space.", - "description": "Get all available features (aligned over runs) in the given project-space.", - "operationId": "getAlignedFeatures", + "summary": "Get compound (group of ion identities) with the given identifier from the specified project-space.", + "description": "Get compound (group of ion identities) with the given identifier from the specified project-space.", + "operationId": "getCompound", "parameters": [ { "name": "projectId", @@ -2153,6 +2275,15 @@ "type": "string" } }, + { + "name": "compoundId", + "in": "path", + "description": "identifier of the compound (group of ion identities) to access.", + "required": true, + "schema": { + "type": "string" + } + }, { "name": "msDataSearchPrepared", "in": "query", @@ -2168,6 +2299,28 @@ "in": "query", "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "consensusAnnotations", + "consensusAnnotationsDeNovo", + "customAnnotations", + "tags" + ] + }, + "default": [ + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", + "required": false, "schema": { "type": "array", "items": { @@ -2191,55 +2344,139 @@ ], "responses": { "200": { - "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", + "description": "Compounds with additional optional fields (if specified).", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeature" - } + "$ref": "#/components/schemas/Compound" } } } } } }, - "post": { + "delete": { "tags": [ - "Features" + "Compounds" ], - "summary": "Import (aligned) features into the project.", - "description": "Import (aligned) features into the project. Features must not exist in the project.\n Otherwise, they will exist twice.", - "operationId": "addAlignedFeatures", + "summary": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", + "description": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", + "operationId": "deleteCompound", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to import into.", + "description": "project-space to delete from.", "required": true, "schema": { "type": "string" } }, { - "name": "profile", + "name": "compoundId", + "in": "path", + "description": "identifier of the compound to delete.", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/projects/{projectId}/compounds/page": { + "get": { + "tags": [ + "Compounds" + ], + "summary": "Page of available compounds (group of ion identities) in the given project-space.", + "description": "Page of available compounds (group of ion identities) in the given project-space.", + "operationId": "getCompoundsPaged", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "page", "in": "query", - "description": "profile describing the instrument used to measure the data. Used to merge spectra.", + "description": "Zero-based page index (0..N)", "required": false, "schema": { - "type": "string", - "nullable": true, - "enum": [ - "QTOF", - "ORBITRAP" - ] + "minimum": 0, + "type": "integer", + "default": 0 + } + }, + { + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, + "schema": { + "minimum": 1, + "type": "integer", + "default": 20 + } + }, + { + "name": "sort", + "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string" + } + } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false } }, { "name": "optFields", "in": "query", - "description": "set of optional fields to be included. Use 'none' to override defaults.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "consensusAnnotations", + "consensusAnnotationsDeNovo", + "customAnnotations", + "tags" + ] + }, + "default": [ + "none" + ] + } + }, + { + "name": "optFieldsFeatures", + "in": "query", "required": false, "schema": { "type": "array", @@ -2262,30 +2499,13 @@ } } ], - "requestBody": { - "description": "the feature data to be imported", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FeatureImport" - } - } - } - }, - "required": true - }, "responses": { "200": { - "description": "the Features that have been imported with specified optional fields", + "description": "Compounds with additional optional fields (if specified).", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AlignedFeature" - } + "$ref": "#/components/schemas/PagedModelCompound" } } } @@ -2293,68 +2513,82 @@ } } }, - "/api/job-configs/{name}": { + "/api/projects/{projectId}/cf-data": { "get": { "tags": [ - "Jobs" + "Projects" ], - "summary": "Request job configuration with given name.", - "description": "Request job configuration with given name.", - "operationId": "getJobConfig", + "summary": "Get CANOPUS prediction vector definition for ClassyFire classes", + "operationId": "getCanopusClassyFireData", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to return", "required": true, "schema": { "type": "string" } }, { - "name": "moveParametersToConfigMap", + "name": "charge", "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", - "required": false, + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "integer", + "format": "int32" } } ], "responses": { "200": { - "description": "{@link JobSubmission JobSubmission} for given name.", + "description": "OK", "content": { - "application/json": { + "application/csv": { "schema": { - "$ref": "#/components/schemas/StoredJobSubmission" + "type": "string" + } + }, + "application/CSV": { + "schema": { + "type": "string" } } } } } - }, - "post": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}": { + "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Add new job configuration with given name.", - "description": "Add new job configuration with given name.", - "operationId": "saveJobConfig", + "summary": "Get feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Get feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "getAlignedFeature", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to add", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "overrideExisting", + "name": "alignedFeatureId", + "in": "path", + "description": "identifier of feature (aligned over runs) to access.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "msDataSearchPrepared", "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", @@ -2362,34 +2596,38 @@ } }, { - "name": "moveParametersToConfigMap", + "name": "optFields", "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters in the return object", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", + "tags" + ] + }, + "default": [ + "none" + ] } } ], - "requestBody": { - "description": "to add", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } - } - }, - "required": true - }, "responses": { "200": { - "description": "StoredJobSubmission that contains the JobSubmission and the probably modified name of the config (to ensure path compatibility).", + "description": "AlignedFeature with additional annotations and MS/MS data (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/StoredJobSubmission" + "$ref": "#/components/schemas/AlignedFeature" } } } @@ -2398,16 +2636,25 @@ }, "delete": { "tags": [ - "Jobs" + "Features" ], - "summary": "Delete job configuration with given name.", - "description": "Delete job configuration with given name.", - "operationId": "deleteJobConfig", + "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", + "operationId": "deleteAlignedFeature", "parameters": [ { - "name": "name", + "name": "projectId", "in": "path", - "description": "name of the job-config to delete", + "description": "project-space to delete from.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "identifier of feature (aligned over runs) to delete.", "required": true, "schema": { "type": "string" @@ -2415,39 +2662,97 @@ } ], "responses": { - "202": { - "description": "Accepted" + "200": { + "description": "OK" } } } }, - "/api/job-configs/get-command": { - "post": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches": { + "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Get a CLI command for the given job configuration.", - "description": "Get a CLI command for the given job configuration.", - "operationId": "getCommand", - "requestBody": { - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } + "summary": "List of spectral library matches for the given 'alignedFeatureId'.", + "description": "List of spectral library matches for the given 'alignedFeatureId'.", + "operationId": "getSpectralLibraryMatches", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" } }, - "required": true - }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "minSharedPeaks", + "in": "query", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": 1 + } + }, + { + "name": "minSimilarity", + "in": "query", + "required": false, + "schema": { + "type": "number", + "format": "double", + "default": 0.2 + } + }, + { + "name": "inchiKey", + "in": "query", + "required": false, + "schema": { + "type": "string", + "default": "" + } + }, + { + "name": "optFields", + "in": "query", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "referenceSpectrum" + ] + }, + "default": [ + "none" + ] + } + } + ], "responses": { "200": { - "description": "OK", + "description": "Spectral library matches of this feature (aligned over runs).", "content": { "application/json": { "schema": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/SpectralLibraryMatch" } } } @@ -2456,232 +2761,267 @@ } } }, - "/api/databases": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}": { "get": { "tags": [ - "Searchable Databases" + "Features" ], - "operationId": "getDatabases", + "summary": "Spectral library match for the given 'alignedFeatureId'.", + "description": "Spectral library match for the given 'alignedFeatureId'.", + "operationId": "getSpectralLibraryMatch", "parameters": [ { - "name": "includeStats", - "in": "query", - "required": false, + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, "schema": { - "type": "boolean", - "default": false + "type": "string" } }, { - "name": "includeWithErrors", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "matchId", + "in": "path", + "description": "id of the library match to be returned.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "optFields", "in": "query", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "referenceSpectrum" + ] + }, + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "OK", + "description": "Spectral library match with requested mathcId.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } + "$ref": "#/components/schemas/SpectralLibraryMatch" } } } } } - }, - "post": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary": { + "get": { "tags": [ - "Searchable Databases" + "Features" ], - "summary": "DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API.", - "operationId": "addDatabases", - "requestBody": { - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } + "summary": "Summarize matched reference spectra for the given 'alignedFeatureId'.", + "description": "Summarize matched reference spectra for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key.", + "operationId": "getSpectralLibraryMatchesSummary", + "parameters": [ + { + "name": "projectId", + "in": "path", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" } }, - "required": true - }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "minSharedPeaks", + "in": "query", + "description": "min threshold of shared peaks.", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": 1 + } + }, + { + "name": "minSimilarity", + "in": "query", + "description": "min spectral similarity threshold.", + "required": false, + "schema": { + "type": "number", + "format": "double", + "default": 0.2 + } + }, + { + "name": "inchiKey", + "in": "query", + "description": "2D inchi key of the compound in the structure database.", + "required": false, + "schema": { + "type": "string", + "default": "" + } + } + ], "responses": { "200": { - "description": "OK", + "description": "Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs).", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } + "$ref": "#/components/schemas/SpectralLibraryMatchSummary" } } } } - }, - "deprecated": true + } } }, - "/api/databases/{databaseId}/import/from-files": { - "post": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page": { + "get": { "tags": [ - "Searchable Databases" + "Features" ], - "summary": "Start import of structure and spectra files into the specified database.", - "description": "Start import of structure and spectra files into the specified database.", - "operationId": "importIntoDatabase", + "summary": "Page of spectral library matches for the given 'alignedFeatureId'.", + "description": "Page of spectral library matches for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key.", + "operationId": "getSpectralLibraryMatchesPaged", "parameters": [ { - "name": "databaseId", + "name": "projectId", "in": "path", - "description": "database to import into", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "bufferSize", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1000 + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" } - } - ], - "requestBody": { - "content": { - "multipart/form-data": { - "schema": { - "required": [ - "inputFiles" - ], - "type": "object", - "properties": { - "inputFiles": { - "type": "array", - "description": "files to be imported", - "items": { - "type": "string", - "format": "binary" - } - }, - "bioTransformerParameters": { - "$ref": "#/components/schemas/BioTransformerParameters" - } - } - }, - "encoding": { - "bioTransformerParameters": { - "contentType": "application/json" - }, - "inputFiles": { - "contentType": "application/octet-stream" - } - } + }, + { + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, + "schema": { + "minimum": 0, + "type": "integer", + "default": 0 } - } - }, - "responses": { - "200": { - "description": "Meta-Information of the affected database after the import has been performed.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/SearchableDatabase" - } + }, + { + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, + "schema": { + "minimum": 1, + "type": "integer", + "default": 20 + } + }, + { + "name": "sort", + "in": "query", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string" } } - } - } - } - }, - "/api/account/logout": { - "post": { - "tags": [ - "Login and Account" - ], - "summary": "Logout from SIRIUS web services.", - "description": "Logout from SIRIUS web services.", - "operationId": "logout", - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/login": { - "post": { - "tags": [ - "Login and Account" - ], - "summary": "Login into SIRIUS web services and activate default subscription if available.", - "description": "Login into SIRIUS web services and activate default subscription if available.", - "operationId": "login", - "parameters": [ + }, { - "name": "acceptTerms", + "name": "minSharedPeaks", "in": "query", - "required": true, + "required": false, "schema": { - "type": "boolean" + "type": "integer", + "format": "int32", + "default": 1 } }, { - "name": "failWhenLoggedIn", + "name": "minSimilarity", "in": "query", - "description": "if true request fails if an active login already exists.", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "number", + "format": "double", + "default": 0.2 } }, { - "name": "includeSubs", + "name": "inchiKey", "in": "query", - "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", "required": false, "schema": { - "type": "boolean", - "default": false + "type": "string", + "default": "" + } + }, + { + "name": "optFields", + "in": "query", + "required": false, + "schema": { + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "referenceSpectrum" + ] + }, + "default": [ + "none" + ] } } ], - "requestBody": { - "description": "used to log in.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AccountCredentials" - } - } - }, - "required": true - }, "responses": { "200": { - "description": "Basic information about the account that has been logged in and its subscriptions.", + "description": "Spectral library matches of this feature (aligned over runs).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AccountInfo" + "$ref": "#/components/schemas/PagedModelSpectralLibraryMatch" } } } @@ -2689,31 +3029,14 @@ } } }, - "/actuator/shutdown": { - "post": { - "tags": [ - "Actuator" - ], - "summary": "Actuator web endpoint 'shutdown'", - "operationId": "shutdown", - "responses": { - "204": { - "description": "No Content" - }, - "400": { - "description": "Bad Request" - } - } - } - }, - "/api/projects/{projectId}/tags/{tagName}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data": { "get": { "tags": [ - "Tags" + "Features" ], - "summary": "[EXPERIMENTAL] Get tag definition by its name in the given project-space", - "description": "[EXPERIMENTAL] Get tag definition by its name in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTag", + "summary": "Mass Spec data (input data) for the given 'alignedFeatureId' .", + "description": "Mass Spec data (input data) for the given 'alignedFeatureId' .", + "operationId": "getMsData", "parameters": [ { "name": "projectId", @@ -2725,132 +3048,113 @@ } }, { - "name": "tagName", + "name": "alignedFeatureId", "in": "path", - "description": "name of the tag", + "description": "feature (aligned over runs) the Mass Spec data belongs to.", "required": true, "schema": { "type": "string" } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } } ], "responses": { "200": { - "description": "Tag definition.", + "description": "Mass Spec data of this feature (aligned over runs).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TagDefinition" + "$ref": "#/components/schemas/MsData" } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas": { + "get": { "tags": [ - "Tags" + "Features" ], - "summary": "[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space", - "description": "[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space.\n
\n This will also remove all tags belonging to this definition from every tagged entity.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteTag", + "summary": "List of FormulaResultContainers available for this feature with minimal information.", + "description": "List of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", + "operationId": "getFormulaCandidates", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "tagName", + "name": "alignedFeatureId", "in": "path", - "description": "name of the tag definition to delete.", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - }, - "patch": { - "tags": [ - "Tags" - ], - "summary": "[EXPERIMENTAL] Add a possible value to the tag definition in the project", - "description": "[EXPERIMENTAL] Add a possible value to the tag definition in the project.\n\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "addPossibleValuesToTagDefinition", - "parameters": [ + }, { - "name": "projectId", - "in": "path", - "description": "project-space to add to.", - "required": true, + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "tagName", - "in": "path", - "description": "the tag definition to add the values to", - "required": true, + "name": "optFields", + "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "required": false, "schema": { - "type": "string" - } - } - ], - "requestBody": { - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "object" - } - } - } - }, - "required": true - }, - "responses": { - "200": { - "description": "the definitions of the tags that have been added", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TagDefinition" - } - } + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "statistics", + "fragmentationTree", + "annotatedSpectrum", + "isotopePattern", + "lipidAnnotation", + "predictedFingerprint", + "compoundClasses", + "canopusPredictions" + ] + }, + "default": [ + "none" + ] } } - } - } - }, - "/api/projects": { - "get": { - "tags": [ - "Projects" ], - "summary": "List opened project spaces.", - "description": "List opened project spaces.", - "operationId": "getProjects", "responses": { "200": { - "description": "OK", + "description": "All FormulaCandidate of this feature with.", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/ProjectInfo" + "$ref": "#/components/schemas/FormulaCandidate" } } } @@ -2859,14 +3163,14 @@ } } }, - "/api/projects/{projectId}/runs/{runId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get run with the given identifier from the specified project-space", - "description": "[EXPERIMENTAL] Get run with the given identifier from the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunExperimental", + "summary": "FormulaResultContainers for the given 'formulaId' with minimal information.", + "description": "FormulaResultContainers for the given 'formulaId' with minimal information.\n Can be enriched with an optional results overview and formula candidate information.", + "operationId": "getFormulaCandidate", "parameters": [ { "name": "projectId", @@ -2878,14 +3182,33 @@ } }, { - "name": "runId", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", "in": "path", - "description": "identifier of run to access.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, { "name": "optFields", "in": "query", @@ -2894,19 +3217,33 @@ "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/RunOptField" + "type": "string", + "nullable": true, + "enum": [ + "none", + "statistics", + "fragmentationTree", + "annotatedSpectrum", + "isotopePattern", + "lipidAnnotation", + "predictedFingerprint", + "compoundClasses", + "canopusPredictions" + ] }, - "default": [] + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "Run with tags (if specified).", + "description": "FormulaCandidate of this feature (aligned over runs) with.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Run" + "$ref": "#/components/schemas/FormulaCandidate" } } } @@ -2914,28 +3251,37 @@ } } }, - "/api/projects/{projectId}/runs/tags/{objectId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Run", - "description": "[EXPERIMENTAL] Get all tags associated with this Run", - "operationId": "getTagsForRunExperimental", + "summary": "Returns Lipid annotation (ElGordo) for the given formulaId", + "description": "Returns Lipid annotation (ElGordo) for the given formulaId.\n
\n ElGordo lipid annotation runs as part of the SIRIUS formula identification step.", + "operationId": "getLipidAnnotation", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to get from.", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "objectId", + "name": "formulaId", "in": "path", - "description": "RunId to get tags for.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" @@ -2944,14 +3290,11 @@ ], "responses": { "200": { - "description": "the tags of the requested object", + "description": "LipidAnnotation", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/LipidAnnotation" } } } @@ -2959,89 +3302,50 @@ } } }, - "/api/projects/{projectId}/runs/tagged": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get runs by tag", - "description": "[EXPERIMENTAL] Get runs by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting)\n for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore).", + "operationId": "getIsotopePatternAnnotation", "parameters": [ { "name": "projectId", "in": "path", - "description": "project space to get runs from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "filter", - "in": "query", - "description": "tag filter.", - "required": false, - "schema": { - "type": "string", - "default": "" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "type": "array", - "items": { - "type": "string" - } + "type": "string" } }, { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/RunOptField" - }, - "default": [] + "type": "string" } } ], "responses": { "200": { - "description": "tagged runs", + "description": "Isotope pattern information", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelRun" + "$ref": "#/components/schemas/IsotopePatternAnnotation" } } } @@ -3049,14 +3353,14 @@ } } }, - "/api/projects/{projectId}/runs/page": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get all available runs in the given project-space", - "description": "[EXPERIMENTAL] Get all available runs in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunPageExperimental", + "summary": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n ", + "description": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n
\n This tree is used to rank formula candidates (treeScore).", + "operationId": "getFragTree", "parameters": [ { "name": "projectId", @@ -3068,60 +3372,31 @@ } }, { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "type": "array", - "items": { - "type": "string" - } + "type": "string" } }, { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/RunOptField" - }, - "default": [] + "type": "string" } } ], "responses": { "200": { - "description": "Runs with tags (if specified).", + "description": "Fragmentation Tree", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelRun" + "$ref": "#/components/schemas/FragmentationTree" } } } @@ -3129,90 +3404,54 @@ } } }, - "/api/projects/{projectId}/runs/grouped": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint": { "get": { "tags": [ - "Runs" + "Features" ], - "summary": "[EXPERIMENTAL] Get runs by tag group", - "description": "[EXPERIMENTAL] Get runs by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getRunsByGroupExperimental", + "summary": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n ", + "description": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n
\n This fingerprint is used to perform structure database search and predict compound classes.", + "operationId": "getFingerprintPrediction", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "groupName", - "in": "query", - "description": "tag group name.", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/RunOptField" - }, - "default": [ - "none" - ] + "type": "string" } } ], "responses": { "200": { - "description": "tagged runs", + "description": "probabilistic fingerprint predicted by CSI:FingerID", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelRun" + "type": "array", + "items": { + "type": "number", + "format": "double" + } } } } @@ -3220,73 +3459,37 @@ } } }, - "/api/projects/{projectId}/npc-data": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures": { "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Get CANOPUS prediction vector definition for NPC classes", - "operationId": "getCanopusNpcData", + "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesByFormula", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "charge", - "in": "query", - "required": true, - "schema": { - "type": "integer", - "format": "int32" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { - "schema": { - "type": "string" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/jobs/{jobId}": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Get job information and its current state and progress (if available).", - "description": "Get job information and its current state and progress (if available).", - "operationId": "getJob", - "parameters": [ - { - "name": "projectId", + "name": "alignedFeatureId", "in": "path", - "description": "project-space to run jobs on", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "jobId", + "name": "formulaId", "in": "path", - "description": "of the job to be returned", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" @@ -3304,97 +3507,66 @@ "nullable": true, "enum": [ "none", - "command", - "progress", - "affectedIds" + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" ] }, "default": [ - "progress" + "none" ] } } ], "responses": { "200": { - "description": "OK", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Job" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateScored" + } } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page": { + "get": { "tags": [ - "Jobs" + "Features" ], - "summary": "Delete job.", - "description": "Delete job. Specify how to behave for running jobs.", - "operationId": "deleteJob", + "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesByFormulaPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete job from", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "jobId", + "name": "alignedFeatureId", "in": "path", - "description": "of the job to be deleted", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "cancelIfRunning", - "in": "query", - "description": "If true, job will be canceled if it is not finished. Otherwise,\n deletion will fail for running jobs or request will block until job has finished.", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - }, - { - "name": "awaitDeletion", - "in": "query", - "description": "If true, request will block until deletion succeeded or failed.\n If the job is still running the request will wait until the job has finished.", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - } - ], - "responses": { - "202": { - "description": "Accepted" - } - } - } - }, - "/api/projects/{projectId}/jobs/page": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Get Page of jobs with information such as current state and progress (if available).", - "description": "Get Page of jobs with information such as current state and progress (if available).", - "operationId": "getJobsPaged", - "parameters": [ - { - "name": "projectId", + "name": "formulaId", "in": "path", - "description": "project-space to run jobs on", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" @@ -3446,9 +3618,10 @@ "nullable": true, "enum": [ "none", - "command", - "progress", - "affectedIds" + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" ] }, "default": [ @@ -3459,11 +3632,11 @@ ], "responses": { "200": { - "description": "OK", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelJob" + "$ref": "#/components/schemas/PagedModelStructureCandidateScored" } } } @@ -3471,82 +3644,75 @@ } } }, - "/api/projects/{projectId}/has-jobs": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures": { "get": { "tags": [ - "Jobs" + "Features" ], - "operationId": "hasJobs", + "summary": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", + "description": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesByFormula", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "includeFinished", - "in": "query", - "required": false, + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "boolean" - } - } + "type": "string" } - } - } - } - }, - "/api/projects/{projectId}/groups": { - "get": { - "tags": [ - "Tags" - ], - "summary": "[EXPERIMENTAL] Get all tag based groups in the given project-space", - "description": "[EXPERIMENTAL] Get all tag based groups in the given project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getGroups", - "parameters": [ + }, { - "name": "projectId", + "name": "formulaId", "in": "path", - "description": "project-space to read from.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, { - "name": "groupType", + "name": "optFields", "in": "query", - "description": "type of the group", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "string" + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" + ] + }, + "default": [ + "none" + ] } } ], "responses": { "200": { - "description": "Groups.", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/TagGroup" + "$ref": "#/components/schemas/StructureCandidateScored" } } } @@ -3555,114 +3721,80 @@ } } }, - "/api/projects/{projectId}/fingerid-data": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page": { "get": { "tags": [ - "Projects" + "Features" ], - "summary": "Get CSI:FingerID fingerprint (prediction vector) definition", - "operationId": "getFingerIdData", + "summary": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", + "description": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesByFormulaPaged", "parameters": [ { "name": "projectId", "in": "path", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "charge", - "in": "query", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { - "type": "integer", - "format": "int32" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { - "schema": { - "type": "string" - } - } + "type": "string" } - } - } - } - }, - "/api/projects/{projectId}/compounds/{compoundId}": { - "get": { - "tags": [ - "Compounds" - ], - "summary": "Get compound (group of ion identities) with the given identifier from the specified project-space.", - "description": "Get compound (group of ion identities) with the given identifier from the specified project-space.", - "operationId": "getCompound", - "parameters": [ + }, { - "name": "projectId", + "name": "formulaId", "in": "path", - "description": "project-space to read from.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, { - "name": "compoundId", - "in": "path", - "description": "identifier of the compound (group of ion identities) to access.", - "required": true, + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, "schema": { - "type": "string" + "minimum": 0, + "type": "integer", + "default": 0 } }, { - "name": "msDataSearchPrepared", + "name": "size", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "description": "The size of the page to be returned", "required": false, "schema": { - "type": "boolean", - "default": false + "minimum": 1, + "type": "integer", + "default": 20 } }, { - "name": "optFields", + "name": "sort", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { "type": "array", "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "consensusAnnotations", - "consensusAnnotationsDeNovo", - "customAnnotations", - "tags" - ] - }, - "default": [ - "none" - ] + "type": "string" + } } }, { - "name": "optFieldsFeatures", + "name": "optFields", "in": "query", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { "type": "array", @@ -3671,12 +3803,10 @@ "nullable": true, "enum": [ "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" ] }, "default": [ @@ -3687,38 +3817,49 @@ ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "StructureCandidate of this formula candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/Compound" + "$ref": "#/components/schemas/PagedModelStructureCandidateScored" } } } } } - }, - "delete": { + } + }, + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction": { + "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", - "description": "Delete compound (group of ion identities) with the given identifier (and the included features) from the\n specified project-space.", - "operationId": "deleteCompound", + "summary": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", + "description": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", + "operationId": "getCanopusPrediction", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" } }, { - "name": "compoundId", + "name": "alignedFeatureId", "in": "path", - "description": "identifier of the compound to delete.", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" @@ -3727,19 +3868,26 @@ ], "responses": { "200": { - "description": "OK" + "description": "Predicted compound classes", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/CanopusPrediction" + } + } + } } } } }, - "/api/projects/{projectId}/compounds/{compoundId}/traces": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Returns the traces of the given compound", - "description": "[EXPERIMENTAL] Returns the traces of the given compound.\n
\n A trace consists of m/z and intensity values over the retention\n time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,\n but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.\n However, this also means that all traces can be directly compared against each other, as they all lie in the same\n retention time axis.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundTracesExperimental", + "summary": "Return Best matching compound classes for given formulaId", + "description": "Return Best matching compound classes for given formulaId.\n
\n Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology,", + "operationId": "getBestMatchingCompoundClasses", "parameters": [ { "name": "projectId", @@ -3751,31 +3899,31 @@ } }, { - "name": "compoundId", + "name": "alignedFeatureId", "in": "path", - "description": "compound which intensities should be read out", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "featureId", - "in": "query", - "required": false, + "name": "formulaId", + "in": "path", + "description": "identifier of the requested formula result", + "required": true, "schema": { - "type": "string", - "default": "" + "type": "string" } } ], "responses": { "200": { - "description": "Traces of the given compound.", + "description": "Best matching Predicted compound classes", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" + "$ref": "#/components/schemas/CompoundClasses" } } } @@ -3783,14 +3931,14 @@ } } }, - "/api/projects/{projectId}/compounds/{compoundId}/quant-table-row": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Returns a single quantification table row for the given compound", - "description": "[EXPERIMENTAL] Returns a single quantification table row for the given compound.\n
\n The quantification table contains a quantification of the feature within all\n samples it is contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundQuantTableRowExperimental", + "summary": "Returns a fragmentation spectrum (e", + "description": "Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier\n
\n These annotations are only available if a fragmentation tree is available.", + "operationId": "getFormulaAnnotatedSpectrum", "parameters": [ { "name": "projectId", @@ -3802,36 +3950,52 @@ } }, { - "name": "compoundId", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "formulaId", "in": "path", - "description": "compound which should be read out", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } }, { - "name": "type", + "name": "spectrumIndex", + "in": "query", + "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", + "required": false, + "schema": { + "type": "integer", + "format": "int32", + "default": -1 + } + }, + { + "name": "searchPrepared", "in": "query", - "description": "quantification type.", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { - "type": "string", - "default": "APEX_HEIGHT", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "OK", + "description": "Fragmentation spectrum annotated with fragment formulas and losses.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "$ref": "#/components/schemas/AnnotatedSpectrum" } } } @@ -3839,44 +4003,60 @@ } } }, - "/api/projects/{projectId}/compounds/tags/{objectId}": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Compound", - "description": "[EXPERIMENTAL] Get all tags associated with this Compound", - "operationId": "getTagsForCompoundExperimental", + "summary": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId", + "description": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.\n
\n Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses\n for the given formula result identifier\n These annotations are only available if a fragmentation tree and the structure candidate are available.", + "operationId": "getFormulaAnnotatedMsMsData", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to get from.", + "description": "project-space to read from.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the formula result belongs to.", "required": true, "schema": { "type": "string" } }, { - "name": "objectId", + "name": "formulaId", "in": "path", - "description": "CompoundId to get tags for.", + "description": "identifier of the requested formula result", "required": true, "schema": { "type": "string" } + }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } } ], "responses": { "200": { - "description": "the tags of the requested Compound", + "description": "Fragmentation spectra annotated with fragment formulas and losses.", "content": { "application/json": { "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } + "$ref": "#/components/schemas/AnnotatedMsMsData" } } } @@ -3884,32 +4064,31 @@ } } }, - "/api/projects/{projectId}/compounds/tagged": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag", - "description": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFoldChangesByCompoundExperimental", + "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", + "operationId": "getDeNovoStructureCandidatesPaged", "parameters": [ { "name": "projectId", @@ -4001,87 +4196,79 @@ } }, { - "name": "objectId", + "name": "alignedFeatureId", "in": "path", - "description": "id of the object the fold changes are assigned to.", + "description": "feature (aligned over runs) the structure candidates belong to.", "required": true, "schema": { "type": "string" } - } - ], - "responses": { - "200": { - "description": "fold changes", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FoldChange" - } - } - } + }, + { + "name": "page", + "in": "query", + "description": "Zero-based page index (0..N)", + "required": false, + "schema": { + "minimum": 0, + "type": "integer", + "default": 0 } - } - } - } - }, - "/api/projects/{projectId}/compounds/statistics/foldchanges/stats-table": { - "get": { - "tags": [ - "Compound Statistics" - ], - "summary": "[EXPERIMENTAL] Get table of all fold changes in the project space", - "description": "[EXPERIMENTAL] Get table of all fold changes in the project space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getCompoundFoldChangeTableExperimental", - "parameters": [ + }, { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, + "name": "size", + "in": "query", + "description": "The size of the page to be returned", + "required": false, "schema": { - "type": "string" + "minimum": 1, + "type": "integer", + "default": 20 } }, { - "name": "aggregation", + "name": "sort", "in": "query", - "description": "aggregation type.", + "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", "required": false, "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] + "type": "array", + "items": { + "type": "string" + } } }, { - "name": "quantification", + "name": "optFields", "in": "query", - "description": "quantification type.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" + ] + }, + "default": [ + "none" ] } } ], "responses": { "200": { - "description": "table of fold changes.", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/StatisticsTable" + "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" } } } @@ -4089,14 +4276,14 @@ } } }, - "/api/projects/{projectId}/compounds/quant-table": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Returns the full quantification table of compounds", - "description": "[EXPERIMENTAL] Returns the full quantification table of compounds.\n
\n The quantification table contains a quantification of the features within all\n runs they are contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*", - "operationId": "getCompoundQuantTableExperimental", + "summary": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", + "description": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidates", "parameters": [ { "name": "projectId", @@ -4108,27 +4295,48 @@ } }, { - "name": "type", + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, + { + "name": "optFields", "in": "query", - "description": "quantification type.", + "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "string", - "default": "APEX_HEIGHT", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" + "type": "array", + "items": { + "type": "string", + "nullable": true, + "enum": [ + "none", + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" + ] + }, + "default": [ + "none" ] } } ], "responses": { "200": { - "description": "OK", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "type": "array", + "items": { + "$ref": "#/components/schemas/StructureCandidateFormula" + } } } } @@ -4136,14 +4344,14 @@ } } }, - "/api/projects/{projectId}/compounds/page": { + "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "Page of available compounds (group of ion identities) in the given project-space.", - "description": "Page of available compounds (group of ion identities) in the given project-space.", - "operationId": "getCompoundsPaged", + "summary": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", + "description": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", + "operationId": "getStructureCandidatesPaged", "parameters": [ { "name": "projectId", @@ -4154,6 +4362,15 @@ "type": "string" } }, + { + "name": "alignedFeatureId", + "in": "path", + "description": "feature (aligned over runs) the structure candidates belong to.", + "required": true, + "schema": { + "type": "string" + } + }, { "name": "page", "in": "query", @@ -4188,16 +4405,6 @@ } } }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, { "name": "optFields", "in": "query", @@ -4210,34 +4417,10 @@ "nullable": true, "enum": [ "none", - "consensusAnnotations", - "consensusAnnotationsDeNovo", - "customAnnotations", - "tags" - ] - }, - "default": [ - "none" - ] - } - }, - { - "name": "optFieldsFeatures", - "in": "query", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" + "fingerprint", + "dbLinks", + "libraryMatches", + "structureSvg" ] }, "default": [ @@ -4248,11 +4431,11 @@ ], "responses": { "200": { - "description": "Compounds with additional optional fields (if specified).", + "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelCompound" + "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" } } } @@ -4260,28 +4443,19 @@ } } }, - "/api/projects/{projectId}/compounds/grouped": { + "/api/projects/{projectId}/aligned-features/page": { "get": { "tags": [ - "Compounds" + "Features" ], - "summary": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag group", - "description": "[EXPERIMENTAL] Get compounds (group of ion identities) by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getCompoundsByGroupExperimental", + "summary": "Get all available features (aligned over runs) in the given project-space.", + "description": "Get all available features (aligned over runs) in the given project-space.", + "operationId": "getAlignedFeaturesPaged", "parameters": [ { "name": "projectId", "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "groupName", - "in": "query", - "description": "tag group name.", + "description": "project-space to read from.", "required": true, "schema": { "type": "string" @@ -4321,6 +4495,16 @@ } } }, + { + "name": "msDataSearchPrepared", + "in": "query", + "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", + "required": false, + "schema": { + "type": "boolean", + "default": false + } + }, { "name": "optFields", "in": "query", @@ -4333,9 +4517,11 @@ "nullable": true, "enum": [ "none", - "consensusAnnotations", - "consensusAnnotationsDeNovo", - "customAnnotations", + "msData", + "topAnnotationsSummary", + "topAnnotations", + "topAnnotationsDeNovo", + "computedTools", "tags" ] }, @@ -4347,11 +4533,11 @@ ], "responses": { "200": { - "description": "tagged compounds (group of ion identities)", + "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/PagedModelCompound" + "$ref": "#/components/schemas/PagedModelAlignedFeature" } } } @@ -4359,192 +4545,155 @@ } } }, - "/api/projects/{projectId}/cf-data": { + "/api/job-configs": { "get": { "tags": [ - "Projects" + "Jobs" ], - "summary": "Get CANOPUS prediction vector definition for ClassyFire classes", - "operationId": "getCanopusClassyFireData", - "parameters": [ - { - "name": "projectId", - "in": "path", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "charge", - "in": "query", - "required": true, - "schema": { - "type": "integer", - "format": "int32" + "summary": "Request all available job configurations", + "description": "Request all available job configurations", + "operationId": "getJobConfigs", + "responses": { + "200": { + "description": "list of available {@link JobSubmission JobSubmission}s", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/StoredJobSubmission" + } + } + } } } + } + } + }, + "/api/job-config-names": { + "get": { + "tags": [ + "Jobs" ], + "summary": "[DEPRECATED] Get all (non-default) job configuration names\n ", + "description": "[DEPRECATED] Get all (non-default) job configuration names\n
\n [DEPRECATED] Use /job-configs to get all configs with names. This endpoint is based on local file paths and will likely be removed in future versions of this API.", + "operationId": "getJobConfigNames", "responses": { "200": { "description": "OK", "content": { - "application/csv": { - "schema": { - "type": "string" - } - }, - "application/CSV": { + "application/json": { "schema": { - "type": "string" + "type": "array", + "items": { + "type": "string" + } } } } } - } + }, + "deprecated": true } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}": { + "/api/info": { "get": { "tags": [ - "Features" + "Info" ], - "summary": "Get feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Get feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "getAlignedFeature", + "operationId": "getInfo", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "identifier of feature (aligned over runs) to access.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", + "name": "serverInfo", "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", "required": false, "schema": { "type": "boolean", - "default": false + "default": true } }, { - "name": "optFields", + "name": "updateInfo", "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", "required": false, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" - ] - }, - "default": [ - "none" - ] + "type": "boolean", + "default": true } } ], "responses": { "200": { - "description": "AlignedFeature with additional annotations and MS/MS data (if specified).", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AlignedFeature" + "$ref": "#/components/schemas/Info" } } } } } - }, - "delete": { + } + }, + "/api/guis": { + "get": { "tags": [ - "Features" - ], - "summary": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "description": "Delete feature (aligned over runs) with the given identifier from the specified project-space.", - "operationId": "deleteAlignedFeature", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "identifier of feature (aligned over runs) to delete.", - "required": true, - "schema": { - "type": "string" - } - } + "Gui" ], + "summary": "Get list of currently running gui windows, managed by this SIRIUS instance.", + "description": "Get list of currently running gui windows, managed by this SIRIUS instance.\n Note this will not show any Clients that are connected from a separate process!", + "operationId": "getGuis", "responses": { "200": { - "description": "OK" + "description": "List of GUI windows that are currently managed by this SIRIUS instance.", + "content": { + "application/json": { + "schema": { + "type": "array", + "items": { + "$ref": "#/components/schemas/GuiInfo" + } + } + } + } } } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces": { + "/api/default-job-config": { "get": { "tags": [ - "Features" + "Jobs" ], - "summary": "[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId).\n
\n Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention\n time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis,\n but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data.\n However, this also means that all traces can be directly compared against each other, as they all lie in the same\n retention time axis.\n By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set,\n it also includes samples in which the same trace appears in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getTracesExperimental", + "summary": "Request default job configuration", + "description": "Request default job configuration", + "operationId": "getDefaultJobConfig", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, + "name": "includeConfigMap", + "in": "query", + "description": "if true, generic configmap with-defaults will be included", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "alignedFeatureId", - "in": "path", - "description": "feature which intensities should be read out", - "required": true, + "name": "moveParametersToConfigMap", + "in": "query", + "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "includeAll", + "name": "includeCustomDbsForStructureSearch", "in": "query", - "description": "when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.", + "description": "if true, default database selection of structure db search\n spectral library search contains also all available custom DB.\n If No custom dbs are selected, spectral library search is disabled by default.", "required": false, "schema": { "type": "boolean", @@ -4554,11 +4703,11 @@ ], "responses": { "200": { - "description": "Traces of the given feature.", + "description": "{@link JobSubmission JobSubmission} with all parameters set to default values.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" + "$ref": "#/components/schemas/JobSubmission" } } } @@ -4566,91 +4715,32 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches": { + "/api/databases/included": { "get": { "tags": [ - "Features" + "Searchable Databases" ], - "summary": "List of spectral library matches for the given 'alignedFeatureId'.", - "description": "List of spectral library matches for the given 'alignedFeatureId'.", - "operationId": "getSpectralLibraryMatches", + "operationId": "getIncludedDatabases", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "minSharedPeaks", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1 - } - }, - { - "name": "minSimilarity", - "in": "query", - "required": false, - "schema": { - "type": "number", - "format": "double", - "default": 0.2 - } - }, - { - "name": "inchiKey", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "" - } - }, - { - "name": "optFields", + "name": "includeStats", "in": "query", "required": false, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "referenceSpectrum" - ] - }, - "default": [ - "none" - ] + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Spectral library matches of this feature (aligned over runs).", + "description": "OK", "content": { "application/json": { "schema": { "type": "array", "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "$ref": "#/components/schemas/SearchableDatabase" } } } @@ -4659,69 +4749,42 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}": { + "/api/databases/custom": { "get": { "tags": [ - "Features" + "Searchable Databases" ], - "summary": "Spectral library match for the given 'alignedFeatureId'.", - "description": "Spectral library match for the given 'alignedFeatureId'.", - "operationId": "getSpectralLibraryMatch", + "operationId": "getCustomDatabases", "parameters": [ { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "matchId", - "in": "path", - "description": "id of the library match to be returned.", - "required": true, + "name": "includeStats", + "in": "query", + "required": false, "schema": { - "type": "string" + "type": "boolean", + "default": false } }, { - "name": "optFields", + "name": "includeWithErrors", "in": "query", "required": false, "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "referenceSpectrum" - ] - }, - "default": [ - "none" - ] + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Spectral library match with requested mathcId.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "type": "array", + "items": { + "$ref": "#/components/schemas/SearchableDatabase" + } } } } @@ -4729,50 +4792,44 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated": { + "/api/connection-status": { "get": { "tags": [ - "Features" + "Info" ], - "summary": "[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations", - "description": "[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedSpectralLibraryMatchExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "matchId", - "in": "path", - "description": "id of the library match to be returned.", - "required": true, - "schema": { - "type": "string" + "operationId": "getConnectionCheck", + "responses": { + "200": { + "description": "OK", + "content": { + "application/json": { + "schema": { + "$ref": "#/components/schemas/ConnectionCheck" + } + } } } + } + } + }, + "/api/account/subscriptions": { + "get": { + "tags": [ + "Login and Account" ], + "summary": "Get available subscriptions of the account currently logged in.", + "description": "Get available subscriptions of the account currently logged in. Fails if not logged in.", + "operationId": "getSubscriptions", "responses": { "200": { - "description": "Spectral library match with requested mathcId.", + "description": "OK", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" + "type": "array", + "items": { + "$ref": "#/components/schemas/Subscription" + } } } } @@ -4780,73 +4837,114 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary": { + "/api/account/signUp": { "get": { "tags": [ - "Features" + "Login and Account" ], - "summary": "Summarize matched reference spectra for the given 'alignedFeatureId'.", - "description": "Summarize matched reference spectra for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key.", - "operationId": "getSpectralLibraryMatchesSummary", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" + "summary": "Open SignUp window in system browser and return signUp link.", + "description": "Open SignUp window in system browser and return signUp link.", + "operationId": "signUp", + "responses": { + "200": { + "description": "OK", + "content": { + "text/plain;charset=UTF-8": { + "schema": { + "type": "string" + } + } } - }, - { - "name": "minSharedPeaks", - "in": "query", - "description": "min threshold of shared peaks.", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1 + } + } + } + }, + "/api/account/signUpURL": { + "get": { + "tags": [ + "Login and Account" + ], + "summary": "Get SignUp URL (For signUp via web browser)", + "description": "Get SignUp URL (For signUp via web browser)", + "operationId": "getSignUpURL", + "responses": { + "200": { + "description": "OK", + "content": { + "text/plain;charset=UTF-8": { + "schema": { + "type": "string" + } + } } - }, - { - "name": "minSimilarity", - "in": "query", - "description": "min spectral similarity threshold.", - "required": false, - "schema": { - "type": "number", - "format": "double", - "default": 0.2 + } + } + } + }, + "/api/account/openPortal": { + "get": { + "tags": [ + "Login and Account" + ], + "summary": "Open User portal in browser.", + "description": "Open User portal in browser. If user is logged in SIRIUS tries to transfer the login state to the browser.", + "operationId": "openPortal", + "responses": { + "200": { + "description": "OK" + } + } + } + }, + "/api/account/isLoggedIn": { + "get": { + "tags": [ + "Login and Account" + ], + "summary": "Check if a user is logged in.", + "description": "Check if a user is logged in.", + "operationId": "isLoggedIn", + "responses": { + "200": { + "description": "true if the user is logged in", + "content": { + "application/json": { + "schema": { + "type": "boolean" + } + } } - }, + } + } + } + }, + "/api/account/": { + "get": { + "tags": [ + "Login and Account" + ], + "summary": "Get information about the account currently logged in.", + "description": "Get information about the account currently logged in. Fails if not logged in.", + "operationId": "getAccountInfo", + "parameters": [ { - "name": "inchiKey", + "name": "includeSubs", "in": "query", - "description": "2D inchi key of the compound in the structure database.", + "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", "required": false, "schema": { - "type": "string", - "default": "" + "type": "boolean", + "default": false } } ], "responses": { "200": { - "description": "Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs).", + "description": "Basic information about the account that has been logged in and its subscriptions.", "content": { "application/json": { "schema": { - "$ref": "#/components/schemas/SpectralLibraryMatchSummary" + "$ref": "#/components/schemas/AccountInfo" } } } @@ -4854,3758 +4952,182 @@ } } }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page": { + "/actuator/health": { "get": { "tags": [ - "Features" - ], - "summary": "Page of spectral library matches for the given 'alignedFeatureId'.", - "description": "Page of spectral library matches for the given 'alignedFeatureId'.\n If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key.", - "operationId": "getSpectralLibraryMatchesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "minSharedPeaks", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": 1 - } - }, - { - "name": "minSimilarity", - "in": "query", - "required": false, - "schema": { - "type": "number", - "format": "double", - "default": 0.2 - } - }, - { - "name": "inchiKey", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "" - } - }, - { - "name": "optFields", - "in": "query", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "referenceSpectrum" - ] - }, - "default": [ - "none" - ] - } - } + "Actuator" ], + "summary": "Actuator web endpoint 'health'", + "operationId": "health", "responses": { "200": { - "description": "Spectral library matches of this feature (aligned over runs).", + "description": "OK", "content": { - "application/json": { + "application/vnd.spring-boot.actuator.v3+json": { "schema": { - "$ref": "#/components/schemas/PagedModelSpectralLibraryMatch" + "type": "object" } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId).\n
\n The quantification table contains a quantity of the feature within all samples it is contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getQuantTableRowExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature which quantity should be read out", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "type", - "in": "query", - "description": "quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.", - "required": false, - "schema": { - "type": "string", - "default": "APEX_HEIGHT", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - } - ], - "responses": { - "200": { - "description": "Quant table row for this feature", - "content": { - "application/json": { + }, + "application/vnd.spring-boot.actuator.v2+json": { "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" + "type": "object" } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)\n ", - "description": "[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)\n
\n Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeatureQualityExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "identifier of feature (aligned over runs) to access.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "AlignedFeatureQuality quality information of the respective feature.", - "content": { + }, "application/json": { "schema": { - "$ref": "#/components/schemas/AlignedFeatureQualityExperimental" + "type": "object" } } } } } } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data": { - "get": { - "tags": [ - "Features" - ], - "summary": "Mass Spec data (input data) for the given 'alignedFeatureId' .", - "description": "Mass Spec data (input data) for the given 'alignedFeatureId' .", - "operationId": "getMsData", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the Mass Spec data belongs to.", - "required": true, - "schema": { - "type": "string" - } + } + }, + "components": { + "schemas": { + "ProjectChangeEvent": { + "type": "object", + "properties": { + "eventType": { + "type": "string", + "enum": [ + "PROJECT_OPENED", + "PROJECT_MOVED", + "PROJECT_CLOSED", + "FEATURE_CREATED", + "FEATURE_UPDATED", + "FEATURE_DELETED", + "RESULT_CREATED", + "RESULT_UPDATED", + "RESULT_DELETED" + ] }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Mass Spec data of this feature (aligned over runs).", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/MsData" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of FormulaResultContainers available for this feature with minimal information.", - "description": "List of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", - "operationId": "getFormulaCandidates", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "statistics", - "fragmentationTree", - "annotatedSpectrum", - "isotopePattern", - "lipidAnnotation", - "predictedFingerprint", - "compoundClasses", - "canopusPredictions" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "All FormulaCandidate of this feature with.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FormulaCandidate" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}": { - "get": { - "tags": [ - "Features" - ], - "summary": "FormulaResultContainers for the given 'formulaId' with minimal information.", - "description": "FormulaResultContainers for the given 'formulaId' with minimal information.\n Can be enriched with an optional results overview and formula candidate information.", - "operationId": "getFormulaCandidate", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "statistics", - "fragmentationTree", - "annotatedSpectrum", - "isotopePattern", - "lipidAnnotation", - "predictedFingerprint", - "compoundClasses", - "canopusPredictions" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "FormulaCandidate of this feature (aligned over runs) with.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/FormulaCandidate" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey\n ", - "description": "[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey\n
\n Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result\n These annotations are only available if a fragmentation tree is available.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedSpectrumExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "inchiKey", - "in": "path", - "description": "2d InChIKey of the structure candidate to be used to annotate the spectrum annotation", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "spectrumIndex", - "in": "query", - "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": -1 - } - }, - { - "name": "searchPrepared", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectrum annotated with fragments and sub-structures.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey", - "description": "[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey.\n
\n Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses\n for the given formula result identifier and structure candidate inChIKey.\n These annotations are only available if a fragmentation tree and the structure candidate are available.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getStructureAnnotatedMsDataExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "inchiKey", - "in": "path", - "description": "2d InChIKey of the structure candidate to be used to annotate the spectrum annotation", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectrum annotated with fragments and sub-structures.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedMsMsData" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns Lipid annotation (ElGordo) for the given formulaId", - "description": "Returns Lipid annotation (ElGordo) for the given formulaId.\n
\n ElGordo lipid annotation runs as part of the SIRIUS formula identification step.", - "operationId": "getLipidAnnotation", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "LipidAnnotation", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/LipidAnnotation" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns Isotope pattern information for given formulaId\n ", - "description": "Returns Isotope pattern information for given formulaId\n
\n Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting)\n for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore).", - "operationId": "getIsotopePatternAnnotation", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Isotope pattern information", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/IsotopePatternAnnotation" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n ", - "description": "Returns fragmentation tree (SIRIUS) for the given formula result identifier\n
\n This tree is used to rank formula candidates (treeScore).", - "operationId": "getFragTree", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Fragmentation Tree", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/FragmentationTree" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n ", - "description": "Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)\n
\n This fingerprint is used to perform structure database search and predict compound classes.", - "operationId": "getFingerprintPrediction", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "probabilistic fingerprint predicted by CSI:FingerID", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesByFormula", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateScored" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesByFormulaPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateScored" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", - "description": "List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesByFormula", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateScored" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.", - "description": "Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesByFormulaPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this formula candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateScored" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction": { - "get": { - "tags": [ - "Features" - ], - "summary": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", - "description": "All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,", - "operationId": "getCanopusPrediction", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Predicted compound classes", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CanopusPrediction" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes": { - "get": { - "tags": [ - "Features" - ], - "summary": "Return Best matching compound classes for given formulaId", - "description": "Return Best matching compound classes for given formulaId.\n
\n Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology,", - "operationId": "getBestMatchingCompoundClasses", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "Best matching Predicted compound classes", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/CompoundClasses" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns a fragmentation spectrum (e", - "description": "Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier\n
\n These annotations are only available if a fragmentation tree is available.", - "operationId": "getFormulaAnnotatedSpectrum", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "spectrumIndex", - "in": "query", - "description": "index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)", - "required": false, - "schema": { - "type": "integer", - "format": "int32", - "default": -1 - } - }, - { - "name": "searchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectrum annotated with fragment formulas and losses.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata": { - "get": { - "tags": [ - "Features" - ], - "summary": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId", - "description": "Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.\n
\n Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses\n for the given formula result identifier\n These annotations are only available if a fragmentation tree and the structure candidate are available.", - "operationId": "getFormulaAnnotatedMsMsData", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "formulaId", - "in": "path", - "description": "identifier of the requested formula result", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Fragmentation spectra annotated with fragment formulas and losses.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AnnotatedMsMsData" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of FormulaResultContainers available for this feature with minimal information.", - "description": "Page of FormulaResultContainers available for this feature with minimal information.\n Can be enriched with an optional results overview.", - "operationId": "getFormulaCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the formula result belongs to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "statistics", - "fragmentationTree", - "annotatedSpectrum", - "isotopePattern", - "lipidAnnotation", - "predictedFingerprint", - "compoundClasses", - "canopusPredictions" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "All FormulaCandidate of this feature with.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelFormulaCandidate" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "description": "Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint.", - "operationId": "getDeNovoStructureCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures": { - "get": { - "tags": [ - "Features" - ], - "summary": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", - "description": "List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidates", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.", - "description": "Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.\n StructureCandidates can be enriched with molecular fingerprint, structure database links.", - "operationId": "getStructureCandidatesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) the structure candidates belong to.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "fingerprint", - "dbLinks", - "libraryMatches", - "structureSvg" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelStructureCandidateFormula" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network", - "description": "[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAdductNetworkWithMergedTracesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "one feature that is considered the main feature of the adduct network", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/TraceSetExperimental" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tags/{objectId}": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get all tags associated with this Object", - "description": "[EXPERIMENTAL] Get all tags associated with this Object", - "operationId": "getTagsForAlignedFeaturesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to get from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "objectId", - "in": "path", - "description": "object to get tags for.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "the tags of the requested object", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Tag" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tagged": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get features (aligned over runs) by tag", - "description": "[EXPERIMENTAL] Get features (aligned over runs) by tag.\n\n
The filter string must contain one or more clauses. A clause is prefÃxed\n by a field name.\n
\n\n Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).\n Tag name based field need to be prefixed with the namespace tags..\n Possible value types of tags are bool, integer, real, text, date, or time - tag value\n\n
The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
\ntags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
\n\ntags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeaturesByTagExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project space to get features (aligned over runs) from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "filter", - "in": "query", - "description": "tag filter.", - "required": false, - "schema": { - "type": "string", - "default": "" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" - ] - }, - "default": [] - } - } - ], - "responses": { - "200": { - "description": "tagged features (aligned over runs)", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId}": { - "get": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] List all fold changes that are associated with an object", - "description": "[EXPERIMENTAL] List all fold changes that are associated with an object.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFoldChangesByAlignedFeatureExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "objectId", - "in": "path", - "description": "id of the object the fold changes are assigned to.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "fold changes", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/FoldChange" - } - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table": { - "get": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] Get table of all fold changes in the project space", - "description": "[EXPERIMENTAL] Get table of all fold changes in the project space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeatureFoldChangeTableExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "description": "aggregation type.", - "required": false, - "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] - } - }, - { - "name": "quantification", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - } - ], - "responses": { - "200": { - "description": "table of fold changes.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/StatisticsTable" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/quant-table": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)", - "description": "[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId).\n
\n Returns the full quantification table. The quantification table contains a quantities of the features within all\n runs they are contained in.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getFeatureQuantTableExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "type", - "in": "query", - "description": "quantification type.", - "required": false, - "schema": { - "type": "string", - "default": "APEX_HEIGHT", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - } - ], - "responses": { - "200": { - "description": "Quant table if akk feature in this project", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/QuantTableExperimental" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/page": { - "get": { - "tags": [ - "Features" - ], - "summary": "Get all available features (aligned over runs) in the given project-space.", - "description": "Get all available features (aligned over runs) in the given project-space.", - "operationId": "getAlignedFeaturesPaged", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to read from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "msDataSearchPrepared", - "in": "query", - "description": "Returns all fragment spectra in a preprocessed form as used for fast\n Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch\n peak assignments and reference spectra.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "AlignedFeatures with additional annotations and MS/MS data (if specified).", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/aligned-features/grouped": { - "get": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Get features (aligned over runs) by tag group", - "description": "[EXPERIMENTAL] Get features (aligned over runs) by tag group.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "getAlignedFeaturesByGroupExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "groupName", - "in": "query", - "description": "tag group name.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "page", - "in": "query", - "description": "Zero-based page index (0..N)", - "required": false, - "schema": { - "minimum": 0, - "type": "integer", - "default": 0 - } - }, - { - "name": "size", - "in": "query", - "description": "The size of the page to be returned", - "required": false, - "schema": { - "minimum": 1, - "type": "integer", - "default": 20 - } - }, - { - "name": "sort", - "in": "query", - "description": "Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - }, - { - "name": "optFields", - "in": "query", - "description": "set of optional fields to be included. Use 'none' only to override defaults.", - "required": false, - "schema": { - "type": "array", - "items": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "msData", - "topAnnotationsSummary", - "topAnnotations", - "topAnnotationsDeNovo", - "computedTools", - "tags" - ] - }, - "default": [ - "none" - ] - } - } - ], - "responses": { - "200": { - "description": "tagged features (aligned over runs)", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/PagedModelAlignedFeature" - } - } - } - } - } - } - }, - "/api/job-configs": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Request all available job configurations", - "description": "Request all available job configurations", - "operationId": "getJobConfigs", - "responses": { - "200": { - "description": "list of available {@link JobSubmission JobSubmission}s", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/StoredJobSubmission" - } - } - } - } - } - } - } - }, - "/api/job-config-names": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "[DEPRECATED] Get all (non-default) job configuration names\n ", - "description": "[DEPRECATED] Get all (non-default) job configuration names\n
\n [DEPRECATED] Use /job-configs to get all configs with names. This endpoint is based on local file paths and will likely be removed in future versions of this API.", - "operationId": "getJobConfigNames", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - } - } - } - } - }, - "deprecated": true - } - }, - "/api/info": { - "get": { - "tags": [ - "Info" - ], - "operationId": "getInfo", - "parameters": [ - { - "name": "serverInfo", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - }, - { - "name": "updateInfo", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": true - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/Info" - } - } - } - } - } - } - }, - "/api/guis": { - "get": { - "tags": [ - "Gui" - ], - "summary": "Get list of currently running gui windows, managed by this SIRIUS instance.", - "description": "Get list of currently running gui windows, managed by this SIRIUS instance.\n Note this will not show any Clients that are connected from a separate process!", - "operationId": "getGuis", - "responses": { - "200": { - "description": "List of GUI windows that are currently managed by this SIRIUS instance.", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/GuiInfo" - } - } - } - } - } - } - } - }, - "/api/default-job-config": { - "get": { - "tags": [ - "Jobs" - ], - "summary": "Request default job configuration", - "description": "Request default job configuration", - "operationId": "getDefaultJobConfig", - "parameters": [ - { - "name": "includeConfigMap", - "in": "query", - "description": "if true, generic configmap with-defaults will be included", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "moveParametersToConfigMap", - "in": "query", - "description": "if true, object-based parameters will be converted to and added to the generic configMap parameters", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "includeCustomDbsForStructureSearch", - "in": "query", - "description": "if true, default database selection of structure db search\n spectral library search contains also all available custom DB.\n If No custom dbs are selected, spectral library search is disabled by default.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "{@link JobSubmission JobSubmission} with all parameters set to default values.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/JobSubmission" - } - } - } - } - } - } - }, - "/api/databases/included": { - "get": { - "tags": [ - "Searchable Databases" - ], - "operationId": "getIncludedDatabases", - "parameters": [ - { - "name": "includeStats", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - } - } - }, - "/api/databases/custom": { - "get": { - "tags": [ - "Searchable Databases" - ], - "operationId": "getCustomDatabases", - "parameters": [ - { - "name": "includeStats", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - }, - { - "name": "includeWithErrors", - "in": "query", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/SearchableDatabase" - } - } - } - } - } - } - } - }, - "/api/connection-status": { - "get": { - "tags": [ - "Info" - ], - "operationId": "getConnectionCheck", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/ConnectionCheck" - } - } - } - } - } - } - }, - "/api/account/subscriptions": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get available subscriptions of the account currently logged in.", - "description": "Get available subscriptions of the account currently logged in. Fails if not logged in.", - "operationId": "getSubscriptions", - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Subscription" - } - } - } - } - } - } - } - }, - "/api/account/signUp": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Open SignUp window in system browser and return signUp link.", - "description": "Open SignUp window in system browser and return signUp link.", - "operationId": "signUp", - "responses": { - "200": { - "description": "OK", - "content": { - "text/plain;charset=UTF-8": { - "schema": { - "type": "string" - } - } - } - } - } - } - }, - "/api/account/signUpURL": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get SignUp URL (For signUp via web browser)", - "description": "Get SignUp URL (For signUp via web browser)", - "operationId": "getSignUpURL", - "responses": { - "200": { - "description": "OK", - "content": { - "text/plain;charset=UTF-8": { - "schema": { - "type": "string" - } - } - } - } - } - } - }, - "/api/account/openPortal": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Open User portal in browser.", - "description": "Open User portal in browser. If user is logged in SIRIUS tries to transfer the login state to the browser.", - "operationId": "openPortal", - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/account/isLoggedIn": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Check if a user is logged in.", - "description": "Check if a user is logged in.", - "operationId": "isLoggedIn", - "responses": { - "200": { - "description": "true if the user is logged in", - "content": { - "application/json": { - "schema": { - "type": "boolean" - } - } - } - } - } - } - }, - "/api/account/": { - "get": { - "tags": [ - "Login and Account" - ], - "summary": "Get information about the account currently logged in.", - "description": "Get information about the account currently logged in. Fails if not logged in.", - "operationId": "getAccountInfo", - "parameters": [ - { - "name": "includeSubs", - "in": "query", - "description": "include available and active subscriptions in {@link AccountInfo AccountInfo}.", - "required": false, - "schema": { - "type": "boolean", - "default": false - } - } - ], - "responses": { - "200": { - "description": "Basic information about the account that has been logged in and its subscriptions.", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/AccountInfo" - } - } - } - } - } - } - }, - "/actuator/health": { - "get": { - "tags": [ - "Actuator" - ], - "summary": "Actuator web endpoint 'health'", - "operationId": "health", - "responses": { - "200": { - "description": "OK", - "content": { - "application/vnd.spring-boot.actuator.v3+json": { - "schema": { - "type": "object" - } - }, - "application/vnd.spring-boot.actuator.v2+json": { - "schema": { - "type": "object" - } - }, - "application/json": { - "schema": { - "type": "object" - } - } - } - } - } - } - }, - "/api/projects/{projectId}/runs/tags/{runId}/{tagName}": { - "delete": { - "tags": [ - "Runs" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromRunExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "runId", - "in": "path", - "description": "run to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds/tags/{compoundId}/{tagName}": { - "delete": { - "tags": [ - "Compounds" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromCompoundExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "compoundId", - "in": "path", - "description": "compound (group of ion identities) to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/compounds/statistics/foldchanges": { - "delete": { - "tags": [ - "Compound Statistics" - ], - "summary": "[EXPERIMENTAL] Delete fold changes", - "description": "[EXPERIMENTAL] Delete fold changes.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteCompoundFoldChangesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "rightGroupName", - "in": "query", - "description": "name of the right group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] - } - }, - { - "name": "quantification", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName}": { - "delete": { - "tags": [ - "Features" - ], - "summary": "[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space", - "description": "[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "removeTagFromAlignedFeatureExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "alignedFeatureId", - "in": "path", - "description": "feature (aligned over runs) to delete tag from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "tagName", - "in": "path", - "description": "name of the tag to delete.", - "required": true, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - }, - "/api/projects/{projectId}/aligned-features/statistics/foldchanges": { - "delete": { - "tags": [ - "Feature Statistics" - ], - "summary": "[EXPERIMENTAL] Delete fold changes", - "description": "[EXPERIMENTAL] Delete fold changes.\n
\n [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.", - "operationId": "deleteAlignedFeatureFoldChangesExperimental", - "parameters": [ - { - "name": "projectId", - "in": "path", - "description": "project-space to delete from.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "leftGroupName", - "in": "query", - "description": "name of the left group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "rightGroupName", - "in": "query", - "description": "name of the right group.", - "required": true, - "schema": { - "type": "string" - } - }, - { - "name": "aggregation", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "AVG", - "enum": [ - "AVG", - "MIN", - "MAX" - ] - } - }, - { - "name": "quantification", - "in": "query", - "required": false, - "schema": { - "type": "string", - "default": "APEX_INTENSITY", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] - } - } - ], - "responses": { - "200": { - "description": "OK" - } - } - } - } - }, - "components": { - "schemas": { - "ProjectChangeEvent": { - "type": "object", - "properties": { - "eventType": { - "type": "string", - "enum": [ - "PROJECT_OPENED", - "PROJECT_MOVED", - "PROJECT_CLOSED", - "FEATURE_CREATED", - "FEATURE_UPDATED", - "FEATURE_DELETED", - "RESULT_CREATED", - "RESULT_UPDATED", - "RESULT_DELETED" - ] - }, - "projectId": { - "type": "string" - }, - "compoundId": { - "type": "string", - "nullable": true - }, - "featuredId": { - "type": "string", - "nullable": true - }, - "formulaId": { - "type": "string", - "nullable": true - }, - "structureInChIKey": { - "type": "string", - "nullable": true - } - } - }, - "DataImportEvent": { - "required": [ - "importedCompoundIds", - "importedFeatureIds" - ], - "type": "object", - "properties": { - "importJobId": { - "type": "string", - "nullable": true - }, - "importedCompoundIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "importedFeatureIds": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "BackgroundComputationsStateEvent": { - "required": [ - "affectedJobs", - "numberOfFinishedJobs", - "numberOfJobs", - "numberOfRunningJobs" - ], - "type": "object", - "properties": { - "affectedJobs": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Job" - } - }, - "numberOfJobs": { - "type": "integer", - "format": "int32" - }, - "numberOfRunningJobs": { - "type": "integer", - "format": "int32" - }, - "numberOfFinishedJobs": { - "type": "integer", - "format": "int32" - } - } - }, - "ProjectInfo": { - "type": "object", - "properties": { "projectId": { - "type": "string", - "description": "a user selected unique name of the project for easy access." - }, - "location": { - "type": "string", - "description": "storage location of the project." - }, - "description": { - "type": "string", - "description": "Description of this project.", - "nullable": true - }, - "type": { - "type": "string", - "description": "Type of this project.\n NULL if project type has not yet been specified by importing data.", - "nullable": true, - "enum": [ - "UNIMPORTED", - "DIRECT_IMPORT", - "PEAKLISTS", - "ALIGNED_RUNS", - "UNALIGNED_RUNS" - ] - }, - "compatible": { - "type": "boolean", - "description": "Indicates whether computed results (e.g. fingerprints, compounds classes) are compatible with the backend.\n If true project is up-to-date and there are no restrictions regarding usage.\n If false project is incompatible and therefore \"read only\" until the incompatible results have been removed. See updateProject endpoint for further information\n If NULL the information has not been requested.", - "nullable": true - }, - "numOfFeatures": { - "type": "integer", - "description": "Number of features (aligned over runs) in this project. If NULL, information has not been requested (See OptField 'sizeInformation').", - "format": "int32", - "nullable": true - }, - "numOfCompounds": { - "type": "integer", - "description": "Number of compounds (group of ion identities) in this project. If NULL, Information has not been requested (See OptField 'sizeInformation') or might be unavailable for this project type.", - "format": "int32", - "nullable": true - }, - "numOfBytes": { - "type": "integer", - "description": "Size in Bytes this project consumes on disk If NULL, Information has not been requested (See OptField 'sizeInformation').", - "format": "int64", - "nullable": true - } - } - }, - "TagDefinitionImport": { - "required": [ - "tagName", - "valueType" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of this tag defined by this definition (key)" - }, - "description": { - "type": "string", - "description": "A human-readable description about the purpose of this tag.", - "nullable": true - }, - "tagType": { - "type": "string", - "description": "A simple string based identifier to specify the type/scope/purpose of this tag.", - "nullable": true - }, - "valueType": { - "type": "string", - "enum": [ - "NONE", - "BOOLEAN", - "INTEGER", - "REAL", - "TEXT", - "DATE", - "TIME" - ] - }, - "possibleValues": { - "type": "array", - "nullable": true, - "items": { - "type": "object", - "nullable": true - } - }, - "minValue": { - "type": "object", - "nullable": true - }, - "maxValue": { - "type": "object", - "nullable": true - } - } - }, - "TagDefinition": { - "required": [ - "tagName", - "valueType" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of this tag defined by this definition (key)" - }, - "description": { - "type": "string", - "description": "A human-readable description about the purpose of this tag.", - "nullable": true - }, - "tagType": { - "type": "string", - "description": "A simple string based identifier to specify the type/scope/purpose of this tag.", - "nullable": true - }, - "valueType": { - "type": "string", - "enum": [ - "NONE", - "BOOLEAN", - "INTEGER", - "REAL", - "TEXT", - "DATE", - "TIME" - ] - }, - "possibleValues": { - "type": "array", - "nullable": true, - "items": { - "type": "object", - "nullable": true - } - }, - "minValue": { - "type": "object", - "nullable": true - }, - "maxValue": { - "type": "object", - "nullable": true - }, - "editable": { - "type": "boolean" - } - } - }, - "Tag": { - "required": [ - "tagName" - ], - "type": "object", - "properties": { - "tagName": { - "type": "string", - "description": "Name of the tag as defined by the corresponding TagDefinition\n Links tag object to their definition." - }, - "value": { - "type": "object", - "description": "Optional value of the tag.\n
\n Generic value of the tag as defined by the corresponding TagDefinition.\n Can be Integer, Double, Boolean and String, whereas String values can represent Text, Date (yyyy-MM-dd) or Time (HH:mm:ss).", - "nullable": true - } - } - }, - "SampleTypeFoldChangeRequest": { - "type": "object", - "properties": { - "sampleRunIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "blankRunIds": { - "type": "array", - "items": { - "type": "string" - } - }, - "controlRunIds": { - "type": "array", - "items": { - "type": "string" - } - } - } - }, - "Job": { - "type": "object", - "properties": { - "id": { - "type": "string", - "description": "Unique identifier to access the job via the API" - }, - "command": { - "type": "string", - "description": "Command string of the executed Task", - "nullable": true - }, - "progress": { - "$ref": "#/components/schemas/JobProgress" - }, - "affectedCompoundIds": { - "type": "array", - "description": "List of compoundIds that are affected by this job.\n This lis will also contain compoundIds where not all features of the compound are affected by the job.\n If this job is creating compounds (e.g. data import jobs) this value will be NULL until the jobs has finished", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "affectedAlignedFeatureIds": { - "type": "array", - "description": "List of alignedFeatureIds that are affected by this job.\n If this job is creating features (e.g. data import jobs) this value will be NULL until the jobs has finished", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "jobEffect": { - "type": "string", - "description": "Effect this job has. The affected ids are added, removed or modified.\n Null if job does not affect features/compounds\n Not available/null if affected Ids are not requested", - "nullable": true, - "enum": [ - "IMPORT", - "COMPUTATION", - "DELETION" - ] - } - }, - "description": "Identifier created by the SIRIUS Nightsky API for a newly created Job.\n Object can be enriched with Job status/progress information ({@link JobProgress JobProgress}) and/or Job command information.\n This is a return value of the API. So nullable values can also be NOT_REQUIRED to allow for easy removal." - }, - "JobProgress": { - "type": "object", - "properties": { - "indeterminate": { - "type": "boolean", - "description": "Is the progress indeterminate or not", - "nullable": true - }, - "state": { - "type": "string", - "description": "Current state of the Jobs in the SIRIUS internal Job scheduler\n\n WAITING: Waiting for submission to ExecutorService (e.g. due to dependent jobs)\n READY: Ready for submission but not yet enqueued for submission to ExecutorService.\n QUEUED: Enqueued for submission to ExecutorService.\n SUBMITTED: Submitted and waiting to be executed.\n RUNNING: Job is running.\n CANCELED: Jobs is finished due to cancellation by user or dependent jobs.\n FAILED: Job is finished but failed.\n DONE: Job finished successfully.", - "enum": [ - "WAITING", - "READY", - "QUEUED", - "SUBMITTED", - "RUNNING", - "CANCELED", - "FAILED", - "DONE" - ] - }, - "currentProgress": { - "type": "integer", - "description": "Current progress value of the job.", - "format": "int64", + "type": "string" + }, + "compoundId": { + "type": "string", "nullable": true }, - "maxProgress": { - "type": "integer", - "description": "Progress value to reach (might also change during execution)", - "format": "int64", + "featuredId": { + "type": "string", "nullable": true }, - "message": { + "formulaId": { "type": "string", - "description": "Progress information and warnings.", "nullable": true }, - "errorMessage": { + "structureInChIKey": { "type": "string", - "description": "Error message if the job did not finish successfully failed.", "nullable": true } - }, - "description": "Progress information of a computation job that has already been submitted to SIRIUS.\n if currentProgress == maxProgress job is finished and should change to state done soon.\n if a job is DONE all results can be accessed via the Project-Spaces api.", - "nullable": true + } }, - "BasicSpectrum": { + "DataImportEvent": { "required": [ - "cosineQuery", - "peaks" + "importedCompoundIds", + "importedFeatureIds" ], "type": "object", "properties": { - "name": { - "type": "string", - "description": "Optional Displayable name of this spectrum.", - "nullable": true - }, - "msLevel": { - "type": "integer", - "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", - "format": "int32", - "nullable": true - }, - "collisionEnergy": { - "type": "string", - "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", - "nullable": true - }, - "instrument": { + "importJobId": { "type": "string", - "description": "Instrument information.", - "nullable": true - }, - "precursorMz": { - "type": "number", - "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", - "format": "double", - "nullable": true - }, - "scanNumber": { - "type": "integer", - "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", - "format": "int32", "nullable": true }, - "cosineQuery": { - "type": "boolean", - "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", - "default": false - }, - "precursorPeak": { - "$ref": "#/components/schemas/SimplePeak" - }, - "peaks": { + "importedCompoundIds": { "type": "array", - "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", "items": { - "$ref": "#/components/schemas/SimplePeak" + "type": "string" } }, - "absIntensityFactor": { - "type": "number", - "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", - "format": "double", - "nullable": true, - "deprecated": true - }, - "maxNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to MAX norm.", - "format": "double", - "nullable": true - }, - "sumNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to SUM norm.", - "format": "double", - "nullable": true - }, - "l2NormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", - "format": "double", - "nullable": true - }, - "firstPeakNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", - "format": "double", - "nullable": true - } - }, - "nullable": true - }, - "BinaryFingerprint": { - "type": "object", - "properties": { - "bitsSet": { + "importedFeatureIds": { "type": "array", - "description": "Array that contains all RELATIVE indices (masked FP) of bits that are set (are 1)", "items": { - "type": "integer", - "format": "int32" + "type": "string" } - }, - "length": { - "type": "integer", - "description": "Size of the fingerprint (masked fp), e.g. to reconstruct the binary array from the array of set bits", - "format": "int32" - } - }, - "nullable": true - }, - "DBLink": { - "required": [ - "name" - ], - "type": "object", - "properties": { - "name": { - "type": "string" - }, - "id": { - "type": "string" - } - }, - "nullable": true - }, - "PeakPair": { - "required": [ - "queryPeak", - "referencePeak" - ], - "type": "object", - "properties": { - "queryPeak": { - "type": "integer", - "format": "int32" - }, - "referencePeak": { - "type": "integer", - "format": "int32" - } - } - }, - "SimplePeak": { - "type": "object", - "properties": { - "mz": { - "type": "number", - "format": "double" - }, - "intensity": { - "type": "number", - "format": "double" } } }, - "SpectralLibraryMatch": { + "BackgroundComputationsStateEvent": { "required": [ - "inchiKey", - "querySpectrumIndex", - "similarity", - "uuid" + "affectedJobs", + "numberOfFinishedJobs", + "numberOfJobs", + "numberOfRunningJobs" ], "type": "object", "properties": { - "specMatchId": { - "type": "string" - }, - "rank": { - "type": "integer", - "format": "int32" - }, - "similarity": { - "type": "number", - "description": "Similarity between query and reference spectrum", - "format": "float" - }, - "sharedPeaks": { - "type": "integer", - "description": "Number of shared/matched peaks", - "format": "int32" - }, - "sharedPeakMapping": { + "affectedJobs": { "type": "array", - "description": "List of paired/matched peak indices.\n\n Maps indices of peaks from the query spectrum (mass sorted)\n to indices of matched peaks in the reference spectrum (mass sorted)", "items": { - "$ref": "#/components/schemas/PeakPair" + "$ref": "#/components/schemas/Job" } }, - "querySpectrumIndex": { + "numberOfJobs": { "type": "integer", "format": "int32" }, - "dbName": { - "type": "string" - }, - "dbId": { - "type": "string" - }, - "uuid": { + "numberOfRunningJobs": { "type": "integer", - "format": "int64" - }, - "splash": { - "type": "string" - }, - "molecularFormula": { - "type": "string" - }, - "adduct": { - "type": "string" - }, - "exactMass": { - "type": "number", - "format": "double" - }, - "smiles": { - "type": "string" - }, - "type": { - "type": "string", - "default": "IDENTITY", - "enum": [ - "IDENTITY", - "ANALOG" - ] - }, - "inchiKey": { - "type": "string" - }, - "referenceSpectrumType": { - "type": "string", - "default": "SPECTRUM", - "enum": [ - "SPECTRUM", - "MERGED_SPECTRUM" - ] - }, - "referenceSpectrum": { - "$ref": "#/components/schemas/BasicSpectrum" + "format": "int32" }, - "querySpectrumType": { - "type": "string", - "enum": [ - "SPECTRUM", - "MERGED_SPECTRUM" - ] + "numberOfFinishedJobs": { + "type": "integer", + "format": "int32" } - }, - "nullable": true + } }, - "StructureCandidateFormula": { + "ProjectInfo": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" + "projectId": { + "type": "string", + "description": "a user selected unique name of the project for easy access." }, - "structureName": { + "location": { "type": "string", - "nullable": true + "description": "storage location of the project." }, - "structureSvg": { + "description": { "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "description": "Description of this project.", "nullable": true }, - "dbLinks": { - "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/DBLink" - } - }, - "spectralLibraryMatches": { - "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "type": { + "type": "string", + "description": "Type of this project.\n NULL if project type has not yet been specified by importing data.", "nullable": true, - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" - } + "enum": [ + "UNIMPORTED", + "DIRECT_IMPORT", + "PEAKLISTS", + "ALIGNED_RUNS", + "UNALIGNED_RUNS" + ] }, - "xlogP": { - "type": "number", - "format": "double", + "compatible": { + "type": "boolean", + "description": "Indicates whether computed results (e.g. fingerprints, compounds classes) are compatible with the backend.\n If true project is up-to-date and there are no restrictions regarding usage.\n If false project is incompatible and therefore \"read only\" until the incompatible results have been removed. See updateProject endpoint for further information\n If NULL the information has not been requested.", "nullable": true }, - "rank": { + "numOfFeatures": { "type": "integer", - "description": "the overall rank of this candidate among all candidates of this feature", - "format": "int32" - }, - "csiScore": { - "type": "number", - "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", - "format": "double" - }, - "tanimotoSimilarity": { - "type": "number", - "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", - "format": "double", + "description": "Number of features (aligned over runs) in this project. If NULL, information has not been requested (See OptField 'sizeInformation').", + "format": "int32", "nullable": true }, - "mcesDistToTopHit": { - "type": "number", - "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", - "format": "double", + "numOfCompounds": { + "type": "integer", + "description": "Number of compounds (group of ion identities) in this project. If NULL, Information has not been requested (See OptField 'sizeInformation') or might be unavailable for this project type.", + "format": "int32", "nullable": true }, - "fingerprint": { - "$ref": "#/components/schemas/BinaryFingerprint" - }, - "molecularFormula": { - "type": "string", - "description": "Molecular formula of this candidate" - }, - "adduct": { - "type": "string", - "description": "Adduct of this candidate" - }, - "formulaId": { - "type": "string", - "description": "Id of the corresponding Formula candidate" + "numOfBytes": { + "type": "integer", + "description": "Size in Bytes this project consumes on disk If NULL, Information has not been requested (See OptField 'sizeInformation').", + "format": "int64", + "nullable": true } } }, @@ -9337,6 +5859,100 @@ }, "nullable": true }, + "Job": { + "type": "object", + "properties": { + "id": { + "type": "string", + "description": "Unique identifier to access the job via the API" + }, + "command": { + "type": "string", + "description": "Command string of the executed Task", + "nullable": true + }, + "progress": { + "$ref": "#/components/schemas/JobProgress" + }, + "affectedCompoundIds": { + "type": "array", + "description": "List of compoundIds that are affected by this job.\n This lis will also contain compoundIds where not all features of the compound are affected by the job.\n If this job is creating compounds (e.g. data import jobs) this value will be NULL until the jobs has finished", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } + }, + "affectedAlignedFeatureIds": { + "type": "array", + "description": "List of alignedFeatureIds that are affected by this job.\n If this job is creating features (e.g. data import jobs) this value will be NULL until the jobs has finished", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } + }, + "jobEffect": { + "type": "string", + "description": "Effect this job has. The affected ids are added, removed or modified.\n Null if job does not affect features/compounds\n Not available/null if affected Ids are not requested", + "nullable": true, + "enum": [ + "IMPORT", + "COMPUTATION", + "DELETION" + ] + } + }, + "description": "Identifier created by the SIRIUS Nightsky API for a newly created Job.\n Object can be enriched with Job status/progress information ({@link JobProgress JobProgress}) and/or Job command information.\n This is a return value of the API. So nullable values can also be NOT_REQUIRED to allow for easy removal." + }, + "JobProgress": { + "type": "object", + "properties": { + "indeterminate": { + "type": "boolean", + "description": "Is the progress indeterminate or not", + "nullable": true + }, + "state": { + "type": "string", + "description": "Current state of the Jobs in the SIRIUS internal Job scheduler\n\n WAITING: Waiting for submission to ExecutorService (e.g. due to dependent jobs)\n READY: Ready for submission but not yet enqueued for submission to ExecutorService.\n QUEUED: Enqueued for submission to ExecutorService.\n SUBMITTED: Submitted and waiting to be executed.\n RUNNING: Job is running.\n CANCELED: Jobs is finished due to cancellation by user or dependent jobs.\n FAILED: Job is finished but failed.\n DONE: Job finished successfully.", + "enum": [ + "WAITING", + "READY", + "QUEUED", + "SUBMITTED", + "RUNNING", + "CANCELED", + "FAILED", + "DONE" + ] + }, + "currentProgress": { + "type": "integer", + "description": "Current progress value of the job.", + "format": "int64", + "nullable": true + }, + "maxProgress": { + "type": "integer", + "description": "Progress value to reach (might also change during execution)", + "format": "int64", + "nullable": true + }, + "message": { + "type": "string", + "description": "Progress information and warnings.", + "nullable": true + }, + "errorMessage": { + "type": "string", + "description": "Error message if the job did not finish successfully failed.", + "nullable": true + } + }, + "description": "Progress information of a computation job that has already been submitted to SIRIUS.\n if currentProgress == maxProgress job is finished and should change to state done soon.\n if a job is DONE all results can be accessed via the Project-Spaces api.", + "nullable": true + }, "ImportResult": { "required": [ "affectedAlignedFeatureIds", @@ -9382,47 +5998,120 @@ "description": "Specifies whether LC/MS runs should be aligned", "default": true }, - "noiseIntensity": { - "type": "number", - "description": "Noise level under which all peaks are considered to be likely noise. A peak has to be at least 3x noise level\n to be picked as feature. Peaks with MS/MS are still picked even though they might be below noise level.\n If not specified, the noise intensity is detected automatically from data. We recommend to NOT specify\n this parameter, as the automated detection is usually sufficient.", - "format": "double", - "default": -1 + "noiseIntensity": { + "type": "number", + "description": "Noise level under which all peaks are considered to be likely noise. A peak has to be at least 3x noise level\n to be picked as feature. Peaks with MS/MS are still picked even though they might be below noise level.\n If not specified, the noise intensity is detected automatically from data. We recommend to NOT specify\n this parameter, as the automated detection is usually sufficient.", + "format": "double", + "default": -1 + }, + "traceMaxMassDeviation": { + "$ref": "#/components/schemas/Deviation" + }, + "alignMaxMassDeviation": { + "$ref": "#/components/schemas/Deviation" + }, + "alignMaxRetentionTimeDeviation": { + "type": "number", + "description": "Maximal allowed retention time error in seconds for aligning features. If not specified, this parameter is estimated from data.", + "format": "double", + "default": -1 + }, + "minSNR": { + "type": "number", + "description": "Minimum ratio between peak height and noise intensity for detecting features. By default, this value is 3. Features with good MS/MS are always picked independent of their intensity. For picking very low intensive features we recommend a min-snr of 2, but this will increase runtime and storage memory", + "format": "double", + "default": 3 + } + } + }, + "BasicSpectrum": { + "required": [ + "cosineQuery", + "peaks" + ], + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Optional Displayable name of this spectrum.", + "nullable": true + }, + "msLevel": { + "type": "integer", + "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", + "format": "int32", + "nullable": true + }, + "collisionEnergy": { + "type": "string", + "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", + "nullable": true + }, + "instrument": { + "type": "string", + "description": "Instrument information.", + "nullable": true + }, + "precursorMz": { + "type": "number", + "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", + "format": "double", + "nullable": true + }, + "scanNumber": { + "type": "integer", + "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", + "format": "int32", + "nullable": true + }, + "cosineQuery": { + "type": "boolean", + "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", + "default": false + }, + "precursorPeak": { + "$ref": "#/components/schemas/SimplePeak" }, - "traceMaxMassDeviation": { - "$ref": "#/components/schemas/Deviation" + "peaks": { + "type": "array", + "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", + "items": { + "$ref": "#/components/schemas/SimplePeak" + } }, - "alignMaxMassDeviation": { - "$ref": "#/components/schemas/Deviation" + "absIntensityFactor": { + "type": "number", + "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", + "format": "double", + "nullable": true, + "deprecated": true }, - "alignMaxRetentionTimeDeviation": { + "maxNormFactor": { "type": "number", - "description": "Maximal allowed retention time error in seconds for aligning features. If not specified, this parameter is estimated from data.", + "description": "Factor to convert absolute intensities to MAX norm.", "format": "double", - "default": -1 + "nullable": true }, - "minSNR": { + "sumNormFactor": { "type": "number", - "description": "Minimum ratio between peak height and noise intensity for detecting features. By default, this value is 3. Features with good MS/MS are always picked independent of their intensity. For picking very low intensive features we recommend a min-snr of 2, but this will increase runtime and storage memory", + "description": "Factor to convert absolute intensities to SUM norm.", "format": "double", - "default": 3 - } - } - }, - "TagGroup": { - "type": "object", - "properties": { - "groupName": { - "type": "string", - "description": "Name of this Grouping query." + "nullable": true }, - "luceneQuery": { - "type": "string", - "description": "Query used to group the entities in lucene format." + "l2NormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", + "format": "double", + "nullable": true }, - "groupType": { - "type": "string" + "firstPeakNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", + "format": "double", + "nullable": true } - } + }, + "nullable": true }, "CompoundImport": { "required": [ @@ -9527,6 +6216,19 @@ }, "description": "Represents an (aligned) feature to be imported into a SIRIUS project.\n At least one of the Mass Spec data sources (e.g. mergedMs1, ms1Spectra, ms2Spectra) needs to be given.\n Otherwise, the import will fail." }, + "SimplePeak": { + "type": "object", + "properties": { + "mz": { + "type": "number", + "format": "double" + }, + "intensity": { + "type": "number", + "format": "double" + } + } + }, "AlignedFeature": { "required": [ "charge", @@ -9641,1599 +6343,1307 @@ "$ref": "#/components/schemas/PeakAnnotation" } } - }, - "AnnotatedSpectrum": { - "required": [ - "cosineQuery", - "peaks" - ], - "type": "object", - "properties": { - "name": { - "type": "string", - "description": "Optional Displayable name of this spectrum.", - "nullable": true - }, - "msLevel": { - "type": "integer", - "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", - "format": "int32", - "nullable": true - }, - "collisionEnergy": { - "type": "string", - "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", - "nullable": true - }, - "instrument": { - "type": "string", - "description": "Instrument information.", - "nullable": true - }, - "precursorMz": { - "type": "number", - "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", - "format": "double", - "nullable": true - }, - "scanNumber": { - "type": "integer", - "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", - "format": "int32", - "nullable": true - }, - "cosineQuery": { - "type": "boolean", - "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", - "default": false - }, - "precursorPeak": { - "$ref": "#/components/schemas/SimplePeak" - }, - "peaks": { - "type": "array", - "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", - "items": { - "$ref": "#/components/schemas/AnnotatedPeak" - } - }, - "absIntensityFactor": { - "type": "number", - "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", - "format": "double", - "nullable": true, - "deprecated": true - }, - "maxNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to MAX norm.", - "format": "double", - "nullable": true - }, - "sumNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to SUM norm.", - "format": "double", - "nullable": true - }, - "l2NormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", - "format": "double", - "nullable": true - }, - "firstPeakNormFactor": { - "type": "number", - "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", - "format": "double", - "nullable": true - }, - "spectrumAnnotation": { - "$ref": "#/components/schemas/SpectrumAnnotation" - } - }, - "description": "Spectrum model with peak annotations based on the fragmentation tree and Epimetheus substructure annotations.\n Molecular formula and adduct of the spectrum are identical to the ones of the corresponding molecular formula candidate and FragmentationTree.\n Fragment molecular formulas and adducts correspond to the FragmentationTree's FragmentNodes", - "nullable": true - }, - "CanopusPrediction": { - "type": "object", - "properties": { - "classyFireClasses": { - "type": "array", - "description": "All predicted ClassyFire classes", - "nullable": true, - "items": { - "$ref": "#/components/schemas/CompoundClass" - } - }, - "npcClasses": { - "type": "array", - "description": "All predicted NPC classes", - "nullable": true, - "items": { - "$ref": "#/components/schemas/CompoundClass" - } - } - }, - "description": "Container class that holds the CANOPUS compound class predictions for alle predictable compound classes.\n This is the full CANOPUS result.", - "nullable": true - }, - "Compound": { - "type": "object", - "properties": { - "compoundId": { - "type": "string", - "description": "uid of this compound Entity" - }, - "name": { - "type": "string", - "description": "Some (optional) human-readable name", - "nullable": true - }, - "rtStartSeconds": { - "type": "number", - "description": "The merged/consensus retention time start (earliest rt) of this compound", - "format": "double", - "nullable": true - }, - "rtEndSeconds": { - "type": "number", - "description": "The merged/consensus retention time end (latest rt) of this compound", - "format": "double", - "nullable": true - }, - "neutralMass": { - "type": "number", - "description": "Neutral mass of this compound. Ion masse minus the mass of the assigned adduct of each feature of\n this compound should result in the same neutral mass", - "format": "double", - "nullable": true - }, - "features": { - "type": "array", - "description": "List of aligned features (adducts) that belong to the same (this) compound", - "items": { - "$ref": "#/components/schemas/AlignedFeature" - } - }, - "consensusAnnotations": { - "$ref": "#/components/schemas/ConsensusAnnotationsCSI" - }, - "consensusAnnotationsDeNovo": { - "$ref": "#/components/schemas/ConsensusAnnotationsDeNovo" - }, - "customAnnotations": { - "$ref": "#/components/schemas/ConsensusAnnotationsCSI" - }, - "tags": { - "type": "object", - "additionalProperties": { - "$ref": "#/components/schemas/Tag" - }, - "description": "Key: tagName, value: tag", - "nullable": true - } - } - }, - "CompoundClass": { - "type": "object", - "properties": { - "type": { - "type": "string", - "description": "Specifies the classification ontology the CompoundClass belongs to.", - "nullable": true, - "enum": [ - "ClassyFire", - "NPC" - ] - }, - "level": { + }, + "AnnotatedSpectrum": { + "required": [ + "cosineQuery", + "peaks" + ], + "type": "object", + "properties": { + "name": { "type": "string", - "description": "Name of the level this compound class belongs to", + "description": "Optional Displayable name of this spectrum.", "nullable": true }, - "levelIndex": { + "msLevel": { "type": "integer", - "description": "Index of the level this compound class belongs to", + "description": "MS level of the measured spectrum.\n Artificial spectra with no msLevel (e.g. Simulated Isotope patterns) use null or zero", "format": "int32", "nullable": true }, - "name": { + "collisionEnergy": { "type": "string", - "description": "Name of the compound class.", + "description": "Collision energy used for MS/MS spectra\n Null for spectra where collision energy is not applicable", "nullable": true }, - "description": { + "instrument": { "type": "string", - "description": "Description of the compound class.", - "nullable": true - }, - "id": { - "type": "integer", - "description": "Unique id of the class. Might be undefined for certain classification ontologies.", - "format": "int32", + "description": "Instrument information.", "nullable": true }, - "probability": { + "precursorMz": { "type": "number", - "description": "prediction probability", - "format": "double" - }, - "index": { - "type": "integer", - "description": "Absolute index of this property in the predicted vector/embedding", - "format": "int32" + "description": "Precursor m/z of the MS/MS spectrum\n Null for spectra where precursor m/z is not applicable", + "format": "double", + "nullable": true }, - "parentId": { + "scanNumber": { "type": "integer", - "description": "Unique id of the parent class. Might be undefined for certain classification ontologies.", + "description": "Scan number of the spectrum.\n Might be null for artificial spectra with no scan number (e.g. Simulated Isotope patterns or merged spectra)", "format": "int32", "nullable": true }, - "parentName": { - "type": "string", - "description": "Name of the parent compound class.", - "nullable": true - } - }, - "description": "Predicted compound class with name, probability and id if available.\n (ClassyFire and NPC). This can be seen as the set of classes a feature most likely belongs to", - "nullable": true - }, - "CompoundClasses": { - "type": "object", - "properties": { - "npcPathway": { - "$ref": "#/components/schemas/CompoundClass" - }, - "npcSuperclass": { - "$ref": "#/components/schemas/CompoundClass" + "cosineQuery": { + "type": "boolean", + "description": "True if spectrum is in cosine query normalized format.\n Such spectrum is compatible with SpectralLibraryMatch peak assignments to reference spectra.", + "default": false }, - "npcClass": { - "$ref": "#/components/schemas/CompoundClass" + "precursorPeak": { + "$ref": "#/components/schemas/SimplePeak" }, - "classyFireLineage": { + "peaks": { "type": "array", - "description": "Most likely ClassyFire lineage from ordered from least specific to most specific class\n classyFireLineage.get(classyFireLineage.size() - 1) gives the most specific ClassyFire compound class annotation", - "nullable": true, + "description": "The peaks of this spectrum which might contain additional annotations such as molecular formulas.", "items": { - "$ref": "#/components/schemas/CompoundClass" + "$ref": "#/components/schemas/AnnotatedPeak" } }, - "classyFireAlternatives": { - "type": "array", - "description": "Alternative ClassyFire classes with high probability that do not fit into the linage", + "absIntensityFactor": { + "type": "number", + "description": "Factor to convert relative intensities to absolute intensities.\n Might be null or 1 for spectra where absolute intensities are not available (E.g. artificial or merged spectra)\n
\n DEPRECATED: Spectra are always returned with raw intensities.\n Use provided normalization factors to normalize on the fly.", + "format": "double", "nullable": true, - "items": { - "$ref": "#/components/schemas/CompoundClass" - } - } - }, - "description": "Container class that holds the most likely compound class for different levels of each ontology for a\n certain Compound/Feature/FormulaCandidate/PredictedFingerprint.", - "nullable": true - }, - "ComputedSubtools": { - "type": "object", - "properties": { - "librarySearch": { - "type": "boolean" - }, - "formulaSearch": { - "type": "boolean" - }, - "zodiac": { - "type": "boolean" - }, - "fingerprint": { - "type": "boolean" - }, - "canopus": { - "type": "boolean" - }, - "structureSearch": { - "type": "boolean" + "deprecated": true }, - "deNovoSearch": { - "type": "boolean" - } - }, - "description": "Specifies which tools have been executed for this feature. Can be used to estimate which results can be expected. Null if it was not requested und non-null otherwise.", - "nullable": true - }, - "ConsensusAnnotationsCSI": { - "type": "object", - "properties": { - "molecularFormula": { - "type": "string", - "description": "Molecular formula of the consensus annotation\n Might be null if no consensus formula is available.", + "maxNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to MAX norm.", + "format": "double", "nullable": true }, - "compoundClasses": { - "$ref": "#/components/schemas/CompoundClasses" - }, - "supportingFeatureIds": { - "type": "array", - "description": "FeatureIds where the topAnnotation supports this annotation.", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } - }, - "selectionCriterion": { - "type": "string", - "description": "Null if this is a custom selection", - "nullable": true, - "enum": [ - "MAJORITY_STRUCTURE", - "CONFIDENCE_STRUCTURE", - "SINGLETON_STRUCTURE", - "MAJORITY_FORMULA", - "TOP_FORMULA", - "SINGLETON_FORMULA" - ] - }, - "csiFingerIdStructure": { - "$ref": "#/components/schemas/StructureCandidate" + "sumNormFactor": { + "type": "number", + "description": "Factor to convert absolute intensities to SUM norm.", + "format": "double", + "nullable": true }, - "confidenceExactMatch": { + "l2NormFactor": { "type": "number", - "description": "Confidence value that represents the certainty that reported consensus structure is exactly the measured one\n If multiple features support this consensus structure the maximum confidence is reported", + "description": "Factor to convert absolute intensities to L2 (Euclidean) norm.", "format": "double", "nullable": true }, - "confidenceApproxMatch": { + "firstPeakNormFactor": { "type": "number", - "description": "Confidence value that represents the certainty that the exact consensus structure or a very similar\n structure (e.g. measured by Maximum Common Edge Subgraph Distance) is the measured one.\n If multiple features support this consensus structure the maximum confidence is reported", + "description": "Factor to convert absolute intensities to normalize intensities by first peak intensity.", "format": "double", "nullable": true + }, + "spectrumAnnotation": { + "$ref": "#/components/schemas/SpectrumAnnotation" } }, + "description": "Spectrum model with peak annotations based on the fragmentation tree and Epimetheus substructure annotations.\n Molecular formula and adduct of the spectrum are identical to the ones of the corresponding molecular formula candidate and FragmentationTree.\n Fragment molecular formulas and adducts correspond to the FragmentationTree's FragmentNodes", "nullable": true }, - "ConsensusAnnotationsDeNovo": { + "BinaryFingerprint": { "type": "object", "properties": { - "molecularFormula": { - "type": "string", - "description": "Molecular formula of the consensus annotation\n Might be null if no consensus formula is available.", - "nullable": true - }, - "compoundClasses": { - "$ref": "#/components/schemas/CompoundClasses" - }, - "supportingFeatureIds": { + "bitsSet": { "type": "array", - "description": "FeatureIds where the topAnnotation supports this annotation.", - "nullable": true, + "description": "Array that contains all RELATIVE indices (masked FP) of bits that are set (are 1)", "items": { - "type": "string", - "nullable": true + "type": "integer", + "format": "int32" } }, - "selectionCriterion": { - "type": "string", - "description": "Criterion that was used to select the consensus annotation.", - "nullable": true, - "enum": [ - "MAJORITY_FORMULA", - "TOP_FORMULA", - "SINGLETON_FORMULA" - ] + "length": { + "type": "integer", + "description": "Size of the fingerprint (masked fp), e.g. to reconstruct the binary array from the array of set bits", + "format": "int32" } }, "nullable": true }, - "FeatureAnnotations": { + "CanopusPrediction": { "type": "object", "properties": { - "formulaAnnotation": { - "$ref": "#/components/schemas/FormulaCandidate" - }, - "structureAnnotation": { - "$ref": "#/components/schemas/StructureCandidateScored" - }, - "compoundClassAnnotation": { - "$ref": "#/components/schemas/CompoundClasses" - }, - "confidenceExactMatch": { - "type": "number", - "description": "Confidence Score that represents the confidence whether the top hit is correct.", - "format": "double", - "nullable": true - }, - "confidenceApproxMatch": { - "type": "number", - "description": "Confidence Score that represents the confidence whether the top hit or a very similar hit (estimated by MCES distance) is correct.", - "format": "double", - "nullable": true - }, - "expansiveSearchState": { - "type": "string", - "description": "Result that shows if structure annotation was expanded by using PubChem as fallback and if so, which confidence mode was used (as per input paramter)", - "nullable": true, - "enum": [ - "OFF", - "EXACT", - "APPROXIMATE" - ] - }, - "specifiedDatabases": { + "classyFireClasses": { "type": "array", - "description": "List of databases that have been specified by for structure db search. Null if no structure db search has been performed.", + "description": "All predicted ClassyFire classes", "nullable": true, "items": { - "type": "string", - "nullable": true + "$ref": "#/components/schemas/CompoundClass" } }, - "expandedDatabases": { + "npcClasses": { "type": "array", - "description": "List of databases that have been used to expand search space during expansive search. Null if no structure db search has been performed.", + "description": "All predicted NPC classes", "nullable": true, "items": { - "type": "string", - "nullable": true + "$ref": "#/components/schemas/CompoundClass" } } }, - "description": "Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature.\n The different annotation fields within this summary object are null if the corresponding\n feature does not contain the represented results. If fields are non-null\n the corresponding result has been computed but might still be empty.", + "description": "Container class that holds the CANOPUS compound class predictions for alle predictable compound classes.\n This is the full CANOPUS result.", "nullable": true }, - "FormulaCandidate": { + "Compound": { "type": "object", "properties": { - "formulaId": { - "type": "string", - "description": "Unique identifier of this formula candidate" - }, - "molecularFormula": { + "compoundId": { "type": "string", - "description": "molecular formula of this formula candidate" + "description": "uid of this compound Entity" }, - "adduct": { + "name": { "type": "string", - "description": "Adduct of this formula candidate" - }, - "rank": { - "type": "integer", - "format": "int32" - }, - "siriusScoreNormalized": { - "type": "number", - "description": "Normalized Sirius Score of the formula candidate.\n If NULL result is not available", - "format": "double", - "nullable": true - }, - "siriusScore": { - "type": "number", - "description": "Sirius Score (isotope + tree score) of the formula candidate.\n If NULL result is not available", - "format": "double", - "nullable": true - }, - "isotopeScore": { - "type": "number", - "format": "double", + "description": "Some (optional) human-readable name", "nullable": true }, - "treeScore": { + "rtStartSeconds": { "type": "number", + "description": "The merged/consensus retention time start (earliest rt) of this compound", "format": "double", "nullable": true }, - "zodiacScore": { + "rtEndSeconds": { "type": "number", - "description": "Zodiac Score of the formula candidate.\n If NULL result is not available", + "description": "The merged/consensus retention time end (latest rt) of this compound", "format": "double", "nullable": true }, - "numOfExplainedPeaks": { - "type": "integer", - "format": "int32", - "nullable": true - }, - "numOfExplainablePeaks": { - "type": "integer", - "format": "int32", - "nullable": true - }, - "totalExplainedIntensity": { + "neutralMass": { "type": "number", + "description": "Neutral mass of this compound. Ion masse minus the mass of the assigned adduct of each feature of\n this compound should result in the same neutral mass", "format": "double", "nullable": true }, - "medianMassDeviation": { - "$ref": "#/components/schemas/Deviation" - }, - "fragmentationTree": { - "$ref": "#/components/schemas/FragmentationTree" - }, - "annotatedSpectrum": { - "$ref": "#/components/schemas/AnnotatedSpectrum" - }, - "isotopePatternAnnotation": { - "$ref": "#/components/schemas/IsotopePatternAnnotation" - }, - "lipidAnnotation": { - "$ref": "#/components/schemas/LipidAnnotation" - }, - "predictedFingerprint": { + "features": { "type": "array", - "description": "Probabilistic molecular fingerprint predicted by CSI:FingerID", - "nullable": true, + "description": "List of aligned features (adducts) that belong to the same (this) compound", "items": { - "type": "number", - "format": "double", - "nullable": true + "$ref": "#/components/schemas/AlignedFeature" } }, - "compoundClasses": { - "$ref": "#/components/schemas/CompoundClasses" + "consensusAnnotations": { + "$ref": "#/components/schemas/ConsensusAnnotationsCSI" }, - "canopusPrediction": { - "$ref": "#/components/schemas/CanopusPrediction" + "consensusAnnotationsDeNovo": { + "$ref": "#/components/schemas/ConsensusAnnotationsDeNovo" + }, + "customAnnotations": { + "$ref": "#/components/schemas/ConsensusAnnotationsCSI" + }, + "tags": { + "type": "object", + "additionalProperties": { + "$ref": "#/components/schemas/Tag" + }, + "description": "Key: tagName, value: tag", + "nullable": true } - }, - "description": "Molecular formula candidate that holds a unique identifier (molecular formula + adduct).\n It can be extended with optional scoring metrics and the raw results\n such as fragmentation trees and simulated isotope pattern.", - "nullable": true + } }, - "FragmentNode": { + "CompoundClass": { "type": "object", "properties": { - "fragmentId": { - "type": "integer", - "format": "int32" + "type": { + "type": "string", + "description": "Specifies the classification ontology the CompoundClass belongs to.", + "nullable": true, + "enum": [ + "ClassyFire", + "NPC" + ] }, - "molecularFormula": { + "level": { "type": "string", - "description": "neutral molecular formula of the fragment without adduct", + "description": "Name of the level this compound class belongs to", "nullable": true }, - "adduct": { - "type": "string", - "description": "This combines the ionization plus adduct of the fragment. In contrast to the {@link FragmentationTree FragmentationTree}s adduct,\n this adduct may not include any in-source loss.", + "levelIndex": { + "type": "integer", + "description": "Index of the level this compound class belongs to", + "format": "int32", "nullable": true }, - "massDeviationDa": { - "type": "number", - "format": "double", + "name": { + "type": "string", + "description": "Name of the compound class.", "nullable": true }, - "massDeviationPpm": { - "type": "number", - "format": "double", + "description": { + "type": "string", + "description": "Description of the compound class.", "nullable": true }, - "score": { - "type": "number", - "format": "double", + "id": { + "type": "integer", + "description": "Unique id of the class. Might be undefined for certain classification ontologies.", + "format": "int32", "nullable": true }, - "intensity": { + "probability": { "type": "number", - "format": "double", + "description": "prediction probability", + "format": "double" + }, + "index": { + "type": "integer", + "description": "Absolute index of this property in the predicted vector/embedding", + "format": "int32" + }, + "parentId": { + "type": "integer", + "description": "Unique id of the parent class. Might be undefined for certain classification ontologies.", + "format": "int32", "nullable": true }, - "mz": { - "type": "number", - "format": "double", + "parentName": { + "type": "string", + "description": "Name of the parent compound class.", "nullable": true } - } + }, + "description": "Predicted compound class with name, probability and id if available.\n (ClassyFire and NPC). This can be seen as the set of classes a feature most likely belongs to", + "nullable": true }, - "FragmentationTree": { + "CompoundClasses": { "type": "object", "properties": { - "fragments": { + "npcPathway": { + "$ref": "#/components/schemas/CompoundClass" + }, + "npcSuperclass": { + "$ref": "#/components/schemas/CompoundClass" + }, + "npcClass": { + "$ref": "#/components/schemas/CompoundClass" + }, + "classyFireLineage": { "type": "array", + "description": "Most likely ClassyFire lineage from ordered from least specific to most specific class\n classyFireLineage.get(classyFireLineage.size() - 1) gives the most specific ClassyFire compound class annotation", + "nullable": true, "items": { - "$ref": "#/components/schemas/FragmentNode" + "$ref": "#/components/schemas/CompoundClass" } }, - "losses": { + "classyFireAlternatives": { "type": "array", + "description": "Alternative ClassyFire classes with high probability that do not fit into the linage", + "nullable": true, "items": { - "$ref": "#/components/schemas/LossEdge" + "$ref": "#/components/schemas/CompoundClass" } + } + }, + "description": "Container class that holds the most likely compound class for different levels of each ontology for a\n certain Compound/Feature/FormulaCandidate/PredictedFingerprint.", + "nullable": true + }, + "ComputedSubtools": { + "type": "object", + "properties": { + "librarySearch": { + "type": "boolean" }, - "treeScore": { - "type": "number", - "format": "double" + "formulaSearch": { + "type": "boolean" }, - "molecularFormula": { - "type": "string" + "zodiac": { + "type": "boolean" }, - "adduct": { - "type": "string" + "fingerprint": { + "type": "boolean" + }, + "canopus": { + "type": "boolean" + }, + "structureSearch": { + "type": "boolean" + }, + "deNovoSearch": { + "type": "boolean" } }, - "description": "Simple and easy serializable fragmentation tree model with annotated fragments/nodes abd losses/edges\n Root fragment has index 0;\n Molecular formula and adduct are identical to the ones of the corresponding molecular formula candidate and SpectrumAnnotation", + "description": "Specifies which tools have been executed for this feature. Can be used to estimate which results can be expected. Null if it was not requested und non-null otherwise.", "nullable": true }, - "IsotopePatternAnnotation": { + "ConsensusAnnotationsCSI": { "type": "object", "properties": { - "isotopePattern": { - "$ref": "#/components/schemas/BasicSpectrum" + "molecularFormula": { + "type": "string", + "description": "Molecular formula of the consensus annotation\n Might be null if no consensus formula is available.", + "nullable": true + }, + "compoundClasses": { + "$ref": "#/components/schemas/CompoundClasses" + }, + "supportingFeatureIds": { + "type": "array", + "description": "FeatureIds where the topAnnotation supports this annotation.", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } + }, + "selectionCriterion": { + "type": "string", + "description": "Null if this is a custom selection", + "nullable": true, + "enum": [ + "MAJORITY_STRUCTURE", + "CONFIDENCE_STRUCTURE", + "SINGLETON_STRUCTURE", + "MAJORITY_FORMULA", + "TOP_FORMULA", + "SINGLETON_FORMULA" + ] }, - "simulatedPattern": { - "$ref": "#/components/schemas/BasicSpectrum" + "csiFingerIdStructure": { + "$ref": "#/components/schemas/StructureCandidate" + }, + "confidenceExactMatch": { + "type": "number", + "description": "Confidence value that represents the certainty that reported consensus structure is exactly the measured one\n If multiple features support this consensus structure the maximum confidence is reported", + "format": "double", + "nullable": true + }, + "confidenceApproxMatch": { + "type": "number", + "description": "Confidence value that represents the certainty that the exact consensus structure or a very similar\n structure (e.g. measured by Maximum Common Edge Subgraph Distance) is the measured one.\n If multiple features support this consensus structure the maximum confidence is reported", + "format": "double", + "nullable": true } }, "nullable": true }, - "LipidAnnotation": { + "ConsensusAnnotationsDeNovo": { "type": "object", "properties": { - "lipidSpecies": { + "molecularFormula": { "type": "string", - "description": "Predicted lipid species in LIPID MAPS notation.\n NULL if not classified as lipid.", + "description": "Molecular formula of the consensus annotation\n Might be null if no consensus formula is available.", "nullable": true }, - "lipidMapsId": { - "type": "string", - "description": "LIPID MAPS id of the predicted lipid class.", - "nullable": true + "compoundClasses": { + "$ref": "#/components/schemas/CompoundClasses" }, - "lipidClassName": { - "type": "string", - "description": "Human-readable name of the predicted lipid class.", - "nullable": true + "supportingFeatureIds": { + "type": "array", + "description": "FeatureIds where the topAnnotation supports this annotation.", + "nullable": true, + "items": { + "type": "string", + "nullable": true + } }, - "hypotheticalStructure": { + "selectionCriterion": { "type": "string", - "description": "Hypothetical molecular structure of the predicted lipid species as SMILES.\n NULL if hypothetical structure not available.", - "nullable": true - }, - "chainsUnknown": { - "type": "boolean", - "description": "True of the formula composition of the chains could not be determined from the MS/MS.", - "nullable": true + "description": "Criterion that was used to select the consensus annotation.", + "nullable": true, + "enum": [ + "MAJORITY_FORMULA", + "TOP_FORMULA", + "SINGLETON_FORMULA" + ] } }, "nullable": true }, - "LossEdge": { + "DBLink": { + "required": [ + "name" + ], "type": "object", "properties": { - "sourceFragmentIdx": { - "type": "integer", - "format": "int32" - }, - "targetFragmentIdx": { - "type": "integer", - "format": "int32" - }, - "molecularFormula": { + "name": { "type": "string" }, - "score": { - "type": "number", - "format": "double" + "id": { + "type": "string" } - } + }, + "nullable": true }, - "MsData": { + "FeatureAnnotations": { "type": "object", "properties": { - "isotopePattern": { - "$ref": "#/components/schemas/BasicSpectrum" + "formulaAnnotation": { + "$ref": "#/components/schemas/FormulaCandidate" }, - "mergedMs1": { - "$ref": "#/components/schemas/BasicSpectrum" + "structureAnnotation": { + "$ref": "#/components/schemas/StructureCandidateScored" }, - "mergedMs2": { - "$ref": "#/components/schemas/BasicSpectrum" + "compoundClassAnnotation": { + "$ref": "#/components/schemas/CompoundClasses" }, - "ms1Spectra": { + "confidenceExactMatch": { + "type": "number", + "description": "Confidence Score that represents the confidence whether the top hit is correct.", + "format": "double", + "nullable": true + }, + "confidenceApproxMatch": { + "type": "number", + "description": "Confidence Score that represents the confidence whether the top hit or a very similar hit (estimated by MCES distance) is correct.", + "format": "double", + "nullable": true + }, + "expansiveSearchState": { + "type": "string", + "description": "Result that shows if structure annotation was expanded by using PubChem as fallback and if so, which confidence mode was used (as per input paramter)", + "nullable": true, + "enum": [ + "OFF", + "EXACT", + "APPROXIMATE" + ] + }, + "specifiedDatabases": { "type": "array", + "description": "List of databases that have been specified by for structure db search. Null if no structure db search has been performed.", + "nullable": true, "items": { - "$ref": "#/components/schemas/BasicSpectrum" + "type": "string", + "nullable": true } }, - "ms2Spectra": { + "expandedDatabases": { "type": "array", + "description": "List of databases that have been used to expand search space during expansive search. Null if no structure db search has been performed.", + "nullable": true, "items": { - "$ref": "#/components/schemas/BasicSpectrum" + "type": "string", + "nullable": true } } }, - "description": "The MsData wraps all spectral input data belonging to a (aligned) feature. All spectra fields are optional.\n However, at least one Spectrum field needs to be set to create a valid MsData Object.\n The different types of spectra fields can be extended to adapt to other MassSpec measurement techniques not covered yet.\n
\n Each Feature can have:\n - One extracted isotope pattern (optional)\n - One merged MS/MS spectrum (optional)\n - One merged MS spectrum (optional)\n - many MS/MS spectra (optional)\n - many MS spectra (optional)\n
\n Each non-merged spectrum has an index which can be used to access the spectrum.\n
\n In the future we might add some additional information like chromatographic peak or something similar", + "description": "Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature.\n The different annotation fields within this summary object are null if the corresponding\n feature does not contain the represented results. If fields are non-null\n the corresponding result has been computed but might still be empty.", "nullable": true }, - "ParentPeak": { - "required": [ - "lossFormula", - "parentFragmentId", - "parentIdx" - ], + "FormulaCandidate": { "type": "object", "properties": { - "parentIdx": { - "type": "integer", - "description": "Index to the parent peak connected by this loss in this particular spectrum", - "format": "int32" - }, - "parentFragmentId": { - "type": "integer", - "description": "Identifier of the parent fragment connected via this loss. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", - "format": "int32" - }, - "lossFormula": { + "formulaId": { "type": "string", - "description": "Molecular formula of the neutral loss that connects these two peaks." - } - }, - "description": "Link from annotated fragment peak to its parent fragment peak connected by their neutral loss.", - "nullable": true - }, - "PeakAnnotation": { - "required": [ - "fragmentId" - ], - "type": "object", - "properties": { - "fragmentId": { - "type": "integer", - "description": "Identifier of the peak/fragment. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", - "format": "int32" + "description": "Unique identifier of this formula candidate" }, "molecularFormula": { "type": "string", - "description": "Molecular formula that has been annotated to this peak", - "nullable": true + "description": "molecular formula of this formula candidate" }, "adduct": { "type": "string", - "description": "Adduct that has been annotated to this peak", + "description": "Adduct of this formula candidate" + }, + "rank": { + "type": "integer", + "format": "int32" + }, + "siriusScoreNormalized": { + "type": "number", + "description": "Normalized Sirius Score of the formula candidate.\n If NULL result is not available", + "format": "double", "nullable": true }, - "exactMass": { + "siriusScore": { "type": "number", - "description": "Exact mass of the annotated molecular formula and adduct", + "description": "Sirius Score (isotope + tree score) of the formula candidate.\n If NULL result is not available", "format": "double", "nullable": true }, - "massDeviationMz": { + "isotopeScore": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the measured peak mass in mDa", "format": "double", "nullable": true }, - "massDeviationPpm": { + "treeScore": { "type": "number", - "description": "Relative mass deviation of the exact mass to the measured peak mass in ppm", "format": "double", "nullable": true }, - "recalibratedMassDeviationMz": { + "zodiacScore": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the recalibrated peak mass in mDa", + "description": "Zodiac Score of the formula candidate.\n If NULL result is not available", "format": "double", "nullable": true }, - "recalibratedMassDeviationPpm": { + "numOfExplainedPeaks": { + "type": "integer", + "format": "int32", + "nullable": true + }, + "numOfExplainablePeaks": { + "type": "integer", + "format": "int32", + "nullable": true + }, + "totalExplainedIntensity": { "type": "number", - "description": "Relative mass deviation of the exact mass to the recalibrated peak mass in ppm", "format": "double", "nullable": true }, - "parentPeak": { - "$ref": "#/components/schemas/ParentPeak" + "medianMassDeviation": { + "$ref": "#/components/schemas/Deviation" }, - "substructureAtoms": { - "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the atoms of the structure candidate that are part of this fragments substructure\n (highlighted atoms)", - "nullable": true, - "items": { - "type": "integer", - "format": "int32", - "nullable": true - } + "fragmentationTree": { + "$ref": "#/components/schemas/FragmentationTree" }, - "substructureBonds": { - "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that are part of this fragments substructure\n (highlighted bonds)\n\n Null if substructure annotation not available or not requested.", - "nullable": true, - "items": { - "type": "integer", - "format": "int32", - "nullable": true - } + "annotatedSpectrum": { + "$ref": "#/components/schemas/AnnotatedSpectrum" }, - "substructureBondsCut": { + "isotopePatternAnnotation": { + "$ref": "#/components/schemas/IsotopePatternAnnotation" + }, + "lipidAnnotation": { + "$ref": "#/components/schemas/LipidAnnotation" + }, + "predictedFingerprint": { "type": "array", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that need to be cut to produce this fragments\n substructure (highlighted cutted bonds).\n\n Null if substructure annotation not available or not requested.", + "description": "Probabilistic molecular fingerprint predicted by CSI:FingerID", "nullable": true, "items": { - "type": "integer", - "format": "int32", + "type": "number", + "format": "double", "nullable": true } }, - "substructureScore": { - "type": "number", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n This score roughly reflects the probability of this fragment forming.\n\n This is the score of the path from root to this node which has the maximal score or \"profit\".\n The score of a path is equal to the sum of scores of its contained fragments and edges.\n Note: Refers to 'totalScore' in CombinatorialNode\n\n Null if substructure annotation not available or not requested.", - "format": "float", - "nullable": true + "compoundClasses": { + "$ref": "#/components/schemas/CompoundClasses" }, - "hydrogenRearrangements": { - "type": "integer", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Number of hydrogens rearrangements needed to match the substructure to the fragment formula.\n\n Null if substructure annotation not available or not requested.", - "format": "int32", - "nullable": true + "canopusPrediction": { + "$ref": "#/components/schemas/CanopusPrediction" } }, + "description": "Molecular formula candidate that holds a unique identifier (molecular formula + adduct).\n It can be extended with optional scoring metrics and the raw results\n such as fragmentation trees and simulated isotope pattern.", "nullable": true }, - "SpectrumAnnotation": { + "FragmentNode": { "type": "object", "properties": { + "fragmentId": { + "type": "integer", + "format": "int32" + }, "molecularFormula": { "type": "string", - "description": "Molecular formula that has been annotated to this spectrum", + "description": "neutral molecular formula of the fragment without adduct", "nullable": true }, "adduct": { "type": "string", - "description": "Adduct that has been annotated to this spectrum", + "description": "This combines the ionization plus adduct of the fragment. In contrast to the {@link FragmentationTree FragmentationTree}s adduct,\n this adduct may not include any in-source loss.", "nullable": true }, - "exactMass": { + "massDeviationDa": { "type": "number", - "description": "Exact mass based on the annotated molecular formula and ionization", "format": "double", "nullable": true }, - "massDeviationMz": { + "massDeviationPpm": { "type": "number", - "description": "Absolute mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in mDa", "format": "double", "nullable": true }, - "massDeviationPpm": { + "score": { "type": "number", - "description": "Relative mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in ppm", "format": "double", "nullable": true }, - "structureAnnotationSmiles": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Smiles of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refer to this specific SMILES.\n If you standardize or canonicalize this SMILES in any way the indices of substructure highlighting might\n not match correctly anymore.\n
\n Null if substructure annotation not available or not requested.", - "nullable": true - }, - "structureAnnotationName": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Name of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation.\n
\n Null if substructure annotation not available or not requested.", - "nullable": true - }, - "structureAnnotationSvg": { - "type": "string", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n SVG graphics of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refers to this SVG.\n
\n Null if substructure annotation not available or not requested.", + "intensity": { + "type": "number", + "format": "double", "nullable": true }, - "structureAnnotationScore": { + "mz": { "type": "number", - "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Overall score of all substructure annotations computed for this structure candidate (structureAnnotationSmiles)\n
\n Null if substructure annotation not available or not requested.", "format": "double", "nullable": true } - }, - "nullable": true + } }, - "StructureCandidate": { + "FragmentationTree": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" - }, - "structureName": { - "type": "string", - "nullable": true - }, - "structureSvg": { - "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true - }, - "dbLinks": { + "fragments": { "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, "items": { - "$ref": "#/components/schemas/DBLink" + "$ref": "#/components/schemas/FragmentNode" } }, - "spectralLibraryMatches": { + "losses": { "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" + "$ref": "#/components/schemas/LossEdge" } }, - "xlogP": { + "treeScore": { "type": "number", - "format": "double", - "nullable": true + "format": "double" + }, + "molecularFormula": { + "type": "string" + }, + "adduct": { + "type": "string" } }, + "description": "Simple and easy serializable fragmentation tree model with annotated fragments/nodes abd losses/edges\n Root fragment has index 0;\n Molecular formula and adduct are identical to the ones of the corresponding molecular formula candidate and SpectrumAnnotation", "nullable": true }, - "StructureCandidateScored": { + "IsotopePatternAnnotation": { "type": "object", "properties": { - "inchiKey": { - "type": "string" - }, - "smiles": { - "type": "string" + "isotopePattern": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "structureName": { + "simulatedPattern": { + "$ref": "#/components/schemas/BasicSpectrum" + } + }, + "nullable": true + }, + "LipidAnnotation": { + "type": "object", + "properties": { + "lipidSpecies": { "type": "string", + "description": "Predicted lipid species in LIPID MAPS notation.\n NULL if not classified as lipid.", "nullable": true }, - "structureSvg": { + "lipidMapsId": { "type": "string", - "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "description": "LIPID MAPS id of the predicted lipid class.", "nullable": true }, - "dbLinks": { - "type": "array", - "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/DBLink" - } - }, - "spectralLibraryMatches": { - "type": "array", - "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", - "nullable": true, - "items": { - "$ref": "#/components/schemas/SpectralLibraryMatch" - } - }, - "xlogP": { - "type": "number", - "format": "double", + "lipidClassName": { + "type": "string", + "description": "Human-readable name of the predicted lipid class.", "nullable": true }, - "rank": { - "type": "integer", - "description": "the overall rank of this candidate among all candidates of this feature", - "format": "int32" - }, - "csiScore": { - "type": "number", - "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", - "format": "double" - }, - "tanimotoSimilarity": { - "type": "number", - "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", - "format": "double", + "hypotheticalStructure": { + "type": "string", + "description": "Hypothetical molecular structure of the predicted lipid species as SMILES.\n NULL if hypothetical structure not available.", "nullable": true }, - "mcesDistToTopHit": { - "type": "number", - "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", - "format": "double", + "chainsUnknown": { + "type": "boolean", + "description": "True of the formula composition of the chains could not be determined from the MS/MS.", "nullable": true - }, - "fingerprint": { - "$ref": "#/components/schemas/BinaryFingerprint" } }, "nullable": true }, - "StoredJobSubmission": { - "required": [ - "editable", - "jobSubmission", - "name" - ], + "LossEdge": { "type": "object", "properties": { - "name": { - "type": "string", - "description": "Unique name to identify this JobSubmission (job config)." + "sourceFragmentIdx": { + "type": "integer", + "format": "int32" }, - "editable": { - "type": "boolean", - "description": "False for predefined configs which are not editable and not removable." + "targetFragmentIdx": { + "type": "integer", + "format": "int32" }, - "jobSubmission": { - "$ref": "#/components/schemas/JobSubmission" + "molecularFormula": { + "type": "string" + }, + "score": { + "type": "number", + "format": "double" } } }, - "BioTransformerParameters": { - "required": [ - "bioTransformerSequenceSteps", - "cyp450Mode", - "p2Mode" - ], + "MsData": { "type": "object", "properties": { - "cyp450Mode": { - "type": "string", - "description": "Specify the Phase I/Cyp450 mode for all provided BioTransformerSequenceSteps. Will only be applied to Steps that\n require the Cyp450 mode as parameter. Can be null in cases where only BioTransformerSequenceSteps are specified\n that do not need the Cyp450 mode.", - "nullable": true, - "default": "COMBINED", - "enum": [ - "RULE_BASED", - "CY_PRODUCT", - "COMBINED" - ] + "isotopePattern": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "p2Mode": { - "type": "string", - "description": "Specify the Phase II mode for all provided BioTransformerSequenceSteps. Will only be applied to Steps that\n require the Phase II mode as parameter. Can be null in cases where only BioTransformerSequenceSteps are specified\n that do not need the Phase II mode.", - "nullable": true, - "default": "BT_RULE_BASED", - "enum": [ - "BT_RULE_BASED", - "P2_RULE_ONLY", - "COMBINED_RULES" - ] + "mergedMs1": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "useDB": { - "type": "boolean", - "description": "\"Specify if you want to enable the retrieving from database (HMDB) feature.\"", - "default": true + "mergedMs2": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "bioTransformerSequenceSteps": { + "ms1Spectra": { "type": "array", - "description": "Specify BioTransformerSequenceSteps to be applied to input structures. MultiStep MetabolicTransformations can\n only be used as singletons (list size of one).", "items": { - "$ref": "#/components/schemas/BioTransformerSequenceStep" + "$ref": "#/components/schemas/BasicSpectrum" } - } - } - }, - "BioTransformerSequenceStep": { - "type": "object", - "properties": { - "metabolicTransformation": { - "type": "string", - "enum": [ - "PHASE_1_CYP450", - "EC_BASED", - "PHASE_2", - "HUMAN_GUT", - "ALL_HUMAN", - "ABIOTIC", - "HUMAN_CUSTOM_MULTI" - ] }, - "iterations": { - "type": "integer", - "format": "int32" + "ms2Spectra": { + "type": "array", + "items": { + "$ref": "#/components/schemas/BasicSpectrum" + } } - } + }, + "description": "The MsData wraps all spectral input data belonging to a (aligned) feature. All spectra fields are optional.\n However, at least one Spectrum field needs to be set to create a valid MsData Object.\n The different types of spectra fields can be extended to adapt to other MassSpec measurement techniques not covered yet.\n
\n Each Feature can have:\n - One extracted isotope pattern (optional)\n - One merged MS/MS spectrum (optional)\n - One merged MS spectrum (optional)\n - many MS/MS spectra (optional)\n - many MS spectra (optional)\n
\n Each non-merged spectrum has an index which can be used to access the spectrum.\n
\n In the future we might add some additional information like chromatographic peak or something similar", + "nullable": true }, - "AccountCredentials": { + "ParentPeak": { + "required": [ + "lossFormula", + "parentFragmentId", + "parentIdx" + ], "type": "object", "properties": { - "username": { - "type": "string", - "nullable": true + "parentIdx": { + "type": "integer", + "description": "Index to the parent peak connected by this loss in this particular spectrum", + "format": "int32" }, - "password": { - "type": "string", - "nullable": true + "parentFragmentId": { + "type": "integer", + "description": "Identifier of the parent fragment connected via this loss. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", + "format": "int32" }, - "refreshToken": { + "lossFormula": { "type": "string", - "nullable": true + "description": "Molecular formula of the neutral loss that connects these two peaks." } }, - "description": "Simple object to hold account credentials, e.g. to perform login operations.\n If refreshToken is given, it is usually preferred over password based authentication.\n But in the end this is up to the respective web service." - }, - "RunOptField": { - "type": "string", - "nullable": true, - "enum": [ - "none", - "tags" - ] + "description": "Link from annotated fragment peak to its parent fragment peak connected by their neutral loss.", + "nullable": true }, - "Run": { + "PeakAnnotation": { + "required": [ + "fragmentId" + ], "type": "object", "properties": { - "runId": { - "type": "string", - "description": "Identifier" + "fragmentId": { + "type": "integer", + "description": "Identifier of the peak/fragment. Can be used to map fragments and peaks\n among fragmentation trees and spectra.", + "format": "int32" }, - "name": { + "molecularFormula": { "type": "string", - "description": "Informative, human-readable name of this run" + "description": "Molecular formula that has been annotated to this peak", + "nullable": true }, - "source": { + "adduct": { "type": "string", - "description": "Source location" + "description": "Adduct that has been annotated to this peak", + "nullable": true }, - "chromatography": { - "type": "string", + "exactMass": { + "type": "number", + "description": "Exact mass of the annotated molecular formula and adduct", + "format": "double", "nullable": true }, - "ionization": { - "type": "string", + "massDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the measured peak mass in mDa", + "format": "double", "nullable": true }, - "fragmentation": { - "type": "string", + "massDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the measured peak mass in ppm", + "format": "double", + "nullable": true + }, + "recalibratedMassDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the recalibrated peak mass in mDa", + "format": "double", + "nullable": true + }, + "recalibratedMassDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the recalibrated peak mass in ppm", + "format": "double", "nullable": true }, - "massAnalyzers": { + "parentPeak": { + "$ref": "#/components/schemas/ParentPeak" + }, + "substructureAtoms": { "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the atoms of the structure candidate that are part of this fragments substructure\n (highlighted atoms)", "nullable": true, "items": { - "type": "string", + "type": "integer", + "format": "int32", "nullable": true } }, - "tags": { - "type": "object", - "additionalProperties": { - "$ref": "#/components/schemas/Tag" - }, - "description": "Key: tagName, value: tag", - "nullable": true - } - } - }, - "PageMetadata": { - "type": "object", - "properties": { - "size": { - "type": "integer", - "format": "int64" + "substructureBonds": { + "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that are part of this fragments substructure\n (highlighted bonds)\n\n Null if substructure annotation not available or not requested.", + "nullable": true, + "items": { + "type": "integer", + "format": "int32", + "nullable": true + } }, - "number": { - "type": "integer", - "format": "int64" + "substructureBondsCut": { + "type": "array", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Array/List of indices of the bonds of the structure candidate that need to be cut to produce this fragments\n substructure (highlighted cutted bonds).\n\n Null if substructure annotation not available or not requested.", + "nullable": true, + "items": { + "type": "integer", + "format": "int32", + "nullable": true + } }, - "totalElements": { - "type": "integer", - "format": "int64" + "substructureScore": { + "type": "number", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n This score roughly reflects the probability of this fragment forming.\n\n This is the score of the path from root to this node which has the maximal score or \"profit\".\n The score of a path is equal to the sum of scores of its contained fragments and edges.\n Note: Refers to 'totalScore' in CombinatorialNode\n\n Null if substructure annotation not available or not requested.", + "format": "float", + "nullable": true }, - "totalPages": { + "hydrogenRearrangements": { "type": "integer", - "format": "int64" + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n\n Number of hydrogens rearrangements needed to match the substructure to the fragment formula.\n\n Null if substructure annotation not available or not requested.", + "format": "int32", + "nullable": true } - } + }, + "nullable": true }, - "PagedModelRun": { + "PeakPair": { + "required": [ + "queryPeak", + "referencePeak" + ], "type": "object", "properties": { - "content": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Run" - } + "queryPeak": { + "type": "integer", + "format": "int32" }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "referencePeak": { + "type": "integer", + "format": "int32" } } }, - "PagedModelJob": { + "SpectralLibraryMatch": { + "required": [ + "inchiKey", + "querySpectrumIndex", + "similarity", + "uuid" + ], "type": "object", "properties": { - "content": { + "specMatchId": { + "type": "string" + }, + "rank": { + "type": "integer", + "format": "int32" + }, + "similarity": { + "type": "number", + "description": "Similarity between query and reference spectrum", + "format": "float" + }, + "sharedPeaks": { + "type": "integer", + "description": "Number of shared/matched peaks", + "format": "int32" + }, + "sharedPeakMapping": { "type": "array", + "description": "List of paired/matched peak indices.\n\n Maps indices of peaks from the query spectrum (mass sorted)\n to indices of matched peaks in the reference spectrum (mass sorted)", "items": { - "$ref": "#/components/schemas/Job" + "$ref": "#/components/schemas/PeakPair" } }, - "page": { - "$ref": "#/components/schemas/PageMetadata" - } - } - }, - "AdductEdgeExperimental": { - "type": "object", - "properties": { - "mzDelta": { - "type": "number", - "format": "double" + "querySpectrumIndex": { + "type": "integer", + "format": "int32" }, - "annotation": { + "dbName": { "type": "string" }, - "from": { - "type": "integer", - "format": "int32" + "dbId": { + "type": "string" }, - "to": { + "uuid": { "type": "integer", - "format": "int32" + "format": "int64" }, - "mergedCorrelation": { - "type": "number", - "format": "float" + "splash": { + "type": "string" }, - "representativeCorrelation": { - "type": "number", - "format": "float" + "molecularFormula": { + "type": "string" }, - "ms2cosine": { - "type": "number", - "format": "float" + "adduct": { + "type": "string" }, - "pvalue": { + "exactMass": { "type": "number", - "format": "float" + "format": "double" }, - "intensityRatioScore": { - "type": "number", - "format": "float" - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "AdductNetworkExperimental": { - "type": "object", - "properties": { - "nodes": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AdductNodeExperimental" - } + "smiles": { + "type": "string" + }, + "type": { + "type": "string", + "default": "IDENTITY", + "enum": [ + "IDENTITY", + "ANALOG" + ] + }, + "inchiKey": { + "type": "string" + }, + "referenceSpectrumType": { + "type": "string", + "default": "SPECTRUM", + "enum": [ + "SPECTRUM", + "MERGED_SPECTRUM" + ] + }, + "referenceSpectrum": { + "$ref": "#/components/schemas/BasicSpectrum" }, - "edges": { - "type": "array", - "items": { - "$ref": "#/components/schemas/AdductEdgeExperimental" - } + "querySpectrumType": { + "type": "string", + "enum": [ + "SPECTRUM", + "MERGED_SPECTRUM" + ] } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "AdductNodeExperimental": { + "SpectrumAnnotation": { "type": "object", "properties": { - "alignedFeatureId": { - "type": "string" + "molecularFormula": { + "type": "string", + "description": "Molecular formula that has been annotated to this spectrum", + "nullable": true }, - "mz": { + "adduct": { + "type": "string", + "description": "Adduct that has been annotated to this spectrum", + "nullable": true + }, + "exactMass": { "type": "number", - "format": "double" + "description": "Exact mass based on the annotated molecular formula and ionization", + "format": "double", + "nullable": true }, - "adductAnnotations": { - "type": "object", - "additionalProperties": { - "type": "number", - "format": "double" - } - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "Axes": { - "type": "object", - "properties": { - "scanNumber": { - "type": "array", - "items": { - "type": "integer", - "format": "int32" - } + "massDeviationMz": { + "type": "number", + "description": "Absolute mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in mDa", + "format": "double", + "nullable": true }, - "scanIds": { - "type": "array", - "items": { - "type": "string" - } + "massDeviationPpm": { + "type": "number", + "description": "Relative mass deviation of the exact mass to the precursor mass (precursorMz) of this spectrum in ppm", + "format": "double", + "nullable": true }, - "retentionTimeInSeconds": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } - } - }, - "TraceAnnotationExperimental": { - "type": "object", - "properties": { - "type": { + "structureAnnotationSmiles": { "type": "string", - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.", - "enum": [ - "FEATURE", - "MS2" - ] + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Smiles of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refer to this specific SMILES.\n If you standardize or canonicalize this SMILES in any way the indices of substructure highlighting might\n not match correctly anymore.\n
\n Null if substructure annotation not available or not requested.", + "nullable": true }, - "description": { + "structureAnnotationName": { "type": "string", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Name of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation.\n
\n Null if substructure annotation not available or not requested.", "nullable": true }, - "index": { - "type": "integer", - "format": "int32" - }, - "from": { - "type": "integer", - "format": "int32", + "structureAnnotationSvg": { + "type": "string", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n SVG graphics of the structure candidate used to derive substructure peak annotations via epimetheus insilico fragmentation\n Substructure highlighting (bond and atom indices) refers to this SVG.\n
\n Null if substructure annotation not available or not requested.", "nullable": true }, - "to": { - "type": "integer", - "format": "int32", + "structureAnnotationScore": { + "type": "number", + "description": "EXPERIMENTAL: This field is experimental and may be changed (or even removed) without notice until it is declared stable.\n
\n Overall score of all substructure annotations computed for this structure candidate (structureAnnotationSmiles)\n
\n Null if substructure annotation not available or not requested.", + "format": "double", "nullable": true } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "TraceExperimental": { + "StructureCandidate": { "type": "object", "properties": { - "id": { + "inchiKey": { + "type": "string" + }, + "smiles": { "type": "string" }, - "sampleId": { + "structureName": { "type": "string", "nullable": true }, - "sampleName": { + "structureSvg": { "type": "string", + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", "nullable": true }, - "label": { - "type": "string" - }, - "color": { - "type": "string" - }, - "intensities": { + "dbLinks": { "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, "items": { - "type": "number", - "format": "double" + "$ref": "#/components/schemas/DBLink" } }, - "annotations": { + "spectralLibraryMatches": { "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, "items": { - "$ref": "#/components/schemas/TraceAnnotationExperimental" + "$ref": "#/components/schemas/SpectralLibraryMatch" } }, - "mz": { - "type": "number", - "format": "double" - }, - "merged": { - "type": "boolean" - }, - "normalizationFactor": { - "type": "number", - "description": "Traces are stored with raw intensity values. The normalization factor maps them to relative intensities,\n such that traces from different samples can be compared.", - "format": "double" - }, - "noiseLevel": { + "xlogP": { "type": "number", - "description": "The noise level is estimated from the median noise in the surrounding scans. It can be used to\n calculate signal-to-noise ratios.", - "format": "double" + "format": "double", + "nullable": true } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "TraceSetExperimental": { + "StructureCandidateScored": { "type": "object", "properties": { - "adductNetwork": { - "$ref": "#/components/schemas/AdductNetworkExperimental" - }, - "sampleId": { + "inchiKey": { "type": "string" }, - "sampleName": { + "smiles": { "type": "string" }, - "axes": { - "$ref": "#/components/schemas/Axes" - }, - "traces": { - "type": "array", - "items": { - "$ref": "#/components/schemas/TraceExperimental" - } - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "QuantTableExperimental": { - "type": "object", - "properties": { - "quantificationMeasure": { + "structureName": { "type": "string", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] + "nullable": true }, - "rowType": { + "structureSvg": { "type": "string", - "enum": [ - "FEATURES", - "COMPOUNDS" - ] + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true }, - "rowIds": { + "dbLinks": { "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", "nullable": true, "items": { - "type": "integer", - "format": "int64", - "nullable": true + "$ref": "#/components/schemas/DBLink" } }, - "columnIds": { + "spectralLibraryMatches": { "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", "nullable": true, "items": { - "type": "integer", - "format": "int64", - "nullable": true + "$ref": "#/components/schemas/SpectralLibraryMatch" } }, - "rowNames": { - "type": "array", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } + "xlogP": { + "type": "number", + "format": "double", + "nullable": true }, - "columnNames": { - "type": "array", - "nullable": true, - "items": { - "type": "string", - "nullable": true - } + "rank": { + "type": "integer", + "description": "the overall rank of this candidate among all candidates of this feature", + "format": "int32" }, - "values": { - "type": "array", - "items": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } + "csiScore": { + "type": "number", + "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", + "format": "double" + }, + "tanimotoSimilarity": { + "type": "number", + "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", + "format": "double", + "nullable": true + }, + "mcesDistToTopHit": { + "type": "number", + "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", + "format": "double", + "nullable": true + }, + "fingerprint": { + "$ref": "#/components/schemas/BinaryFingerprint" } }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." + "nullable": true }, - "PagedModelCompound": { + "Tag": { + "required": [ + "tagName" + ], "type": "object", "properties": { - "content": { - "type": "array", - "items": { - "$ref": "#/components/schemas/Compound" - } + "tagName": { + "type": "string", + "description": "Name of the tag as defined by the corresponding TagDefinition\n Links tag object to their definition." }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "value": { + "type": "object", + "description": "Optional value of the tag.\n
\n Generic value of the tag as defined by the corresponding TagDefinition.\n Can be Integer, Double, Boolean and String, whereas String values can represent Text, Date (yyyy-MM-dd) or Time (HH:mm:ss).", + "nullable": true } - } + }, + "nullable": true }, - "FoldChange": { + "StoredJobSubmission": { "required": [ - "foldChange", - "objectId", - "quantType" + "editable", + "jobSubmission", + "name" ], "type": "object", "properties": { - "leftGroup": { - "type": "string" - }, - "rightGroup": { - "type": "string" - }, - "aggregation": { + "name": { "type": "string", - "enum": [ - "AVG", - "MIN", - "MAX" - ] + "description": "Unique name to identify this JobSubmission (job config)." }, - "quantification": { + "editable": { + "type": "boolean", + "description": "False for predefined configs which are not editable and not removable." + }, + "jobSubmission": { + "$ref": "#/components/schemas/JobSubmission" + } + } + }, + "BioTransformerParameters": { + "required": [ + "bioTransformerSequenceSteps", + "cyp450Mode", + "p2Mode" + ], + "type": "object", + "properties": { + "cyp450Mode": { "type": "string", + "description": "Specify the Phase I/Cyp450 mode for all provided BioTransformerSequenceSteps. Will only be applied to Steps that\n require the Cyp450 mode as parameter. Can be null in cases where only BioTransformerSequenceSteps are specified\n that do not need the Cyp450 mode.", + "nullable": true, + "default": "COMBINED", "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" + "RULE_BASED", + "CY_PRODUCT", + "COMBINED" ] }, - "quantType": { + "p2Mode": { "type": "string", + "description": "Specify the Phase II mode for all provided BioTransformerSequenceSteps. Will only be applied to Steps that\n require the Phase II mode as parameter. Can be null in cases where only BioTransformerSequenceSteps are specified\n that do not need the Phase II mode.", + "nullable": true, + "default": "BT_RULE_BASED", "enum": [ - "FEATURES", - "COMPOUNDS" + "BT_RULE_BASED", + "P2_RULE_ONLY", + "COMBINED_RULES" ] }, - "objectId": { - "type": "string" + "useDB": { + "type": "boolean", + "description": "\"Specify if you want to enable the retrieving from database (HMDB) feature.\"", + "default": true }, - "foldChange": { - "type": "number", - "format": "double" + "bioTransformerSequenceSteps": { + "type": "array", + "description": "Specify BioTransformerSequenceSteps to be applied to input structures. MultiStep MetabolicTransformations can\n only be used as singletons (list size of one).", + "items": { + "$ref": "#/components/schemas/BioTransformerSequenceStep" + } } } }, - "StatisticsTable": { + "BioTransformerSequenceStep": { "type": "object", "properties": { - "statisticsType": { + "metabolicTransformation": { "type": "string", "enum": [ - "FOLD_CHANGE" + "PHASE_1_CYP450", + "EC_BASED", + "PHASE_2", + "HUMAN_GUT", + "ALL_HUMAN", + "ABIOTIC", + "HUMAN_CUSTOM_MULTI" ] }, - "aggregationType": { + "iterations": { + "type": "integer", + "format": "int32" + } + } + }, + "AccountCredentials": { + "type": "object", + "properties": { + "username": { "type": "string", - "enum": [ - "AVG", - "MIN", - "MAX" - ] + "nullable": true }, - "quantificationMeasure": { + "password": { "type": "string", - "enum": [ - "APEX_INTENSITY", - "AREA_UNDER_CURVE" - ] + "nullable": true }, - "rowType": { + "refreshToken": { "type": "string", - "enum": [ - "FEATURES", - "COMPOUNDS" - ] + "nullable": true + } + }, + "description": "Simple object to hold account credentials, e.g. to perform login operations.\n If refreshToken is given, it is usually preferred over password based authentication.\n But in the end this is up to the respective web service." + }, + "PageMetadata": { + "type": "object", + "properties": { + "size": { + "type": "integer", + "format": "int64" }, - "rowIds": { - "type": "array", - "items": { - "type": "string" - } + "number": { + "type": "integer", + "format": "int64" }, - "columnNames": { - "type": "array", - "items": { - "type": "string" - } + "totalElements": { + "type": "integer", + "format": "int64" }, - "columnLeftGroups": { + "totalPages": { + "type": "integer", + "format": "int64" + } + } + }, + "PagedModelJob": { + "type": "object", + "properties": { + "content": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/Job" } }, - "columnRightGroups": { + "page": { + "$ref": "#/components/schemas/PageMetadata" + } + } + }, + "PagedModelCompound": { + "type": "object", + "properties": { + "content": { "type": "array", "items": { - "type": "string" + "$ref": "#/components/schemas/Compound" } }, - "values": { - "type": "array", - "items": { - "type": "array", - "items": { - "type": "number", - "format": "double" - } - } + "page": { + "$ref": "#/components/schemas/PageMetadata" } } }, @@ -11276,89 +7686,17 @@ } } }, - "AlignedFeatureQualityExperimental": { - "required": [ - "alignedFeatureId", - "categories", - "overallQuality" - ], - "type": "object", - "properties": { - "alignedFeatureId": { - "type": "string", - "description": "Id of the feature (aligned over runs) this quality information belongs to." - }, - "overallQuality": { - "type": "string", - "description": "Overall Quality", - "nullable": true, - "enum": [ - "NOT_APPLICABLE", - "LOWEST", - "BAD", - "DECENT", - "GOOD" - ] - }, - "categories": { - "type": "object", - "additionalProperties": { - "$ref": "#/components/schemas/Category" - }, - "description": "Contains all pre-computation quality information that belong to\n this feature (aligned over runs), such as information about the quality of the peak shape, MS2 spectrum etc.," - } - }, - "description": "EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable." - }, - "Category": { + "PagedModelStructureCandidateScored": { "type": "object", "properties": { - "categoryName": { - "type": "string" - }, - "overallQuality": { - "type": "string", - "nullable": true, - "enum": [ - "NOT_APPLICABLE", - "LOWEST", - "BAD", - "DECENT", - "GOOD" - ] - }, - "items": { + "content": { "type": "array", "items": { - "$ref": "#/components/schemas/QualityItem" + "$ref": "#/components/schemas/StructureCandidateScored" } - } - } - }, - "QualityItem": { - "type": "object", - "properties": { - "description": { - "type": "string" - }, - "quality": { - "type": "string", - "nullable": true, - "enum": [ - "NOT_APPLICABLE", - "LOWEST", - "BAD", - "DECENT", - "GOOD" - ] }, - "weight": { - "type": "string", - "enum": [ - "MINOR", - "MAJOR", - "CRITICAL" - ] + "page": { + "$ref": "#/components/schemas/PageMetadata" } } }, @@ -11380,13 +7718,13 @@ } } }, - "PagedModelStructureCandidateScored": { + "PagedModelFormulaCandidate": { "type": "object", "properties": { "content": { "type": "array", "items": { - "$ref": "#/components/schemas/StructureCandidateScored" + "$ref": "#/components/schemas/FormulaCandidate" } }, "page": { @@ -11394,13 +7732,13 @@ } } }, - "PagedModelFormulaCandidate": { + "PagedModelStructureCandidateFormula": { "type": "object", "properties": { "content": { "type": "array", "items": { - "$ref": "#/components/schemas/FormulaCandidate" + "$ref": "#/components/schemas/StructureCandidateFormula" } }, "page": { @@ -11408,17 +7746,81 @@ } } }, - "PagedModelStructureCandidateFormula": { + "StructureCandidateFormula": { "type": "object", "properties": { - "content": { + "inchiKey": { + "type": "string" + }, + "smiles": { + "type": "string" + }, + "structureName": { + "type": "string", + "nullable": true + }, + "structureSvg": { + "type": "string", + "description": "SVG graphics of the structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true + }, + "dbLinks": { "type": "array", + "description": "List of structure database links belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, "items": { - "$ref": "#/components/schemas/StructureCandidateFormula" + "$ref": "#/components/schemas/DBLink" } }, - "page": { - "$ref": "#/components/schemas/PageMetadata" + "spectralLibraryMatches": { + "type": "array", + "description": "List of spectral library matches belonging to this structure candidate\n OPTIONAL: needs to be added by parameter", + "nullable": true, + "items": { + "$ref": "#/components/schemas/SpectralLibraryMatch" + } + }, + "xlogP": { + "type": "number", + "format": "double", + "nullable": true + }, + "rank": { + "type": "integer", + "description": "the overall rank of this candidate among all candidates of this feature", + "format": "int32" + }, + "csiScore": { + "type": "number", + "description": "CSI:FingerID score of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID\n This is the score used for ranking structure candidates", + "format": "double" + }, + "tanimotoSimilarity": { + "type": "number", + "description": "Tanimoto similarly of the fingerprint of this compound to the predicted fingerprint of CSI:FingerID", + "format": "double", + "nullable": true + }, + "mcesDistToTopHit": { + "type": "number", + "description": "Maximum Common Edge Subgraph (MCES) distance to the top scoring hit (CSI:FingerID) in a candidate list.", + "format": "double", + "nullable": true + }, + "fingerprint": { + "$ref": "#/components/schemas/BinaryFingerprint" + }, + "molecularFormula": { + "type": "string", + "description": "Molecular formula of this candidate" + }, + "adduct": { + "type": "string", + "description": "Adduct of this candidate" + }, + "formulaId": { + "type": "string", + "description": "Id of the corresponding Formula candidate" } } }, diff --git a/.updater/api/packageVersion.txt b/.updater/api/packageVersion.txt index 7849b73d..8ac3c445 100644 --- a/.updater/api/packageVersion.txt +++ b/.updater/api/packageVersion.txt @@ -1 +1 @@ -6.3.3 +6.3.4 diff --git a/client-api_python/generated/.openapi-generator/FILES b/client-api_python/generated/.openapi-generator/FILES index bb345b9c..8ec52fa8 100644 --- a/client-api_python/generated/.openapi-generator/FILES +++ b/client-api_python/generated/.openapi-generator/FILES @@ -2,18 +2,14 @@ PySirius/__init__.py PySirius/api/__init__.py PySirius/api/actuator_api.py -PySirius/api/compound_statistics_api.py PySirius/api/compounds_api.py -PySirius/api/feature_statistics_api.py PySirius/api/features_api.py PySirius/api/gui_api.py PySirius/api/info_api.py PySirius/api/jobs_api.py PySirius/api/login_and_account_api.py PySirius/api/projects_api.py -PySirius/api/runs_api.py PySirius/api/searchable_databases_api.py -PySirius/api/tags_api.py PySirius/api_client.py PySirius/api_response.py PySirius/configuration.py @@ -21,19 +17,13 @@ PySirius/exceptions.py PySirius/models/__init__.py PySirius/models/account_credentials.py PySirius/models/account_info.py -PySirius/models/adduct_edge_experimental.py -PySirius/models/adduct_network_experimental.py -PySirius/models/adduct_node_experimental.py -PySirius/models/aggregation_type.py PySirius/models/aligned_feature.py PySirius/models/aligned_feature_opt_field.py -PySirius/models/aligned_feature_quality_experimental.py PySirius/models/allowed_features.py PySirius/models/annotated_ms_ms_data.py PySirius/models/annotated_peak.py PySirius/models/annotated_spectrum.py PySirius/models/api_version.py -PySirius/models/axes.py PySirius/models/background_computations_state_event.py PySirius/models/basic_spectrum.py PySirius/models/binary_fingerprint.py @@ -41,7 +31,6 @@ PySirius/models/bio_transformer_parameters.py PySirius/models/bio_transformer_sequence_step.py PySirius/models/canopus.py PySirius/models/canopus_prediction.py -PySirius/models/category.py PySirius/models/compound.py PySirius/models/compound_class.py PySirius/models/compound_class_type.py @@ -66,7 +55,6 @@ PySirius/models/deviation.py PySirius/models/feature_annotations.py PySirius/models/feature_import.py PySirius/models/fingerprint_prediction.py -PySirius/models/fold_change.py PySirius/models/formula_candidate.py PySirius/models/formula_candidate_opt_field.py PySirius/models/fragment_node.py @@ -96,7 +84,6 @@ PySirius/models/paged_model_aligned_feature.py PySirius/models/paged_model_compound.py PySirius/models/paged_model_formula_candidate.py PySirius/models/paged_model_job.py -PySirius/models/paged_model_run.py PySirius/models/paged_model_spectral_library_match.py PySirius/models/paged_model_structure_candidate_formula.py PySirius/models/paged_model_structure_candidate_scored.py @@ -108,14 +95,6 @@ PySirius/models/project_event_type.py PySirius/models/project_info.py PySirius/models/project_info_opt_field.py PySirius/models/project_type.py -PySirius/models/quality_item.py -PySirius/models/quality_weight.py -PySirius/models/quant_measure.py -PySirius/models/quant_row_type.py -PySirius/models/quant_table_experimental.py -PySirius/models/run.py -PySirius/models/run_opt_field.py -PySirius/models/sample_type_fold_change_request.py PySirius/models/searchable_database.py PySirius/models/searchable_database_parameters.py PySirius/models/security_context.py @@ -131,8 +110,6 @@ PySirius/models/spectral_match_type.py PySirius/models/spectral_matching_type.py PySirius/models/spectrum_annotation.py PySirius/models/spectrum_type.py -PySirius/models/statistics_table.py -PySirius/models/statistics_type.py PySirius/models/stored_job_submission.py PySirius/models/structure_candidate.py PySirius/models/structure_candidate_formula.py @@ -142,17 +119,9 @@ PySirius/models/structure_db_search.py PySirius/models/subscription.py PySirius/models/subscription_consumables.py PySirius/models/tag.py -PySirius/models/tag_definition.py -PySirius/models/tag_definition_import.py -PySirius/models/tag_group.py PySirius/models/term.py PySirius/models/timeout.py -PySirius/models/trace_annotation_experimental.py -PySirius/models/trace_annotation_type_experimental.py -PySirius/models/trace_experimental.py -PySirius/models/trace_set_experimental.py PySirius/models/use_heuristic.py -PySirius/models/value_type.py PySirius/models/web_server_namespace.py PySirius/models/zodiac.py PySirius/models/zodiac_analogue_nodes.py @@ -165,19 +134,13 @@ README.md docs/AccountCredentials.md docs/AccountInfo.md docs/ActuatorApi.md -docs/AdductEdgeExperimental.md -docs/AdductNetworkExperimental.md -docs/AdductNodeExperimental.md -docs/AggregationType.md docs/AlignedFeature.md docs/AlignedFeatureOptField.md -docs/AlignedFeatureQualityExperimental.md docs/AllowedFeatures.md docs/AnnotatedMsMsData.md docs/AnnotatedPeak.md docs/AnnotatedSpectrum.md docs/ApiVersion.md -docs/Axes.md docs/BackgroundComputationsStateEvent.md docs/BasicSpectrum.md docs/BinaryFingerprint.md @@ -185,14 +148,12 @@ docs/BioTransformerParameters.md docs/BioTransformerSequenceStep.md docs/Canopus.md docs/CanopusPrediction.md -docs/Category.md docs/Compound.md docs/CompoundClass.md docs/CompoundClassType.md docs/CompoundClasses.md docs/CompoundImport.md docs/CompoundOptField.md -docs/CompoundStatisticsApi.md docs/CompoundsApi.md docs/ComputedSubtools.md docs/ConfidenceMode.md @@ -211,10 +172,8 @@ docs/DataQuality.md docs/Deviation.md docs/FeatureAnnotations.md docs/FeatureImport.md -docs/FeatureStatisticsApi.md docs/FeaturesApi.md docs/FingerprintPrediction.md -docs/FoldChange.md docs/FormulaCandidate.md docs/FormulaCandidateOptField.md docs/FragmentNode.md @@ -248,7 +207,6 @@ docs/PagedModelAlignedFeature.md docs/PagedModelCompound.md docs/PagedModelFormulaCandidate.md docs/PagedModelJob.md -docs/PagedModelRun.md docs/PagedModelSpectralLibraryMatch.md docs/PagedModelStructureCandidateFormula.md docs/PagedModelStructureCandidateScored.md @@ -261,15 +219,6 @@ docs/ProjectInfo.md docs/ProjectInfoOptField.md docs/ProjectType.md docs/ProjectsApi.md -docs/QualityItem.md -docs/QualityWeight.md -docs/QuantMeasure.md -docs/QuantRowType.md -docs/QuantTableExperimental.md -docs/Run.md -docs/RunOptField.md -docs/RunsApi.md -docs/SampleTypeFoldChangeRequest.md docs/SearchableDatabase.md docs/SearchableDatabaseParameters.md docs/SearchableDatabasesApi.md @@ -286,8 +235,6 @@ docs/SpectralMatchType.md docs/SpectralMatchingType.md docs/SpectrumAnnotation.md docs/SpectrumType.md -docs/StatisticsTable.md -docs/StatisticsType.md docs/StoredJobSubmission.md docs/StructureCandidate.md docs/StructureCandidateFormula.md @@ -297,18 +244,9 @@ docs/StructureDbSearch.md docs/Subscription.md docs/SubscriptionConsumables.md docs/Tag.md -docs/TagDefinition.md -docs/TagDefinitionImport.md -docs/TagGroup.md -docs/TagsApi.md docs/Term.md docs/Timeout.md -docs/TraceAnnotationExperimental.md -docs/TraceAnnotationTypeExperimental.md -docs/TraceExperimental.md -docs/TraceSetExperimental.md docs/UseHeuristic.md -docs/ValueType.md docs/WebServerNamespace.md docs/Zodiac.md docs/ZodiacAnalogueNodes.md diff --git a/client-api_python/generated/PySirius/__init__.py b/client-api_python/generated/PySirius/__init__.py index a4a5c768..aa52cadd 100644 --- a/client-api_python/generated/PySirius/__init__.py +++ b/client-api_python/generated/PySirius/__init__.py @@ -12,23 +12,19 @@ """ # noqa: E501 -__version__ = "6.3.3" +__version__ = "6.3.4" # Define package exports __all__ = [ "ActuatorApi", - "CompoundStatisticsApi", "CompoundsApi", - "FeatureStatisticsApi", "FeaturesApi", "GuiApi", "InfoApi", "JobsApi", "LoginAndAccountApi", "ProjectsApi", - "RunsApi", "SearchableDatabasesApi", - "TagsApi", "ApiResponse", "ApiClient", "Configuration", @@ -40,19 +36,13 @@ "ApiException", "AccountCredentials", "AccountInfo", - "AdductEdgeExperimental", - "AdductNetworkExperimental", - "AdductNodeExperimental", - "AggregationType", "AlignedFeature", "AlignedFeatureOptField", - "AlignedFeatureQualityExperimental", "AllowedFeatures", "AnnotatedMsMsData", "AnnotatedPeak", "AnnotatedSpectrum", "ApiVersion", - "Axes", "BackgroundComputationsStateEvent", "BasicSpectrum", "BinaryFingerprint", @@ -60,7 +50,6 @@ "BioTransformerSequenceStep", "Canopus", "CanopusPrediction", - "Category", "Compound", "CompoundClass", "CompoundClassType", @@ -85,7 +74,6 @@ "FeatureAnnotations", "FeatureImport", "FingerprintPrediction", - "FoldChange", "FormulaCandidate", "FormulaCandidateOptField", "FragmentNode", @@ -115,7 +103,6 @@ "PagedModelCompound", "PagedModelFormulaCandidate", "PagedModelJob", - "PagedModelRun", "PagedModelSpectralLibraryMatch", "PagedModelStructureCandidateFormula", "PagedModelStructureCandidateScored", @@ -127,14 +114,6 @@ "ProjectInfo", "ProjectInfoOptField", "ProjectType", - "QualityItem", - "QualityWeight", - "QuantMeasure", - "QuantRowType", - "QuantTableExperimental", - "Run", - "RunOptField", - "SampleTypeFoldChangeRequest", "SearchableDatabase", "SearchableDatabaseParameters", "SecurityContext", @@ -150,8 +129,6 @@ "SpectralMatchingType", "SpectrumAnnotation", "SpectrumType", - "StatisticsTable", - "StatisticsType", "StoredJobSubmission", "StructureCandidate", "StructureCandidateFormula", @@ -161,17 +138,9 @@ "Subscription", "SubscriptionConsumables", "Tag", - "TagDefinition", - "TagDefinitionImport", - "TagGroup", "Term", "Timeout", - "TraceAnnotationExperimental", - "TraceAnnotationTypeExperimental", - "TraceExperimental", - "TraceSetExperimental", "UseHeuristic", - "ValueType", "WebServerNamespace", "Zodiac", "ZodiacAnalogueNodes", @@ -185,18 +154,14 @@ # import apis into sdk package from PySirius.api.actuator_api import ActuatorApi as ActuatorApi -from PySirius.api.compound_statistics_api import CompoundStatisticsApi as CompoundStatisticsApi from PySirius.api.compounds_api import CompoundsApi as CompoundsApi -from PySirius.api.feature_statistics_api import FeatureStatisticsApi as FeatureStatisticsApi from PySirius.api.features_api import FeaturesApi as FeaturesApi from PySirius.api.gui_api import GuiApi as GuiApi from PySirius.api.info_api import InfoApi as InfoApi from PySirius.api.jobs_api import JobsApi as JobsApi from PySirius.api.login_and_account_api import LoginAndAccountApi as LoginAndAccountApi from PySirius.api.projects_api import ProjectsApi as ProjectsApi -from PySirius.api.runs_api import RunsApi as RunsApi from PySirius.api.searchable_databases_api import SearchableDatabasesApi as SearchableDatabasesApi -from PySirius.api.tags_api import TagsApi as TagsApi # import ApiClient from PySirius.api_response import ApiResponse as ApiResponse @@ -212,19 +177,13 @@ # import models into sdk package from PySirius.models.account_credentials import AccountCredentials as AccountCredentials from PySirius.models.account_info import AccountInfo as AccountInfo -from PySirius.models.adduct_edge_experimental import AdductEdgeExperimental as AdductEdgeExperimental -from PySirius.models.adduct_network_experimental import AdductNetworkExperimental as AdductNetworkExperimental -from PySirius.models.adduct_node_experimental import AdductNodeExperimental as AdductNodeExperimental -from PySirius.models.aggregation_type import AggregationType as AggregationType from PySirius.models.aligned_feature import AlignedFeature as AlignedFeature from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField as AlignedFeatureOptField -from PySirius.models.aligned_feature_quality_experimental import AlignedFeatureQualityExperimental as AlignedFeatureQualityExperimental from PySirius.models.allowed_features import AllowedFeatures as AllowedFeatures from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData as AnnotatedMsMsData from PySirius.models.annotated_peak import AnnotatedPeak as AnnotatedPeak from PySirius.models.annotated_spectrum import AnnotatedSpectrum as AnnotatedSpectrum from PySirius.models.api_version import ApiVersion as ApiVersion -from PySirius.models.axes import Axes as Axes from PySirius.models.background_computations_state_event import BackgroundComputationsStateEvent as BackgroundComputationsStateEvent from PySirius.models.basic_spectrum import BasicSpectrum as BasicSpectrum from PySirius.models.binary_fingerprint import BinaryFingerprint as BinaryFingerprint @@ -232,7 +191,6 @@ from PySirius.models.bio_transformer_sequence_step import BioTransformerSequenceStep as BioTransformerSequenceStep from PySirius.models.canopus import Canopus as Canopus from PySirius.models.canopus_prediction import CanopusPrediction as CanopusPrediction -from PySirius.models.category import Category as Category from PySirius.models.compound import Compound as Compound from PySirius.models.compound_class import CompoundClass as CompoundClass from PySirius.models.compound_class_type import CompoundClassType as CompoundClassType @@ -257,7 +215,6 @@ from PySirius.models.feature_annotations import FeatureAnnotations as FeatureAnnotations from PySirius.models.feature_import import FeatureImport as FeatureImport from PySirius.models.fingerprint_prediction import FingerprintPrediction as FingerprintPrediction -from PySirius.models.fold_change import FoldChange as FoldChange from PySirius.models.formula_candidate import FormulaCandidate as FormulaCandidate from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField as FormulaCandidateOptField from PySirius.models.fragment_node import FragmentNode as FragmentNode @@ -287,7 +244,6 @@ from PySirius.models.paged_model_compound import PagedModelCompound as PagedModelCompound from PySirius.models.paged_model_formula_candidate import PagedModelFormulaCandidate as PagedModelFormulaCandidate from PySirius.models.paged_model_job import PagedModelJob as PagedModelJob -from PySirius.models.paged_model_run import PagedModelRun as PagedModelRun from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch as PagedModelSpectralLibraryMatch from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula as PagedModelStructureCandidateFormula from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored as PagedModelStructureCandidateScored @@ -299,14 +255,6 @@ from PySirius.models.project_info import ProjectInfo as ProjectInfo from PySirius.models.project_info_opt_field import ProjectInfoOptField as ProjectInfoOptField from PySirius.models.project_type import ProjectType as ProjectType -from PySirius.models.quality_item import QualityItem as QualityItem -from PySirius.models.quality_weight import QualityWeight as QualityWeight -from PySirius.models.quant_measure import QuantMeasure as QuantMeasure -from PySirius.models.quant_row_type import QuantRowType as QuantRowType -from PySirius.models.quant_table_experimental import QuantTableExperimental as QuantTableExperimental -from PySirius.models.run import Run as Run -from PySirius.models.run_opt_field import RunOptField as RunOptField -from PySirius.models.sample_type_fold_change_request import SampleTypeFoldChangeRequest as SampleTypeFoldChangeRequest from PySirius.models.searchable_database import SearchableDatabase as SearchableDatabase from PySirius.models.searchable_database_parameters import SearchableDatabaseParameters as SearchableDatabaseParameters from PySirius.models.security_context import SecurityContext as SecurityContext @@ -322,8 +270,6 @@ from PySirius.models.spectral_matching_type import SpectralMatchingType as SpectralMatchingType from PySirius.models.spectrum_annotation import SpectrumAnnotation as SpectrumAnnotation from PySirius.models.spectrum_type import SpectrumType as SpectrumType -from PySirius.models.statistics_table import StatisticsTable as StatisticsTable -from PySirius.models.statistics_type import StatisticsType as StatisticsType from PySirius.models.stored_job_submission import StoredJobSubmission as StoredJobSubmission from PySirius.models.structure_candidate import StructureCandidate as StructureCandidate from PySirius.models.structure_candidate_formula import StructureCandidateFormula as StructureCandidateFormula @@ -333,17 +279,9 @@ from PySirius.models.subscription import Subscription as Subscription from PySirius.models.subscription_consumables import SubscriptionConsumables as SubscriptionConsumables from PySirius.models.tag import Tag as Tag -from PySirius.models.tag_definition import TagDefinition as TagDefinition -from PySirius.models.tag_definition_import import TagDefinitionImport as TagDefinitionImport -from PySirius.models.tag_group import TagGroup as TagGroup from PySirius.models.term import Term as Term from PySirius.models.timeout import Timeout as Timeout -from PySirius.models.trace_annotation_experimental import TraceAnnotationExperimental as TraceAnnotationExperimental -from PySirius.models.trace_annotation_type_experimental import TraceAnnotationTypeExperimental as TraceAnnotationTypeExperimental -from PySirius.models.trace_experimental import TraceExperimental as TraceExperimental -from PySirius.models.trace_set_experimental import TraceSetExperimental as TraceSetExperimental from PySirius.models.use_heuristic import UseHeuristic as UseHeuristic -from PySirius.models.value_type import ValueType as ValueType from PySirius.models.web_server_namespace import WebServerNamespace as WebServerNamespace from PySirius.models.zodiac import Zodiac as Zodiac from PySirius.models.zodiac_analogue_nodes import ZodiacAnalogueNodes as ZodiacAnalogueNodes diff --git a/client-api_python/generated/PySirius/api/__init__.py b/client-api_python/generated/PySirius/api/__init__.py index 06ea846e..d9129a5a 100644 --- a/client-api_python/generated/PySirius/api/__init__.py +++ b/client-api_python/generated/PySirius/api/__init__.py @@ -2,16 +2,12 @@ # import apis into api package from PySirius.api.actuator_api import ActuatorApi -from PySirius.api.compound_statistics_api import CompoundStatisticsApi from PySirius.api.compounds_api import CompoundsApi -from PySirius.api.feature_statistics_api import FeatureStatisticsApi from PySirius.api.features_api import FeaturesApi from PySirius.api.gui_api import GuiApi from PySirius.api.info_api import InfoApi from PySirius.api.jobs_api import JobsApi from PySirius.api.login_and_account_api import LoginAndAccountApi from PySirius.api.projects_api import ProjectsApi -from PySirius.api.runs_api import RunsApi from PySirius.api.searchable_databases_api import SearchableDatabasesApi -from PySirius.api.tags_api import TagsApi diff --git a/client-api_python/generated/PySirius/api/compound_statistics_api.py b/client-api_python/generated/PySirius/api/compound_statistics_api.py deleted file mode 100644 index 9de9e08b..00000000 --- a/client-api_python/generated/PySirius/api/compound_statistics_api.py +++ /dev/null @@ -1,1278 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - -import warnings -from pydantic import validate_call, Field, StrictFloat, StrictStr, StrictInt -from typing import Any, Dict, List, Optional, Tuple, Union -from typing_extensions import Annotated - -from pydantic import Field, StrictStr -from typing import List, Optional -from typing_extensions import Annotated -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.fold_change import FoldChange -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.statistics_table import StatisticsTable - -from PySirius.api_client import ApiClient, RequestSerialized -from PySirius.api_response import ApiResponse -from PySirius.rest import RESTResponseType - - -class CompoundStatisticsApi: - """NOTE: This class is auto generated by OpenAPI Generator - Ref: https://openapi-generator.tech - - Do not edit the class manually. - """ - - def __init__(self, api_client=None) -> None: - if api_client is None: - api_client = ApiClient.get_default() - self.api_client = api_client - - - @validate_call - def compute_compound_fold_changes_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> Job: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def compute_compound_fold_changes_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[Job]: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def compute_compound_fold_changes_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _compute_compound_fold_changes_experimental_serialize( - self, - project_id, - left_group_name, - right_group_name, - aggregation, - quantification, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if left_group_name is not None: - - _query_params.append(('leftGroupName', left_group_name)) - - if right_group_name is not None: - - _query_params.append(('rightGroupName', right_group_name)) - - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/compounds/statistics/foldchange/compute', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def delete_compound_fold_changes_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def delete_compound_fold_changes_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def delete_compound_fold_changes_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_compound_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _delete_compound_fold_changes_experimental_serialize( - self, - project_id, - left_group_name, - right_group_name, - aggregation, - quantification, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if left_group_name is not None: - - _query_params.append(('leftGroupName', left_group_name)) - - if right_group_name is not None: - - _query_params.append(('rightGroupName', right_group_name)) - - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/compounds/statistics/foldchanges', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compound_fold_change_table_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> StatisticsTable: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_compound_fold_change_table_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[StatisticsTable]: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_compound_fold_change_table_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_compound_fold_change_table_experimental_serialize( - self, - project_id, - aggregation, - quantification, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds/statistics/foldchanges/stats-table', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_fold_changes_by_compound_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[FoldChange]: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_compound_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_fold_changes_by_compound_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[FoldChange]]: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_compound_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_fold_changes_by_compound_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_compound_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_fold_changes_by_compound_experimental_serialize( - self, - project_id, - object_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if object_id is not None: - _path_params['objectId'] = object_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds/statistics/foldchanges/{objectId}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - diff --git a/client-api_python/generated/PySirius/api/compounds_api.py b/client-api_python/generated/PySirius/api/compounds_api.py index 9c90a007..e5e5ece3 100644 --- a/client-api_python/generated/PySirius/api/compounds_api.py +++ b/client-api_python/generated/PySirius/api/compounds_api.py @@ -23,10 +23,6 @@ from PySirius.models.compound_opt_field import CompoundOptField from PySirius.models.instrument_profile import InstrumentProfile from PySirius.models.paged_model_compound import PagedModelCompound -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.models.tag import Tag -from PySirius.models.trace_set_experimental import TraceSetExperimental from PySirius.api_client import ApiClient, RequestSerialized from PySirius.api_response import ApiResponse @@ -389,11 +385,10 @@ def _add_compounds_serialize( @validate_call - def add_tags_to_compound_experimental( + def delete_compound( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - compound_id: Annotated[StrictStr, Field(description="compound (group of ion identities) to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -406,17 +401,15 @@ def add_tags_to_compound_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[Tag]: - """[EXPERIMENTAL] Tags with the same name will be overwritten + ) -> None: + """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - [EXPERIMENTAL] Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param compound_id: compound (group of ion identities) to add tags to. (required) + :param compound_id: identifier of the compound to delete. (required) :type compound_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -439,10 +432,9 @@ def add_tags_to_compound_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_compound_experimental_serialize( + _param = self._delete_compound_serialize( project_id=project_id, compound_id=compound_id, - tag=tag, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -450,7 +442,7 @@ def add_tags_to_compound_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -464,11 +456,10 @@ def add_tags_to_compound_experimental( @validate_call - def add_tags_to_compound_experimental_with_http_info( + def delete_compound_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - compound_id: Annotated[StrictStr, Field(description="compound (group of ion identities) to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -481,17 +472,15 @@ def add_tags_to_compound_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[Tag]]: - """[EXPERIMENTAL] Tags with the same name will be overwritten + ) -> ApiResponse[None]: + """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - [EXPERIMENTAL] Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param compound_id: compound (group of ion identities) to add tags to. (required) + :param compound_id: identifier of the compound to delete. (required) :type compound_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -514,10 +503,9 @@ def add_tags_to_compound_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_compound_experimental_serialize( + _param = self._delete_compound_serialize( project_id=project_id, compound_id=compound_id, - tag=tag, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -525,7 +513,7 @@ def add_tags_to_compound_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -539,11 +527,10 @@ def add_tags_to_compound_experimental_with_http_info( @validate_call - def add_tags_to_compound_experimental_without_preload_content( + def delete_compound_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - compound_id: Annotated[StrictStr, Field(description="compound (group of ion identities) to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -557,16 +544,14 @@ def add_tags_to_compound_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Tags with the same name will be overwritten + """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - [EXPERIMENTAL] Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param compound_id: compound (group of ion identities) to add tags to. (required) + :param compound_id: identifier of the compound to delete. (required) :type compound_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -589,10 +574,9 @@ def add_tags_to_compound_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_compound_experimental_serialize( + _param = self._delete_compound_serialize( project_id=project_id, compound_id=compound_id, - tag=tag, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -600,7 +584,7 @@ def add_tags_to_compound_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -609,11 +593,10 @@ def add_tags_to_compound_experimental_without_preload_content( return response_data.response - def _add_tags_to_compound_experimental_serialize( + def _delete_compound_serialize( self, project_id, compound_id, - tag, _request_auth, _content_type, _headers, @@ -623,7 +606,6 @@ def _add_tags_to_compound_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { - 'Tag': '', } _path_params: Dict[str, str] = {} @@ -644,39 +626,17 @@ def _add_tags_to_compound_experimental_serialize( # process the header parameters # process the form parameters # process the body parameter - if tag is not None: - _body_params = tag - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) - ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type # authentication setting _auth_settings: List[str] = [ ] return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/compounds/tags/{compoundId}', + method='DELETE', + resource_path='/api/projects/{projectId}/compounds/{compoundId}', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -693,10 +653,13 @@ def _add_tags_to_compound_experimental_serialize( @validate_call - def delete_compound( + def get_compound( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -709,15 +672,21 @@ def delete_compound( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + ) -> Compound: + """Get compound (group of ion identities) with the given identifier from the specified project-space. - Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + Get compound (group of ion identities) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound to delete. (required) + :param compound_id: identifier of the compound (group of ion identities) to access. (required) :type compound_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -740,9 +709,12 @@ def delete_compound( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_compound_serialize( + _param = self._get_compound_serialize( project_id=project_id, compound_id=compound_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -750,7 +722,7 @@ def delete_compound( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "Compound", } response_data = self.api_client.call_api( *_param, @@ -764,10 +736,13 @@ def delete_compound( @validate_call - def delete_compound_with_http_info( + def get_compound_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -780,15 +755,21 @@ def delete_compound_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + ) -> ApiResponse[Compound]: + """Get compound (group of ion identities) with the given identifier from the specified project-space. - Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + Get compound (group of ion identities) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound to delete. (required) + :param compound_id: identifier of the compound (group of ion identities) to access. (required) :type compound_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -811,9 +792,12 @@ def delete_compound_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_compound_serialize( + _param = self._get_compound_serialize( project_id=project_id, compound_id=compound_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -821,7 +805,7 @@ def delete_compound_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "Compound", } response_data = self.api_client.call_api( *_param, @@ -835,10 +819,13 @@ def delete_compound_with_http_info( @validate_call - def delete_compound_without_preload_content( + def get_compound_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -852,14 +839,20 @@ def delete_compound_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + """Get compound (group of ion identities) with the given identifier from the specified project-space. - Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. + Get compound (group of ion identities) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound to delete. (required) + :param compound_id: identifier of the compound (group of ion identities) to access. (required) :type compound_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -882,9 +875,12 @@ def delete_compound_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_compound_serialize( + _param = self._get_compound_serialize( project_id=project_id, compound_id=compound_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -892,7 +888,7 @@ def delete_compound_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "Compound", } response_data = self.api_client.call_api( *_param, @@ -901,10 +897,13 @@ def delete_compound_without_preload_content( return response_data.response - def _delete_compound_serialize( + def _get_compound_serialize( self, project_id, compound_id, + ms_data_search_prepared, + opt_fields, + opt_fields_features, _request_auth, _content_type, _headers, @@ -914,6 +913,8 @@ def _delete_compound_serialize( _host = None _collection_formats: Dict[str, str] = { + 'optFields': 'multi', + 'optFieldsFeatures': 'multi', } _path_params: Dict[str, str] = {} @@ -931,11 +932,30 @@ def _delete_compound_serialize( if compound_id is not None: _path_params['compoundId'] = compound_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + + if opt_fields_features is not None: + + _query_params.append(('optFieldsFeatures', opt_fields_features)) + # process the header parameters # process the form parameters # process the body parameter + # set the HTTP header `Accept` + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] + ) # authentication setting @@ -943,7 +963,7 @@ def _delete_compound_serialize( ] return self.api_client.param_serialize( - method='DELETE', + method='GET', resource_path='/api/projects/{projectId}/compounds/{compoundId}', path_params=_path_params, query_params=_query_params, @@ -961,10 +981,9 @@ def _delete_compound_serialize( @validate_call - def get_compound( + def get_compounds( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, @@ -980,15 +999,13 @@ def get_compound( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> Compound: - """Get compound (group of ion identities) with the given identifier from the specified project-space. + ) -> List[Compound]: + """List of all available compounds (group of ion identities) in the given project-space. - Get compound (group of ion identities) with the given identifier from the specified project-space. + List of all available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound (group of ion identities) to access. (required) - :type compound_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. @@ -1017,9 +1034,8 @@ def get_compound( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_serialize( + _param = self._get_compounds_serialize( project_id=project_id, - compound_id=compound_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features, @@ -1030,7 +1046,7 @@ def get_compound( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "Compound", + '200': "List[Compound]", } response_data = self.api_client.call_api( *_param, @@ -1044,10 +1060,9 @@ def get_compound( @validate_call - def get_compound_with_http_info( + def get_compounds_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, @@ -1063,15 +1078,13 @@ def get_compound_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[Compound]: - """Get compound (group of ion identities) with the given identifier from the specified project-space. + ) -> ApiResponse[List[Compound]]: + """List of all available compounds (group of ion identities) in the given project-space. - Get compound (group of ion identities) with the given identifier from the specified project-space. + List of all available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound (group of ion identities) to access. (required) - :type compound_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. @@ -1100,9 +1113,8 @@ def get_compound_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_serialize( + _param = self._get_compounds_serialize( project_id=project_id, - compound_id=compound_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features, @@ -1113,7 +1125,7 @@ def get_compound_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "Compound", + '200': "List[Compound]", } response_data = self.api_client.call_api( *_param, @@ -1127,10 +1139,9 @@ def get_compound_with_http_info( @validate_call - def get_compound_without_preload_content( + def get_compounds_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="identifier of the compound (group of ion identities) to access.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, @@ -1147,14 +1158,12 @@ def get_compound_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Get compound (group of ion identities) with the given identifier from the specified project-space. + """List of all available compounds (group of ion identities) in the given project-space. - Get compound (group of ion identities) with the given identifier from the specified project-space. + List of all available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param compound_id: identifier of the compound (group of ion identities) to access. (required) - :type compound_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. @@ -1183,9 +1192,8 @@ def get_compound_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_serialize( + _param = self._get_compounds_serialize( project_id=project_id, - compound_id=compound_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features, @@ -1196,7 +1204,7 @@ def get_compound_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "Compound", + '200': "List[Compound]", } response_data = self.api_client.call_api( *_param, @@ -1205,10 +1213,9 @@ def get_compound_without_preload_content( return response_data.response - def _get_compound_serialize( + def _get_compounds_serialize( self, project_id, - compound_id, ms_data_search_prepared, opt_fields, opt_fields_features, @@ -1237,8 +1244,6 @@ def _get_compound_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id - if compound_id is not None: - _path_params['compoundId'] = compound_id # process the query parameters if ms_data_search_prepared is not None: @@ -1272,7 +1277,7 @@ def _get_compound_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/compounds/{compoundId}', + resource_path='/api/projects/{projectId}/compounds', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -1289,10 +1294,15 @@ def _get_compound_serialize( @validate_call - def get_compound_quant_table_experimental( + def get_compounds_paged( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1305,15 +1315,25 @@ def get_compound_quant_table_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> QuantTableExperimental: - """[EXPERIMENTAL] Returns the full quantification table of compounds + ) -> PagedModelCompound: + """Page of available compounds (group of ion identities) in the given project-space. - [EXPERIMENTAL] Returns the full quantification table of compounds.
The quantification table contains a quantification of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* + Page of available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1336,9 +1356,14 @@ def get_compound_quant_table_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_quant_table_experimental_serialize( + _param = self._get_compounds_paged_serialize( project_id=project_id, - type=type, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1346,7 +1371,7 @@ def get_compound_quant_table_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "PagedModelCompound", } response_data = self.api_client.call_api( *_param, @@ -1360,10 +1385,15 @@ def get_compound_quant_table_experimental( @validate_call - def get_compound_quant_table_experimental_with_http_info( + def get_compounds_paged_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1376,15 +1406,25 @@ def get_compound_quant_table_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[QuantTableExperimental]: - """[EXPERIMENTAL] Returns the full quantification table of compounds + ) -> ApiResponse[PagedModelCompound]: + """Page of available compounds (group of ion identities) in the given project-space. - [EXPERIMENTAL] Returns the full quantification table of compounds.
The quantification table contains a quantification of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* + Page of available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1407,9 +1447,14 @@ def get_compound_quant_table_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_quant_table_experimental_serialize( + _param = self._get_compounds_paged_serialize( project_id=project_id, - type=type, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1417,7 +1462,7 @@ def get_compound_quant_table_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "PagedModelCompound", } response_data = self.api_client.call_api( *_param, @@ -1431,10 +1476,15 @@ def get_compound_quant_table_experimental_with_http_info( @validate_call - def get_compound_quant_table_experimental_without_preload_content( + def get_compounds_paged_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1448,14 +1498,24 @@ def get_compound_quant_table_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Returns the full quantification table of compounds + """Page of available compounds (group of ion identities) in the given project-space. - [EXPERIMENTAL] Returns the full quantification table of compounds.
The quantification table contains a quantification of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* + Page of available compounds (group of ion identities) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[CompoundOptField] + :param opt_fields_features: + :type opt_fields_features: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1478,9 +1538,14 @@ def get_compound_quant_table_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_compound_quant_table_experimental_serialize( + _param = self._get_compounds_paged_serialize( project_id=project_id, - type=type, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, + opt_fields_features=opt_fields_features, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1488,7 +1553,7 @@ def get_compound_quant_table_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "PagedModelCompound", } response_data = self.api_client.call_api( *_param, @@ -1497,10 +1562,15 @@ def get_compound_quant_table_experimental_without_preload_content( return response_data.response - def _get_compound_quant_table_experimental_serialize( + def _get_compounds_paged_serialize( self, project_id, - type, + page, + size, + sort, + ms_data_search_prepared, + opt_fields, + opt_fields_features, _request_auth, _content_type, _headers, @@ -1510,6 +1580,9 @@ def _get_compound_quant_table_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { + 'sort': 'multi', + 'optFields': 'multi', + 'optFieldsFeatures': 'multi', } _path_params: Dict[str, str] = {} @@ -1525,9 +1598,29 @@ def _get_compound_quant_table_experimental_serialize( if project_id is not None: _path_params['projectId'] = project_id # process the query parameters - if type is not None: + if page is not None: + + _query_params.append(('page', page)) + + if size is not None: + + _query_params.append(('size', size)) + + if sort is not None: + + _query_params.append(('sort', sort)) + + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + + if opt_fields_features is not None: - _query_params.append(('type', type.value)) + _query_params.append(('optFieldsFeatures', opt_fields_features)) # process the header parameters # process the form parameters @@ -1549,2521 +1642,7 @@ def _get_compound_quant_table_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/compounds/quant-table', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compound_quant_table_row_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> QuantTableExperimental: - """[EXPERIMENTAL] Returns a single quantification table row for the given compound - - [EXPERIMENTAL] Returns a single quantification table row for the given compound.
The quantification table contains a quantification of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which should be read out (required) - :type compound_id: str - :param type: quantification type. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_quant_table_row_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_compound_quant_table_row_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[QuantTableExperimental]: - """[EXPERIMENTAL] Returns a single quantification table row for the given compound - - [EXPERIMENTAL] Returns a single quantification table row for the given compound.
The quantification table contains a quantification of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which should be read out (required) - :type compound_id: str - :param type: quantification type. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_quant_table_row_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_compound_quant_table_row_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Returns a single quantification table row for the given compound - - [EXPERIMENTAL] Returns a single quantification table row for the given compound.
The quantification table contains a quantification of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which should be read out (required) - :type compound_id: str - :param type: quantification type. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_quant_table_row_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_compound_quant_table_row_experimental_serialize( - self, - project_id, - compound_id, - type, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if compound_id is not None: - _path_params['compoundId'] = compound_id - # process the query parameters - if type is not None: - - _query_params.append(('type', type.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds/{compoundId}/quant-table-row', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compound_traces_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which intensities should be read out")], - feature_id: Optional[StrictStr] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TraceSetExperimental: - """[EXPERIMENTAL] Returns the traces of the given compound - - [EXPERIMENTAL] Returns the traces of the given compound.
A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which intensities should be read out (required) - :type compound_id: str - :param feature_id: - :type feature_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_traces_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - feature_id=feature_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_compound_traces_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which intensities should be read out")], - feature_id: Optional[StrictStr] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TraceSetExperimental]: - """[EXPERIMENTAL] Returns the traces of the given compound - - [EXPERIMENTAL] Returns the traces of the given compound.
A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which intensities should be read out (required) - :type compound_id: str - :param feature_id: - :type feature_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_traces_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - feature_id=feature_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_compound_traces_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - compound_id: Annotated[StrictStr, Field(description="compound which intensities should be read out")], - feature_id: Optional[StrictStr] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Returns the traces of the given compound - - [EXPERIMENTAL] Returns the traces of the given compound.
A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - - :param project_id: project-space to read from. (required) - :type project_id: str - :param compound_id: compound which intensities should be read out (required) - :type compound_id: str - :param feature_id: - :type feature_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compound_traces_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - feature_id=feature_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_compound_traces_experimental_serialize( - self, - project_id, - compound_id, - feature_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if compound_id is not None: - _path_params['compoundId'] = compound_id - # process the query parameters - if feature_id is not None: - - _query_params.append(('featureId', feature_id)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds/{compoundId}/traces', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compounds( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[Compound]: - """List of all available compounds (group of ion identities) in the given project-space. - - List of all available compounds (group of ion identities) in the given project-space. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param opt_fields_features: - :type opt_fields_features: List[AlignedFeatureOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_serialize( - project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, - opt_fields_features=opt_fields_features, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Compound]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_compounds_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[Compound]]: - """List of all available compounds (group of ion identities) in the given project-space. - - List of all available compounds (group of ion identities) in the given project-space. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param opt_fields_features: - :type opt_fields_features: List[AlignedFeatureOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_serialize( - project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, - opt_fields_features=opt_fields_features, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Compound]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_compounds_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - opt_fields_features: Optional[List[Optional[AlignedFeatureOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """List of all available compounds (group of ion identities) in the given project-space. - - List of all available compounds (group of ion identities) in the given project-space. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param opt_fields_features: - :type opt_fields_features: List[AlignedFeatureOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_serialize( - project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, - opt_fields_features=opt_fields_features, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Compound]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_compounds_serialize( - self, - project_id, - ms_data_search_prepared, - opt_fields, - opt_fields_features, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - 'optFieldsFeatures': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - if opt_fields_features is not None: - - _query_params.append(('optFieldsFeatures', opt_fields_features)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compounds_by_group_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelCompound: - """[EXPERIMENTAL] Get compounds (group of ion identities) by tag group - - [EXPERIMENTAL] Get compounds (group of ion identities) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelCompound", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_compounds_by_group_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelCompound]: - """[EXPERIMENTAL] Get compounds (group of ion identities) by tag group - - [EXPERIMENTAL] Get compounds (group of ion identities) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelCompound", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_compounds_by_group_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get compounds (group of ion identities) by tag group - - [EXPERIMENTAL] Get compounds (group of ion identities) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[CompoundOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_compounds_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelCompound", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_compounds_by_group_experimental_serialize( - self, - project_id, - group_name, - page, - size, - sort, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if group_name is not None: - - _query_params.append(('groupName', group_name)) - - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/compounds/grouped', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_compounds_by_tag_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project space to get compounds (group of ion identities) from.")], - filter: Annotated[Optional[StrictStr], Field(description="tag filter.")] = None, - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[CompoundOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelCompound: - """[EXPERIMENTAL] Get compounds (group of ion identities) by tag - - [EXPERIMENTAL] Get compounds (group of ion identities) by tag.
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param compound_id: compound (group of ion identities) to delete tag from. (required) - :type compound_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_compound_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def remove_tag_from_compound_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - compound_id: Annotated[StrictStr, Field(description="compound (group of ion identities) to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space - - [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param compound_id: compound (group of ion identities) to delete tag from. (required) - :type compound_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_compound_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def remove_tag_from_compound_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - compound_id: Annotated[StrictStr, Field(description="compound (group of ion identities) to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space - - [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param compound_id: compound (group of ion identities) to delete tag from. (required) - :type compound_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_compound_experimental_serialize( - project_id=project_id, - compound_id=compound_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _remove_tag_from_compound_experimental_serialize( - self, - project_id, - compound_id, - tag_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if compound_id is not None: - _path_params['compoundId'] = compound_id - if tag_name is not None: - _path_params['tagName'] = tag_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/compounds/tags/{compoundId}/{tagName}', + resource_path='/api/projects/{projectId}/compounds/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, diff --git a/client-api_python/generated/PySirius/api/feature_statistics_api.py b/client-api_python/generated/PySirius/api/feature_statistics_api.py deleted file mode 100644 index 36dc5cac..00000000 --- a/client-api_python/generated/PySirius/api/feature_statistics_api.py +++ /dev/null @@ -1,1278 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - -import warnings -from pydantic import validate_call, Field, StrictFloat, StrictStr, StrictInt -from typing import Any, Dict, List, Optional, Tuple, Union -from typing_extensions import Annotated - -from pydantic import Field, StrictStr -from typing import List, Optional -from typing_extensions import Annotated -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.fold_change import FoldChange -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.statistics_table import StatisticsTable - -from PySirius.api_client import ApiClient, RequestSerialized -from PySirius.api_response import ApiResponse -from PySirius.rest import RESTResponseType - - -class FeatureStatisticsApi: - """NOTE: This class is auto generated by OpenAPI Generator - Ref: https://openapi-generator.tech - - Do not edit the class manually. - """ - - def __init__(self, api_client=None) -> None: - if api_client is None: - api_client = ApiClient.get_default() - self.api_client = api_client - - - @validate_call - def compute_aligned_feature_fold_changes_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> Job: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def compute_aligned_feature_fold_changes_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[Job]: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def compute_aligned_feature_fold_changes_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left tag group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right tag group.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Compute the fold change between two groups of runs - - [EXPERIMENTAL] Compute the fold change between two groups of runs.
The runs need to be tagged and grouped.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param left_group_name: name of the left tag group. (required) - :type left_group_name: str - :param right_group_name: name of the right tag group. (required) - :type right_group_name: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _compute_aligned_feature_fold_changes_experimental_serialize( - self, - project_id, - left_group_name, - right_group_name, - aggregation, - quantification, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if left_group_name is not None: - - _query_params.append(('leftGroupName', left_group_name)) - - if right_group_name is not None: - - _query_params.append(('rightGroupName', right_group_name)) - - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/aligned-features/statistics/foldchange/compute', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def delete_aligned_feature_fold_changes_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def delete_aligned_feature_fold_changes_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def delete_aligned_feature_fold_changes_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - left_group_name: Annotated[StrictStr, Field(description="name of the left group.")], - right_group_name: Annotated[StrictStr, Field(description="name of the right group.")], - aggregation: Optional[AggregationType] = None, - quantification: Optional[QuantMeasure] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete fold changes - - [EXPERIMENTAL] Delete fold changes.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param left_group_name: name of the left group. (required) - :type left_group_name: str - :param right_group_name: name of the right group. (required) - :type right_group_name: str - :param aggregation: - :type aggregation: AggregationType - :param quantification: - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_aligned_feature_fold_changes_experimental_serialize( - project_id=project_id, - left_group_name=left_group_name, - right_group_name=right_group_name, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _delete_aligned_feature_fold_changes_experimental_serialize( - self, - project_id, - left_group_name, - right_group_name, - aggregation, - quantification, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if left_group_name is not None: - - _query_params.append(('leftGroupName', left_group_name)) - - if right_group_name is not None: - - _query_params.append(('rightGroupName', right_group_name)) - - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/aligned-features/statistics/foldchanges', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_aligned_feature_fold_change_table_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> StatisticsTable: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_aligned_feature_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_aligned_feature_fold_change_table_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[StatisticsTable]: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_aligned_feature_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_aligned_feature_fold_change_table_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aggregation: Annotated[Optional[AggregationType], Field(description="aggregation type.")] = None, - quantification: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get table of all fold changes in the project space - - [EXPERIMENTAL] Get table of all fold changes in the project space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aggregation: aggregation type. - :type aggregation: AggregationType - :param quantification: quantification type. - :type quantification: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_aligned_feature_fold_change_table_experimental_serialize( - project_id=project_id, - aggregation=aggregation, - quantification=quantification, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "StatisticsTable", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_aligned_feature_fold_change_table_experimental_serialize( - self, - project_id, - aggregation, - quantification, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if aggregation is not None: - - _query_params.append(('aggregation', aggregation.value)) - - if quantification is not None: - - _query_params.append(('quantification', quantification.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_fold_changes_by_aligned_feature_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[FoldChange]: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_aligned_feature_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_fold_changes_by_aligned_feature_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[FoldChange]]: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_aligned_feature_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_fold_changes_by_aligned_feature_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - object_id: Annotated[StrictStr, Field(description="id of the object the fold changes are assigned to.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] List all fold changes that are associated with an object - - [EXPERIMENTAL] List all fold changes that are associated with an object.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param object_id: id of the object the fold changes are assigned to. (required) - :type object_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_fold_changes_by_aligned_feature_experimental_serialize( - project_id=project_id, - object_id=object_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FoldChange]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_fold_changes_by_aligned_feature_experimental_serialize( - self, - project_id, - object_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if object_id is not None: - _path_params['objectId'] = object_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - diff --git a/client-api_python/generated/PySirius/api/features_api.py b/client-api_python/generated/PySirius/api/features_api.py index a81aefc8..05b9ea09 100644 --- a/client-api_python/generated/PySirius/api/features_api.py +++ b/client-api_python/generated/PySirius/api/features_api.py @@ -19,7 +19,6 @@ from typing_extensions import Annotated from PySirius.models.aligned_feature import AlignedFeature from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField -from PySirius.models.aligned_feature_quality_experimental import AlignedFeatureQualityExperimental from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData from PySirius.models.annotated_spectrum import AnnotatedSpectrum from PySirius.models.canopus_prediction import CanopusPrediction @@ -37,16 +36,12 @@ from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental from PySirius.models.spectral_library_match import SpectralLibraryMatch from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField from PySirius.models.spectral_library_match_summary import SpectralLibraryMatchSummary from PySirius.models.structure_candidate_formula import StructureCandidateFormula from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField from PySirius.models.structure_candidate_scored import StructureCandidateScored -from PySirius.models.tag import Tag -from PySirius.models.trace_set_experimental import TraceSetExperimental from PySirius.api_client import ApiClient, RequestSerialized from PySirius.api_response import ApiResponse @@ -391,11 +386,10 @@ def _add_aligned_features_serialize( @validate_call - def add_de_novo_structure_candidate( + def delete_aligned_feature( self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - smiles: Annotated[Optional[StrictStr], Field(description="smiles")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -408,17 +402,15 @@ def add_de_novo_structure_candidate( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[StructureCandidateFormula]: - """[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. + ) -> None: + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to read from. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) :type aligned_feature_id: str - :param smiles: smiles - :type smiles: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -441,10 +433,9 @@ def add_de_novo_structure_candidate( :return: Returns the result object. """ # noqa: E501 - _param = self._add_de_novo_structure_candidate_serialize( + _param = self._delete_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - smiles=smiles, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -452,7 +443,7 @@ def add_de_novo_structure_candidate( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -466,11 +457,10 @@ def add_de_novo_structure_candidate( @validate_call - def add_de_novo_structure_candidate_with_http_info( + def delete_aligned_feature_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - smiles: Annotated[Optional[StrictStr], Field(description="smiles")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -483,17 +473,15 @@ def add_de_novo_structure_candidate_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[StructureCandidateFormula]]: - """[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. + ) -> ApiResponse[None]: + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to read from. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) :type aligned_feature_id: str - :param smiles: smiles - :type smiles: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -516,10 +504,9 @@ def add_de_novo_structure_candidate_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._add_de_novo_structure_candidate_serialize( + _param = self._delete_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - smiles=smiles, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -527,7 +514,7 @@ def add_de_novo_structure_candidate_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -541,11 +528,10 @@ def add_de_novo_structure_candidate_with_http_info( @validate_call - def add_de_novo_structure_candidate_without_preload_content( + def delete_aligned_feature_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - smiles: Annotated[Optional[StrictStr], Field(description="smiles")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -559,16 +545,14 @@ def add_de_novo_structure_candidate_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to read from. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) :type aligned_feature_id: str - :param smiles: smiles - :type smiles: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -591,10 +575,9 @@ def add_de_novo_structure_candidate_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._add_de_novo_structure_candidate_serialize( + _param = self._delete_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - smiles=smiles, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -602,7 +585,7 @@ def add_de_novo_structure_candidate_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -611,11 +594,10 @@ def add_de_novo_structure_candidate_without_preload_content( return response_data.response - def _add_de_novo_structure_candidate_serialize( + def _delete_aligned_feature_serialize( self, project_id, aligned_feature_id, - smiles, _request_auth, _content_type, _headers, @@ -642,22 +624,11 @@ def _add_de_novo_structure_candidate_serialize( if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters - if smiles is not None: - - _query_params.append(('smiles', smiles)) - # process the header parameters # process the form parameters # process the body parameter - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) # authentication setting @@ -665,8 +636,8 @@ def _add_de_novo_structure_candidate_serialize( ] return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures', + method='DELETE', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -683,11 +654,10 @@ def _add_de_novo_structure_candidate_serialize( @validate_call - def add_tags_to_aligned_feature_experimental( + def delete_aligned_features( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - aligned_feature_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + request_body: List[StrictStr], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -700,17 +670,15 @@ def add_tags_to_aligned_feature_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[Tag]: - """[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project + ) -> None: + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: run to add tags to. (required) - :type aligned_feature_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] + :param request_body: (required) + :type request_body: List[str] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -733,10 +701,9 @@ def add_tags_to_aligned_feature_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_aligned_feature_experimental_serialize( + _param = self._delete_aligned_features_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, - tag=tag, + request_body=request_body, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -744,7 +711,7 @@ def add_tags_to_aligned_feature_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -758,11 +725,10 @@ def add_tags_to_aligned_feature_experimental( @validate_call - def add_tags_to_aligned_feature_experimental_with_http_info( + def delete_aligned_features_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - aligned_feature_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + request_body: List[StrictStr], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -775,17 +741,15 @@ def add_tags_to_aligned_feature_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[Tag]]: - """[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project + ) -> ApiResponse[None]: + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: run to add tags to. (required) - :type aligned_feature_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] + :param request_body: (required) + :type request_body: List[str] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -808,10 +772,9 @@ def add_tags_to_aligned_feature_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_aligned_feature_experimental_serialize( + _param = self._delete_aligned_features_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, - tag=tag, + request_body=request_body, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -819,7 +782,7 @@ def add_tags_to_aligned_feature_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -833,11 +796,10 @@ def add_tags_to_aligned_feature_experimental_with_http_info( @validate_call - def add_tags_to_aligned_feature_experimental_without_preload_content( + def delete_aligned_features_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - aligned_feature_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], + project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], + request_body: List[StrictStr], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -851,16 +813,14 @@ def add_tags_to_aligned_feature_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project + """Delete feature (aligned over runs) with the given identifier from the specified project-space. - [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Delete feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to add to. (required) + :param project_id: project-space to delete from. (required) :type project_id: str - :param aligned_feature_id: run to add tags to. (required) - :type aligned_feature_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] + :param request_body: (required) + :type request_body: List[str] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -883,10 +843,9 @@ def add_tags_to_aligned_feature_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._add_tags_to_aligned_feature_experimental_serialize( + _param = self._delete_aligned_features_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, - tag=tag, + request_body=request_body, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -894,7 +853,7 @@ def add_tags_to_aligned_feature_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': None, } response_data = self.api_client.call_api( *_param, @@ -903,11 +862,10 @@ def add_tags_to_aligned_feature_experimental_without_preload_content( return response_data.response - def _add_tags_to_aligned_feature_experimental_serialize( + def _delete_aligned_features_serialize( self, project_id, - aligned_feature_id, - tag, + request_body, _request_auth, _content_type, _headers, @@ -917,7 +875,7 @@ def _add_tags_to_aligned_feature_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { - 'Tag': '', + 'request_body': '', } _path_params: Dict[str, str] = {} @@ -932,23 +890,14 @@ def _add_tags_to_aligned_feature_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters # process the header parameters # process the form parameters # process the body parameter - if tag is not None: - _body_params = tag + if request_body is not None: + _body_params = request_body - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) # set the HTTP header `Content-Type` if _content_type: @@ -970,7 +919,7 @@ def _add_tags_to_aligned_feature_experimental_serialize( return self.api_client.param_serialize( method='PUT', - resource_path='/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}', + resource_path='/api/projects/{projectId}/aligned-features/delete', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -987,10 +936,12 @@ def _add_tags_to_aligned_feature_experimental_serialize( @validate_call - def delete_aligned_feature( + def get_aligned_feature( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1003,15 +954,19 @@ def delete_aligned_feature( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + ) -> AlignedFeature: + """Get feature (aligned over runs) with the given identifier from the specified project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) :type aligned_feature_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1034,9 +989,11 @@ def delete_aligned_feature( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_feature_serialize( + _param = self._get_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1044,7 +1001,7 @@ def delete_aligned_feature( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "AlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1058,10 +1015,12 @@ def delete_aligned_feature( @validate_call - def delete_aligned_feature_with_http_info( + def get_aligned_feature_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1074,15 +1033,19 @@ def delete_aligned_feature_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + ) -> ApiResponse[AlignedFeature]: + """Get feature (aligned over runs) with the given identifier from the specified project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) :type aligned_feature_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1105,9 +1068,11 @@ def delete_aligned_feature_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_feature_serialize( + _param = self._get_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1115,7 +1080,7 @@ def delete_aligned_feature_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "AlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1129,10 +1094,12 @@ def delete_aligned_feature_with_http_info( @validate_call - def delete_aligned_feature_without_preload_content( + def get_aligned_feature_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1146,14 +1113,18 @@ def delete_aligned_feature_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + """Get feature (aligned over runs) with the given identifier from the specified project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get feature (aligned over runs) with the given identifier from the specified project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to delete. (required) + :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) :type aligned_feature_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1176,9 +1147,11 @@ def delete_aligned_feature_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_feature_serialize( + _param = self._get_aligned_feature_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1186,7 +1159,7 @@ def delete_aligned_feature_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "AlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1195,10 +1168,12 @@ def delete_aligned_feature_without_preload_content( return response_data.response - def _delete_aligned_feature_serialize( + def _get_aligned_feature_serialize( self, project_id, aligned_feature_id, + ms_data_search_prepared, + opt_fields, _request_auth, _content_type, _headers, @@ -1208,6 +1183,7 @@ def _delete_aligned_feature_serialize( _host = None _collection_formats: Dict[str, str] = { + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -1225,11 +1201,26 @@ def _delete_aligned_feature_serialize( if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + # process the header parameters # process the form parameters # process the body parameter + # set the HTTP header `Accept` + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] + ) # authentication setting @@ -1237,7 +1228,7 @@ def _delete_aligned_feature_serialize( ] return self.api_client.param_serialize( - method='DELETE', + method='GET', resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}', path_params=_path_params, query_params=_query_params, @@ -1255,10 +1246,11 @@ def _delete_aligned_feature_serialize( @validate_call - def delete_aligned_features( + def get_aligned_features( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - request_body: List[StrictStr], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1271,15 +1263,17 @@ def delete_aligned_features( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + ) -> List[AlignedFeature]: + """Get all available features (aligned over runs) in the given project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get all available features (aligned over runs) in the given project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param request_body: (required) - :type request_body: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1302,9 +1296,10 @@ def delete_aligned_features( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_features_serialize( + _param = self._get_aligned_features_serialize( project_id=project_id, - request_body=request_body, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1312,7 +1307,7 @@ def delete_aligned_features( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "List[AlignedFeature]", } response_data = self.api_client.call_api( *_param, @@ -1326,10 +1321,11 @@ def delete_aligned_features( @validate_call - def delete_aligned_features_with_http_info( + def get_aligned_features_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - request_body: List[StrictStr], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1342,15 +1338,17 @@ def delete_aligned_features_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + ) -> ApiResponse[List[AlignedFeature]]: + """Get all available features (aligned over runs) in the given project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get all available features (aligned over runs) in the given project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param request_body: (required) - :type request_body: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1373,9 +1371,10 @@ def delete_aligned_features_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_features_serialize( + _param = self._get_aligned_features_serialize( project_id=project_id, - request_body=request_body, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1383,7 +1382,7 @@ def delete_aligned_features_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "List[AlignedFeature]", } response_data = self.api_client.call_api( *_param, @@ -1397,10 +1396,11 @@ def delete_aligned_features_with_http_info( @validate_call - def delete_aligned_features_without_preload_content( + def get_aligned_features_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - request_body: List[StrictStr], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1414,14 +1414,16 @@ def delete_aligned_features_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Delete feature (aligned over runs) with the given identifier from the specified project-space. + """Get all available features (aligned over runs) in the given project-space. - Delete feature (aligned over runs) with the given identifier from the specified project-space. + Get all available features (aligned over runs) in the given project-space. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param request_body: (required) - :type request_body: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1444,9 +1446,10 @@ def delete_aligned_features_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._delete_aligned_features_serialize( + _param = self._get_aligned_features_serialize( project_id=project_id, - request_body=request_body, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1454,7 +1457,7 @@ def delete_aligned_features_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "List[AlignedFeature]", } response_data = self.api_client.call_api( *_param, @@ -1463,10 +1466,11 @@ def delete_aligned_features_without_preload_content( return response_data.response - def _delete_aligned_features_serialize( + def _get_aligned_features_serialize( self, project_id, - request_body, + ms_data_search_prepared, + opt_fields, _request_auth, _content_type, _headers, @@ -1476,7 +1480,7 @@ def _delete_aligned_features_serialize( _host = None _collection_formats: Dict[str, str] = { - 'request_body': '', + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -1492,35 +1496,35 @@ def _delete_aligned_features_serialize( if project_id is not None: _path_params['projectId'] = project_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + # process the header parameters # process the form parameters # process the body parameter - if request_body is not None: - _body_params = request_body - - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) + # set the HTTP header `Accept` + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type + # authentication setting _auth_settings: List[str] = [ ] return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/aligned-features/delete', + method='GET', + resource_path='/api/projects/{projectId}/aligned-features', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -1537,10 +1541,14 @@ def _delete_aligned_features_serialize( @validate_call - def get_adduct_network_with_merged_traces_experimental( + def get_aligned_features_paged( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="one feature that is considered the main feature of the adduct network")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1553,15 +1561,23 @@ def get_adduct_network_with_merged_traces_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TraceSetExperimental: - """[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network + ) -> PagedModelAlignedFeature: + """Get all available features (aligned over runs) in the given project-space. - [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Get all available features (aligned over runs) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: one feature that is considered the main feature of the adduct network (required) - :type aligned_feature_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1584,9 +1600,13 @@ def get_adduct_network_with_merged_traces_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_adduct_network_with_merged_traces_experimental_serialize( + _param = self._get_aligned_features_paged_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1594,7 +1614,7 @@ def get_adduct_network_with_merged_traces_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelAlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1608,10 +1628,14 @@ def get_adduct_network_with_merged_traces_experimental( @validate_call - def get_adduct_network_with_merged_traces_experimental_with_http_info( + def get_aligned_features_paged_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="one feature that is considered the main feature of the adduct network")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1624,15 +1648,23 @@ def get_adduct_network_with_merged_traces_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TraceSetExperimental]: - """[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network + ) -> ApiResponse[PagedModelAlignedFeature]: + """Get all available features (aligned over runs) in the given project-space. - [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Get all available features (aligned over runs) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: one feature that is considered the main feature of the adduct network (required) - :type aligned_feature_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1655,9 +1687,13 @@ def get_adduct_network_with_merged_traces_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_adduct_network_with_merged_traces_experimental_serialize( + _param = self._get_aligned_features_paged_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1665,7 +1701,7 @@ def get_adduct_network_with_merged_traces_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelAlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1679,10 +1715,14 @@ def get_adduct_network_with_merged_traces_experimental_with_http_info( @validate_call - def get_adduct_network_with_merged_traces_experimental_without_preload_content( + def get_aligned_features_paged_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="one feature that is considered the main feature of the adduct network")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1696,14 +1736,22 @@ def get_adduct_network_with_merged_traces_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network + """Get all available features (aligned over runs) in the given project-space. - [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Get all available features (aligned over runs) in the given project-space. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: one feature that is considered the main feature of the adduct network (required) - :type aligned_feature_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[AlignedFeatureOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1726,9 +1774,13 @@ def get_adduct_network_with_merged_traces_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_adduct_network_with_merged_traces_experimental_serialize( + _param = self._get_aligned_features_paged_serialize( project_id=project_id, - aligned_feature_id=aligned_feature_id, + page=page, + size=size, + sort=sort, + ms_data_search_prepared=ms_data_search_prepared, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1736,7 +1788,7 @@ def get_adduct_network_with_merged_traces_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelAlignedFeature", } response_data = self.api_client.call_api( *_param, @@ -1745,10 +1797,14 @@ def get_adduct_network_with_merged_traces_experimental_without_preload_content( return response_data.response - def _get_adduct_network_with_merged_traces_experimental_serialize( + def _get_aligned_features_paged_serialize( self, project_id, - aligned_feature_id, + page, + size, + sort, + ms_data_search_prepared, + opt_fields, _request_auth, _content_type, _headers, @@ -1758,6 +1814,8 @@ def _get_adduct_network_with_merged_traces_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { + 'sort': 'multi', + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -1772,9 +1830,27 @@ def _get_adduct_network_with_merged_traces_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters + if page is not None: + + _query_params.append(('page', page)) + + if size is not None: + + _query_params.append(('size', size)) + + if sort is not None: + + _query_params.append(('sort', sort)) + + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + # process the header parameters # process the form parameters # process the body parameter @@ -1795,7 +1871,7 @@ def _get_adduct_network_with_merged_traces_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts', + resource_path='/api/projects/{projectId}/aligned-features/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -1812,12 +1888,11 @@ def _get_adduct_network_with_merged_traces_experimental_serialize( @validate_call - def get_aligned_feature( + def get_best_matching_compound_classes( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1830,19 +1905,17 @@ def get_aligned_feature( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AlignedFeature: - """Get feature (aligned over runs) with the given identifier from the specified project-space. + ) -> CompoundClasses: + """Return Best matching compound classes for given formulaId - Get feature (aligned over runs) with the given identifier from the specified project-space. + Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1865,11 +1938,10 @@ def get_aligned_feature( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_serialize( + _param = self._get_best_matching_compound_classes_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1877,7 +1949,7 @@ def get_aligned_feature( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeature", + '200': "CompoundClasses", } response_data = self.api_client.call_api( *_param, @@ -1891,12 +1963,11 @@ def get_aligned_feature( @validate_call - def get_aligned_feature_with_http_info( + def get_best_matching_compound_classes_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1909,19 +1980,17 @@ def get_aligned_feature_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AlignedFeature]: - """Get feature (aligned over runs) with the given identifier from the specified project-space. + ) -> ApiResponse[CompoundClasses]: + """Return Best matching compound classes for given formulaId - Get feature (aligned over runs) with the given identifier from the specified project-space. + Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -1944,11 +2013,10 @@ def get_aligned_feature_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_serialize( + _param = self._get_best_matching_compound_classes_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -1956,7 +2024,7 @@ def get_aligned_feature_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeature", + '200': "CompoundClasses", } response_data = self.api_client.call_api( *_param, @@ -1970,12 +2038,11 @@ def get_aligned_feature_with_http_info( @validate_call - def get_aligned_feature_without_preload_content( + def get_best_matching_compound_classes_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -1989,18 +2056,16 @@ def get_aligned_feature_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Get feature (aligned over runs) with the given identifier from the specified project-space. + """Return Best matching compound classes for given formulaId - Get feature (aligned over runs) with the given identifier from the specified project-space. + Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2023,11 +2088,10 @@ def get_aligned_feature_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_serialize( + _param = self._get_best_matching_compound_classes_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -2035,7 +2099,7 @@ def get_aligned_feature_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeature", + '200': "CompoundClasses", } response_data = self.api_client.call_api( *_param, @@ -2044,12 +2108,11 @@ def get_aligned_feature_without_preload_content( return response_data.response - def _get_aligned_feature_serialize( + def _get_best_matching_compound_classes_serialize( self, project_id, aligned_feature_id, - ms_data_search_prepared, - opt_fields, + formula_id, _request_auth, _content_type, _headers, @@ -2059,7 +2122,6 @@ def _get_aligned_feature_serialize( _host = None _collection_formats: Dict[str, str] = { - 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -2076,15 +2138,9 @@ def _get_aligned_feature_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - # process the header parameters # process the form parameters # process the body parameter @@ -2105,7 +2161,7 @@ def _get_aligned_feature_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -2122,10 +2178,11 @@ def _get_aligned_feature_serialize( @validate_call - def get_aligned_feature_quality_experimental( + def get_canopus_prediction( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2138,15 +2195,17 @@ def get_aligned_feature_quality_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AlignedFeatureQualityExperimental: - """[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) + ) -> CanopusPrediction: + """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, - [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2169,9 +2228,10 @@ def get_aligned_feature_quality_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_quality_experimental_serialize( + _param = self._get_canopus_prediction_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -2179,7 +2239,7 @@ def get_aligned_feature_quality_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeatureQualityExperimental", + '200': "CanopusPrediction", } response_data = self.api_client.call_api( *_param, @@ -2193,10 +2253,11 @@ def get_aligned_feature_quality_experimental( @validate_call - def get_aligned_feature_quality_experimental_with_http_info( + def get_canopus_prediction_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2209,15 +2270,17 @@ def get_aligned_feature_quality_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AlignedFeatureQualityExperimental]: - """[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) + ) -> ApiResponse[CanopusPrediction]: + """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, - [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2240,9 +2303,10 @@ def get_aligned_feature_quality_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_quality_experimental_serialize( + _param = self._get_canopus_prediction_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -2250,7 +2314,7 @@ def get_aligned_feature_quality_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeatureQualityExperimental", + '200': "CanopusPrediction", } response_data = self.api_client.call_api( *_param, @@ -2264,10 +2328,11 @@ def get_aligned_feature_quality_experimental_with_http_info( @validate_call - def get_aligned_feature_quality_experimental_without_preload_content( + def get_canopus_prediction_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="identifier of feature (aligned over runs) to access.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2281,14 +2346,16 @@ def get_aligned_feature_quality_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) + """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, - [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: identifier of feature (aligned over runs) to access. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2311,9 +2378,10 @@ def get_aligned_feature_quality_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_feature_quality_experimental_serialize( + _param = self._get_canopus_prediction_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -2321,7 +2389,7 @@ def get_aligned_feature_quality_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AlignedFeatureQualityExperimental", + '200': "CanopusPrediction", } response_data = self.api_client.call_api( *_param, @@ -2330,10 +2398,11 @@ def get_aligned_feature_quality_experimental_without_preload_content( return response_data.response - def _get_aligned_feature_quality_experimental_serialize( + def _get_canopus_prediction_serialize( self, project_id, aligned_feature_id, + formula_id, _request_auth, _content_type, _headers, @@ -2359,6 +2428,8 @@ def _get_aligned_feature_quality_experimental_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters # process the header parameters # process the form parameters @@ -2380,7 +2451,7 @@ def _get_aligned_feature_quality_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -2397,11 +2468,12 @@ def _get_aligned_feature_quality_experimental_serialize( @validate_call - def get_aligned_features( + def get_de_novo_structure_candidates_by_formula( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2414,17 +2486,19 @@ def get_aligned_features( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[AlignedFeature]: - """Get all available features (aligned over runs) in the given project-space. + ) -> List[StructureCandidateScored]: + """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - Get all available features (aligned over runs) in the given project-space. + List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. :param project_id: project-space to read from. (required) :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2447,9 +2521,10 @@ def get_aligned_features( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_serialize( project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -2458,7 +2533,7 @@ def get_aligned_features( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[AlignedFeature]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -2472,11 +2547,12 @@ def get_aligned_features( @validate_call - def get_aligned_features_with_http_info( + def get_de_novo_structure_candidates_by_formula_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2489,17 +2565,19 @@ def get_aligned_features_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[AlignedFeature]]: - """Get all available features (aligned over runs) in the given project-space. + ) -> ApiResponse[List[StructureCandidateScored]]: + """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - Get all available features (aligned over runs) in the given project-space. + List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. :param project_id: project-space to read from. (required) :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2522,9 +2600,10 @@ def get_aligned_features_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_serialize( project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -2533,7 +2612,7 @@ def get_aligned_features_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[AlignedFeature]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -2547,11 +2626,12 @@ def get_aligned_features_with_http_info( @validate_call - def get_aligned_features_without_preload_content( + def get_de_novo_structure_candidates_by_formula_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2565,16 +2645,18 @@ def get_aligned_features_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Get all available features (aligned over runs) in the given project-space. + """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - Get all available features (aligned over runs) in the given project-space. + List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. :param project_id: project-space to read from. (required) :type project_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2597,9 +2679,10 @@ def get_aligned_features_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_serialize( project_id=project_id, - ms_data_search_prepared=ms_data_search_prepared, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -2608,7 +2691,7 @@ def get_aligned_features_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[AlignedFeature]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -2617,10 +2700,11 @@ def get_aligned_features_without_preload_content( return response_data.response - def _get_aligned_features_serialize( + def _get_de_novo_structure_candidates_by_formula_serialize( self, project_id, - ms_data_search_prepared, + aligned_feature_id, + formula_id, opt_fields, _request_auth, _content_type, @@ -2646,11 +2730,11 @@ def _get_aligned_features_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - if opt_fields is not None: _query_params.append(('optFields', opt_fields)) @@ -2675,7 +2759,7 @@ def _get_aligned_features_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -2692,14 +2776,15 @@ def _get_aligned_features_serialize( @validate_call - def get_aligned_features_by_group_experimental( + def get_de_novo_structure_candidates_by_formula_paged( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2712,15 +2797,17 @@ def get_aligned_features_by_group_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelAlignedFeature: - """[EXPERIMENTAL] Get features (aligned over runs) by tag group + ) -> PagedModelStructureCandidateScored: + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -2728,7 +2815,7 @@ def get_aligned_features_by_group_experimental( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2751,9 +2838,10 @@ def get_aligned_features_by_group_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_group_experimental_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( project_id=project_id, - group_name=group_name, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, page=page, size=size, sort=sort, @@ -2765,7 +2853,7 @@ def get_aligned_features_by_group_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -2779,14 +2867,15 @@ def get_aligned_features_by_group_experimental( @validate_call - def get_aligned_features_by_group_experimental_with_http_info( + def get_de_novo_structure_candidates_by_formula_paged_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2799,15 +2888,17 @@ def get_aligned_features_by_group_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelAlignedFeature]: - """[EXPERIMENTAL] Get features (aligned over runs) by tag group + ) -> ApiResponse[PagedModelStructureCandidateScored]: + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -2815,7 +2906,7 @@ def get_aligned_features_by_group_experimental_with_http_info( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2838,9 +2929,10 @@ def get_aligned_features_by_group_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_group_experimental_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( project_id=project_id, - group_name=group_name, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, page=page, size=size, sort=sort, @@ -2852,7 +2944,7 @@ def get_aligned_features_by_group_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -2866,14 +2958,15 @@ def get_aligned_features_by_group_experimental_with_http_info( @validate_call - def get_aligned_features_by_group_experimental_without_preload_content( + def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -2887,14 +2980,16 @@ def get_aligned_features_by_group_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Get features (aligned over runs) by tag group + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -2902,7 +2997,7 @@ def get_aligned_features_by_group_experimental_without_preload_content( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -2925,10 +3020,11 @@ def get_aligned_features_by_group_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_group_experimental_serialize( + _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( project_id=project_id, - group_name=group_name, - page=page, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + page=page, size=size, sort=sort, opt_fields=opt_fields, @@ -2939,7 +3035,7 @@ def get_aligned_features_by_group_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -2948,10 +3044,11 @@ def get_aligned_features_by_group_experimental_without_preload_content( return response_data.response - def _get_aligned_features_by_group_experimental_serialize( + def _get_de_novo_structure_candidates_by_formula_paged_serialize( self, project_id, - group_name, + aligned_feature_id, + formula_id, page, size, sort, @@ -2981,11 +3078,11 @@ def _get_aligned_features_by_group_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if group_name is not None: - - _query_params.append(('groupName', group_name)) - if page is not None: _query_params.append(('page', page)) @@ -3022,7 +3119,7 @@ def _get_aligned_features_by_group_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/grouped', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -3039,14 +3136,14 @@ def _get_aligned_features_by_group_experimental_serialize( @validate_call - def get_aligned_features_by_tag_experimental( + def get_de_novo_structure_candidates_paged( self, - project_id: Annotated[StrictStr, Field(description="project space to get features (aligned over runs) from.")], - filter: Annotated[Optional[StrictStr], Field(description="tag filter.")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3059,15 +3156,15 @@ def get_aligned_features_by_tag_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelAlignedFeature: - """[EXPERIMENTAL] Get features (aligned over runs) by tag + ) -> PagedModelStructureCandidateFormula: + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag.
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value
The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project space to get features (aligned over runs) from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param filter: tag filter. - :type filter: str + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :type aligned_feature_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -3075,7 +3172,7 @@ def get_aligned_features_by_tag_experimental( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3098,9 +3195,9 @@ def get_aligned_features_by_tag_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_tag_experimental_serialize( + _param = self._get_de_novo_structure_candidates_paged_serialize( project_id=project_id, - filter=filter, + aligned_feature_id=aligned_feature_id, page=page, size=size, sort=sort, @@ -3112,7 +3209,7 @@ def get_aligned_features_by_tag_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -3126,14 +3223,14 @@ def get_aligned_features_by_tag_experimental( @validate_call - def get_aligned_features_by_tag_experimental_with_http_info( + def get_de_novo_structure_candidates_paged_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project space to get features (aligned over runs) from.")], - filter: Annotated[Optional[StrictStr], Field(description="tag filter.")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3146,15 +3243,15 @@ def get_aligned_features_by_tag_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelAlignedFeature]: - """[EXPERIMENTAL] Get features (aligned over runs) by tag + ) -> ApiResponse[PagedModelStructureCandidateFormula]: + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag.
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value
The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project space to get features (aligned over runs) from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param filter: tag filter. - :type filter: str + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :type aligned_feature_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -3162,7 +3259,7 @@ def get_aligned_features_by_tag_experimental_with_http_info( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3185,9 +3282,9 @@ def get_aligned_features_by_tag_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_tag_experimental_serialize( + _param = self._get_de_novo_structure_candidates_paged_serialize( project_id=project_id, - filter=filter, + aligned_feature_id=aligned_feature_id, page=page, size=size, sort=sort, @@ -3199,7 +3296,7 @@ def get_aligned_features_by_tag_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -3213,14 +3310,14 @@ def get_aligned_features_by_tag_experimental_with_http_info( @validate_call - def get_aligned_features_by_tag_experimental_without_preload_content( + def get_de_novo_structure_candidates_paged_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project space to get features (aligned over runs) from.")], - filter: Annotated[Optional[StrictStr], Field(description="tag filter.")] = None, + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3234,14 +3331,14 @@ def get_aligned_features_by_tag_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Get features (aligned over runs) by tag + """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - [EXPERIMENTAL] Get features (aligned over runs) by tag.
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value
The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - :param project_id: project space to get features (aligned over runs) from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param filter: tag filter. - :type filter: str + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :type aligned_feature_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned @@ -3249,7 +3346,7 @@ def get_aligned_features_by_tag_experimental_without_preload_content( :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3272,9 +3369,9 @@ def get_aligned_features_by_tag_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_by_tag_experimental_serialize( + _param = self._get_de_novo_structure_candidates_paged_serialize( project_id=project_id, - filter=filter, + aligned_feature_id=aligned_feature_id, page=page, size=size, sort=sort, @@ -3286,7 +3383,7 @@ def get_aligned_features_by_tag_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -3295,10 +3392,10 @@ def get_aligned_features_by_tag_experimental_without_preload_content( return response_data.response - def _get_aligned_features_by_tag_experimental_serialize( + def _get_de_novo_structure_candidates_paged_serialize( self, project_id, - filter, + aligned_feature_id, page, size, sort, @@ -3328,11 +3425,9 @@ def _get_aligned_features_by_tag_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters - if filter is not None: - - _query_params.append(('filter', filter)) - if page is not None: _query_params.append(('page', page)) @@ -3369,7 +3464,7 @@ def _get_aligned_features_by_tag_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/tagged', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -3386,14 +3481,11 @@ def _get_aligned_features_by_tag_experimental_serialize( @validate_call - def get_aligned_features_paged( + def get_fingerprint_prediction( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3406,23 +3498,17 @@ def get_aligned_features_paged( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelAlignedFeature: - """Get all available features (aligned over runs) in the given project-space. + ) -> List[float]: + """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) - Get all available features (aligned over runs) in the given project-space. + Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. :param project_id: project-space to read from. (required) :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3445,13 +3531,10 @@ def get_aligned_features_paged( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_paged_serialize( + _param = self._get_fingerprint_prediction_serialize( project_id=project_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3459,7 +3542,7 @@ def get_aligned_features_paged( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "List[float]", } response_data = self.api_client.call_api( *_param, @@ -3473,14 +3556,11 @@ def get_aligned_features_paged( @validate_call - def get_aligned_features_paged_with_http_info( + def get_fingerprint_prediction_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3493,23 +3573,17 @@ def get_aligned_features_paged_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelAlignedFeature]: - """Get all available features (aligned over runs) in the given project-space. + ) -> ApiResponse[List[float]]: + """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) - Get all available features (aligned over runs) in the given project-space. + Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. :param project_id: project-space to read from. (required) :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3532,13 +3606,10 @@ def get_aligned_features_paged_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_paged_serialize( + _param = self._get_fingerprint_prediction_serialize( project_id=project_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3546,7 +3617,7 @@ def get_aligned_features_paged_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "List[float]", } response_data = self.api_client.call_api( *_param, @@ -3560,14 +3631,11 @@ def get_aligned_features_paged_with_http_info( @validate_call - def get_aligned_features_paged_without_preload_content( + def get_fingerprint_prediction_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[AlignedFeatureOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3581,22 +3649,16 @@ def get_aligned_features_paged_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Get all available features (aligned over runs) in the given project-space. + """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) - Get all available features (aligned over runs) in the given project-space. + Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. :param project_id: project-space to read from. (required) :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[AlignedFeatureOptField] + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3619,13 +3681,10 @@ def get_aligned_features_paged_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_aligned_features_paged_serialize( + _param = self._get_fingerprint_prediction_serialize( project_id=project_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3633,7 +3692,7 @@ def get_aligned_features_paged_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelAlignedFeature", + '200': "List[float]", } response_data = self.api_client.call_api( *_param, @@ -3642,14 +3701,11 @@ def get_aligned_features_paged_without_preload_content( return response_data.response - def _get_aligned_features_paged_serialize( + def _get_fingerprint_prediction_serialize( self, project_id, - page, - size, - sort, - ms_data_search_prepared, - opt_fields, + aligned_feature_id, + formula_id, _request_auth, _content_type, _headers, @@ -3659,8 +3715,6 @@ def _get_aligned_features_paged_serialize( _host = None _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -3675,27 +3729,11 @@ def _get_aligned_features_paged_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - # process the header parameters # process the form parameters # process the body parameter @@ -3716,7 +3754,7 @@ def _get_aligned_features_paged_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/page', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -3733,11 +3771,12 @@ def _get_aligned_features_paged_serialize( @validate_call - def get_best_matching_compound_classes( + def get_formula_annotated_ms_ms_data( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3750,10 +3789,10 @@ def get_best_matching_compound_classes( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> CompoundClasses: - """Return Best matching compound classes for given formulaId + ) -> AnnotatedMsMsData: + """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId - Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, + Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. :param project_id: project-space to read from. (required) :type project_id: str @@ -3761,6 +3800,8 @@ def get_best_matching_compound_classes( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3783,10 +3824,11 @@ def get_best_matching_compound_classes( :return: Returns the result object. """ # noqa: E501 - _param = self._get_best_matching_compound_classes_serialize( + _param = self._get_formula_annotated_ms_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3794,7 +3836,7 @@ def get_best_matching_compound_classes( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CompoundClasses", + '200': "AnnotatedMsMsData", } response_data = self.api_client.call_api( *_param, @@ -3808,11 +3850,12 @@ def get_best_matching_compound_classes( @validate_call - def get_best_matching_compound_classes_with_http_info( + def get_formula_annotated_ms_ms_data_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3825,10 +3868,10 @@ def get_best_matching_compound_classes_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[CompoundClasses]: - """Return Best matching compound classes for given formulaId + ) -> ApiResponse[AnnotatedMsMsData]: + """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId - Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, + Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. :param project_id: project-space to read from. (required) :type project_id: str @@ -3836,6 +3879,8 @@ def get_best_matching_compound_classes_with_http_info( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3858,10 +3903,11 @@ def get_best_matching_compound_classes_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_best_matching_compound_classes_serialize( + _param = self._get_formula_annotated_ms_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3869,7 +3915,7 @@ def get_best_matching_compound_classes_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CompoundClasses", + '200': "AnnotatedMsMsData", } response_data = self.api_client.call_api( *_param, @@ -3883,11 +3929,12 @@ def get_best_matching_compound_classes_with_http_info( @validate_call - def get_best_matching_compound_classes_without_preload_content( + def get_formula_annotated_ms_ms_data_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -3901,9 +3948,9 @@ def get_best_matching_compound_classes_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Return Best matching compound classes for given formulaId + """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId - Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, + Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. :param project_id: project-space to read from. (required) :type project_id: str @@ -3911,6 +3958,8 @@ def get_best_matching_compound_classes_without_preload_content( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -3933,10 +3982,11 @@ def get_best_matching_compound_classes_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_best_matching_compound_classes_serialize( + _param = self._get_formula_annotated_ms_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -3944,7 +3994,7 @@ def get_best_matching_compound_classes_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CompoundClasses", + '200': "AnnotatedMsMsData", } response_data = self.api_client.call_api( *_param, @@ -3953,11 +4003,12 @@ def get_best_matching_compound_classes_without_preload_content( return response_data.response - def _get_best_matching_compound_classes_serialize( + def _get_formula_annotated_ms_ms_data_serialize( self, project_id, aligned_feature_id, formula_id, + ms_data_search_prepared, _request_auth, _content_type, _headers, @@ -3986,6 +4037,10 @@ def _get_best_matching_compound_classes_serialize( if formula_id is not None: _path_params['formulaId'] = formula_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + # process the header parameters # process the form parameters # process the body parameter @@ -4006,7 +4061,7 @@ def _get_best_matching_compound_classes_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -4023,11 +4078,13 @@ def _get_best_matching_compound_classes_serialize( @validate_call - def get_canopus_prediction( + def get_formula_annotated_spectrum( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, + search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4040,10 +4097,10 @@ def get_canopus_prediction( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> CanopusPrediction: - """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + ) -> AnnotatedSpectrum: + """Returns a fragmentation spectrum (e - All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. :param project_id: project-space to read from. (required) :type project_id: str @@ -4051,6 +4108,10 @@ def get_canopus_prediction( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) + :type spectrum_index: int + :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4073,10 +4134,12 @@ def get_canopus_prediction( :return: Returns the result object. """ # noqa: E501 - _param = self._get_canopus_prediction_serialize( + _param = self._get_formula_annotated_spectrum_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + spectrum_index=spectrum_index, + search_prepared=search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -4084,7 +4147,7 @@ def get_canopus_prediction( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CanopusPrediction", + '200': "AnnotatedSpectrum", } response_data = self.api_client.call_api( *_param, @@ -4098,11 +4161,13 @@ def get_canopus_prediction( @validate_call - def get_canopus_prediction_with_http_info( + def get_formula_annotated_spectrum_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, + search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4115,10 +4180,10 @@ def get_canopus_prediction_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[CanopusPrediction]: - """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + ) -> ApiResponse[AnnotatedSpectrum]: + """Returns a fragmentation spectrum (e - All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. :param project_id: project-space to read from. (required) :type project_id: str @@ -4126,6 +4191,10 @@ def get_canopus_prediction_with_http_info( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) + :type spectrum_index: int + :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4148,10 +4217,12 @@ def get_canopus_prediction_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_canopus_prediction_serialize( + _param = self._get_formula_annotated_spectrum_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + spectrum_index=spectrum_index, + search_prepared=search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -4159,7 +4230,7 @@ def get_canopus_prediction_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CanopusPrediction", + '200': "AnnotatedSpectrum", } response_data = self.api_client.call_api( *_param, @@ -4173,11 +4244,13 @@ def get_canopus_prediction_with_http_info( @validate_call - def get_canopus_prediction_without_preload_content( + def get_formula_annotated_spectrum_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, + search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4191,9 +4264,9 @@ def get_canopus_prediction_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + """Returns a fragmentation spectrum (e - All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. :param project_id: project-space to read from. (required) :type project_id: str @@ -4201,6 +4274,10 @@ def get_canopus_prediction_without_preload_content( :type aligned_feature_id: str :param formula_id: identifier of the requested formula result (required) :type formula_id: str + :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) + :type spectrum_index: int + :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type search_prepared: bool :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4223,10 +4300,12 @@ def get_canopus_prediction_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_canopus_prediction_serialize( + _param = self._get_formula_annotated_spectrum_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, + spectrum_index=spectrum_index, + search_prepared=search_prepared, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -4234,7 +4313,7 @@ def get_canopus_prediction_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "CanopusPrediction", + '200': "AnnotatedSpectrum", } response_data = self.api_client.call_api( *_param, @@ -4243,11 +4322,13 @@ def get_canopus_prediction_without_preload_content( return response_data.response - def _get_canopus_prediction_serialize( + def _get_formula_annotated_spectrum_serialize( self, project_id, aligned_feature_id, formula_id, + spectrum_index, + search_prepared, _request_auth, _content_type, _headers, @@ -4276,6 +4357,14 @@ def _get_canopus_prediction_serialize( if formula_id is not None: _path_params['formulaId'] = formula_id # process the query parameters + if spectrum_index is not None: + + _query_params.append(('spectrumIndex', spectrum_index)) + + if search_prepared is not None: + + _query_params.append(('searchPrepared', search_prepared)) + # process the header parameters # process the form parameters # process the body parameter @@ -4296,7 +4385,7 @@ def _get_canopus_prediction_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -4313,11 +4402,13 @@ def _get_canopus_prediction_serialize( @validate_call - def get_de_novo_structure_candidates( + def get_formula_candidate( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4330,17 +4421,21 @@ def get_de_novo_structure_candidates( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[StructureCandidateFormula]: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> FormulaCandidate: + """FormulaResultContainers for the given 'formulaId' with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4363,9 +4458,11 @@ def get_de_novo_structure_candidates( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_serialize( + _param = self._get_formula_candidate_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4374,7 +4471,7 @@ def get_de_novo_structure_candidates( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': "FormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -4388,11 +4485,13 @@ def get_de_novo_structure_candidates( @validate_call - def get_de_novo_structure_candidates_with_http_info( + def get_formula_candidate_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4405,17 +4504,21 @@ def get_de_novo_structure_candidates_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[StructureCandidateFormula]]: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> ApiResponse[FormulaCandidate]: + """FormulaResultContainers for the given 'formulaId' with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4438,9 +4541,11 @@ def get_de_novo_structure_candidates_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_serialize( + _param = self._get_formula_candidate_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4449,7 +4554,7 @@ def get_de_novo_structure_candidates_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': "FormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -4463,11 +4568,13 @@ def get_de_novo_structure_candidates_with_http_info( @validate_call - def get_de_novo_structure_candidates_without_preload_content( + def get_formula_candidate_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4481,16 +4588,20 @@ def get_de_novo_structure_candidates_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + """FormulaResultContainers for the given 'formulaId' with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4513,9 +4624,11 @@ def get_de_novo_structure_candidates_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_serialize( + _param = self._get_formula_candidate_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4524,7 +4637,7 @@ def get_de_novo_structure_candidates_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", + '200': "FormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -4533,10 +4646,12 @@ def get_de_novo_structure_candidates_without_preload_content( return response_data.response - def _get_de_novo_structure_candidates_serialize( + def _get_formula_candidate_serialize( self, project_id, aligned_feature_id, + formula_id, + ms_data_search_prepared, opt_fields, _request_auth, _content_type, @@ -4564,7 +4679,13 @@ def _get_de_novo_structure_candidates_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + if opt_fields is not None: _query_params.append(('optFields', opt_fields)) @@ -4589,7 +4710,7 @@ def _get_de_novo_structure_candidates_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -4606,12 +4727,12 @@ def _get_de_novo_structure_candidates_serialize( @validate_call - def get_de_novo_structure_candidates_by_formula( + def get_formula_candidates( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4624,19 +4745,19 @@ def get_de_novo_structure_candidates_by_formula( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[StructureCandidateScored]: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> List[FormulaCandidate]: + """List of FormulaResultContainers available for this feature with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4659,10 +4780,10 @@ def get_de_novo_structure_candidates_by_formula( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_serialize( + _param = self._get_formula_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4671,7 +4792,7 @@ def get_de_novo_structure_candidates_by_formula( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", + '200': "List[FormulaCandidate]", } response_data = self.api_client.call_api( *_param, @@ -4685,12 +4806,12 @@ def get_de_novo_structure_candidates_by_formula( @validate_call - def get_de_novo_structure_candidates_by_formula_with_http_info( + def get_formula_candidates_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4703,19 +4824,19 @@ def get_de_novo_structure_candidates_by_formula_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[StructureCandidateScored]]: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> ApiResponse[List[FormulaCandidate]]: + """List of FormulaResultContainers available for this feature with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4738,10 +4859,10 @@ def get_de_novo_structure_candidates_by_formula_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_serialize( + _param = self._get_formula_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4750,7 +4871,7 @@ def get_de_novo_structure_candidates_by_formula_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", + '200': "List[FormulaCandidate]", } response_data = self.api_client.call_api( *_param, @@ -4764,12 +4885,12 @@ def get_de_novo_structure_candidates_by_formula_with_http_info( @validate_call - def get_de_novo_structure_candidates_by_formula_without_preload_content( + def get_formula_candidates_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4783,18 +4904,18 @@ def get_de_novo_structure_candidates_by_formula_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + """List of FormulaResultContainers available for this feature with minimal information. - List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4817,10 +4938,10 @@ def get_de_novo_structure_candidates_by_formula_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_serialize( + _param = self._get_formula_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4829,7 +4950,7 @@ def get_de_novo_structure_candidates_by_formula_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", + '200': "List[FormulaCandidate]", } response_data = self.api_client.call_api( *_param, @@ -4838,11 +4959,11 @@ def get_de_novo_structure_candidates_by_formula_without_preload_content( return response_data.response - def _get_de_novo_structure_candidates_by_formula_serialize( + def _get_formula_candidates_serialize( self, project_id, aligned_feature_id, - formula_id, + ms_data_search_prepared, opt_fields, _request_auth, _content_type, @@ -4870,9 +4991,11 @@ def _get_de_novo_structure_candidates_by_formula_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id # process the query parameters + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + if opt_fields is not None: _query_params.append(('optFields', opt_fields)) @@ -4897,7 +5020,7 @@ def _get_de_novo_structure_candidates_by_formula_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -4914,15 +5037,15 @@ def _get_de_novo_structure_candidates_by_formula_serialize( @validate_call - def get_de_novo_structure_candidates_by_formula_paged( + def get_formula_candidates_paged( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -4935,25 +5058,25 @@ def get_de_novo_structure_candidates_by_formula_paged( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelStructureCandidateScored: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> PagedModelFormulaCandidate: + """Page of FormulaResultContainers available for this feature with minimal information. - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned :type size: int :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -4976,13 +5099,13 @@ def get_de_novo_structure_candidates_by_formula_paged( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( + _param = self._get_formula_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, page=page, size=size, sort=sort, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -4991,7 +5114,7 @@ def get_de_novo_structure_candidates_by_formula_paged( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", + '200': "PagedModelFormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -5005,15 +5128,15 @@ def get_de_novo_structure_candidates_by_formula_paged( @validate_call - def get_de_novo_structure_candidates_by_formula_paged_with_http_info( + def get_formula_candidates_paged_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5026,25 +5149,25 @@ def get_de_novo_structure_candidates_by_formula_paged_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelStructureCandidateScored]: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> ApiResponse[PagedModelFormulaCandidate]: + """Page of FormulaResultContainers available for this feature with minimal information. - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned :type size: int :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5067,13 +5190,13 @@ def get_de_novo_structure_candidates_by_formula_paged_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( + _param = self._get_formula_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, page=page, size=size, sort=sort, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -5082,7 +5205,7 @@ def get_de_novo_structure_candidates_by_formula_paged_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", + '200': "PagedModelFormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -5096,15 +5219,15 @@ def get_de_novo_structure_candidates_by_formula_paged_with_http_info( @validate_call - def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( + def get_formula_candidates_paged_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5118,24 +5241,24 @@ def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + """Page of FormulaResultContainers available for this feature with minimal information. - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param page: Zero-based page index (0..N) :type page: int :param size: The size of the page to be returned :type size: int :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. :type sort: List[str] + :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. + :type ms_data_search_prepared: bool :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :type opt_fields: List[FormulaCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5158,13 +5281,13 @@ def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_by_formula_paged_serialize( + _param = self._get_formula_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, page=page, size=size, sort=sort, + ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -5173,7 +5296,7 @@ def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", + '200': "PagedModelFormulaCandidate", } response_data = self.api_client.call_api( *_param, @@ -5182,14 +5305,14 @@ def get_de_novo_structure_candidates_by_formula_paged_without_preload_content( return response_data.response - def _get_de_novo_structure_candidates_by_formula_paged_serialize( + def _get_formula_candidates_paged_serialize( self, project_id, aligned_feature_id, - formula_id, page, size, sort, + ms_data_search_prepared, opt_fields, _request_auth, _content_type, @@ -5218,8 +5341,6 @@ def _get_de_novo_structure_candidates_by_formula_paged_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id # process the query parameters if page is not None: @@ -5233,6 +5354,10 @@ def _get_de_novo_structure_candidates_by_formula_paged_serialize( _query_params.append(('sort', sort)) + if ms_data_search_prepared is not None: + + _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + if opt_fields is not None: _query_params.append(('optFields', opt_fields)) @@ -5257,7 +5382,7 @@ def _get_de_novo_structure_candidates_by_formula_paged_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -5274,14 +5399,11 @@ def _get_de_novo_structure_candidates_by_formula_paged_serialize( @validate_call - def get_de_novo_structure_candidates_paged( + def get_frag_tree( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5294,23 +5416,17 @@ def get_de_novo_structure_candidates_paged( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelStructureCandidateFormula: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> FragmentationTree: + """Returns fragmentation tree (SIRIUS) for the given formula result identifier - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5333,13 +5449,10 @@ def get_de_novo_structure_candidates_paged( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_paged_serialize( + _param = self._get_frag_tree_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5347,7 +5460,7 @@ def get_de_novo_structure_candidates_paged( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "FragmentationTree", } response_data = self.api_client.call_api( *_param, @@ -5361,14 +5474,11 @@ def get_de_novo_structure_candidates_paged( @validate_call - def get_de_novo_structure_candidates_paged_with_http_info( + def get_frag_tree_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5381,23 +5491,17 @@ def get_de_novo_structure_candidates_paged_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelStructureCandidateFormula]: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + ) -> ApiResponse[FragmentationTree]: + """Returns fragmentation tree (SIRIUS) for the given formula result identifier - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5420,13 +5524,10 @@ def get_de_novo_structure_candidates_paged_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_paged_serialize( + _param = self._get_frag_tree_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5434,7 +5535,7 @@ def get_de_novo_structure_candidates_paged_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "FragmentationTree", } response_data = self.api_client.call_api( *_param, @@ -5448,14 +5549,11 @@ def get_de_novo_structure_candidates_paged_with_http_info( @validate_call - def get_de_novo_structure_candidates_paged_without_preload_content( + def get_frag_tree_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5469,22 +5567,16 @@ def get_de_novo_structure_candidates_paged_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + """Returns fragmentation tree (SIRIUS) for the given formula result identifier - Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5507,13 +5599,10 @@ def get_de_novo_structure_candidates_paged_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_de_novo_structure_candidates_paged_serialize( + _param = self._get_frag_tree_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5521,7 +5610,7 @@ def get_de_novo_structure_candidates_paged_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "FragmentationTree", } response_data = self.api_client.call_api( *_param, @@ -5530,14 +5619,11 @@ def get_de_novo_structure_candidates_paged_without_preload_content( return response_data.response - def _get_de_novo_structure_candidates_paged_serialize( + def _get_frag_tree_serialize( self, project_id, aligned_feature_id, - page, - size, - sort, - opt_fields, + formula_id, _request_auth, _content_type, _headers, @@ -5547,8 +5633,6 @@ def _get_de_novo_structure_candidates_paged_serialize( _host = None _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -5565,23 +5649,9 @@ def _get_de_novo_structure_candidates_paged_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - # process the header parameters # process the form parameters # process the body parameter @@ -5602,7 +5672,7 @@ def _get_de_novo_structure_candidates_paged_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -5619,10 +5689,11 @@ def _get_de_novo_structure_candidates_paged_serialize( @validate_call - def get_feature_quant_table_experimental( + def get_isotope_pattern_annotation( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5635,15 +5706,17 @@ def get_feature_quant_table_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> QuantTableExperimental: - """[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) + ) -> IsotopePatternAnnotation: + """Returns Isotope pattern information for given formulaId - [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId).
Returns the full quantification table. The quantification table contains a quantities of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5666,9 +5739,10 @@ def get_feature_quant_table_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_feature_quant_table_experimental_serialize( + _param = self._get_isotope_pattern_annotation_serialize( project_id=project_id, - type=type, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5676,7 +5750,7 @@ def get_feature_quant_table_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "IsotopePatternAnnotation", } response_data = self.api_client.call_api( *_param, @@ -5690,10 +5764,11 @@ def get_feature_quant_table_experimental( @validate_call - def get_feature_quant_table_experimental_with_http_info( + def get_isotope_pattern_annotation_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5706,15 +5781,17 @@ def get_feature_quant_table_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[QuantTableExperimental]: - """[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) + ) -> ApiResponse[IsotopePatternAnnotation]: + """Returns Isotope pattern information for given formulaId - [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId).
Returns the full quantification table. The quantification table contains a quantities of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5737,9 +5814,10 @@ def get_feature_quant_table_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_feature_quant_table_experimental_serialize( + _param = self._get_isotope_pattern_annotation_serialize( project_id=project_id, - type=type, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5747,7 +5825,7 @@ def get_feature_quant_table_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "IsotopePatternAnnotation", } response_data = self.api_client.call_api( *_param, @@ -5761,10 +5839,11 @@ def get_feature_quant_table_experimental_with_http_info( @validate_call - def get_feature_quant_table_experimental_without_preload_content( + def get_isotope_pattern_annotation_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -5778,14 +5857,16 @@ def get_feature_quant_table_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) + """Returns Isotope pattern information for given formulaId - [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId).
Returns the full quantification table. The quantification table contains a quantities of the features within all runs they are contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). :param project_id: project-space to read from. (required) :type project_id: str - :param type: quantification type. - :type type: QuantMeasure + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -5808,9 +5889,10 @@ def get_feature_quant_table_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_feature_quant_table_experimental_serialize( + _param = self._get_isotope_pattern_annotation_serialize( project_id=project_id, - type=type, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -5818,7 +5900,7 @@ def get_feature_quant_table_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", + '200': "IsotopePatternAnnotation", } response_data = self.api_client.call_api( *_param, @@ -5827,10 +5909,11 @@ def get_feature_quant_table_experimental_without_preload_content( return response_data.response - def _get_feature_quant_table_experimental_serialize( + def _get_isotope_pattern_annotation_serialize( self, project_id, - type, + aligned_feature_id, + formula_id, _request_auth, _content_type, _headers, @@ -5854,11 +5937,11 @@ def _get_feature_quant_table_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if type is not None: - - _query_params.append(('type', type.value)) - # process the header parameters # process the form parameters # process the body parameter @@ -5879,7 +5962,7 @@ def _get_feature_quant_table_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/quant-table', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -5896,7 +5979,7 @@ def _get_feature_quant_table_experimental_serialize( @validate_call - def get_fingerprint_prediction( + def get_lipid_annotation( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], @@ -5913,10 +5996,10 @@ def get_fingerprint_prediction( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[float]: - """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) + ) -> LipidAnnotation: + """Returns Lipid annotation (ElGordo) for the given formulaId - Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. + Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. :param project_id: project-space to read from. (required) :type project_id: str @@ -5946,7 +6029,7 @@ def get_fingerprint_prediction( :return: Returns the result object. """ # noqa: E501 - _param = self._get_fingerprint_prediction_serialize( + _param = self._get_lipid_annotation_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, @@ -5957,7 +6040,7 @@ def get_fingerprint_prediction( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[float]", + '200': "LipidAnnotation", } response_data = self.api_client.call_api( *_param, @@ -5971,7 +6054,7 @@ def get_fingerprint_prediction( @validate_call - def get_fingerprint_prediction_with_http_info( + def get_lipid_annotation_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], @@ -5988,10 +6071,10 @@ def get_fingerprint_prediction_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[float]]: - """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) + ) -> ApiResponse[LipidAnnotation]: + """Returns Lipid annotation (ElGordo) for the given formulaId - Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. + Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. :param project_id: project-space to read from. (required) :type project_id: str @@ -6021,7 +6104,7 @@ def get_fingerprint_prediction_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_fingerprint_prediction_serialize( + _param = self._get_lipid_annotation_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, @@ -6032,7 +6115,7 @@ def get_fingerprint_prediction_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[float]", + '200': "LipidAnnotation", } response_data = self.api_client.call_api( *_param, @@ -6046,7 +6129,7 @@ def get_fingerprint_prediction_with_http_info( @validate_call - def get_fingerprint_prediction_without_preload_content( + def get_lipid_annotation_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], @@ -6064,9 +6147,9 @@ def get_fingerprint_prediction_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) + """Returns Lipid annotation (ElGordo) for the given formulaId - Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes. + Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. :param project_id: project-space to read from. (required) :type project_id: str @@ -6096,7 +6179,7 @@ def get_fingerprint_prediction_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_fingerprint_prediction_serialize( + _param = self._get_lipid_annotation_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, formula_id=formula_id, @@ -6107,7 +6190,7 @@ def get_fingerprint_prediction_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[float]", + '200': "LipidAnnotation", } response_data = self.api_client.call_api( *_param, @@ -6116,7 +6199,7 @@ def get_fingerprint_prediction_without_preload_content( return response_data.response - def _get_fingerprint_prediction_serialize( + def _get_lipid_annotation_serialize( self, project_id, aligned_feature_id, @@ -6169,7 +6252,7 @@ def _get_fingerprint_prediction_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -6186,11 +6269,10 @@ def _get_fingerprint_prediction_serialize( @validate_call - def get_formula_annotated_ms_ms_data( + def get_ms_data( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, @@ -6204,17 +6286,15 @@ def get_formula_annotated_ms_ms_data( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AnnotatedMsMsData: - """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId + ) -> MsData: + """Mass Spec data (input data) for the given 'alignedFeatureId' . - Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. + Mass Spec data (input data) for the given 'alignedFeatureId' . :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one @@ -6239,10 +6319,9 @@ def get_formula_annotated_ms_ms_data( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_ms_ms_data_serialize( + _param = self._get_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, @@ -6251,7 +6330,7 @@ def get_formula_annotated_ms_ms_data( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", + '200': "MsData", } response_data = self.api_client.call_api( *_param, @@ -6265,11 +6344,10 @@ def get_formula_annotated_ms_ms_data( @validate_call - def get_formula_annotated_ms_ms_data_with_http_info( + def get_ms_data_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, @@ -6283,17 +6361,15 @@ def get_formula_annotated_ms_ms_data_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AnnotatedMsMsData]: - """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId + ) -> ApiResponse[MsData]: + """Mass Spec data (input data) for the given 'alignedFeatureId' . - Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. + Mass Spec data (input data) for the given 'alignedFeatureId' . :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one @@ -6318,10 +6394,9 @@ def get_formula_annotated_ms_ms_data_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_ms_ms_data_serialize( + _param = self._get_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, @@ -6330,7 +6405,7 @@ def get_formula_annotated_ms_ms_data_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", + '200': "MsData", } response_data = self.api_client.call_api( *_param, @@ -6344,11 +6419,10 @@ def get_formula_annotated_ms_ms_data_with_http_info( @validate_call - def get_formula_annotated_ms_ms_data_without_preload_content( + def get_ms_data_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, _request_timeout: Union[ None, @@ -6363,16 +6437,14 @@ def get_formula_annotated_ms_ms_data_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId + """Mass Spec data (input data) for the given 'alignedFeatureId' . - Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available. + Mass Spec data (input data) for the given 'alignedFeatureId' . :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. :type ms_data_search_prepared: bool :param _request_timeout: timeout setting for this request. If one @@ -6397,10 +6469,9 @@ def get_formula_annotated_ms_ms_data_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_ms_ms_data_serialize( + _param = self._get_ms_data_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, ms_data_search_prepared=ms_data_search_prepared, _request_auth=_request_auth, _content_type=_content_type, @@ -6409,7 +6480,7 @@ def get_formula_annotated_ms_ms_data_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", + '200': "MsData", } response_data = self.api_client.call_api( *_param, @@ -6418,11 +6489,10 @@ def get_formula_annotated_ms_ms_data_without_preload_content( return response_data.response - def _get_formula_annotated_ms_ms_data_serialize( + def _get_ms_data_serialize( self, project_id, aligned_feature_id, - formula_id, ms_data_search_prepared, _request_auth, _content_type, @@ -6449,8 +6519,6 @@ def _get_formula_annotated_ms_ms_data_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id # process the query parameters if ms_data_search_prepared is not None: @@ -6476,7 +6544,7 @@ def _get_formula_annotated_ms_ms_data_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -6493,13 +6561,12 @@ def _get_formula_annotated_ms_ms_data_serialize( @validate_call - def get_formula_annotated_spectrum( + def get_spectral_library_match( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -6512,21 +6579,19 @@ def get_formula_annotated_spectrum( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AnnotatedSpectrum: - """Returns a fragmentation spectrum (e + ) -> SpectralLibraryMatch: + """Spectral library match for the given 'alignedFeatureId'. - Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. + Spectral library match for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type search_prepared: bool + :param match_id: id of the library match to be returned. (required) + :type match_id: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -6549,12 +6614,11 @@ def get_formula_annotated_spectrum( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_spectrum_serialize( + _param = self._get_spectral_library_match_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - spectrum_index=spectrum_index, - search_prepared=search_prepared, + match_id=match_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -6562,7 +6626,7 @@ def get_formula_annotated_spectrum( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", + '200': "SpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -6576,13 +6640,12 @@ def get_formula_annotated_spectrum( @validate_call - def get_formula_annotated_spectrum_with_http_info( + def get_spectral_library_match_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -6595,21 +6658,19 @@ def get_formula_annotated_spectrum_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AnnotatedSpectrum]: - """Returns a fragmentation spectrum (e + ) -> ApiResponse[SpectralLibraryMatch]: + """Spectral library match for the given 'alignedFeatureId'. - Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. + Spectral library match for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type search_prepared: bool + :param match_id: id of the library match to be returned. (required) + :type match_id: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -6632,12 +6693,11 @@ def get_formula_annotated_spectrum_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_spectrum_serialize( + _param = self._get_spectral_library_match_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - spectrum_index=spectrum_index, - search_prepared=search_prepared, + match_id=match_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -6645,7 +6705,7 @@ def get_formula_annotated_spectrum_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", + '200': "SpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -6659,13 +6719,12 @@ def get_formula_annotated_spectrum_with_http_info( @validate_call - def get_formula_annotated_spectrum_without_preload_content( + def get_spectral_library_match_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -6679,20 +6738,18 @@ def get_formula_annotated_spectrum_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Returns a fragmentation spectrum (e + """Spectral library match for the given 'alignedFeatureId'. - Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available. + Spectral library match for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type search_prepared: bool + :param match_id: id of the library match to be returned. (required) + :type match_id: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -6715,12 +6772,11 @@ def get_formula_annotated_spectrum_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_annotated_spectrum_serialize( + _param = self._get_spectral_library_match_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - spectrum_index=spectrum_index, - search_prepared=search_prepared, + match_id=match_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -6728,7 +6784,7 @@ def get_formula_annotated_spectrum_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", + '200': "SpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -6737,13 +6793,12 @@ def get_formula_annotated_spectrum_without_preload_content( return response_data.response - def _get_formula_annotated_spectrum_serialize( + def _get_spectral_library_match_serialize( self, project_id, aligned_feature_id, - formula_id, - spectrum_index, - search_prepared, + match_id, + opt_fields, _request_auth, _content_type, _headers, @@ -6753,6 +6808,7 @@ def _get_formula_annotated_spectrum_serialize( _host = None _collection_formats: Dict[str, str] = { + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -6769,16 +6825,12 @@ def _get_formula_annotated_spectrum_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id + if match_id is not None: + _path_params['matchId'] = match_id # process the query parameters - if spectrum_index is not None: - - _query_params.append(('spectrumIndex', spectrum_index)) - - if search_prepared is not None: + if opt_fields is not None: - _query_params.append(('searchPrepared', search_prepared)) + _query_params.append(('optFields', opt_fields)) # process the header parameters # process the form parameters @@ -6800,7 +6852,7 @@ def _get_formula_annotated_spectrum_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -6817,14 +6869,15 @@ def _get_formula_annotated_spectrum_serialize( @validate_call - def get_formula_candidate( + def get_spectral_library_matches( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, + _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], Tuple[ @@ -6836,21 +6889,23 @@ def get_formula_candidate( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> FormulaCandidate: - """FormulaResultContainers for the given 'formulaId' with minimal information. + ) -> List[SpectralLibraryMatch]: + """List of spectral library matches for the given 'alignedFeatureId'. - FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. + List of spectral library matches for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -6873,11 +6928,12 @@ def get_formula_candidate( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidate_serialize( + _param = self._get_spectral_library_matches_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - ms_data_search_prepared=ms_data_search_prepared, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -6886,7 +6942,7 @@ def get_formula_candidate( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "FormulaCandidate", + '200': "List[SpectralLibraryMatch]", } response_data = self.api_client.call_api( *_param, @@ -6900,13 +6956,14 @@ def get_formula_candidate( @validate_call - def get_formula_candidate_with_http_info( + def get_spectral_library_matches_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -6919,21 +6976,23 @@ def get_formula_candidate_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[FormulaCandidate]: - """FormulaResultContainers for the given 'formulaId' with minimal information. + ) -> ApiResponse[List[SpectralLibraryMatch]]: + """List of spectral library matches for the given 'alignedFeatureId'. - FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. + List of spectral library matches for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -6956,11 +7015,12 @@ def get_formula_candidate_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidate_serialize( + _param = self._get_spectral_library_matches_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - ms_data_search_prepared=ms_data_search_prepared, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -6969,7 +7029,7 @@ def get_formula_candidate_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "FormulaCandidate", + '200': "List[SpectralLibraryMatch]", } response_data = self.api_client.call_api( *_param, @@ -6983,13 +7043,14 @@ def get_formula_candidate_with_http_info( @validate_call - def get_formula_candidate_without_preload_content( + def get_spectral_library_matches_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -7003,20 +7064,22 @@ def get_formula_candidate_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """FormulaResultContainers for the given 'formulaId' with minimal information. + """List of spectral library matches for the given 'alignedFeatureId'. - FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information. + List of spectral library matches for the given 'alignedFeatureId'. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -7039,11 +7102,12 @@ def get_formula_candidate_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidate_serialize( + _param = self._get_spectral_library_matches_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - ms_data_search_prepared=ms_data_search_prepared, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -7052,7 +7116,7 @@ def get_formula_candidate_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "FormulaCandidate", + '200': "List[SpectralLibraryMatch]", } response_data = self.api_client.call_api( *_param, @@ -7061,12 +7125,13 @@ def get_formula_candidate_without_preload_content( return response_data.response - def _get_formula_candidate_serialize( + def _get_spectral_library_matches_serialize( self, project_id, aligned_feature_id, - formula_id, - ms_data_search_prepared, + min_shared_peaks, + min_similarity, + inchi_key, opt_fields, _request_auth, _content_type, @@ -7094,12 +7159,18 @@ def _get_formula_candidate_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id # process the query parameters - if ms_data_search_prepared is not None: + if min_shared_peaks is not None: - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + _query_params.append(('minSharedPeaks', min_shared_peaks)) + + if min_similarity is not None: + + _query_params.append(('minSimilarity', min_similarity)) + + if inchi_key is not None: + + _query_params.append(('inchiKey', inchi_key)) if opt_fields is not None: @@ -7125,7 +7196,7 @@ def _get_formula_candidate_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -7142,12 +7213,17 @@ def _get_formula_candidate_serialize( @validate_call - def get_formula_candidates( + def get_spectral_library_matches_paged( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -7160,19 +7236,29 @@ def get_formula_candidates( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[FormulaCandidate]: - """List of FormulaResultContainers available for this feature with minimal information. + ) -> PagedModelSpectralLibraryMatch: + """Page of spectral library matches for the given 'alignedFeatureId'. - List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. + Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -7195,10 +7281,15 @@ def get_formula_candidates( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidates_serialize( + _param = self._get_spectral_library_matches_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, + page=page, + size=size, + sort=sort, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -7207,7 +7298,7 @@ def get_formula_candidates( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FormulaCandidate]", + '200': "PagedModelSpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -7221,12 +7312,17 @@ def get_formula_candidates( @validate_call - def get_formula_candidates_with_http_info( + def get_spectral_library_matches_paged_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -7239,19 +7335,29 @@ def get_formula_candidates_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[FormulaCandidate]]: - """List of FormulaResultContainers available for this feature with minimal information. + ) -> ApiResponse[PagedModelSpectralLibraryMatch]: + """Page of spectral library matches for the given 'alignedFeatureId'. - List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. + Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -7274,10 +7380,15 @@ def get_formula_candidates_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidates_serialize( + _param = self._get_spectral_library_matches_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, + page=page, + size=size, + sort=sort, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -7286,7 +7397,7 @@ def get_formula_candidates_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FormulaCandidate]", + '200': "PagedModelSpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -7300,12 +7411,17 @@ def get_formula_candidates_with_http_info( @validate_call - def get_formula_candidates_without_preload_content( + def get_spectral_library_matches_paged_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + min_shared_peaks: Optional[StrictInt] = None, + min_similarity: Optional[float] = None, + inchi_key: Optional[StrictStr] = None, + opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -7319,18 +7435,28 @@ def get_formula_candidates_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """List of FormulaResultContainers available for this feature with minimal information. + """Page of spectral library matches for the given 'alignedFeatureId'. - List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. + Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param min_shared_peaks: + :type min_shared_peaks: int + :param min_similarity: + :type min_similarity: float + :param inchi_key: + :type inchi_key: str + :param opt_fields: + :type opt_fields: List[SpectralLibraryMatchOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -7353,10 +7479,15 @@ def get_formula_candidates_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidates_serialize( + _param = self._get_spectral_library_matches_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, + page=page, + size=size, + sort=sort, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -7365,7 +7496,7 @@ def get_formula_candidates_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[FormulaCandidate]", + '200': "PagedModelSpectralLibraryMatch", } response_data = self.api_client.call_api( *_param, @@ -7374,11 +7505,16 @@ def get_formula_candidates_without_preload_content( return response_data.response - def _get_formula_candidates_serialize( + def _get_spectral_library_matches_paged_serialize( self, project_id, aligned_feature_id, - ms_data_search_prepared, + page, + size, + sort, + min_shared_peaks, + min_similarity, + inchi_key, opt_fields, _request_auth, _content_type, @@ -7389,6 +7525,7 @@ def _get_formula_candidates_serialize( _host = None _collection_formats: Dict[str, str] = { + 'sort': 'multi', 'optFields': 'multi', } @@ -7407,9 +7544,29 @@ def _get_formula_candidates_serialize( if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters - if ms_data_search_prepared is not None: + if page is not None: - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) + _query_params.append(('page', page)) + + if size is not None: + + _query_params.append(('size', size)) + + if sort is not None: + + _query_params.append(('sort', sort)) + + if min_shared_peaks is not None: + + _query_params.append(('minSharedPeaks', min_shared_peaks)) + + if min_similarity is not None: + + _query_params.append(('minSimilarity', min_similarity)) + + if inchi_key is not None: + + _query_params.append(('inchiKey', inchi_key)) if opt_fields is not None: @@ -7435,7 +7592,7 @@ def _get_formula_candidates_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -7452,15 +7609,13 @@ def _get_formula_candidates_serialize( @validate_call - def get_formula_candidates_paged( + def get_spectral_library_matches_summary( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, + min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, + inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -7473,25 +7628,21 @@ def get_formula_candidates_paged( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelFormulaCandidate: - """Page of FormulaResultContainers available for this feature with minimal information. + ) -> SpectralLibraryMatchSummary: + """Summarize matched reference spectra for the given 'alignedFeatureId'. - Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. + Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] + :param min_shared_peaks: min threshold of shared peaks. + :type min_shared_peaks: int + :param min_similarity: min spectral similarity threshold. + :type min_similarity: float + :param inchi_key: 2D inchi key of the compound in the structure database. + :type inchi_key: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -7514,14 +7665,12 @@ def get_formula_candidates_paged( :return: Returns the result object. """ # noqa: E501 - _param = self._get_formula_candidates_paged_serialize( + _param = self._get_spectral_library_matches_summary_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -7529,7 +7678,7 @@ def get_formula_candidates_paged( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelFormulaCandidate", + '200': "SpectralLibraryMatchSummary", } response_data = self.api_client.call_api( *_param, @@ -7543,4757 +7692,13 @@ def get_formula_candidates_paged( @validate_call - def get_formula_candidates_paged_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelFormulaCandidate]: - """Page of FormulaResultContainers available for this feature with minimal information. - - Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_formula_candidates_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelFormulaCandidate", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_formula_candidates_paged_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - opt_fields: Annotated[Optional[List[Optional[FormulaCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Page of FormulaResultContainers available for this feature with minimal information. - - Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[FormulaCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_formula_candidates_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - ms_data_search_prepared=ms_data_search_prepared, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelFormulaCandidate", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_formula_candidates_paged_serialize( - self, - project_id, - aligned_feature_id, - page, - size, - sort, - ms_data_search_prepared, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_frag_tree( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> FragmentationTree: - """Returns fragmentation tree (SIRIUS) for the given formula result identifier - - Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_frag_tree_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "FragmentationTree", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_frag_tree_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[FragmentationTree]: - """Returns fragmentation tree (SIRIUS) for the given formula result identifier - - Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_frag_tree_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "FragmentationTree", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_frag_tree_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Returns fragmentation tree (SIRIUS) for the given formula result identifier - - Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_frag_tree_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "FragmentationTree", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_frag_tree_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_isotope_pattern_annotation( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> IsotopePatternAnnotation: - """Returns Isotope pattern information for given formulaId - - Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_isotope_pattern_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "IsotopePatternAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_isotope_pattern_annotation_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[IsotopePatternAnnotation]: - """Returns Isotope pattern information for given formulaId - - Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_isotope_pattern_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "IsotopePatternAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_isotope_pattern_annotation_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Returns Isotope pattern information for given formulaId - - Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_isotope_pattern_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "IsotopePatternAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_isotope_pattern_annotation_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_lipid_annotation( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> LipidAnnotation: - """Returns Lipid annotation (ElGordo) for the given formulaId - - Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_lipid_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "LipidAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_lipid_annotation_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[LipidAnnotation]: - """Returns Lipid annotation (ElGordo) for the given formulaId - - Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_lipid_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "LipidAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_lipid_annotation_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Returns Lipid annotation (ElGordo) for the given formulaId - - Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_lipid_annotation_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "LipidAnnotation", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_lipid_annotation_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_ms_data( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> MsData: - """Mass Spec data (input data) for the given 'alignedFeatureId' . - - Mass Spec data (input data) for the given 'alignedFeatureId' . - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) - :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_ms_data_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "MsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_ms_data_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[MsData]: - """Mass Spec data (input data) for the given 'alignedFeatureId' . - - Mass Spec data (input data) for the given 'alignedFeatureId' . - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) - :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_ms_data_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "MsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_ms_data_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the Mass Spec data belongs to.")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Mass Spec data (input data) for the given 'alignedFeatureId' . - - Mass Spec data (input data) for the given 'alignedFeatureId' . - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the Mass Spec data belongs to. (required) - :type aligned_feature_id: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_ms_data_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "MsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_ms_data_serialize( - self, - project_id, - aligned_feature_id, - ms_data_search_prepared, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_quant_table_row_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which quantity should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> QuantTableExperimental: - """[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) - - [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId).
The quantification table contains a quantity of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature which quantity should be read out (required) - :type aligned_feature_id: str - :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_quant_table_row_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_quant_table_row_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which quantity should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[QuantTableExperimental]: - """[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) - - [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId).
The quantification table contains a quantity of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature which quantity should be read out (required) - :type aligned_feature_id: str - :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_quant_table_row_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_quant_table_row_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which quantity should be read out")], - type: Annotated[Optional[QuantMeasure], Field(description="quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) - - [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId).
The quantification table contains a quantity of the feature within all samples it is contained in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature which quantity should be read out (required) - :type aligned_feature_id: str - :param type: quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. - :type type: QuantMeasure - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_quant_table_row_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - type=type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "QuantTableExperimental", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_quant_table_row_experimental_serialize( - self, - project_id, - aligned_feature_id, - type, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if type is not None: - - _query_params.append(('type', type.value)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_spectral_library_match( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> SpectralLibraryMatch: - """Spectral library match for the given 'alignedFeatureId'. - - Spectral library match for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_match_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_spectral_library_match_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[SpectralLibraryMatch]: - """Spectral library match for the given 'alignedFeatureId'. - - Spectral library match for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_match_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_spectral_library_match_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Spectral library match for the given 'alignedFeatureId'. - - Spectral library match for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_match_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_spectral_library_match_serialize( - self, - project_id, - aligned_feature_id, - match_id, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if match_id is not None: - _path_params['matchId'] = match_id - # process the query parameters - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_spectral_library_matches( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[SpectralLibraryMatch]: - """List of spectral library matches for the given 'alignedFeatureId'. - - List of spectral library matches for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[SpectralLibraryMatch]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_spectral_library_matches_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[SpectralLibraryMatch]]: - """List of spectral library matches for the given 'alignedFeatureId'. - - List of spectral library matches for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[SpectralLibraryMatch]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_spectral_library_matches_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """List of spectral library matches for the given 'alignedFeatureId'. - - List of spectral library matches for the given 'alignedFeatureId'. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[SpectralLibraryMatch]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_spectral_library_matches_serialize( - self, - project_id, - aligned_feature_id, - min_shared_peaks, - min_similarity, - inchi_key, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if min_shared_peaks is not None: - - _query_params.append(('minSharedPeaks', min_shared_peaks)) - - if min_similarity is not None: - - _query_params.append(('minSimilarity', min_similarity)) - - if inchi_key is not None: - - _query_params.append(('inchiKey', inchi_key)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_spectral_library_matches_paged( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelSpectralLibraryMatch: - """Page of spectral library matches for the given 'alignedFeatureId'. - - Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelSpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_spectral_library_matches_paged_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelSpectralLibraryMatch]: - """Page of spectral library matches for the given 'alignedFeatureId'. - - Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelSpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_spectral_library_matches_paged_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - min_shared_peaks: Optional[StrictInt] = None, - min_similarity: Optional[float] = None, - inchi_key: Optional[StrictStr] = None, - opt_fields: Optional[List[Optional[SpectralLibraryMatchOptField]]] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Page of spectral library matches for the given 'alignedFeatureId'. - - Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param min_shared_peaks: - :type min_shared_peaks: int - :param min_similarity: - :type min_similarity: float - :param inchi_key: - :type inchi_key: str - :param opt_fields: - :type opt_fields: List[SpectralLibraryMatchOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelSpectralLibraryMatch", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_spectral_library_matches_paged_serialize( - self, - project_id, - aligned_feature_id, - page, - size, - sort, - min_shared_peaks, - min_similarity, - inchi_key, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if min_shared_peaks is not None: - - _query_params.append(('minSharedPeaks', min_shared_peaks)) - - if min_similarity is not None: - - _query_params.append(('minSimilarity', min_similarity)) - - if inchi_key is not None: - - _query_params.append(('inchiKey', inchi_key)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_spectral_library_matches_summary( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, - min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, - inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> SpectralLibraryMatchSummary: - """Summarize matched reference spectra for the given 'alignedFeatureId'. - - Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: min threshold of shared peaks. - :type min_shared_peaks: int - :param min_similarity: min spectral similarity threshold. - :type min_similarity: float - :param inchi_key: 2D inchi key of the compound in the structure database. - :type inchi_key: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_summary_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatchSummary", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_spectral_library_matches_summary_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, - min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, - inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[SpectralLibraryMatchSummary]: - """Summarize matched reference spectra for the given 'alignedFeatureId'. - - Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: min threshold of shared peaks. - :type min_shared_peaks: int - :param min_similarity: min spectral similarity threshold. - :type min_similarity: float - :param inchi_key: 2D inchi key of the compound in the structure database. - :type inchi_key: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_summary_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatchSummary", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_spectral_library_matches_summary_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, - min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, - inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """Summarize matched reference spectra for the given 'alignedFeatureId'. - - Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param min_shared_peaks: min threshold of shared peaks. - :type min_shared_peaks: int - :param min_similarity: min spectral similarity threshold. - :type min_similarity: float - :param inchi_key: 2D inchi key of the compound in the structure database. - :type inchi_key: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_spectral_library_matches_summary_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - min_shared_peaks=min_shared_peaks, - min_similarity=min_similarity, - inchi_key=inchi_key, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "SpectralLibraryMatchSummary", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_spectral_library_matches_summary_serialize( - self, - project_id, - aligned_feature_id, - min_shared_peaks, - min_similarity, - inchi_key, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if min_shared_peaks is not None: - - _query_params.append(('minSharedPeaks', min_shared_peaks)) - - if min_similarity is not None: - - _query_params.append(('minSimilarity', min_similarity)) - - if inchi_key is not None: - - _query_params.append(('inchiKey', inchi_key)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_annotated_ms_data_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AnnotatedMsMsData: - """[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey - - [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey.
Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses for the given formula result identifier and structure candidate inChIKey. These annotations are only available if a fragmentation tree and the structure candidate are available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_ms_data_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_annotated_ms_data_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AnnotatedMsMsData]: - """[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey - - [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey.
Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses for the given formula result identifier and structure candidate inChIKey. These annotations are only available if a fragmentation tree and the structure candidate are available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_ms_data_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_structure_annotated_ms_data_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - ms_data_search_prepared: Annotated[Optional[StrictBool], Field(description="Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey - - [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey.
Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses for the given formula result identifier and structure candidate inChIKey. These annotations are only available if a fragmentation tree and the structure candidate are available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param ms_data_search_prepared: Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. - :type ms_data_search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_ms_data_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - ms_data_search_prepared=ms_data_search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedMsMsData", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_structure_annotated_ms_data_experimental_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - inchi_key, - ms_data_search_prepared, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - if inchi_key is not None: - _path_params['inchiKey'] = inchi_key - # process the query parameters - if ms_data_search_prepared is not None: - - _query_params.append(('msDataSearchPrepared', ms_data_search_prepared)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_annotated_spectral_library_match_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AnnotatedSpectrum: - """[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations - - [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectral_library_match_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_annotated_spectral_library_match_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AnnotatedSpectrum]: - """[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations - - [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectral_library_match_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_structure_annotated_spectral_library_match_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - match_id: Annotated[StrictStr, Field(description="id of the library match to be returned.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations - - [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param match_id: id of the library match to be returned. (required) - :type match_id: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectral_library_match_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - match_id=match_id, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_structure_annotated_spectral_library_match_experimental_serialize( - self, - project_id, - aligned_feature_id, - match_id, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if match_id is not None: - _path_params['matchId'] = match_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_annotated_spectrum_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Optional[StrictBool] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> AnnotatedSpectrum: - """[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey - - [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result These annotations are only available if a fragmentation tree is available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: - :type search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectrum_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - spectrum_index=spectrum_index, - search_prepared=search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_annotated_spectrum_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Optional[StrictBool] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[AnnotatedSpectrum]: - """[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey - - [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result These annotations are only available if a fragmentation tree is available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: - :type search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectrum_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - spectrum_index=spectrum_index, - search_prepared=search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_structure_annotated_spectrum_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - inchi_key: Annotated[StrictStr, Field(description="2d InChIKey of the structure candidate to be used to annotate the spectrum annotation")], - spectrum_index: Annotated[Optional[StrictInt], Field(description="index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default)")] = None, - search_prepared: Optional[StrictBool] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey - - [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result These annotations are only available if a fragmentation tree is available.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param inchi_key: 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation (required) - :type inchi_key: str - :param spectrum_index: index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) - :type spectrum_index: int - :param search_prepared: - :type search_prepared: bool - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_annotated_spectrum_experimental_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - inchi_key=inchi_key, - spectrum_index=spectrum_index, - search_prepared=search_prepared, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "AnnotatedSpectrum", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_structure_annotated_spectrum_experimental_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - inchi_key, - spectrum_index, - search_prepared, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - if inchi_key is not None: - _path_params['inchiKey'] = inchi_key - # process the query parameters - if spectrum_index is not None: - - _query_params.append(('spectrumIndex', spectrum_index)) - - if search_prepared is not None: - - _query_params.append(('searchPrepared', search_prepared)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_candidates( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[StructureCandidateFormula]: - """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - - List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_candidates_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[StructureCandidateFormula]]: - """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - - List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_structure_candidates_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - - List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) - :type aligned_feature_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateFormula]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_structure_candidates_serialize( - self, - project_id, - aligned_feature_id, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - # process the query parameters - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_candidates_by_formula( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[StructureCandidateScored]: - """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - - List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_by_formula_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_candidates_by_formula_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[StructureCandidateScored]]: - """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - - List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_by_formula_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_structure_candidates_by_formula_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - - List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_by_formula_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[StructureCandidateScored]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_structure_candidates_by_formula_serialize( - self, - project_id, - aligned_feature_id, - formula_id, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if aligned_feature_id is not None: - _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id - # process the query parameters - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_structure_candidates_by_formula_paged( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelStructureCandidateScored: - """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - - Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) - :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_structure_candidates_by_formula_paged_serialize( - project_id=project_id, - aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_structure_candidates_by_formula_paged_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + def get_spectral_library_matches_summary_with_http_info( + self, + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, + min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, + inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -12306,25 +7711,21 @@ def get_structure_candidates_by_formula_paged_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelStructureCandidateScored]: - """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. + ) -> ApiResponse[SpectralLibraryMatchSummary]: + """Summarize matched reference spectra for the given 'alignedFeatureId'. - Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. + Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :param min_shared_peaks: min threshold of shared peaks. + :type min_shared_peaks: int + :param min_similarity: min spectral similarity threshold. + :type min_similarity: float + :param inchi_key: 2D inchi key of the compound in the structure database. + :type inchi_key: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -12347,14 +7748,12 @@ def get_structure_candidates_by_formula_paged_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_structure_candidates_by_formula_paged_serialize( + _param = self._get_spectral_library_matches_summary_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -12362,7 +7761,7 @@ def get_structure_candidates_by_formula_paged_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", + '200': "SpectralLibraryMatchSummary", } response_data = self.api_client.call_api( *_param, @@ -12376,15 +7775,13 @@ def get_structure_candidates_by_formula_paged_with_http_info( @validate_call - def get_structure_candidates_by_formula_paged_without_preload_content( + def get_spectral_library_matches_summary_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], - formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + min_shared_peaks: Annotated[Optional[StrictInt], Field(description="min threshold of shared peaks.")] = None, + min_similarity: Annotated[Optional[float], Field(description="min spectral similarity threshold.")] = None, + inchi_key: Annotated[Optional[StrictStr], Field(description="2D inchi key of the compound in the structure database.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -12398,24 +7795,20 @@ def get_structure_candidates_by_formula_paged_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. + """Summarize matched reference spectra for the given 'alignedFeatureId'. - Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. + Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param formula_id: identifier of the requested formula result (required) - :type formula_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[StructureCandidateOptField] + :param min_shared_peaks: min threshold of shared peaks. + :type min_shared_peaks: int + :param min_similarity: min spectral similarity threshold. + :type min_similarity: float + :param inchi_key: 2D inchi key of the compound in the structure database. + :type inchi_key: str :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -12438,14 +7831,12 @@ def get_structure_candidates_by_formula_paged_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_structure_candidates_by_formula_paged_serialize( + _param = self._get_spectral_library_matches_summary_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - formula_id=formula_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, + min_shared_peaks=min_shared_peaks, + min_similarity=min_similarity, + inchi_key=inchi_key, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -12453,7 +7844,7 @@ def get_structure_candidates_by_formula_paged_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateScored", + '200': "SpectralLibraryMatchSummary", } response_data = self.api_client.call_api( *_param, @@ -12462,15 +7853,13 @@ def get_structure_candidates_by_formula_paged_without_preload_content( return response_data.response - def _get_structure_candidates_by_formula_paged_serialize( + def _get_spectral_library_matches_summary_serialize( self, project_id, aligned_feature_id, - formula_id, - page, - size, - sort, - opt_fields, + min_shared_peaks, + min_similarity, + inchi_key, _request_auth, _content_type, _headers, @@ -12480,8 +7869,6 @@ def _get_structure_candidates_by_formula_paged_serialize( _host = None _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -12498,24 +7885,18 @@ def _get_structure_candidates_by_formula_paged_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if formula_id is not None: - _path_params['formulaId'] = formula_id # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: + if min_shared_peaks is not None: - _query_params.append(('size', size)) + _query_params.append(('minSharedPeaks', min_shared_peaks)) - if sort is not None: + if min_similarity is not None: - _query_params.append(('sort', sort)) + _query_params.append(('minSimilarity', min_similarity)) - if opt_fields is not None: + if inchi_key is not None: - _query_params.append(('optFields', opt_fields)) + _query_params.append(('inchiKey', inchi_key)) # process the header parameters # process the form parameters @@ -12537,7 +7918,7 @@ def _get_structure_candidates_by_formula_paged_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -12554,13 +7935,10 @@ def _get_structure_candidates_by_formula_paged_serialize( @validate_call - def get_structure_candidates_paged( + def get_structure_candidates( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, @@ -12574,21 +7952,15 @@ def get_structure_candidates_paged( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelStructureCandidateFormula: - """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. + ) -> List[StructureCandidateFormula]: + """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. + List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one @@ -12613,12 +7985,9 @@ def get_structure_candidates_paged( :return: Returns the result object. """ # noqa: E501 - _param = self._get_structure_candidates_paged_serialize( + _param = self._get_structure_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -12627,7 +7996,7 @@ def get_structure_candidates_paged( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "List[StructureCandidateFormula]", } response_data = self.api_client.call_api( *_param, @@ -12641,13 +8010,10 @@ def get_structure_candidates_paged( @validate_call - def get_structure_candidates_paged_with_http_info( + def get_structure_candidates_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, @@ -12661,21 +8027,15 @@ def get_structure_candidates_paged_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelStructureCandidateFormula]: - """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. + ) -> ApiResponse[List[StructureCandidateFormula]]: + """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. + List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one @@ -12700,12 +8060,9 @@ def get_structure_candidates_paged_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_structure_candidates_paged_serialize( + _param = self._get_structure_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -12714,7 +8071,7 @@ def get_structure_candidates_paged_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "List[StructureCandidateFormula]", } response_data = self.api_client.call_api( *_param, @@ -12728,13 +8085,10 @@ def get_structure_candidates_paged_with_http_info( @validate_call - def get_structure_candidates_paged_without_preload_content( + def get_structure_candidates_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, @@ -12749,20 +8103,14 @@ def get_structure_candidates_paged_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. + """List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. + List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one @@ -12787,12 +8135,9 @@ def get_structure_candidates_paged_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_structure_candidates_paged_serialize( + _param = self._get_structure_candidates_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - page=page, - size=size, - sort=sort, opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, @@ -12801,7 +8146,7 @@ def get_structure_candidates_paged_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelStructureCandidateFormula", + '200': "List[StructureCandidateFormula]", } response_data = self.api_client.call_api( *_param, @@ -12810,13 +8155,10 @@ def get_structure_candidates_paged_without_preload_content( return response_data.response - def _get_structure_candidates_paged_serialize( + def _get_structure_candidates_serialize( self, project_id, aligned_feature_id, - page, - size, - sort, opt_fields, _request_auth, _content_type, @@ -12827,7 +8169,6 @@ def _get_structure_candidates_paged_serialize( _host = None _collection_formats: Dict[str, str] = { - 'sort': 'multi', 'optFields': 'multi', } @@ -12846,18 +8187,6 @@ def _get_structure_candidates_paged_serialize( if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - if opt_fields is not None: _query_params.append(('optFields', opt_fields)) @@ -12882,7 +8211,7 @@ def _get_structure_candidates_paged_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -12899,10 +8228,12 @@ def _get_structure_candidates_paged_serialize( @validate_call - def get_tags_for_aligned_features_experimental( + def get_structure_candidates_by_formula( self, - project_id: Annotated[StrictStr, Field(description="project-space to get from.")], - object_id: Annotated[StrictStr, Field(description="object to get tags for.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -12915,15 +8246,19 @@ def get_tags_for_aligned_features_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[Tag]: - """[EXPERIMENTAL] Get all tags associated with this Object + ) -> List[StructureCandidateScored]: + """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Get all tags associated with this Object + List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to get from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param object_id: object to get tags for. (required) - :type object_id: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -12946,9 +8281,11 @@ def get_tags_for_aligned_features_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_tags_for_aligned_features_experimental_serialize( + _param = self._get_structure_candidates_by_formula_serialize( project_id=project_id, - object_id=object_id, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -12956,7 +8293,7 @@ def get_tags_for_aligned_features_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -12970,10 +8307,12 @@ def get_tags_for_aligned_features_experimental( @validate_call - def get_tags_for_aligned_features_experimental_with_http_info( + def get_structure_candidates_by_formula_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to get from.")], - object_id: Annotated[StrictStr, Field(description="object to get tags for.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -12986,15 +8325,19 @@ def get_tags_for_aligned_features_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[Tag]]: - """[EXPERIMENTAL] Get all tags associated with this Object + ) -> ApiResponse[List[StructureCandidateScored]]: + """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Get all tags associated with this Object + List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to get from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param object_id: object to get tags for. (required) - :type object_id: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13017,9 +8360,11 @@ def get_tags_for_aligned_features_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_tags_for_aligned_features_experimental_serialize( + _param = self._get_structure_candidates_by_formula_serialize( project_id=project_id, - object_id=object_id, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13027,7 +8372,7 @@ def get_tags_for_aligned_features_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -13041,10 +8386,12 @@ def get_tags_for_aligned_features_experimental_with_http_info( @validate_call - def get_tags_for_aligned_features_experimental_without_preload_content( + def get_structure_candidates_by_formula_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to get from.")], - object_id: Annotated[StrictStr, Field(description="object to get tags for.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13058,14 +8405,18 @@ def get_tags_for_aligned_features_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Get all tags associated with this Object + """List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Get all tags associated with this Object + List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to get from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param object_id: object to get tags for. (required) - :type object_id: str + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) + :type aligned_feature_id: str + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13088,9 +8439,11 @@ def get_tags_for_aligned_features_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_tags_for_aligned_features_experimental_serialize( + _param = self._get_structure_candidates_by_formula_serialize( project_id=project_id, - object_id=object_id, + aligned_feature_id=aligned_feature_id, + formula_id=formula_id, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13098,7 +8451,7 @@ def get_tags_for_aligned_features_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", + '200': "List[StructureCandidateScored]", } response_data = self.api_client.call_api( *_param, @@ -13107,10 +8460,12 @@ def get_tags_for_aligned_features_experimental_without_preload_content( return response_data.response - def _get_tags_for_aligned_features_experimental_serialize( + def _get_structure_candidates_by_formula_serialize( self, project_id, - object_id, + aligned_feature_id, + formula_id, + opt_fields, _request_auth, _content_type, _headers, @@ -13120,6 +8475,7 @@ def _get_tags_for_aligned_features_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -13134,9 +8490,15 @@ def _get_tags_for_aligned_features_experimental_serialize( # process the path parameters if project_id is not None: _path_params['projectId'] = project_id - if object_id is not None: - _path_params['objectId'] = object_id + if aligned_feature_id is not None: + _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + # process the header parameters # process the form parameters # process the body parameter @@ -13157,7 +8519,7 @@ def _get_tags_for_aligned_features_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/tags/{objectId}', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -13174,11 +8536,15 @@ def _get_tags_for_aligned_features_experimental_serialize( @validate_call - def get_traces_experimental( + def get_structure_candidates_by_formula_paged( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")], - include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13191,17 +8557,25 @@ def get_traces_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TraceSetExperimental: - """[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) + ) -> PagedModelStructureCandidateScored: + """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId).
Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis. By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set, it also includes samples in which the same trace appears in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature which intensities should be read out (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. - :type include_all: bool + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13224,10 +8598,14 @@ def get_traces_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._get_traces_experimental_serialize( + _param = self._get_structure_candidates_by_formula_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - include_all=include_all, + formula_id=formula_id, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13235,7 +8613,7 @@ def get_traces_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -13249,11 +8627,15 @@ def get_traces_experimental( @validate_call - def get_traces_experimental_with_http_info( + def get_structure_candidates_by_formula_paged_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")], - include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13266,17 +8648,25 @@ def get_traces_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TraceSetExperimental]: - """[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) + ) -> ApiResponse[PagedModelStructureCandidateScored]: + """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId).
Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis. By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set, it also includes samples in which the same trace appears in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature which intensities should be read out (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. - :type include_all: bool + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13299,10 +8689,14 @@ def get_traces_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._get_traces_experimental_serialize( + _param = self._get_structure_candidates_by_formula_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - include_all=include_all, + formula_id=formula_id, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13310,7 +8704,7 @@ def get_traces_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -13324,11 +8718,15 @@ def get_traces_experimental_with_http_info( @validate_call - def get_traces_experimental_without_preload_content( + def get_structure_candidates_by_formula_paged_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature which intensities should be read out")], - include_all: Annotated[Optional[StrictBool], Field(description="when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature.")] = None, + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the formula result belongs to.")], + formula_id: Annotated[StrictStr, Field(description="identifier of the requested formula result")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13342,16 +8740,24 @@ def get_traces_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) + """Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. - [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId).
Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis. By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set, it also includes samples in which the same trace appears in.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature which intensities should be read out (required) + :param aligned_feature_id: feature (aligned over runs) the formula result belongs to. (required) :type aligned_feature_id: str - :param include_all: when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. - :type include_all: bool + :param formula_id: identifier of the requested formula result (required) + :type formula_id: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13374,10 +8780,14 @@ def get_traces_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._get_traces_experimental_serialize( + _param = self._get_structure_candidates_by_formula_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - include_all=include_all, + formula_id=formula_id, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13385,7 +8795,7 @@ def get_traces_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': "TraceSetExperimental", + '200': "PagedModelStructureCandidateScored", } response_data = self.api_client.call_api( *_param, @@ -13394,11 +8804,15 @@ def get_traces_experimental_without_preload_content( return response_data.response - def _get_traces_experimental_serialize( + def _get_structure_candidates_by_formula_paged_serialize( self, project_id, aligned_feature_id, - include_all, + formula_id, + page, + size, + sort, + opt_fields, _request_auth, _content_type, _headers, @@ -13408,6 +8822,8 @@ def _get_traces_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { + 'sort': 'multi', + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -13424,10 +8840,24 @@ def _get_traces_experimental_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id + if formula_id is not None: + _path_params['formulaId'] = formula_id # process the query parameters - if include_all is not None: + if page is not None: + + _query_params.append(('page', page)) + + if size is not None: + + _query_params.append(('size', size)) + + if sort is not None: + + _query_params.append(('sort', sort)) + + if opt_fields is not None: - _query_params.append(('includeAll', include_all)) + _query_params.append(('optFields', opt_fields)) # process the header parameters # process the form parameters @@ -13449,7 +8879,7 @@ def _get_traces_experimental_serialize( return self.api_client.param_serialize( method='GET', - resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, @@ -13466,11 +8896,14 @@ def _get_traces_experimental_serialize( @validate_call - def remove_tag_from_aligned_feature_experimental( + def get_structure_candidates_paged( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13483,17 +8916,23 @@ def remove_tag_from_aligned_feature_experimental( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space + ) -> PagedModelStructureCandidateFormula: + """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) to delete tag from. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13516,10 +8955,13 @@ def remove_tag_from_aligned_feature_experimental( :return: Returns the result object. """ # noqa: E501 - _param = self._remove_tag_from_aligned_feature_experimental_serialize( + _param = self._get_structure_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - tag_name=tag_name, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13527,7 +8969,7 @@ def remove_tag_from_aligned_feature_experimental( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -13541,11 +8983,14 @@ def remove_tag_from_aligned_feature_experimental( @validate_call - def remove_tag_from_aligned_feature_experimental_with_http_info( + def get_structure_candidates_paged_with_http_info( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13558,17 +9003,23 @@ def remove_tag_from_aligned_feature_experimental_with_http_info( _content_type: Optional[StrictStr] = None, _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space + ) -> ApiResponse[PagedModelStructureCandidateFormula]: + """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) to delete tag from. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13591,10 +9042,13 @@ def remove_tag_from_aligned_feature_experimental_with_http_info( :return: Returns the result object. """ # noqa: E501 - _param = self._remove_tag_from_aligned_feature_experimental_serialize( + _param = self._get_structure_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - tag_name=tag_name, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13602,7 +9056,7 @@ def remove_tag_from_aligned_feature_experimental_with_http_info( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -13616,11 +9070,14 @@ def remove_tag_from_aligned_feature_experimental_with_http_info( @validate_call - def remove_tag_from_aligned_feature_experimental_without_preload_content( + def get_structure_candidates_paged_without_preload_content( self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], + project_id: Annotated[StrictStr, Field(description="project-space to read from.")], + aligned_feature_id: Annotated[StrictStr, Field(description="feature (aligned over runs) the structure candidates belong to.")], + page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, + size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, + sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, + opt_fields: Annotated[Optional[List[Optional[StructureCandidateOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ None, Annotated[StrictFloat, Field(gt=0)], @@ -13634,16 +9091,22 @@ def remove_tag_from_aligned_feature_experimental_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space + """Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. + Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links. - :param project_id: project-space to delete from. (required) + :param project_id: project-space to read from. (required) :type project_id: str - :param aligned_feature_id: feature (aligned over runs) to delete tag from. (required) + :param aligned_feature_id: feature (aligned over runs) the structure candidates belong to. (required) :type aligned_feature_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str + :param page: Zero-based page index (0..N) + :type page: int + :param size: The size of the page to be returned + :type size: int + :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. + :type sort: List[str] + :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. + :type opt_fields: List[StructureCandidateOptField] :param _request_timeout: timeout setting for this request. If one number provided, it will be total request timeout. It can also be a pair (tuple) of @@ -13666,10 +9129,13 @@ def remove_tag_from_aligned_feature_experimental_without_preload_content( :return: Returns the result object. """ # noqa: E501 - _param = self._remove_tag_from_aligned_feature_experimental_serialize( + _param = self._get_structure_candidates_paged_serialize( project_id=project_id, aligned_feature_id=aligned_feature_id, - tag_name=tag_name, + page=page, + size=size, + sort=sort, + opt_fields=opt_fields, _request_auth=_request_auth, _content_type=_content_type, _headers=_headers, @@ -13677,7 +9143,7 @@ def remove_tag_from_aligned_feature_experimental_without_preload_content( ) _response_types_map: Dict[str, Optional[str]] = { - '200': None, + '200': "PagedModelStructureCandidateFormula", } response_data = self.api_client.call_api( *_param, @@ -13686,11 +9152,14 @@ def remove_tag_from_aligned_feature_experimental_without_preload_content( return response_data.response - def _remove_tag_from_aligned_feature_experimental_serialize( + def _get_structure_candidates_paged_serialize( self, project_id, aligned_feature_id, - tag_name, + page, + size, + sort, + opt_fields, _request_auth, _content_type, _headers, @@ -13700,6 +9169,8 @@ def _remove_tag_from_aligned_feature_experimental_serialize( _host = None _collection_formats: Dict[str, str] = { + 'sort': 'multi', + 'optFields': 'multi', } _path_params: Dict[str, str] = {} @@ -13716,14 +9187,35 @@ def _remove_tag_from_aligned_feature_experimental_serialize( _path_params['projectId'] = project_id if aligned_feature_id is not None: _path_params['alignedFeatureId'] = aligned_feature_id - if tag_name is not None: - _path_params['tagName'] = tag_name # process the query parameters + if page is not None: + + _query_params.append(('page', page)) + + if size is not None: + + _query_params.append(('size', size)) + + if sort is not None: + + _query_params.append(('sort', sort)) + + if opt_fields is not None: + + _query_params.append(('optFields', opt_fields)) + # process the header parameters # process the form parameters # process the body parameter + # set the HTTP header `Accept` + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] + ) # authentication setting @@ -13731,8 +9223,8 @@ def _remove_tag_from_aligned_feature_experimental_serialize( ] return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName}', + method='GET', + resource_path='/api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page', path_params=_path_params, query_params=_query_params, header_params=_header_params, diff --git a/client-api_python/generated/PySirius/api/projects_api.py b/client-api_python/generated/PySirius/api/projects_api.py index 506ca817..3ec8d73f 100644 --- a/client-api_python/generated/PySirius/api/projects_api.py +++ b/client-api_python/generated/PySirius/api/projects_api.py @@ -1959,7 +1959,7 @@ def _get_projects_serialize( def import_ms_run_data( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, _request_timeout: Union[ None, @@ -1980,7 +1980,7 @@ def import_ms_run_data( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2034,7 +2034,7 @@ def import_ms_run_data( def import_ms_run_data_with_http_info( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, _request_timeout: Union[ None, @@ -2055,7 +2055,7 @@ def import_ms_run_data_with_http_info( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2109,7 +2109,7 @@ def import_ms_run_data_with_http_info( def import_ms_run_data_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, _request_timeout: Union[ None, @@ -2130,7 +2130,7 @@ def import_ms_run_data_without_preload_content( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2272,7 +2272,7 @@ def _import_ms_run_data_serialize( def import_ms_run_data_as_job( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="Set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ @@ -2294,7 +2294,7 @@ def import_ms_run_data_as_job( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2351,7 +2351,7 @@ def import_ms_run_data_as_job( def import_ms_run_data_as_job_with_http_info( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="Set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ @@ -2373,7 +2373,7 @@ def import_ms_run_data_as_job_with_http_info( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2430,7 +2430,7 @@ def import_ms_run_data_as_job_with_http_info( def import_ms_run_data_as_job_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="Project-space to import into.")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="Files to import into project.")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], parameters: LcmsSubmissionParameters, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="Set of optional fields to be included. Use 'none' only to override defaults.")] = None, _request_timeout: Union[ @@ -2452,7 +2452,7 @@ def import_ms_run_data_as_job_without_preload_content( :param project_id: Project-space to import into. (required) :type project_id: str - :param input_files: Files to import into project. (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param parameters: (required) :type parameters: LcmsSubmissionParameters @@ -2926,7 +2926,7 @@ def _import_preprocessed_data_serialize( def import_preprocessed_data_as_job( self, project_id: Annotated[StrictStr, Field(description="project-space to import into.")], - input_files: List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], ignore_formulas: Optional[StrictBool] = None, allow_ms1_only: Optional[StrictBool] = None, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, @@ -2949,7 +2949,7 @@ def import_preprocessed_data_as_job( :param project_id: project-space to import into. (required) :type project_id: str - :param input_files: (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param ignore_formulas: :type ignore_formulas: bool @@ -3009,7 +3009,7 @@ def import_preprocessed_data_as_job( def import_preprocessed_data_as_job_with_http_info( self, project_id: Annotated[StrictStr, Field(description="project-space to import into.")], - input_files: List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], ignore_formulas: Optional[StrictBool] = None, allow_ms1_only: Optional[StrictBool] = None, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, @@ -3032,7 +3032,7 @@ def import_preprocessed_data_as_job_with_http_info( :param project_id: project-space to import into. (required) :type project_id: str - :param input_files: (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param ignore_formulas: :type ignore_formulas: bool @@ -3092,7 +3092,7 @@ def import_preprocessed_data_as_job_with_http_info( def import_preprocessed_data_as_job_without_preload_content( self, project_id: Annotated[StrictStr, Field(description="project-space to import into.")], - input_files: List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], ignore_formulas: Optional[StrictBool] = None, allow_ms1_only: Optional[StrictBool] = None, opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, @@ -3115,7 +3115,7 @@ def import_preprocessed_data_as_job_without_preload_content( :param project_id: project-space to import into. (required) :type project_id: str - :param input_files: (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param ignore_formulas: :type ignore_formulas: bool diff --git a/client-api_python/generated/PySirius/api/runs_api.py b/client-api_python/generated/PySirius/api/runs_api.py deleted file mode 100644 index a0cadfba..00000000 --- a/client-api_python/generated/PySirius/api/runs_api.py +++ /dev/null @@ -1,2528 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - -import warnings -from pydantic import validate_call, Field, StrictFloat, StrictStr, StrictInt -from typing import Any, Dict, List, Optional, Tuple, Union -from typing_extensions import Annotated - -from pydantic import Field, StrictStr -from typing import List, Optional -from typing_extensions import Annotated -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.paged_model_run import PagedModelRun -from PySirius.models.run import Run -from PySirius.models.run_opt_field import RunOptField -from PySirius.models.sample_type_fold_change_request import SampleTypeFoldChangeRequest -from PySirius.models.tag import Tag - -from PySirius.api_client import ApiClient, RequestSerialized -from PySirius.api_response import ApiResponse -from PySirius.rest import RESTResponseType - - -class RunsApi: - """NOTE: This class is auto generated by OpenAPI Generator - Ref: https://openapi-generator.tech - - Do not edit the class manually. - """ - - def __init__(self, api_client=None) -> None: - if api_client is None: - api_client = ApiClient.get_default() - self.api_client = api_client - - - @validate_call - def add_tags_to_run_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - run_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[Tag]: - """[EXPERIMENTAL] Add tags to a run in the project - - [EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param run_id: run to add tags to. (required) - :type run_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_tags_to_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag=tag, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def add_tags_to_run_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - run_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[Tag]]: - """[EXPERIMENTAL] Add tags to a run in the project - - [EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param run_id: run to add tags to. (required) - :type run_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_tags_to_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag=tag, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def add_tags_to_run_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - run_id: Annotated[StrictStr, Field(description="run to add tags to.")], - tag: Annotated[List[Tag], Field(description="tags to add.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Add tags to a run in the project - - [EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param run_id: run to add tags to. (required) - :type run_id: str - :param tag: tags to add. (required) - :type tag: List[Tag] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_tags_to_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag=tag, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[Tag]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _add_tags_to_run_experimental_serialize( - self, - project_id, - run_id, - tag, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'Tag': '', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if run_id is not None: - _path_params['runId'] = run_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - if tag is not None: - _body_params = tag - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) - ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/runs/tags/{runId}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def compute_fold_change_for_blank_subtraction( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - sample_type_fold_change_request: Annotated[SampleTypeFoldChangeRequest, Field(description="request with lists of run IDs that are sample, blank, and control runs")], - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> Job: - """**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter - - **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter.
This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
- - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param sample_type_fold_change_request: request with lists of run IDs that are sample, blank, and control runs (required) - :type sample_type_fold_change_request: SampleTypeFoldChangeRequest - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_fold_change_for_blank_subtraction_serialize( - project_id=project_id, - sample_type_fold_change_request=sample_type_fold_change_request, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def compute_fold_change_for_blank_subtraction_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - sample_type_fold_change_request: Annotated[SampleTypeFoldChangeRequest, Field(description="request with lists of run IDs that are sample, blank, and control runs")], - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[Job]: - """**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter - - **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter.This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
- - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param sample_type_fold_change_request: request with lists of run IDs that are sample, blank, and control runs (required) - :type sample_type_fold_change_request: SampleTypeFoldChangeRequest - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_fold_change_for_blank_subtraction_serialize( - project_id=project_id, - sample_type_fold_change_request=sample_type_fold_change_request, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def compute_fold_change_for_blank_subtraction_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to compute the fold change in.")], - sample_type_fold_change_request: Annotated[SampleTypeFoldChangeRequest, Field(description="request with lists of run IDs that are sample, blank, and control runs")], - opt_fields: Annotated[Optional[List[Optional[JobOptField]]], Field(description="job opt fields.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter - - **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter.This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
- - :param project_id: project-space to compute the fold change in. (required) - :type project_id: str - :param sample_type_fold_change_request: request with lists of run IDs that are sample, blank, and control runs (required) - :type sample_type_fold_change_request: SampleTypeFoldChangeRequest - :param opt_fields: job opt fields. - :type opt_fields: List[JobOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._compute_fold_change_for_blank_subtraction_serialize( - project_id=project_id, - sample_type_fold_change_request=sample_type_fold_change_request, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Job", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _compute_fold_change_for_blank_subtraction_serialize( - self, - project_id, - sample_type_fold_change_request, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - if sample_type_fold_change_request is not None: - _body_params = sample_type_fold_change_request - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) - ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/runs/blanksubtract/compute', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_run_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - run_id: Annotated[StrictStr, Field(description="identifier of run to access.")], - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> Run: - """[EXPERIMENTAL] Get run with the given identifier from the specified project-space - - [EXPERIMENTAL] Get run with the given identifier from the specified project-space.[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param run_id: identifier of run to access. (required) - :type run_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Run", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_run_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - run_id: Annotated[StrictStr, Field(description="identifier of run to access.")], - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[Run]: - """[EXPERIMENTAL] Get run with the given identifier from the specified project-space - - [EXPERIMENTAL] Get run with the given identifier from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param run_id: identifier of run to access. (required) - :type run_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Run", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_run_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - run_id: Annotated[StrictStr, Field(description="identifier of run to access.")], - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get run with the given identifier from the specified project-space - - [EXPERIMENTAL] Get run with the given identifier from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param run_id: identifier of run to access. (required) - :type run_id: str - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "Run", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_run_experimental_serialize( - self, - project_id, - run_id, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if run_id is not None: - _path_params['runId'] = run_id - # process the query parameters - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/runs/{runId}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_run_page_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelRun: - """[EXPERIMENTAL] Get all available runs in the given project-space - - [EXPERIMENTAL] Get all available runs in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_page_experimental_serialize( - project_id=project_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_run_page_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelRun]: - """[EXPERIMENTAL] Get all available runs in the given project-space - - [EXPERIMENTAL] Get all available runs in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_page_experimental_serialize( - project_id=project_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_run_page_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get all available runs in the given project-space - - [EXPERIMENTAL] Get all available runs in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_run_page_experimental_serialize( - project_id=project_id, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_run_page_experimental_serialize( - self, - project_id, - page, - size, - sort, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/runs/page', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_runs_by_group_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelRun: - """[EXPERIMENTAL] Get runs by tag group - - [EXPERIMENTAL] Get runs by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_runs_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_runs_by_group_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[PagedModelRun]: - """[EXPERIMENTAL] Get runs by tag group - - [EXPERIMENTAL] Get runs by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_runs_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_runs_by_group_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="tag group name.")], - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get runs by tag group - - [EXPERIMENTAL] Get runs by tag group.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: tag group name. (required) - :type group_name: str - :param page: Zero-based page index (0..N) - :type page: int - :param size: The size of the page to be returned - :type size: int - :param sort: Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. - :type sort: List[str] - :param opt_fields: set of optional fields to be included. Use 'none' only to override defaults. - :type opt_fields: List[RunOptField] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_runs_by_group_experimental_serialize( - project_id=project_id, - group_name=group_name, - page=page, - size=size, - sort=sort, - opt_fields=opt_fields, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "PagedModelRun", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_runs_by_group_experimental_serialize( - self, - project_id, - group_name, - page, - size, - sort, - opt_fields, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'sort': 'multi', - 'optFields': 'multi', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if group_name is not None: - - _query_params.append(('groupName', group_name)) - - if page is not None: - - _query_params.append(('page', page)) - - if size is not None: - - _query_params.append(('size', size)) - - if sort is not None: - - _query_params.append(('sort', sort)) - - if opt_fields is not None: - - _query_params.append(('optFields', opt_fields)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/runs/grouped', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_runs_by_tag_experimental( - self, - project_id: Annotated[StrictStr, Field(description="project space to get runs from.")], - filter: Annotated[Optional[StrictStr], Field(description="tag filter.")] = None, - page: Annotated[Optional[Annotated[int, Field(strict=True, ge=0)]], Field(description="Zero-based page index (0..N)")] = None, - size: Annotated[Optional[Annotated[int, Field(strict=True, ge=1)]], Field(description="The size of the page to be returned")] = None, - sort: Annotated[Optional[List[StrictStr]], Field(description="Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported.")] = None, - opt_fields: Annotated[Optional[List[Optional[RunOptField]]], Field(description="set of optional fields to be included. Use 'none' only to override defaults.")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> PagedModelRun: - """[EXPERIMENTAL] Get runs by tag - - [EXPERIMENTAL] Get runs by tag.
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
The filter string must contain one or more clauses. A clause is prefÃxed by a field name.
Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value The format of the date type is yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
A clause may be:
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param run_id: run to delete tag from. (required) - :type run_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def remove_tag_from_run_experimental_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - run_id: Annotated[StrictStr, Field(description="run to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space - - [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param run_id: run to delete tag from. (required) - :type run_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def remove_tag_from_run_experimental_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - run_id: Annotated[StrictStr, Field(description="run to delete tag from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space - - [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param run_id: run to delete tag from. (required) - :type run_id: str - :param tag_name: name of the tag to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._remove_tag_from_run_experimental_serialize( - project_id=project_id, - run_id=run_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _remove_tag_from_run_experimental_serialize( - self, - project_id, - run_id, - tag_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if run_id is not None: - _path_params['runId'] = run_id - if tag_name is not None: - _path_params['tagName'] = tag_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/runs/tags/{runId}/{tagName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - diff --git a/client-api_python/generated/PySirius/api/searchable_databases_api.py b/client-api_python/generated/PySirius/api/searchable_databases_api.py index b50242ec..2dea322c 100644 --- a/client-api_python/generated/PySirius/api/searchable_databases_api.py +++ b/client-api_python/generated/PySirius/api/searchable_databases_api.py @@ -56,7 +56,7 @@ def add_databases( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> List[SearchableDatabase]: - """(Deprecated) DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. + """(Deprecated) [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. :param request_body: (required) @@ -123,7 +123,7 @@ def add_databases_with_http_info( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> ApiResponse[List[SearchableDatabase]]: - """(Deprecated) DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. + """(Deprecated) [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. :param request_body: (required) @@ -190,7 +190,7 @@ def add_databases_without_preload_content( _headers: Optional[Dict[StrictStr, Any]] = None, _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, ) -> RESTResponseType: - """(Deprecated) DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. + """(Deprecated) [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. :param request_body: (required) @@ -1687,7 +1687,7 @@ def _get_included_databases_serialize( def import_into_database( self, database_id: Annotated[StrictStr, Field(description="database to import into")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to be imported")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], buffer_size: Optional[StrictInt] = None, bio_transformer_parameters: Optional[BioTransformerParameters] = None, _request_timeout: Union[ @@ -1709,7 +1709,7 @@ def import_into_database( :param database_id: database to import into (required) :type database_id: str - :param input_files: files to be imported (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param buffer_size: :type buffer_size: int @@ -1766,7 +1766,7 @@ def import_into_database( def import_into_database_with_http_info( self, database_id: Annotated[StrictStr, Field(description="database to import into")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to be imported")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], buffer_size: Optional[StrictInt] = None, bio_transformer_parameters: Optional[BioTransformerParameters] = None, _request_timeout: Union[ @@ -1788,7 +1788,7 @@ def import_into_database_with_http_info( :param database_id: database to import into (required) :type database_id: str - :param input_files: files to be imported (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param buffer_size: :type buffer_size: int @@ -1845,7 +1845,7 @@ def import_into_database_with_http_info( def import_into_database_without_preload_content( self, database_id: Annotated[StrictStr, Field(description="database to import into")], - input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to be imported")], + input_files: Annotated[List[Union[StrictBytes, StrictStr, Tuple[StrictStr, StrictBytes]]], Field(description="files to import into project")], buffer_size: Optional[StrictInt] = None, bio_transformer_parameters: Optional[BioTransformerParameters] = None, _request_timeout: Union[ @@ -1867,7 +1867,7 @@ def import_into_database_without_preload_content( :param database_id: database to import into (required) :type database_id: str - :param input_files: files to be imported (required) + :param input_files: files to import into project (required) :type input_files: List[bytearray] :param buffer_size: :type buffer_size: int diff --git a/client-api_python/generated/PySirius/api/tags_api.py b/client-api_python/generated/PySirius/api/tags_api.py deleted file mode 100644 index 15a380d8..00000000 --- a/client-api_python/generated/PySirius/api/tags_api.py +++ /dev/null @@ -1,2581 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - -import warnings -from pydantic import validate_call, Field, StrictFloat, StrictStr, StrictInt -from typing import Any, Dict, List, Optional, Tuple, Union -from typing_extensions import Annotated - -from pydantic import Field, StrictStr -from typing import Any, Dict, List, Optional -from typing_extensions import Annotated -from PySirius.models.tag_definition import TagDefinition -from PySirius.models.tag_definition_import import TagDefinitionImport -from PySirius.models.tag_group import TagGroup - -from PySirius.api_client import ApiClient, RequestSerialized -from PySirius.api_response import ApiResponse -from PySirius.rest import RESTResponseType - - -class TagsApi: - """NOTE: This class is auto generated by OpenAPI Generator - Ref: https://openapi-generator.tech - - Do not edit the class manually. - """ - - def __init__(self, api_client=None) -> None: - if api_client is None: - api_client = ApiClient.get_default() - self.api_client = api_client - - - @validate_call - def add_group( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - group_name: Annotated[StrictStr, Field(description="name of the new group")], - filter: Annotated[StrictStr, Field(description="filter query to create the group")], - type: Annotated[StrictStr, Field(description="type of the group")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TagGroup: - """[EXPERIMENTAL] Group tags in the project - - [EXPERIMENTAL] Group tags in the project. The group name must not exist in the project.
See /tagged for filter syntax.
See /tagged for filter syntax.
See /tagged for filter syntax.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_name: the tag definition to add the values to (required) - :type tag_name: str - :param request_body: (required) - :type request_body: List[object] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_possible_values_to_tag_definition_serialize( - project_id=project_id, - tag_name=tag_name, - request_body=request_body, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def add_possible_values_to_tag_definition_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - tag_name: Annotated[StrictStr, Field(description="the tag definition to add the values to")], - request_body: List[Dict[str, Any]], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TagDefinition]: - """[EXPERIMENTAL] Add a possible value to the tag definition in the project - - [EXPERIMENTAL] Add a possible value to the tag definition in the project.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_name: the tag definition to add the values to (required) - :type tag_name: str - :param request_body: (required) - :type request_body: List[object] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_possible_values_to_tag_definition_serialize( - project_id=project_id, - tag_name=tag_name, - request_body=request_body, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def add_possible_values_to_tag_definition_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - tag_name: Annotated[StrictStr, Field(description="the tag definition to add the values to")], - request_body: List[Dict[str, Any]], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Add a possible value to the tag definition in the project - - [EXPERIMENTAL] Add a possible value to the tag definition in the project.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_name: the tag definition to add the values to (required) - :type tag_name: str - :param request_body: (required) - :type request_body: List[object] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._add_possible_values_to_tag_definition_serialize( - project_id=project_id, - tag_name=tag_name, - request_body=request_body, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _add_possible_values_to_tag_definition_serialize( - self, - project_id, - tag_name, - request_body, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'request_body': '', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if tag_name is not None: - _path_params['tagName'] = tag_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - if request_body is not None: - _body_params = request_body - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) - ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PATCH', - resource_path='/api/projects/{projectId}/tags/{tagName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def create_tags( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - tag_definition_import: Annotated[List[TagDefinitionImport], Field(description="the tag definitions to be created")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[TagDefinition]: - """[EXPERIMENTAL] Add tags to the project - - [EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_definition_import: the tag definitions to be created (required) - :type tag_definition_import: List[TagDefinitionImport] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._create_tags_serialize( - project_id=project_id, - tag_definition_import=tag_definition_import, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def create_tags_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - tag_definition_import: Annotated[List[TagDefinitionImport], Field(description="the tag definitions to be created")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[TagDefinition]]: - """[EXPERIMENTAL] Add tags to the project - - [EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_definition_import: the tag definitions to be created (required) - :type tag_definition_import: List[TagDefinitionImport] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._create_tags_serialize( - project_id=project_id, - tag_definition_import=tag_definition_import, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def create_tags_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to add to.")], - tag_definition_import: Annotated[List[TagDefinitionImport], Field(description="the tag definitions to be created")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Add tags to the project - - [EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to add to. (required) - :type project_id: str - :param tag_definition_import: the tag definitions to be created (required) - :type tag_definition_import: List[TagDefinitionImport] - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._create_tags_serialize( - project_id=project_id, - tag_definition_import=tag_definition_import, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _create_tags_serialize( - self, - project_id, - tag_definition_import, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - 'TagDefinitionImport': '', - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - if tag_definition_import is not None: - _body_params = tag_definition_import - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - # set the HTTP header `Content-Type` - if _content_type: - _header_params['Content-Type'] = _content_type - else: - _default_content_type = ( - self.api_client.select_header_content_type( - [ - 'application/json' - ] - ) - ) - if _default_content_type is not None: - _header_params['Content-Type'] = _default_content_type - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='PUT', - resource_path='/api/projects/{projectId}/tags', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def delete_group( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="name of group to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: name of group to delete. (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_group_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def delete_group_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="name of group to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: name of group to delete. (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_group_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def delete_group_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - group_name: Annotated[StrictStr, Field(description="name of group to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param group_name: name of group to delete. (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_group_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _delete_group_serialize( - self, - project_id, - group_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if group_name is not None: - _path_params['groupName'] = group_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/groups/{groupName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def delete_tag( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag definition to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> None: - """[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space.
This will also remove all tags belonging to this definition from every tagged entity.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param tag_name: name of the tag definition to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def delete_tag_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag definition to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[None]: - """[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space.This will also remove all tags belonging to this definition from every tagged entity.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param tag_name: name of the tag definition to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def delete_tag_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to delete from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag definition to delete.")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space - - [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space.This will also remove all tags belonging to this definition from every tagged entity.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to delete from. (required) - :type project_id: str - :param tag_name: name of the tag definition to delete. (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._delete_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': None, - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _delete_tag_serialize( - self, - project_id, - tag_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if tag_name is not None: - _path_params['tagName'] = tag_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='DELETE', - resource_path='/api/projects/{projectId}/tags/{tagName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_group_by_name( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_name: Annotated[StrictStr, Field(description="name of the group")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TagGroup: - """[EXPERIMENTAL] Get tag group by name in the given project-space - - [EXPERIMENTAL] Get tag group by name in the given project-space.[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_name: name of the group (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_group_by_name_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagGroup", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_group_by_name_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_name: Annotated[StrictStr, Field(description="name of the group")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TagGroup]: - """[EXPERIMENTAL] Get tag group by name in the given project-space - - [EXPERIMENTAL] Get tag group by name in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_name: name of the group (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_group_by_name_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagGroup", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_group_by_name_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_name: Annotated[StrictStr, Field(description="name of the group")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get tag group by name in the given project-space - - [EXPERIMENTAL] Get tag group by name in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_name: name of the group (required) - :type group_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_group_by_name_serialize( - project_id=project_id, - group_name=group_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagGroup", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_group_by_name_serialize( - self, - project_id, - group_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if group_name is not None: - _path_params['groupName'] = group_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/groups/{groupName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_groups( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_type: Annotated[Optional[StrictStr], Field(description="type of the group")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[TagGroup]: - """[EXPERIMENTAL] Get all tag based groups in the given project-space - - [EXPERIMENTAL] Get all tag based groups in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_type: type of the group - :type group_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_groups_serialize( - project_id=project_id, - group_type=group_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagGroup]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_groups_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_type: Annotated[Optional[StrictStr], Field(description="type of the group")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[TagGroup]]: - """[EXPERIMENTAL] Get all tag based groups in the given project-space - - [EXPERIMENTAL] Get all tag based groups in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_type: type of the group - :type group_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_groups_serialize( - project_id=project_id, - group_type=group_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagGroup]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_groups_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - group_type: Annotated[Optional[StrictStr], Field(description="type of the group")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get all tag based groups in the given project-space - - [EXPERIMENTAL] Get all tag based groups in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param group_type: type of the group - :type group_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_groups_serialize( - project_id=project_id, - group_type=group_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagGroup]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_groups_serialize( - self, - project_id, - group_type, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if group_type is not None: - - _query_params.append(('groupType', group_type)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/groups', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_tag( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> TagDefinition: - """[EXPERIMENTAL] Get tag definition by its name in the given project-space - - [EXPERIMENTAL] Get tag definition by its name in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_name: name of the tag (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_tag_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[TagDefinition]: - """[EXPERIMENTAL] Get tag definition by its name in the given project-space - - [EXPERIMENTAL] Get tag definition by its name in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_name: name of the tag (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_tag_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_name: Annotated[StrictStr, Field(description="name of the tag")], - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get tag definition by its name in the given project-space - - [EXPERIMENTAL] Get tag definition by its name in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_name: name of the tag (required) - :type tag_name: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tag_serialize( - project_id=project_id, - tag_name=tag_name, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "TagDefinition", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_tag_serialize( - self, - project_id, - tag_name, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - if tag_name is not None: - _path_params['tagName'] = tag_name - # process the query parameters - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/tags/{tagName}', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - - - - @validate_call - def get_tags( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_type: Annotated[Optional[StrictStr], Field(description="scope of the tag (optional)")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> List[TagDefinition]: - """[EXPERIMENTAL] Get all tag definitions in the given project-space - - [EXPERIMENTAL] Get all tag definitions in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_type: scope of the tag (optional) - :type tag_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tags_serialize( - project_id=project_id, - tag_type=tag_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ).data - - - @validate_call - def get_tags_with_http_info( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_type: Annotated[Optional[StrictStr], Field(description="scope of the tag (optional)")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> ApiResponse[List[TagDefinition]]: - """[EXPERIMENTAL] Get all tag definitions in the given project-space - - [EXPERIMENTAL] Get all tag definitions in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_type: scope of the tag (optional) - :type tag_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tags_serialize( - project_id=project_id, - tag_type=tag_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - response_data.read() - return self.api_client.response_deserialize( - response_data=response_data, - response_types_map=_response_types_map, - ) - - - @validate_call - def get_tags_without_preload_content( - self, - project_id: Annotated[StrictStr, Field(description="project-space to read from.")], - tag_type: Annotated[Optional[StrictStr], Field(description="scope of the tag (optional)")] = None, - _request_timeout: Union[ - None, - Annotated[StrictFloat, Field(gt=0)], - Tuple[ - Annotated[StrictFloat, Field(gt=0)], - Annotated[StrictFloat, Field(gt=0)] - ] - ] = None, - _request_auth: Optional[Dict[StrictStr, Any]] = None, - _content_type: Optional[StrictStr] = None, - _headers: Optional[Dict[StrictStr, Any]] = None, - _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0, - ) -> RESTResponseType: - """[EXPERIMENTAL] Get all tag definitions in the given project-space - - [EXPERIMENTAL] Get all tag definitions in the given project-space.
[EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - - :param project_id: project-space to read from. (required) - :type project_id: str - :param tag_type: scope of the tag (optional) - :type tag_type: str - :param _request_timeout: timeout setting for this request. If one - number provided, it will be total request - timeout. It can also be a pair (tuple) of - (connection, read) timeouts. - :type _request_timeout: int, tuple(int, int), optional - :param _request_auth: set to override the auth_settings for an a single - request; this effectively ignores the - authentication in the spec for a single request. - :type _request_auth: dict, optional - :param _content_type: force content-type for the request. - :type _content_type: str, Optional - :param _headers: set to override the headers for a single - request; this effectively ignores the headers - in the spec for a single request. - :type _headers: dict, optional - :param _host_index: set to override the host_index for a single - request; this effectively ignores the host_index - in the spec for a single request. - :type _host_index: int, optional - :return: Returns the result object. - """ # noqa: E501 - - _param = self._get_tags_serialize( - project_id=project_id, - tag_type=tag_type, - _request_auth=_request_auth, - _content_type=_content_type, - _headers=_headers, - _host_index=_host_index - ) - - _response_types_map: Dict[str, Optional[str]] = { - '200': "List[TagDefinition]", - } - response_data = self.api_client.call_api( - *_param, - _request_timeout=_request_timeout - ) - return response_data.response - - - def _get_tags_serialize( - self, - project_id, - tag_type, - _request_auth, - _content_type, - _headers, - _host_index, - ) -> RequestSerialized: - - _host = None - - _collection_formats: Dict[str, str] = { - } - - _path_params: Dict[str, str] = {} - _query_params: List[Tuple[str, str]] = [] - _header_params: Dict[str, Optional[str]] = _headers or {} - _form_params: List[Tuple[str, str]] = [] - _files: Dict[ - str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] - ] = {} - _body_params: Optional[bytes] = None - - # process the path parameters - if project_id is not None: - _path_params['projectId'] = project_id - # process the query parameters - if tag_type is not None: - - _query_params.append(('tagType', tag_type)) - - # process the header parameters - # process the form parameters - # process the body parameter - - - # set the HTTP header `Accept` - if 'Accept' not in _header_params: - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) - - - # authentication setting - _auth_settings: List[str] = [ - ] - - return self.api_client.param_serialize( - method='GET', - resource_path='/api/projects/{projectId}/tags', - path_params=_path_params, - query_params=_query_params, - header_params=_header_params, - body=_body_params, - post_params=_form_params, - files=_files, - auth_settings=_auth_settings, - collection_formats=_collection_formats, - _host=_host, - _request_auth=_request_auth - ) - - diff --git a/client-api_python/generated/PySirius/api_client.py b/client-api_python/generated/PySirius/api_client.py index e041ec92..7444e089 100644 --- a/client-api_python/generated/PySirius/api_client.py +++ b/client-api_python/generated/PySirius/api_client.py @@ -89,7 +89,7 @@ def __init__( self.default_headers[header_name] = header_value self.cookie = cookie # Set default User-Agent. - self.user_agent = 'OpenAPI-Generator/6.3.3/python' + self.user_agent = 'OpenAPI-Generator/6.3.4/python' self.client_side_validation = configuration.client_side_validation def __enter__(self): diff --git a/client-api_python/generated/PySirius/configuration.py b/client-api_python/generated/PySirius/configuration.py index 76401975..23d7581e 100644 --- a/client-api_python/generated/PySirius/configuration.py +++ b/client-api_python/generated/PySirius/configuration.py @@ -499,7 +499,7 @@ def to_debug_report(self) -> str: "OS: {env}\n"\ "Python Version: {pyversion}\n"\ "Version of the API: 3.1\n"\ - "SDK Package Version: 6.3.3".\ + "SDK Package Version: 6.3.4".\ format(env=sys.platform, pyversion=sys.version) def get_host_settings(self) -> List[HostSetting]: diff --git a/client-api_python/generated/PySirius/models/__init__.py b/client-api_python/generated/PySirius/models/__init__.py index b9e10406..ba6cc11a 100644 --- a/client-api_python/generated/PySirius/models/__init__.py +++ b/client-api_python/generated/PySirius/models/__init__.py @@ -13,19 +13,13 @@ # import models into model package from PySirius.models.account_credentials import AccountCredentials from PySirius.models.account_info import AccountInfo -from PySirius.models.adduct_edge_experimental import AdductEdgeExperimental -from PySirius.models.adduct_network_experimental import AdductNetworkExperimental -from PySirius.models.adduct_node_experimental import AdductNodeExperimental -from PySirius.models.aggregation_type import AggregationType from PySirius.models.aligned_feature import AlignedFeature from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField -from PySirius.models.aligned_feature_quality_experimental import AlignedFeatureQualityExperimental from PySirius.models.allowed_features import AllowedFeatures from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData from PySirius.models.annotated_peak import AnnotatedPeak from PySirius.models.annotated_spectrum import AnnotatedSpectrum from PySirius.models.api_version import ApiVersion -from PySirius.models.axes import Axes from PySirius.models.background_computations_state_event import BackgroundComputationsStateEvent from PySirius.models.basic_spectrum import BasicSpectrum from PySirius.models.binary_fingerprint import BinaryFingerprint @@ -33,7 +27,6 @@ from PySirius.models.bio_transformer_sequence_step import BioTransformerSequenceStep from PySirius.models.canopus import Canopus from PySirius.models.canopus_prediction import CanopusPrediction -from PySirius.models.category import Category from PySirius.models.compound import Compound from PySirius.models.compound_class import CompoundClass from PySirius.models.compound_class_type import CompoundClassType @@ -58,7 +51,6 @@ from PySirius.models.feature_annotations import FeatureAnnotations from PySirius.models.feature_import import FeatureImport from PySirius.models.fingerprint_prediction import FingerprintPrediction -from PySirius.models.fold_change import FoldChange from PySirius.models.formula_candidate import FormulaCandidate from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField from PySirius.models.fragment_node import FragmentNode @@ -88,7 +80,6 @@ from PySirius.models.paged_model_compound import PagedModelCompound from PySirius.models.paged_model_formula_candidate import PagedModelFormulaCandidate from PySirius.models.paged_model_job import PagedModelJob -from PySirius.models.paged_model_run import PagedModelRun from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored @@ -100,14 +91,6 @@ from PySirius.models.project_info import ProjectInfo from PySirius.models.project_info_opt_field import ProjectInfoOptField from PySirius.models.project_type import ProjectType -from PySirius.models.quality_item import QualityItem -from PySirius.models.quality_weight import QualityWeight -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_row_type import QuantRowType -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.models.run import Run -from PySirius.models.run_opt_field import RunOptField -from PySirius.models.sample_type_fold_change_request import SampleTypeFoldChangeRequest from PySirius.models.searchable_database import SearchableDatabase from PySirius.models.searchable_database_parameters import SearchableDatabaseParameters from PySirius.models.security_context import SecurityContext @@ -123,8 +106,6 @@ from PySirius.models.spectral_matching_type import SpectralMatchingType from PySirius.models.spectrum_annotation import SpectrumAnnotation from PySirius.models.spectrum_type import SpectrumType -from PySirius.models.statistics_table import StatisticsTable -from PySirius.models.statistics_type import StatisticsType from PySirius.models.stored_job_submission import StoredJobSubmission from PySirius.models.structure_candidate import StructureCandidate from PySirius.models.structure_candidate_formula import StructureCandidateFormula @@ -134,17 +115,9 @@ from PySirius.models.subscription import Subscription from PySirius.models.subscription_consumables import SubscriptionConsumables from PySirius.models.tag import Tag -from PySirius.models.tag_definition import TagDefinition -from PySirius.models.tag_definition_import import TagDefinitionImport -from PySirius.models.tag_group import TagGroup from PySirius.models.term import Term from PySirius.models.timeout import Timeout -from PySirius.models.trace_annotation_experimental import TraceAnnotationExperimental -from PySirius.models.trace_annotation_type_experimental import TraceAnnotationTypeExperimental -from PySirius.models.trace_experimental import TraceExperimental -from PySirius.models.trace_set_experimental import TraceSetExperimental from PySirius.models.use_heuristic import UseHeuristic -from PySirius.models.value_type import ValueType from PySirius.models.web_server_namespace import WebServerNamespace from PySirius.models.zodiac import Zodiac from PySirius.models.zodiac_analogue_nodes import ZodiacAnalogueNodes diff --git a/client-api_python/generated/PySirius/models/adduct_edge_experimental.py b/client-api_python/generated/PySirius/models/adduct_edge_experimental.py deleted file mode 100644 index 90d9fc77..00000000 --- a/client-api_python/generated/PySirius/models/adduct_edge_experimental.py +++ /dev/null @@ -1,101 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from typing import Optional, Set -from typing_extensions import Self - -class AdductEdgeExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - mz_delta: Optional[float] = Field(default=None, alias="mzDelta") - annotation: Optional[StrictStr] = None - var_from: Optional[StrictInt] = Field(default=None, alias="from") - to: Optional[StrictInt] = None - merged_correlation: Optional[float] = Field(default=None, alias="mergedCorrelation") - representative_correlation: Optional[float] = Field(default=None, alias="representativeCorrelation") - ms2cosine: Optional[float] = None - pvalue: Optional[float] = None - intensity_ratio_score: Optional[float] = Field(default=None, alias="intensityRatioScore") - __properties: ClassVar[List[str]] = ["mzDelta", "annotation", "from", "to", "mergedCorrelation", "representativeCorrelation", "ms2cosine", "pvalue", "intensityRatioScore"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of AdductEdgeExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of AdductEdgeExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "mzDelta": obj.get("mzDelta"), - "annotation": obj.get("annotation"), - "from": obj.get("from"), - "to": obj.get("to"), - "mergedCorrelation": obj.get("mergedCorrelation"), - "representativeCorrelation": obj.get("representativeCorrelation"), - "ms2cosine": obj.get("ms2cosine"), - "pvalue": obj.get("pvalue"), - "intensityRatioScore": obj.get("intensityRatioScore") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/adduct_network_experimental.py b/client-api_python/generated/PySirius/models/adduct_network_experimental.py deleted file mode 100644 index ee62d773..00000000 --- a/client-api_python/generated/PySirius/models/adduct_network_experimental.py +++ /dev/null @@ -1,103 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.adduct_edge_experimental import AdductEdgeExperimental -from PySirius.models.adduct_node_experimental import AdductNodeExperimental -from typing import Optional, Set -from typing_extensions import Self - -class AdductNetworkExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - nodes: Optional[List[AdductNodeExperimental]] = None - edges: Optional[List[AdductEdgeExperimental]] = None - __properties: ClassVar[List[str]] = ["nodes", "edges"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of AdductNetworkExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each item in nodes (list) - _items = [] - if self.nodes: - for _item_nodes in self.nodes: - if _item_nodes: - _items.append(_item_nodes.to_dict()) - _dict['nodes'] = _items - # override the default output from pydantic by calling `to_dict()` of each item in edges (list) - _items = [] - if self.edges: - for _item_edges in self.edges: - if _item_edges: - _items.append(_item_edges.to_dict()) - _dict['edges'] = _items - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of AdductNetworkExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "nodes": [AdductNodeExperimental.from_dict(_item) for _item in obj["nodes"]] if obj.get("nodes") is not None else None, - "edges": [AdductEdgeExperimental.from_dict(_item) for _item in obj["edges"]] if obj.get("edges") is not None else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/adduct_node_experimental.py b/client-api_python/generated/PySirius/models/adduct_node_experimental.py deleted file mode 100644 index e81fc02b..00000000 --- a/client-api_python/generated/PySirius/models/adduct_node_experimental.py +++ /dev/null @@ -1,89 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from typing import Optional, Set -from typing_extensions import Self - -class AdductNodeExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - aligned_feature_id: Optional[StrictStr] = Field(default=None, alias="alignedFeatureId") - mz: Optional[float] = None - adduct_annotations: Optional[Dict[str, float]] = Field(default=None, alias="adductAnnotations") - __properties: ClassVar[List[str]] = ["alignedFeatureId", "mz", "adductAnnotations"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of AdductNodeExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of AdductNodeExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "alignedFeatureId": obj.get("alignedFeatureId"), - "mz": obj.get("mz"), - "adductAnnotations": obj.get("adductAnnotations") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/aggregation_type.py b/client-api_python/generated/PySirius/models/aggregation_type.py deleted file mode 100644 index f22d6cfa..00000000 --- a/client-api_python/generated/PySirius/models/aggregation_type.py +++ /dev/null @@ -1,36 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class AggregationType(str, Enum): - """ - AggregationType - """ - - """ - allowed enum values - """ - AVG = 'AVG' - MIN = 'MIN' - MAX = 'MAX' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of AggregationType from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/aligned_feature.py b/client-api_python/generated/PySirius/models/aligned_feature.py index 0f4e0a7e..73df3fe4 100644 --- a/client-api_python/generated/PySirius/models/aligned_feature.py +++ b/client-api_python/generated/PySirius/models/aligned_feature.py @@ -47,7 +47,7 @@ class AlignedFeature(BaseModel): top_annotations_de_novo: Optional[FeatureAnnotations] = Field(default=None, alias="topAnnotationsDeNovo") computing: Optional[StrictBool] = Field(default=None, description="Write lock for this feature. If the feature is locked no write operations are possible. True if any computation is modifying this feature or its results") computed_tools: Optional[ComputedSubtools] = Field(default=None, alias="computedTools") - tags: Optional[Dict[str, Tag]] = Field(default=None, description="Key: tagName, value: tag") + tags: Optional[Dict[str, Optional[Tag]]] = Field(default=None, description="Key: tagName, value: tag") __properties: ClassVar[List[str]] = ["alignedFeatureId", "compoundId", "name", "externalFeatureId", "ionMass", "charge", "detectedAdducts", "rtStartSeconds", "rtEndSeconds", "rtApexSeconds", "quality", "hasMs1", "hasMsMs", "msData", "topAnnotations", "topAnnotationsDeNovo", "computing", "computedTools", "tags"] model_config = ConfigDict( diff --git a/client-api_python/generated/PySirius/models/aligned_feature_quality_experimental.py b/client-api_python/generated/PySirius/models/aligned_feature_quality_experimental.py deleted file mode 100644 index 39577290..00000000 --- a/client-api_python/generated/PySirius/models/aligned_feature_quality_experimental.py +++ /dev/null @@ -1,108 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.category import Category -from PySirius.models.data_quality import DataQuality -from typing import Optional, Set -from typing_extensions import Self - -class AlignedFeatureQualityExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - aligned_feature_id: StrictStr = Field(description="Id of the feature (aligned over runs) this quality information belongs to.", alias="alignedFeatureId") - overall_quality: Optional[DataQuality] = Field(alias="overallQuality") - categories: Dict[str, Category] = Field(description="Contains all pre-computation quality information that belong to this feature (aligned over runs), such as information about the quality of the peak shape, MS2 spectrum etc.,") - __properties: ClassVar[List[str]] = ["alignedFeatureId", "overallQuality", "categories"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of AlignedFeatureQualityExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each value in categories (dict) - _field_dict = {} - if self.categories: - for _key_categories in self.categories: - if self.categories[_key_categories]: - _field_dict[_key_categories] = self.categories[_key_categories].to_dict() - _dict['categories'] = _field_dict - # set to None if overall_quality (nullable) is None - # and model_fields_set contains the field - if self.overall_quality is None and "overall_quality" in self.model_fields_set: - _dict['overallQuality'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of AlignedFeatureQualityExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "alignedFeatureId": obj.get("alignedFeatureId"), - "overallQuality": obj.get("overallQuality"), - "categories": dict( - (_k, Category.from_dict(_v)) - for _k, _v in obj["categories"].items() - ) - if obj.get("categories") is not None - else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/axes.py b/client-api_python/generated/PySirius/models/axes.py deleted file mode 100644 index 1534b5eb..00000000 --- a/client-api_python/generated/PySirius/models/axes.py +++ /dev/null @@ -1,89 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from typing import Optional, Set -from typing_extensions import Self - -class Axes(BaseModel): - """ - Axes - """ # noqa: E501 - scan_number: Optional[List[StrictInt]] = Field(default=None, alias="scanNumber") - scan_ids: Optional[List[StrictStr]] = Field(default=None, alias="scanIds") - retention_time_in_seconds: Optional[List[float]] = Field(default=None, alias="retentionTimeInSeconds") - __properties: ClassVar[List[str]] = ["scanNumber", "scanIds", "retentionTimeInSeconds"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of Axes from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of Axes from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "scanNumber": obj.get("scanNumber"), - "scanIds": obj.get("scanIds"), - "retentionTimeInSeconds": obj.get("retentionTimeInSeconds") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/category.py b/client-api_python/generated/PySirius/models/category.py deleted file mode 100644 index 919bc6e9..00000000 --- a/client-api_python/generated/PySirius/models/category.py +++ /dev/null @@ -1,103 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.data_quality import DataQuality -from PySirius.models.quality_item import QualityItem -from typing import Optional, Set -from typing_extensions import Self - -class Category(BaseModel): - """ - Category - """ # noqa: E501 - category_name: Optional[StrictStr] = Field(default=None, alias="categoryName") - overall_quality: Optional[DataQuality] = Field(default=None, alias="overallQuality") - items: Optional[List[QualityItem]] = None - __properties: ClassVar[List[str]] = ["categoryName", "overallQuality", "items"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of Category from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each item in items (list) - _items = [] - if self.items: - for _item_items in self.items: - if _item_items: - _items.append(_item_items.to_dict()) - _dict['items'] = _items - # set to None if overall_quality (nullable) is None - # and model_fields_set contains the field - if self.overall_quality is None and "overall_quality" in self.model_fields_set: - _dict['overallQuality'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of Category from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "categoryName": obj.get("categoryName"), - "overallQuality": obj.get("overallQuality"), - "items": [QualityItem.from_dict(_item) for _item in obj["items"]] if obj.get("items") is not None else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/compound.py b/client-api_python/generated/PySirius/models/compound.py index 879593a0..1a8cf130 100644 --- a/client-api_python/generated/PySirius/models/compound.py +++ b/client-api_python/generated/PySirius/models/compound.py @@ -37,7 +37,7 @@ class Compound(BaseModel): consensus_annotations: Optional[ConsensusAnnotationsCSI] = Field(default=None, alias="consensusAnnotations") consensus_annotations_de_novo: Optional[ConsensusAnnotationsDeNovo] = Field(default=None, alias="consensusAnnotationsDeNovo") custom_annotations: Optional[ConsensusAnnotationsCSI] = Field(default=None, alias="customAnnotations") - tags: Optional[Dict[str, Tag]] = Field(default=None, description="Key: tagName, value: tag") + tags: Optional[Dict[str, Optional[Tag]]] = Field(default=None, description="Key: tagName, value: tag") __properties: ClassVar[List[str]] = ["compoundId", "name", "rtStartSeconds", "rtEndSeconds", "neutralMass", "features", "consensusAnnotations", "consensusAnnotationsDeNovo", "customAnnotations", "tags"] model_config = ConfigDict( diff --git a/client-api_python/generated/PySirius/models/fold_change.py b/client-api_python/generated/PySirius/models/fold_change.py deleted file mode 100644 index 8b55b0d0..00000000 --- a/client-api_python/generated/PySirius/models/fold_change.py +++ /dev/null @@ -1,100 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_row_type import QuantRowType -from typing import Optional, Set -from typing_extensions import Self - -class FoldChange(BaseModel): - """ - FoldChange - """ # noqa: E501 - left_group: Optional[StrictStr] = Field(default=None, alias="leftGroup") - right_group: Optional[StrictStr] = Field(default=None, alias="rightGroup") - aggregation: Optional[AggregationType] = None - quantification: Optional[QuantMeasure] = None - quant_type: QuantRowType = Field(alias="quantType") - object_id: StrictStr = Field(alias="objectId") - fold_change: float = Field(alias="foldChange") - __properties: ClassVar[List[str]] = ["leftGroup", "rightGroup", "aggregation", "quantification", "quantType", "objectId", "foldChange"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of FoldChange from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of FoldChange from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "leftGroup": obj.get("leftGroup"), - "rightGroup": obj.get("rightGroup"), - "aggregation": obj.get("aggregation"), - "quantification": obj.get("quantification"), - "quantType": obj.get("quantType"), - "objectId": obj.get("objectId"), - "foldChange": obj.get("foldChange") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/paged_model_run.py b/client-api_python/generated/PySirius/models/paged_model_run.py deleted file mode 100644 index 90f4f94d..00000000 --- a/client-api_python/generated/PySirius/models/paged_model_run.py +++ /dev/null @@ -1,99 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.page_metadata import PageMetadata -from PySirius.models.run import Run -from typing import Optional, Set -from typing_extensions import Self - -class PagedModelRun(BaseModel): - """ - PagedModelRun - """ # noqa: E501 - content: Optional[List[Run]] = None - page: Optional[PageMetadata] = None - __properties: ClassVar[List[str]] = ["content", "page"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of PagedModelRun from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each item in content (list) - _items = [] - if self.content: - for _item_content in self.content: - if _item_content: - _items.append(_item_content.to_dict()) - _dict['content'] = _items - # override the default output from pydantic by calling `to_dict()` of page - if self.page: - _dict['page'] = self.page.to_dict() - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of PagedModelRun from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "content": [Run.from_dict(_item) for _item in obj["content"]] if obj.get("content") is not None else None, - "page": PageMetadata.from_dict(obj["page"]) if obj.get("page") is not None else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/quality_item.py b/client-api_python/generated/PySirius/models/quality_item.py deleted file mode 100644 index 591e2bbe..00000000 --- a/client-api_python/generated/PySirius/models/quality_item.py +++ /dev/null @@ -1,96 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.data_quality import DataQuality -from PySirius.models.quality_weight import QualityWeight -from typing import Optional, Set -from typing_extensions import Self - -class QualityItem(BaseModel): - """ - QualityItem - """ # noqa: E501 - description: Optional[StrictStr] = None - quality: Optional[DataQuality] = None - weight: Optional[QualityWeight] = None - __properties: ClassVar[List[str]] = ["description", "quality", "weight"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of QualityItem from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # set to None if quality (nullable) is None - # and model_fields_set contains the field - if self.quality is None and "quality" in self.model_fields_set: - _dict['quality'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of QualityItem from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "description": obj.get("description"), - "quality": obj.get("quality"), - "weight": obj.get("weight") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/quality_weight.py b/client-api_python/generated/PySirius/models/quality_weight.py deleted file mode 100644 index dc3c2d20..00000000 --- a/client-api_python/generated/PySirius/models/quality_weight.py +++ /dev/null @@ -1,36 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class QualityWeight(str, Enum): - """ - QualityWeight - """ - - """ - allowed enum values - """ - MINOR = 'MINOR' - MAJOR = 'MAJOR' - CRITICAL = 'CRITICAL' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of QualityWeight from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/quant_measure.py b/client-api_python/generated/PySirius/models/quant_measure.py deleted file mode 100644 index e2def182..00000000 --- a/client-api_python/generated/PySirius/models/quant_measure.py +++ /dev/null @@ -1,35 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class QuantMeasure(str, Enum): - """ - QuantMeasure - """ - - """ - allowed enum values - """ - APEX_INTENSITY = 'APEX_INTENSITY' - AREA_UNDER_CURVE = 'AREA_UNDER_CURVE' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of QuantMeasure from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/quant_row_type.py b/client-api_python/generated/PySirius/models/quant_row_type.py deleted file mode 100644 index 6ef94cd0..00000000 --- a/client-api_python/generated/PySirius/models/quant_row_type.py +++ /dev/null @@ -1,35 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class QuantRowType(str, Enum): - """ - QuantRowType - """ - - """ - allowed enum values - """ - FEATURES = 'FEATURES' - COMPOUNDS = 'COMPOUNDS' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of QuantRowType from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/quant_table_experimental.py b/client-api_python/generated/PySirius/models/quant_table_experimental.py deleted file mode 100644 index db9bba10..00000000 --- a/client-api_python/generated/PySirius/models/quant_table_experimental.py +++ /dev/null @@ -1,119 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_row_type import QuantRowType -from typing import Optional, Set -from typing_extensions import Self - -class QuantTableExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - quantification_measure: Optional[QuantMeasure] = Field(default=None, alias="quantificationMeasure") - row_type: Optional[QuantRowType] = Field(default=None, alias="rowType") - row_ids: Optional[List[Optional[StrictInt]]] = Field(default=None, alias="rowIds") - column_ids: Optional[List[Optional[StrictInt]]] = Field(default=None, alias="columnIds") - row_names: Optional[List[Optional[StrictStr]]] = Field(default=None, alias="rowNames") - column_names: Optional[List[Optional[StrictStr]]] = Field(default=None, alias="columnNames") - values: Optional[List[List[float]]] = None - __properties: ClassVar[List[str]] = ["quantificationMeasure", "rowType", "rowIds", "columnIds", "rowNames", "columnNames", "values"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of QuantTableExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # set to None if row_ids (nullable) is None - # and model_fields_set contains the field - if self.row_ids is None and "row_ids" in self.model_fields_set: - _dict['rowIds'] = None - - # set to None if column_ids (nullable) is None - # and model_fields_set contains the field - if self.column_ids is None and "column_ids" in self.model_fields_set: - _dict['columnIds'] = None - - # set to None if row_names (nullable) is None - # and model_fields_set contains the field - if self.row_names is None and "row_names" in self.model_fields_set: - _dict['rowNames'] = None - - # set to None if column_names (nullable) is None - # and model_fields_set contains the field - if self.column_names is None and "column_names" in self.model_fields_set: - _dict['columnNames'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of QuantTableExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "quantificationMeasure": obj.get("quantificationMeasure"), - "rowType": obj.get("rowType"), - "rowIds": obj.get("rowIds"), - "columnIds": obj.get("columnIds"), - "rowNames": obj.get("rowNames"), - "columnNames": obj.get("columnNames"), - "values": obj.get("values") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/run.py b/client-api_python/generated/PySirius/models/run.py deleted file mode 100644 index 494ceae2..00000000 --- a/client-api_python/generated/PySirius/models/run.py +++ /dev/null @@ -1,137 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.tag import Tag -from typing import Optional, Set -from typing_extensions import Self - -class Run(BaseModel): - """ - Run - """ # noqa: E501 - run_id: Optional[StrictStr] = Field(default=None, description="Identifier", alias="runId") - name: Optional[StrictStr] = Field(default=None, description="Informative, human-readable name of this run") - source: Optional[StrictStr] = Field(default=None, description="Source location") - chromatography: Optional[StrictStr] = None - ionization: Optional[StrictStr] = None - fragmentation: Optional[StrictStr] = None - mass_analyzers: Optional[List[Optional[StrictStr]]] = Field(default=None, alias="massAnalyzers") - tags: Optional[Dict[str, Tag]] = Field(default=None, description="Key: tagName, value: tag") - __properties: ClassVar[List[str]] = ["runId", "name", "source", "chromatography", "ionization", "fragmentation", "massAnalyzers", "tags"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of Run from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each value in tags (dict) - _field_dict = {} - if self.tags: - for _key_tags in self.tags: - if self.tags[_key_tags]: - _field_dict[_key_tags] = self.tags[_key_tags].to_dict() - _dict['tags'] = _field_dict - # set to None if chromatography (nullable) is None - # and model_fields_set contains the field - if self.chromatography is None and "chromatography" in self.model_fields_set: - _dict['chromatography'] = None - - # set to None if ionization (nullable) is None - # and model_fields_set contains the field - if self.ionization is None and "ionization" in self.model_fields_set: - _dict['ionization'] = None - - # set to None if fragmentation (nullable) is None - # and model_fields_set contains the field - if self.fragmentation is None and "fragmentation" in self.model_fields_set: - _dict['fragmentation'] = None - - # set to None if mass_analyzers (nullable) is None - # and model_fields_set contains the field - if self.mass_analyzers is None and "mass_analyzers" in self.model_fields_set: - _dict['massAnalyzers'] = None - - # set to None if tags (nullable) is None - # and model_fields_set contains the field - if self.tags is None and "tags" in self.model_fields_set: - _dict['tags'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of Run from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "runId": obj.get("runId"), - "name": obj.get("name"), - "source": obj.get("source"), - "chromatography": obj.get("chromatography"), - "ionization": obj.get("ionization"), - "fragmentation": obj.get("fragmentation"), - "massAnalyzers": obj.get("massAnalyzers"), - "tags": dict( - (_k, Tag.from_dict(_v)) - for _k, _v in obj["tags"].items() - ) - if obj.get("tags") is not None - else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/run_opt_field.py b/client-api_python/generated/PySirius/models/run_opt_field.py deleted file mode 100644 index 3d595746..00000000 --- a/client-api_python/generated/PySirius/models/run_opt_field.py +++ /dev/null @@ -1,35 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class RunOptField(str, Enum): - """ - RunOptField - """ - - """ - allowed enum values - """ - NONE = 'none' - TAGS = 'tags' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of RunOptField from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/sample_type_fold_change_request.py b/client-api_python/generated/PySirius/models/sample_type_fold_change_request.py deleted file mode 100644 index f639f6b2..00000000 --- a/client-api_python/generated/PySirius/models/sample_type_fold_change_request.py +++ /dev/null @@ -1,89 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from typing import Optional, Set -from typing_extensions import Self - -class SampleTypeFoldChangeRequest(BaseModel): - """ - SampleTypeFoldChangeRequest - """ # noqa: E501 - sample_run_ids: Optional[List[StrictStr]] = Field(default=None, alias="sampleRunIds") - blank_run_ids: Optional[List[StrictStr]] = Field(default=None, alias="blankRunIds") - control_run_ids: Optional[List[StrictStr]] = Field(default=None, alias="controlRunIds") - __properties: ClassVar[List[str]] = ["sampleRunIds", "blankRunIds", "controlRunIds"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of SampleTypeFoldChangeRequest from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of SampleTypeFoldChangeRequest from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "sampleRunIds": obj.get("sampleRunIds"), - "blankRunIds": obj.get("blankRunIds"), - "controlRunIds": obj.get("controlRunIds") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/statistics_table.py b/client-api_python/generated/PySirius/models/statistics_table.py deleted file mode 100644 index 1b7ac186..00000000 --- a/client-api_python/generated/PySirius/models/statistics_table.py +++ /dev/null @@ -1,105 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_row_type import QuantRowType -from PySirius.models.statistics_type import StatisticsType -from typing import Optional, Set -from typing_extensions import Self - -class StatisticsTable(BaseModel): - """ - StatisticsTable - """ # noqa: E501 - statistics_type: Optional[StatisticsType] = Field(default=None, alias="statisticsType") - aggregation_type: Optional[AggregationType] = Field(default=None, alias="aggregationType") - quantification_measure: Optional[QuantMeasure] = Field(default=None, alias="quantificationMeasure") - row_type: Optional[QuantRowType] = Field(default=None, alias="rowType") - row_ids: Optional[List[StrictStr]] = Field(default=None, alias="rowIds") - column_names: Optional[List[StrictStr]] = Field(default=None, alias="columnNames") - column_left_groups: Optional[List[StrictStr]] = Field(default=None, alias="columnLeftGroups") - column_right_groups: Optional[List[StrictStr]] = Field(default=None, alias="columnRightGroups") - values: Optional[List[List[float]]] = None - __properties: ClassVar[List[str]] = ["statisticsType", "aggregationType", "quantificationMeasure", "rowType", "rowIds", "columnNames", "columnLeftGroups", "columnRightGroups", "values"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of StatisticsTable from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of StatisticsTable from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "statisticsType": obj.get("statisticsType"), - "aggregationType": obj.get("aggregationType"), - "quantificationMeasure": obj.get("quantificationMeasure"), - "rowType": obj.get("rowType"), - "rowIds": obj.get("rowIds"), - "columnNames": obj.get("columnNames"), - "columnLeftGroups": obj.get("columnLeftGroups"), - "columnRightGroups": obj.get("columnRightGroups"), - "values": obj.get("values") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/statistics_type.py b/client-api_python/generated/PySirius/models/statistics_type.py deleted file mode 100644 index ca7f9dc1..00000000 --- a/client-api_python/generated/PySirius/models/statistics_type.py +++ /dev/null @@ -1,34 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class StatisticsType(str, Enum): - """ - StatisticsType - """ - - """ - allowed enum values - """ - FOLD_CHANGE = 'FOLD_CHANGE' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of StatisticsType from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/tag_definition.py b/client-api_python/generated/PySirius/models/tag_definition.py deleted file mode 100644 index e69dc3e0..00000000 --- a/client-api_python/generated/PySirius/models/tag_definition.py +++ /dev/null @@ -1,125 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictBool, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.value_type import ValueType -from typing import Optional, Set -from typing_extensions import Self - -class TagDefinition(BaseModel): - """ - TagDefinition - """ # noqa: E501 - tag_name: StrictStr = Field(description="Name of this tag defined by this definition (key)", alias="tagName") - description: Optional[StrictStr] = Field(default=None, description="A human-readable description about the purpose of this tag.") - tag_type: Optional[StrictStr] = Field(default=None, description="A simple string based identifier to specify the type/scope/purpose of this tag.", alias="tagType") - value_type: ValueType = Field(alias="valueType") - possible_values: Optional[List[Optional[Dict[str, Any]]]] = Field(default=None, alias="possibleValues") - min_value: Optional[Dict[str, Any]] = Field(default=None, alias="minValue") - max_value: Optional[Dict[str, Any]] = Field(default=None, alias="maxValue") - editable: Optional[StrictBool] = None - __properties: ClassVar[List[str]] = ["tagName", "description", "tagType", "valueType", "possibleValues", "minValue", "maxValue", "editable"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TagDefinition from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # set to None if description (nullable) is None - # and model_fields_set contains the field - if self.description is None and "description" in self.model_fields_set: - _dict['description'] = None - - # set to None if tag_type (nullable) is None - # and model_fields_set contains the field - if self.tag_type is None and "tag_type" in self.model_fields_set: - _dict['tagType'] = None - - # set to None if possible_values (nullable) is None - # and model_fields_set contains the field - if self.possible_values is None and "possible_values" in self.model_fields_set: - _dict['possibleValues'] = None - - # set to None if min_value (nullable) is None - # and model_fields_set contains the field - if self.min_value is None and "min_value" in self.model_fields_set: - _dict['minValue'] = None - - # set to None if max_value (nullable) is None - # and model_fields_set contains the field - if self.max_value is None and "max_value" in self.model_fields_set: - _dict['maxValue'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TagDefinition from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "tagName": obj.get("tagName"), - "description": obj.get("description"), - "tagType": obj.get("tagType"), - "valueType": obj.get("valueType"), - "possibleValues": obj.get("possibleValues"), - "minValue": obj.get("minValue"), - "maxValue": obj.get("maxValue"), - "editable": obj.get("editable") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/tag_definition_import.py b/client-api_python/generated/PySirius/models/tag_definition_import.py deleted file mode 100644 index 5aaa4016..00000000 --- a/client-api_python/generated/PySirius/models/tag_definition_import.py +++ /dev/null @@ -1,123 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.value_type import ValueType -from typing import Optional, Set -from typing_extensions import Self - -class TagDefinitionImport(BaseModel): - """ - TagDefinitionImport - """ # noqa: E501 - tag_name: StrictStr = Field(description="Name of this tag defined by this definition (key)", alias="tagName") - description: Optional[StrictStr] = Field(default=None, description="A human-readable description about the purpose of this tag.") - tag_type: Optional[StrictStr] = Field(default=None, description="A simple string based identifier to specify the type/scope/purpose of this tag.", alias="tagType") - value_type: ValueType = Field(alias="valueType") - possible_values: Optional[List[Optional[Dict[str, Any]]]] = Field(default=None, alias="possibleValues") - min_value: Optional[Dict[str, Any]] = Field(default=None, alias="minValue") - max_value: Optional[Dict[str, Any]] = Field(default=None, alias="maxValue") - __properties: ClassVar[List[str]] = ["tagName", "description", "tagType", "valueType", "possibleValues", "minValue", "maxValue"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TagDefinitionImport from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # set to None if description (nullable) is None - # and model_fields_set contains the field - if self.description is None and "description" in self.model_fields_set: - _dict['description'] = None - - # set to None if tag_type (nullable) is None - # and model_fields_set contains the field - if self.tag_type is None and "tag_type" in self.model_fields_set: - _dict['tagType'] = None - - # set to None if possible_values (nullable) is None - # and model_fields_set contains the field - if self.possible_values is None and "possible_values" in self.model_fields_set: - _dict['possibleValues'] = None - - # set to None if min_value (nullable) is None - # and model_fields_set contains the field - if self.min_value is None and "min_value" in self.model_fields_set: - _dict['minValue'] = None - - # set to None if max_value (nullable) is None - # and model_fields_set contains the field - if self.max_value is None and "max_value" in self.model_fields_set: - _dict['maxValue'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TagDefinitionImport from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "tagName": obj.get("tagName"), - "description": obj.get("description"), - "tagType": obj.get("tagType"), - "valueType": obj.get("valueType"), - "possibleValues": obj.get("possibleValues"), - "minValue": obj.get("minValue"), - "maxValue": obj.get("maxValue") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/tag_group.py b/client-api_python/generated/PySirius/models/tag_group.py deleted file mode 100644 index 489d27f2..00000000 --- a/client-api_python/generated/PySirius/models/tag_group.py +++ /dev/null @@ -1,89 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from typing import Optional, Set -from typing_extensions import Self - -class TagGroup(BaseModel): - """ - TagGroup - """ # noqa: E501 - group_name: Optional[StrictStr] = Field(default=None, description="Name of this Grouping query.", alias="groupName") - lucene_query: Optional[StrictStr] = Field(default=None, description="Query used to group the entities in lucene format.", alias="luceneQuery") - group_type: Optional[StrictStr] = Field(default=None, alias="groupType") - __properties: ClassVar[List[str]] = ["groupName", "luceneQuery", "groupType"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TagGroup from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TagGroup from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "groupName": obj.get("groupName"), - "luceneQuery": obj.get("luceneQuery"), - "groupType": obj.get("groupType") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/trace_annotation_experimental.py b/client-api_python/generated/PySirius/models/trace_annotation_experimental.py deleted file mode 100644 index 70726427..00000000 --- a/client-api_python/generated/PySirius/models/trace_annotation_experimental.py +++ /dev/null @@ -1,109 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictInt, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.trace_annotation_type_experimental import TraceAnnotationTypeExperimental -from typing import Optional, Set -from typing_extensions import Self - -class TraceAnnotationExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - type: Optional[TraceAnnotationTypeExperimental] = None - description: Optional[StrictStr] = None - index: Optional[StrictInt] = None - var_from: Optional[StrictInt] = Field(default=None, alias="from") - to: Optional[StrictInt] = None - __properties: ClassVar[List[str]] = ["type", "description", "index", "from", "to"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TraceAnnotationExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # set to None if description (nullable) is None - # and model_fields_set contains the field - if self.description is None and "description" in self.model_fields_set: - _dict['description'] = None - - # set to None if var_from (nullable) is None - # and model_fields_set contains the field - if self.var_from is None and "var_from" in self.model_fields_set: - _dict['from'] = None - - # set to None if to (nullable) is None - # and model_fields_set contains the field - if self.to is None and "to" in self.model_fields_set: - _dict['to'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TraceAnnotationExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "type": obj.get("type"), - "description": obj.get("description"), - "index": obj.get("index"), - "from": obj.get("from"), - "to": obj.get("to") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/trace_annotation_type_experimental.py b/client-api_python/generated/PySirius/models/trace_annotation_type_experimental.py deleted file mode 100644 index ccf899dc..00000000 --- a/client-api_python/generated/PySirius/models/trace_annotation_type_experimental.py +++ /dev/null @@ -1,35 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class TraceAnnotationTypeExperimental(str, Enum): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ - - """ - allowed enum values - """ - FEATURE = 'FEATURE' - MS2 = 'MS2' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of TraceAnnotationTypeExperimental from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/PySirius/models/trace_experimental.py b/client-api_python/generated/PySirius/models/trace_experimental.py deleted file mode 100644 index 88091bec..00000000 --- a/client-api_python/generated/PySirius/models/trace_experimental.py +++ /dev/null @@ -1,123 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictBool, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.trace_annotation_experimental import TraceAnnotationExperimental -from typing import Optional, Set -from typing_extensions import Self - -class TraceExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - id: Optional[StrictStr] = None - sample_id: Optional[StrictStr] = Field(default=None, alias="sampleId") - sample_name: Optional[StrictStr] = Field(default=None, alias="sampleName") - label: Optional[StrictStr] = None - color: Optional[StrictStr] = None - intensities: Optional[List[float]] = None - annotations: Optional[List[TraceAnnotationExperimental]] = None - mz: Optional[float] = None - merged: Optional[StrictBool] = None - normalization_factor: Optional[float] = Field(default=None, description="Traces are stored with raw intensity values. The normalization factor maps them to relative intensities, such that traces from different samples can be compared.", alias="normalizationFactor") - noise_level: Optional[float] = Field(default=None, description="The noise level is estimated from the median noise in the surrounding scans. It can be used to calculate signal-to-noise ratios.", alias="noiseLevel") - __properties: ClassVar[List[str]] = ["id", "sampleId", "sampleName", "label", "color", "intensities", "annotations", "mz", "merged", "normalizationFactor", "noiseLevel"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TraceExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of each item in annotations (list) - _items = [] - if self.annotations: - for _item_annotations in self.annotations: - if _item_annotations: - _items.append(_item_annotations.to_dict()) - _dict['annotations'] = _items - # set to None if sample_id (nullable) is None - # and model_fields_set contains the field - if self.sample_id is None and "sample_id" in self.model_fields_set: - _dict['sampleId'] = None - - # set to None if sample_name (nullable) is None - # and model_fields_set contains the field - if self.sample_name is None and "sample_name" in self.model_fields_set: - _dict['sampleName'] = None - - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TraceExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "id": obj.get("id"), - "sampleId": obj.get("sampleId"), - "sampleName": obj.get("sampleName"), - "label": obj.get("label"), - "color": obj.get("color"), - "intensities": obj.get("intensities"), - "annotations": [TraceAnnotationExperimental.from_dict(_item) for _item in obj["annotations"]] if obj.get("annotations") is not None else None, - "mz": obj.get("mz"), - "merged": obj.get("merged"), - "normalizationFactor": obj.get("normalizationFactor"), - "noiseLevel": obj.get("noiseLevel") - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/trace_set_experimental.py b/client-api_python/generated/PySirius/models/trace_set_experimental.py deleted file mode 100644 index 5d1f1ab0..00000000 --- a/client-api_python/generated/PySirius/models/trace_set_experimental.py +++ /dev/null @@ -1,109 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import pprint -import re # noqa: F401 -import json - -from pydantic import BaseModel, ConfigDict, Field, StrictStr -from typing import Any, ClassVar, Dict, List, Optional -from PySirius.models.adduct_network_experimental import AdductNetworkExperimental -from PySirius.models.axes import Axes -from PySirius.models.trace_experimental import TraceExperimental -from typing import Optional, Set -from typing_extensions import Self - -class TraceSetExperimental(BaseModel): - """ - EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - """ # noqa: E501 - adduct_network: Optional[AdductNetworkExperimental] = Field(default=None, alias="adductNetwork") - sample_id: Optional[StrictStr] = Field(default=None, alias="sampleId") - sample_name: Optional[StrictStr] = Field(default=None, alias="sampleName") - axes: Optional[Axes] = None - traces: Optional[List[TraceExperimental]] = None - __properties: ClassVar[List[str]] = ["adductNetwork", "sampleId", "sampleName", "axes", "traces"] - - model_config = ConfigDict( - populate_by_name=True, - validate_assignment=True, - protected_namespaces=(), - ) - - - def to_str(self) -> str: - """Returns the string representation of the model using alias""" - return pprint.pformat(self.model_dump(by_alias=True)) - - def to_json(self) -> str: - """Returns the JSON representation of the model using alias""" - # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead - return json.dumps(self.to_dict()) - - @classmethod - def from_json(cls, json_str: str) -> Optional[Self]: - """Create an instance of TraceSetExperimental from a JSON string""" - return cls.from_dict(json.loads(json_str)) - - def to_dict(self) -> Dict[str, Any]: - """Return the dictionary representation of the model using alias. - - This has the following differences from calling pydantic's - `self.model_dump(by_alias=True)`: - - * `None` is only added to the output dict for nullable fields that - were set at model initialization. Other fields with value `None` - are ignored. - """ - excluded_fields: Set[str] = set([ - ]) - - _dict = self.model_dump( - by_alias=True, - exclude=excluded_fields, - exclude_none=True, - ) - # override the default output from pydantic by calling `to_dict()` of adduct_network - if self.adduct_network: - _dict['adductNetwork'] = self.adduct_network.to_dict() - # override the default output from pydantic by calling `to_dict()` of axes - if self.axes: - _dict['axes'] = self.axes.to_dict() - # override the default output from pydantic by calling `to_dict()` of each item in traces (list) - _items = [] - if self.traces: - for _item_traces in self.traces: - if _item_traces: - _items.append(_item_traces.to_dict()) - _dict['traces'] = _items - return _dict - - @classmethod - def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: - """Create an instance of TraceSetExperimental from a dict""" - if obj is None: - return None - - if not isinstance(obj, dict): - return cls.model_validate(obj) - - _obj = cls.model_validate({ - "adductNetwork": AdductNetworkExperimental.from_dict(obj["adductNetwork"]) if obj.get("adductNetwork") is not None else None, - "sampleId": obj.get("sampleId"), - "sampleName": obj.get("sampleName"), - "axes": Axes.from_dict(obj["axes"]) if obj.get("axes") is not None else None, - "traces": [TraceExperimental.from_dict(_item) for _item in obj["traces"]] if obj.get("traces") is not None else None - }) - return _obj - - diff --git a/client-api_python/generated/PySirius/models/value_type.py b/client-api_python/generated/PySirius/models/value_type.py deleted file mode 100644 index c90e7151..00000000 --- a/client-api_python/generated/PySirius/models/value_type.py +++ /dev/null @@ -1,40 +0,0 @@ -# coding: utf-8 - -""" - SIRIUS Nightsky API - - - Generated by OpenAPI Generator (https://openapi-generator.tech) - - Do not edit the class manually. -""" # noqa: E501 - - -from __future__ import annotations -import json -from enum import Enum -from typing_extensions import Self - - -class ValueType(str, Enum): - """ - ValueType - """ - - """ - allowed enum values - """ - NONE = 'NONE' - BOOLEAN = 'BOOLEAN' - INTEGER = 'INTEGER' - REAL = 'REAL' - TEXT = 'TEXT' - DATE = 'DATE' - TIME = 'TIME' - - @classmethod - def from_json(cls, json_str: str) -> Self: - """Create an instance of ValueType from a JSON string""" - return cls(json.loads(json_str)) - - diff --git a/client-api_python/generated/README.md b/client-api_python/generated/README.md index e799e198..2c336bee 100644 --- a/client-api_python/generated/README.md +++ b/client-api_python/generated/README.md @@ -4,7 +4,7 @@ REST API that provides the full functionality of SIRIUS and its web services as This Python package is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project: - API version: 3.1 -- Package version: 6.3.3 +- Package version: 6.3.4 - Generator version: 7.16.0 - Build package: org.openapitools.codegen.languages.PythonClientCodegen @@ -86,46 +86,22 @@ Class | Method | HTTP request | Description ------------ | ------------- | ------------- | ------------- *ActuatorApi* | [**health**](docs/ActuatorApi.md#health) | **GET** /actuator/health | Actuator web endpoint 'health' *ActuatorApi* | [**shutdown**](docs/ActuatorApi.md#shutdown) | **POST** /actuator/shutdown | Actuator web endpoint 'shutdown' -*CompoundStatisticsApi* | [**compute_compound_fold_changes_experimental**](docs/CompoundStatisticsApi.md#compute_compound_fold_changes_experimental) | **PUT** /api/projects/{projectId}/compounds/statistics/foldchange/compute | [EXPERIMENTAL] Compute the fold change between two groups of runs -*CompoundStatisticsApi* | [**delete_compound_fold_changes_experimental**](docs/CompoundStatisticsApi.md#delete_compound_fold_changes_experimental) | **DELETE** /api/projects/{projectId}/compounds/statistics/foldchanges | [EXPERIMENTAL] Delete fold changes -*CompoundStatisticsApi* | [**get_compound_fold_change_table_experimental**](docs/CompoundStatisticsApi.md#get_compound_fold_change_table_experimental) | **GET** /api/projects/{projectId}/compounds/statistics/foldchanges/stats-table | [EXPERIMENTAL] Get table of all fold changes in the project space -*CompoundStatisticsApi* | [**get_fold_changes_by_compound_experimental**](docs/CompoundStatisticsApi.md#get_fold_changes_by_compound_experimental) | **GET** /api/projects/{projectId}/compounds/statistics/foldchanges/{objectId} | [EXPERIMENTAL] List all fold changes that are associated with an object *CompoundsApi* | [**add_compounds**](docs/CompoundsApi.md#add_compounds) | **POST** /api/projects/{projectId}/compounds | Import Compounds and its contained features. -*CompoundsApi* | [**add_tags_to_compound_experimental**](docs/CompoundsApi.md#add_tags_to_compound_experimental) | **PUT** /api/projects/{projectId}/compounds/tags/{compoundId} | [EXPERIMENTAL] Tags with the same name will be overwritten *CompoundsApi* | [**delete_compound**](docs/CompoundsApi.md#delete_compound) | **DELETE** /api/projects/{projectId}/compounds/{compoundId} | Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. *CompoundsApi* | [**get_compound**](docs/CompoundsApi.md#get_compound) | **GET** /api/projects/{projectId}/compounds/{compoundId} | Get compound (group of ion identities) with the given identifier from the specified project-space. -*CompoundsApi* | [**get_compound_quant_table_experimental**](docs/CompoundsApi.md#get_compound_quant_table_experimental) | **GET** /api/projects/{projectId}/compounds/quant-table | [EXPERIMENTAL] Returns the full quantification table of compounds -*CompoundsApi* | [**get_compound_quant_table_row_experimental**](docs/CompoundsApi.md#get_compound_quant_table_row_experimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given compound -*CompoundsApi* | [**get_compound_traces_experimental**](docs/CompoundsApi.md#get_compound_traces_experimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/traces | [EXPERIMENTAL] Returns the traces of the given compound *CompoundsApi* | [**get_compounds**](docs/CompoundsApi.md#get_compounds) | **GET** /api/projects/{projectId}/compounds | List of all available compounds (group of ion identities) in the given project-space. -*CompoundsApi* | [**get_compounds_by_group_experimental**](docs/CompoundsApi.md#get_compounds_by_group_experimental) | **GET** /api/projects/{projectId}/compounds/grouped | [EXPERIMENTAL] Get compounds (group of ion identities) by tag group -*CompoundsApi* | [**get_compounds_by_tag_experimental**](docs/CompoundsApi.md#get_compounds_by_tag_experimental) | **GET** /api/projects/{projectId}/compounds/tagged | [EXPERIMENTAL] Get compounds (group of ion identities) by tag *CompoundsApi* | [**get_compounds_paged**](docs/CompoundsApi.md#get_compounds_paged) | **GET** /api/projects/{projectId}/compounds/page | Page of available compounds (group of ion identities) in the given project-space. -*CompoundsApi* | [**get_tags_for_compound_experimental**](docs/CompoundsApi.md#get_tags_for_compound_experimental) | **GET** /api/projects/{projectId}/compounds/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Compound -*CompoundsApi* | [**remove_tag_from_compound_experimental**](docs/CompoundsApi.md#remove_tag_from_compound_experimental) | **DELETE** /api/projects/{projectId}/compounds/tags/{compoundId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space -*FeatureStatisticsApi* | [**compute_aligned_feature_fold_changes_experimental**](docs/FeatureStatisticsApi.md#compute_aligned_feature_fold_changes_experimental) | **PUT** /api/projects/{projectId}/aligned-features/statistics/foldchange/compute | [EXPERIMENTAL] Compute the fold change between two groups of runs -*FeatureStatisticsApi* | [**delete_aligned_feature_fold_changes_experimental**](docs/FeatureStatisticsApi.md#delete_aligned_feature_fold_changes_experimental) | **DELETE** /api/projects/{projectId}/aligned-features/statistics/foldchanges | [EXPERIMENTAL] Delete fold changes -*FeatureStatisticsApi* | [**get_aligned_feature_fold_change_table_experimental**](docs/FeatureStatisticsApi.md#get_aligned_feature_fold_change_table_experimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table | [EXPERIMENTAL] Get table of all fold changes in the project space -*FeatureStatisticsApi* | [**get_fold_changes_by_aligned_feature_experimental**](docs/FeatureStatisticsApi.md#get_fold_changes_by_aligned_feature_experimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId} | [EXPERIMENTAL] List all fold changes that are associated with an object *FeaturesApi* | [**add_aligned_features**](docs/FeaturesApi.md#add_aligned_features) | **POST** /api/projects/{projectId}/aligned-features | Import (aligned) features into the project. -*FeaturesApi* | [**add_de_novo_structure_candidate**](docs/FeaturesApi.md#add_de_novo_structure_candidate) | **PUT** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. -*FeaturesApi* | [**add_tags_to_aligned_feature_experimental**](docs/FeaturesApi.md#add_tags_to_aligned_feature_experimental) | **PUT** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId} | [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project *FeaturesApi* | [**delete_aligned_feature**](docs/FeaturesApi.md#delete_aligned_feature) | **DELETE** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Delete feature (aligned over runs) with the given identifier from the specified project-space. *FeaturesApi* | [**delete_aligned_features**](docs/FeaturesApi.md#delete_aligned_features) | **PUT** /api/projects/{projectId}/aligned-features/delete | Delete feature (aligned over runs) with the given identifier from the specified project-space. -*FeaturesApi* | [**get_adduct_network_with_merged_traces_experimental**](docs/FeaturesApi.md#get_adduct_network_with_merged_traces_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts | [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network *FeaturesApi* | [**get_aligned_feature**](docs/FeaturesApi.md#get_aligned_feature) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Get feature (aligned over runs) with the given identifier from the specified project-space. -*FeaturesApi* | [**get_aligned_feature_quality_experimental**](docs/FeaturesApi.md#get_aligned_feature_quality_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report | [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) *FeaturesApi* | [**get_aligned_features**](docs/FeaturesApi.md#get_aligned_features) | **GET** /api/projects/{projectId}/aligned-features | Get all available features (aligned over runs) in the given project-space. -*FeaturesApi* | [**get_aligned_features_by_group_experimental**](docs/FeaturesApi.md#get_aligned_features_by_group_experimental) | **GET** /api/projects/{projectId}/aligned-features/grouped | [EXPERIMENTAL] Get features (aligned over runs) by tag group -*FeaturesApi* | [**get_aligned_features_by_tag_experimental**](docs/FeaturesApi.md#get_aligned_features_by_tag_experimental) | **GET** /api/projects/{projectId}/aligned-features/tagged | [EXPERIMENTAL] Get features (aligned over runs) by tag *FeaturesApi* | [**get_aligned_features_paged**](docs/FeaturesApi.md#get_aligned_features_paged) | **GET** /api/projects/{projectId}/aligned-features/page | Get all available features (aligned over runs) in the given project-space. *FeaturesApi* | [**get_best_matching_compound_classes**](docs/FeaturesApi.md#get_best_matching_compound_classes) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes | Return Best matching compound classes for given formulaId *FeaturesApi* | [**get_canopus_prediction**](docs/FeaturesApi.md#get_canopus_prediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction | All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, -*FeaturesApi* | [**get_de_novo_structure_candidates**](docs/FeaturesApi.md#get_de_novo_structure_candidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. *FeaturesApi* | [**get_de_novo_structure_candidates_by_formula**](docs/FeaturesApi.md#get_de_novo_structure_candidates_by_formula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. *FeaturesApi* | [**get_de_novo_structure_candidates_by_formula_paged**](docs/FeaturesApi.md#get_de_novo_structure_candidates_by_formula_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. *FeaturesApi* | [**get_de_novo_structure_candidates_paged**](docs/FeaturesApi.md#get_de_novo_structure_candidates_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. -*FeaturesApi* | [**get_feature_quant_table_experimental**](docs/FeaturesApi.md#get_feature_quant_table_experimental) | **GET** /api/projects/{projectId}/aligned-features/quant-table | [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) *FeaturesApi* | [**get_fingerprint_prediction**](docs/FeaturesApi.md#get_fingerprint_prediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint | Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) *FeaturesApi* | [**get_formula_annotated_ms_ms_data**](docs/FeaturesApi.md#get_formula_annotated_ms_ms_data) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata | Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId *FeaturesApi* | [**get_formula_annotated_spectrum**](docs/FeaturesApi.md#get_formula_annotated_spectrum) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum | Returns a fragmentation spectrum (e @@ -136,21 +112,14 @@ Class | Method | HTTP request | Description *FeaturesApi* | [**get_isotope_pattern_annotation**](docs/FeaturesApi.md#get_isotope_pattern_annotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern | Returns Isotope pattern information for given formulaId *FeaturesApi* | [**get_lipid_annotation**](docs/FeaturesApi.md#get_lipid_annotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation | Returns Lipid annotation (ElGordo) for the given formulaId *FeaturesApi* | [**get_ms_data**](docs/FeaturesApi.md#get_ms_data) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data | Mass Spec data (input data) for the given 'alignedFeatureId' . -*FeaturesApi* | [**get_quant_table_row_experimental**](docs/FeaturesApi.md#get_quant_table_row_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) *FeaturesApi* | [**get_spectral_library_match**](docs/FeaturesApi.md#get_spectral_library_match) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId} | Spectral library match for the given 'alignedFeatureId'. *FeaturesApi* | [**get_spectral_library_matches**](docs/FeaturesApi.md#get_spectral_library_matches) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches | List of spectral library matches for the given 'alignedFeatureId'. *FeaturesApi* | [**get_spectral_library_matches_paged**](docs/FeaturesApi.md#get_spectral_library_matches_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page | Page of spectral library matches for the given 'alignedFeatureId'. *FeaturesApi* | [**get_spectral_library_matches_summary**](docs/FeaturesApi.md#get_spectral_library_matches_summary) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary | Summarize matched reference spectra for the given 'alignedFeatureId'. -*FeaturesApi* | [**get_structure_annotated_ms_data_experimental**](docs/FeaturesApi.md#get_structure_annotated_ms_data_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata | [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey -*FeaturesApi* | [**get_structure_annotated_spectral_library_match_experimental**](docs/FeaturesApi.md#get_structure_annotated_spectral_library_match_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated | [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations -*FeaturesApi* | [**get_structure_annotated_spectrum_experimental**](docs/FeaturesApi.md#get_structure_annotated_spectrum_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum | [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey *FeaturesApi* | [**get_structure_candidates**](docs/FeaturesApi.md#get_structure_candidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures | List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. *FeaturesApi* | [**get_structure_candidates_by_formula**](docs/FeaturesApi.md#get_structure_candidates_by_formula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures | List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. *FeaturesApi* | [**get_structure_candidates_by_formula_paged**](docs/FeaturesApi.md#get_structure_candidates_by_formula_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page | Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. *FeaturesApi* | [**get_structure_candidates_paged**](docs/FeaturesApi.md#get_structure_candidates_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page | Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. -*FeaturesApi* | [**get_tags_for_aligned_features_experimental**](docs/FeaturesApi.md#get_tags_for_aligned_features_experimental) | **GET** /api/projects/{projectId}/aligned-features/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Object -*FeaturesApi* | [**get_traces_experimental**](docs/FeaturesApi.md#get_traces_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces | [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) -*FeaturesApi* | [**remove_tag_from_aligned_feature_experimental**](docs/FeaturesApi.md#remove_tag_from_aligned_feature_experimental) | **DELETE** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space *GuiApi* | [**close_gui**](docs/GuiApi.md#close_gui) | **DELETE** /api/projects/{projectId}/gui | Close GUI instance of given project-space if available. *GuiApi* | [**get_guis**](docs/GuiApi.md#get_guis) | **GET** /api/guis | Get list of currently running gui windows, managed by this SIRIUS instance. *GuiApi* | [**open_gui**](docs/GuiApi.md#open_gui) | **POST** /api/projects/{projectId}/gui | Open GUI instance on specified project-space and bring the GUI window to foreground. @@ -192,15 +161,7 @@ Class | Method | HTTP request | Description *ProjectsApi* | [**import_preprocessed_data**](docs/ProjectsApi.md#import_preprocessed_data) | **POST** /api/projects/{projectId}/import/preprocessed-data-files | Import already preprocessed ms/ms data from various formats into the specified project Possible formats (ms, mgf, cef, msp) *ProjectsApi* | [**import_preprocessed_data_as_job**](docs/ProjectsApi.md#import_preprocessed_data_as_job) | **POST** /api/projects/{projectId}/import/preprocessed-data-files-job | Import ms/ms data from the given format into the specified project-space as background job. *ProjectsApi* | [**open_project**](docs/ProjectsApi.md#open_project) | **PUT** /api/projects/{projectId} | Open an existing project-space and make it accessible via the given projectId. -*RunsApi* | [**add_tags_to_run_experimental**](docs/RunsApi.md#add_tags_to_run_experimental) | **PUT** /api/projects/{projectId}/runs/tags/{runId} | [EXPERIMENTAL] Add tags to a run in the project -*RunsApi* | [**compute_fold_change_for_blank_subtraction**](docs/RunsApi.md#compute_fold_change_for_blank_subtraction) | **PUT** /api/projects/{projectId}/runs/blanksubtract/compute | **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter -*RunsApi* | [**get_run_experimental**](docs/RunsApi.md#get_run_experimental) | **GET** /api/projects/{projectId}/runs/{runId} | [EXPERIMENTAL] Get run with the given identifier from the specified project-space -*RunsApi* | [**get_run_page_experimental**](docs/RunsApi.md#get_run_page_experimental) | **GET** /api/projects/{projectId}/runs/page | [EXPERIMENTAL] Get all available runs in the given project-space -*RunsApi* | [**get_runs_by_group_experimental**](docs/RunsApi.md#get_runs_by_group_experimental) | **GET** /api/projects/{projectId}/runs/grouped | [EXPERIMENTAL] Get runs by tag group -*RunsApi* | [**get_runs_by_tag_experimental**](docs/RunsApi.md#get_runs_by_tag_experimental) | **GET** /api/projects/{projectId}/runs/tagged | [EXPERIMENTAL] Get runs by tag -*RunsApi* | [**get_tags_for_run_experimental**](docs/RunsApi.md#get_tags_for_run_experimental) | **GET** /api/projects/{projectId}/runs/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Run -*RunsApi* | [**remove_tag_from_run_experimental**](docs/RunsApi.md#remove_tag_from_run_experimental) | **DELETE** /api/projects/{projectId}/runs/tags/{runId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space -*SearchableDatabasesApi* | [**add_databases**](docs/SearchableDatabasesApi.md#add_databases) | **POST** /api/databases | DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. +*SearchableDatabasesApi* | [**add_databases**](docs/SearchableDatabasesApi.md#add_databases) | **POST** /api/databases | [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. *SearchableDatabasesApi* | [**create_database**](docs/SearchableDatabasesApi.md#create_database) | **POST** /api/databases/{databaseId} | *SearchableDatabasesApi* | [**get_custom_databases**](docs/SearchableDatabasesApi.md#get_custom_databases) | **GET** /api/databases/custom | *SearchableDatabasesApi* | [**get_database**](docs/SearchableDatabasesApi.md#get_database) | **GET** /api/databases/{databaseId} | @@ -209,34 +170,19 @@ Class | Method | HTTP request | Description *SearchableDatabasesApi* | [**import_into_database**](docs/SearchableDatabasesApi.md#import_into_database) | **POST** /api/databases/{databaseId}/import/from-files | Start import of structure and spectra files into the specified database. *SearchableDatabasesApi* | [**remove_database**](docs/SearchableDatabasesApi.md#remove_database) | **DELETE** /api/databases/{databaseId} | *SearchableDatabasesApi* | [**update_database**](docs/SearchableDatabasesApi.md#update_database) | **PUT** /api/databases/{databaseId} | -*TagsApi* | [**add_group**](docs/TagsApi.md#add_group) | **POST** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Group tags in the project -*TagsApi* | [**add_possible_values_to_tag_definition**](docs/TagsApi.md#add_possible_values_to_tag_definition) | **PATCH** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Add a possible value to the tag definition in the project -*TagsApi* | [**create_tags**](docs/TagsApi.md#create_tags) | **PUT** /api/projects/{projectId}/tags | [EXPERIMENTAL] Add tags to the project -*TagsApi* | [**delete_group**](docs/TagsApi.md#delete_group) | **DELETE** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space -*TagsApi* | [**delete_tag**](docs/TagsApi.md#delete_tag) | **DELETE** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space -*TagsApi* | [**get_group_by_name**](docs/TagsApi.md#get_group_by_name) | **GET** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Get tag group by name in the given project-space -*TagsApi* | [**get_groups**](docs/TagsApi.md#get_groups) | **GET** /api/projects/{projectId}/groups | [EXPERIMENTAL] Get all tag based groups in the given project-space -*TagsApi* | [**get_tag**](docs/TagsApi.md#get_tag) | **GET** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Get tag definition by its name in the given project-space -*TagsApi* | [**get_tags**](docs/TagsApi.md#get_tags) | **GET** /api/projects/{projectId}/tags | [EXPERIMENTAL] Get all tag definitions in the given project-space ## Documentation For Models - [AccountCredentials](docs/AccountCredentials.md) - [AccountInfo](docs/AccountInfo.md) - - [AdductEdgeExperimental](docs/AdductEdgeExperimental.md) - - [AdductNetworkExperimental](docs/AdductNetworkExperimental.md) - - [AdductNodeExperimental](docs/AdductNodeExperimental.md) - - [AggregationType](docs/AggregationType.md) - [AlignedFeature](docs/AlignedFeature.md) - [AlignedFeatureOptField](docs/AlignedFeatureOptField.md) - - [AlignedFeatureQualityExperimental](docs/AlignedFeatureQualityExperimental.md) - [AllowedFeatures](docs/AllowedFeatures.md) - [AnnotatedMsMsData](docs/AnnotatedMsMsData.md) - [AnnotatedPeak](docs/AnnotatedPeak.md) - [AnnotatedSpectrum](docs/AnnotatedSpectrum.md) - [ApiVersion](docs/ApiVersion.md) - - [Axes](docs/Axes.md) - [BackgroundComputationsStateEvent](docs/BackgroundComputationsStateEvent.md) - [BasicSpectrum](docs/BasicSpectrum.md) - [BinaryFingerprint](docs/BinaryFingerprint.md) @@ -244,7 +190,6 @@ Class | Method | HTTP request | Description - [BioTransformerSequenceStep](docs/BioTransformerSequenceStep.md) - [Canopus](docs/Canopus.md) - [CanopusPrediction](docs/CanopusPrediction.md) - - [Category](docs/Category.md) - [Compound](docs/Compound.md) - [CompoundClass](docs/CompoundClass.md) - [CompoundClassType](docs/CompoundClassType.md) @@ -269,7 +214,6 @@ Class | Method | HTTP request | Description - [FeatureAnnotations](docs/FeatureAnnotations.md) - [FeatureImport](docs/FeatureImport.md) - [FingerprintPrediction](docs/FingerprintPrediction.md) - - [FoldChange](docs/FoldChange.md) - [FormulaCandidate](docs/FormulaCandidate.md) - [FormulaCandidateOptField](docs/FormulaCandidateOptField.md) - [FragmentNode](docs/FragmentNode.md) @@ -299,7 +243,6 @@ Class | Method | HTTP request | Description - [PagedModelCompound](docs/PagedModelCompound.md) - [PagedModelFormulaCandidate](docs/PagedModelFormulaCandidate.md) - [PagedModelJob](docs/PagedModelJob.md) - - [PagedModelRun](docs/PagedModelRun.md) - [PagedModelSpectralLibraryMatch](docs/PagedModelSpectralLibraryMatch.md) - [PagedModelStructureCandidateFormula](docs/PagedModelStructureCandidateFormula.md) - [PagedModelStructureCandidateScored](docs/PagedModelStructureCandidateScored.md) @@ -311,14 +254,6 @@ Class | Method | HTTP request | Description - [ProjectInfo](docs/ProjectInfo.md) - [ProjectInfoOptField](docs/ProjectInfoOptField.md) - [ProjectType](docs/ProjectType.md) - - [QualityItem](docs/QualityItem.md) - - [QualityWeight](docs/QualityWeight.md) - - [QuantMeasure](docs/QuantMeasure.md) - - [QuantRowType](docs/QuantRowType.md) - - [QuantTableExperimental](docs/QuantTableExperimental.md) - - [Run](docs/Run.md) - - [RunOptField](docs/RunOptField.md) - - [SampleTypeFoldChangeRequest](docs/SampleTypeFoldChangeRequest.md) - [SearchableDatabase](docs/SearchableDatabase.md) - [SearchableDatabaseParameters](docs/SearchableDatabaseParameters.md) - [SecurityContext](docs/SecurityContext.md) @@ -334,8 +269,6 @@ Class | Method | HTTP request | Description - [SpectralMatchingType](docs/SpectralMatchingType.md) - [SpectrumAnnotation](docs/SpectrumAnnotation.md) - [SpectrumType](docs/SpectrumType.md) - - [StatisticsTable](docs/StatisticsTable.md) - - [StatisticsType](docs/StatisticsType.md) - [StoredJobSubmission](docs/StoredJobSubmission.md) - [StructureCandidate](docs/StructureCandidate.md) - [StructureCandidateFormula](docs/StructureCandidateFormula.md) @@ -345,17 +278,9 @@ Class | Method | HTTP request | Description - [Subscription](docs/Subscription.md) - [SubscriptionConsumables](docs/SubscriptionConsumables.md) - [Tag](docs/Tag.md) - - [TagDefinition](docs/TagDefinition.md) - - [TagDefinitionImport](docs/TagDefinitionImport.md) - - [TagGroup](docs/TagGroup.md) - [Term](docs/Term.md) - [Timeout](docs/Timeout.md) - - [TraceAnnotationExperimental](docs/TraceAnnotationExperimental.md) - - [TraceAnnotationTypeExperimental](docs/TraceAnnotationTypeExperimental.md) - - [TraceExperimental](docs/TraceExperimental.md) - - [TraceSetExperimental](docs/TraceSetExperimental.md) - [UseHeuristic](docs/UseHeuristic.md) - - [ValueType](docs/ValueType.md) - [WebServerNamespace](docs/WebServerNamespace.md) - [Zodiac](docs/Zodiac.md) - [ZodiacAnalogueNodes](docs/ZodiacAnalogueNodes.md) diff --git a/client-api_python/generated/docs/AdductEdgeExperimental.md b/client-api_python/generated/docs/AdductEdgeExperimental.md deleted file mode 100644 index e0be3313..00000000 --- a/client-api_python/generated/docs/AdductEdgeExperimental.md +++ /dev/null @@ -1,38 +0,0 @@ -# AdductEdgeExperimental - -EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**mz_delta** | **float** | | [optional] -**annotation** | **str** | | [optional] -**var_from** | **int** | | [optional] -**to** | **int** | | [optional] -**merged_correlation** | **float** | | [optional] -**representative_correlation** | **float** | | [optional] -**ms2cosine** | **float** | | [optional] -**pvalue** | **float** | | [optional] -**intensity_ratio_score** | **float** | | [optional] - -## Example - -```python -from PySirius.models.adduct_edge_experimental import AdductEdgeExperimental - -# TODO update the JSON string below -json = "{}" -# create an instance of AdductEdgeExperimental from a JSON string -adduct_edge_experimental_instance = AdductEdgeExperimental.from_json(json) -# print the JSON string representation of the object -print(AdductEdgeExperimental.to_json()) - -# convert the object into a dict -adduct_edge_experimental_dict = adduct_edge_experimental_instance.to_dict() -# create an instance of AdductEdgeExperimental from a dict -adduct_edge_experimental_from_dict = AdductEdgeExperimental.from_dict(adduct_edge_experimental_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/AdductNetworkExperimental.md b/client-api_python/generated/docs/AdductNetworkExperimental.md deleted file mode 100644 index 1f2ddf89..00000000 --- a/client-api_python/generated/docs/AdductNetworkExperimental.md +++ /dev/null @@ -1,31 +0,0 @@ -# AdductNetworkExperimental - -EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**nodes** | [**List[AdductNodeExperimental]**](AdductNodeExperimental.md) | | [optional] -**edges** | [**List[AdductEdgeExperimental]**](AdductEdgeExperimental.md) | | [optional] - -## Example - -```python -from PySirius.models.adduct_network_experimental import AdductNetworkExperimental - -# TODO update the JSON string below -json = "{}" -# create an instance of AdductNetworkExperimental from a JSON string -adduct_network_experimental_instance = AdductNetworkExperimental.from_json(json) -# print the JSON string representation of the object -print(AdductNetworkExperimental.to_json()) - -# convert the object into a dict -adduct_network_experimental_dict = adduct_network_experimental_instance.to_dict() -# create an instance of AdductNetworkExperimental from a dict -adduct_network_experimental_from_dict = AdductNetworkExperimental.from_dict(adduct_network_experimental_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/AdductNodeExperimental.md b/client-api_python/generated/docs/AdductNodeExperimental.md deleted file mode 100644 index e14d1ed1..00000000 --- a/client-api_python/generated/docs/AdductNodeExperimental.md +++ /dev/null @@ -1,32 +0,0 @@ -# AdductNodeExperimental - -EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**aligned_feature_id** | **str** | | [optional] -**mz** | **float** | | [optional] -**adduct_annotations** | **Dict[str, float]** | | [optional] - -## Example - -```python -from PySirius.models.adduct_node_experimental import AdductNodeExperimental - -# TODO update the JSON string below -json = "{}" -# create an instance of AdductNodeExperimental from a JSON string -adduct_node_experimental_instance = AdductNodeExperimental.from_json(json) -# print the JSON string representation of the object -print(AdductNodeExperimental.to_json()) - -# convert the object into a dict -adduct_node_experimental_dict = adduct_node_experimental_instance.to_dict() -# create an instance of AdductNodeExperimental from a dict -adduct_node_experimental_from_dict = AdductNodeExperimental.from_dict(adduct_node_experimental_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/AggregationType.md b/client-api_python/generated/docs/AggregationType.md deleted file mode 100644 index 1751dc71..00000000 --- a/client-api_python/generated/docs/AggregationType.md +++ /dev/null @@ -1,14 +0,0 @@ -# AggregationType - - -## Enum - -* `AVG` (value: `'AVG'`) - -* `MIN` (value: `'MIN'`) - -* `MAX` (value: `'MAX'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/AlignedFeatureQualityExperimental.md b/client-api_python/generated/docs/AlignedFeatureQualityExperimental.md deleted file mode 100644 index e095cfa1..00000000 --- a/client-api_python/generated/docs/AlignedFeatureQualityExperimental.md +++ /dev/null @@ -1,32 +0,0 @@ -# AlignedFeatureQualityExperimental - -EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**aligned_feature_id** | **str** | Id of the feature (aligned over runs) this quality information belongs to. | -**overall_quality** | [**DataQuality**](DataQuality.md) | | -**categories** | [**Dict[str, Category]**](Category.md) | Contains all pre-computation quality information that belong to this feature (aligned over runs), such as information about the quality of the peak shape, MS2 spectrum etc., | - -## Example - -```python -from PySirius.models.aligned_feature_quality_experimental import AlignedFeatureQualityExperimental - -# TODO update the JSON string below -json = "{}" -# create an instance of AlignedFeatureQualityExperimental from a JSON string -aligned_feature_quality_experimental_instance = AlignedFeatureQualityExperimental.from_json(json) -# print the JSON string representation of the object -print(AlignedFeatureQualityExperimental.to_json()) - -# convert the object into a dict -aligned_feature_quality_experimental_dict = aligned_feature_quality_experimental_instance.to_dict() -# create an instance of AlignedFeatureQualityExperimental from a dict -aligned_feature_quality_experimental_from_dict = AlignedFeatureQualityExperimental.from_dict(aligned_feature_quality_experimental_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/Axes.md b/client-api_python/generated/docs/Axes.md deleted file mode 100644 index 47fad4cf..00000000 --- a/client-api_python/generated/docs/Axes.md +++ /dev/null @@ -1,31 +0,0 @@ -# Axes - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**scan_number** | **List[int]** | | [optional] -**scan_ids** | **List[str]** | | [optional] -**retention_time_in_seconds** | **List[float]** | | [optional] - -## Example - -```python -from PySirius.models.axes import Axes - -# TODO update the JSON string below -json = "{}" -# create an instance of Axes from a JSON string -axes_instance = Axes.from_json(json) -# print the JSON string representation of the object -print(Axes.to_json()) - -# convert the object into a dict -axes_dict = axes_instance.to_dict() -# create an instance of Axes from a dict -axes_from_dict = Axes.from_dict(axes_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/Category.md b/client-api_python/generated/docs/Category.md deleted file mode 100644 index 5a3dce1a..00000000 --- a/client-api_python/generated/docs/Category.md +++ /dev/null @@ -1,31 +0,0 @@ -# Category - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**category_name** | **str** | | [optional] -**overall_quality** | [**DataQuality**](DataQuality.md) | | [optional] -**items** | [**List[QualityItem]**](QualityItem.md) | | [optional] - -## Example - -```python -from PySirius.models.category import Category - -# TODO update the JSON string below -json = "{}" -# create an instance of Category from a JSON string -category_instance = Category.from_json(json) -# print the JSON string representation of the object -print(Category.to_json()) - -# convert the object into a dict -category_dict = category_instance.to_dict() -# create an instance of Category from a dict -category_from_dict = Category.from_dict(category_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/CompoundStatisticsApi.md b/client-api_python/generated/docs/CompoundStatisticsApi.md deleted file mode 100644 index 8532566b..00000000 --- a/client-api_python/generated/docs/CompoundStatisticsApi.md +++ /dev/null @@ -1,322 +0,0 @@ -# PySirius.CompoundStatisticsApi - -All URIs are relative to *http://localhost:8080* - -Method | HTTP request | Description -------------- | ------------- | ------------- -[**compute_compound_fold_changes_experimental**](CompoundStatisticsApi.md#compute_compound_fold_changes_experimental) | **PUT** /api/projects/{projectId}/compounds/statistics/foldchange/compute | [EXPERIMENTAL] Compute the fold change between two groups of runs -[**delete_compound_fold_changes_experimental**](CompoundStatisticsApi.md#delete_compound_fold_changes_experimental) | **DELETE** /api/projects/{projectId}/compounds/statistics/foldchanges | [EXPERIMENTAL] Delete fold changes -[**get_compound_fold_change_table_experimental**](CompoundStatisticsApi.md#get_compound_fold_change_table_experimental) | **GET** /api/projects/{projectId}/compounds/statistics/foldchanges/stats-table | [EXPERIMENTAL] Get table of all fold changes in the project space -[**get_fold_changes_by_compound_experimental**](CompoundStatisticsApi.md#get_fold_changes_by_compound_experimental) | **GET** /api/projects/{projectId}/compounds/statistics/foldchanges/{objectId} | [EXPERIMENTAL] List all fold changes that are associated with an object - - -# **compute_compound_fold_changes_experimental** -> Job compute_compound_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification, opt_fields=opt_fields) - -[EXPERIMENTAL] Compute the fold change between two groups of runs - -[EXPERIMENTAL] Compute the fold change between two groups of runs. -
- The runs need to be tagged and grouped. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.quant_measure import QuantMeasure -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to compute the fold change in. - left_group_name = 'left_group_name_example' # str | name of the left tag group. - right_group_name = 'right_group_name_example' # str | name of the right tag group. - aggregation = PySirius.AggregationType() # AggregationType | aggregation type. (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - opt_fields = ["progress"] # List[JobOptField] | job opt fields. (optional) (default to ["progress"]) - - try: - # [EXPERIMENTAL] Compute the fold change between two groups of runs - api_response = api_instance.compute_compound_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification, opt_fields=opt_fields) - print("The response of CompoundStatisticsApi->compute_compound_fold_changes_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundStatisticsApi->compute_compound_fold_changes_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to compute the fold change in. | - **left_group_name** | **str**| name of the left tag group. | - **right_group_name** | **str**| name of the right tag group. | - **aggregation** | [**AggregationType**](.md)| aggregation type. | [optional] - **quantification** | [**QuantMeasure**](.md)| quantification type. | [optional] - **opt_fields** | [**List[JobOptField]**](JobOptField.md)| job opt fields. | [optional] [default to ["progress"]] - -### Return type - -[**Job**](Job.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **delete_compound_fold_changes_experimental** -> delete_compound_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification) - -[EXPERIMENTAL] Delete fold changes - -[EXPERIMENTAL] Delete fold changes. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - left_group_name = 'left_group_name_example' # str | name of the left group. - right_group_name = 'right_group_name_example' # str | name of the right group. - aggregation = PySirius.AggregationType() # AggregationType | (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | (optional) - - try: - # [EXPERIMENTAL] Delete fold changes - api_instance.delete_compound_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification) - except Exception as e: - print("Exception when calling CompoundStatisticsApi->delete_compound_fold_changes_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **left_group_name** | **str**| name of the left group. | - **right_group_name** | **str**| name of the right group. | - **aggregation** | [**AggregationType**](.md)| | [optional] - **quantification** | [**QuantMeasure**](.md)| | [optional] - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_compound_fold_change_table_experimental** -> StatisticsTable get_compound_fold_change_table_experimental(project_id, aggregation=aggregation, quantification=quantification) - -[EXPERIMENTAL] Get table of all fold changes in the project space - -[EXPERIMENTAL] Get table of all fold changes in the project space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.statistics_table import StatisticsTable -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aggregation = PySirius.AggregationType() # AggregationType | aggregation type. (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - - try: - # [EXPERIMENTAL] Get table of all fold changes in the project space - api_response = api_instance.get_compound_fold_change_table_experimental(project_id, aggregation=aggregation, quantification=quantification) - print("The response of CompoundStatisticsApi->get_compound_fold_change_table_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundStatisticsApi->get_compound_fold_change_table_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aggregation** | [**AggregationType**](.md)| aggregation type. | [optional] - **quantification** | [**QuantMeasure**](.md)| quantification type. | [optional] - -### Return type - -[**StatisticsTable**](StatisticsTable.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | table of fold changes. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_fold_changes_by_compound_experimental** -> List[FoldChange] get_fold_changes_by_compound_experimental(project_id, object_id) - -[EXPERIMENTAL] List all fold changes that are associated with an object - -[EXPERIMENTAL] List all fold changes that are associated with an object. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.fold_change import FoldChange -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - object_id = 'object_id_example' # str | id of the object the fold changes are assigned to. - - try: - # [EXPERIMENTAL] List all fold changes that are associated with an object - api_response = api_instance.get_fold_changes_by_compound_experimental(project_id, object_id) - print("The response of CompoundStatisticsApi->get_fold_changes_by_compound_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundStatisticsApi->get_fold_changes_by_compound_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **object_id** | **str**| id of the object the fold changes are assigned to. | - -### Return type - -[**List[FoldChange]**](FoldChange.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | fold changes | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - diff --git a/client-api_python/generated/docs/CompoundsApi.md b/client-api_python/generated/docs/CompoundsApi.md index 29f799a7..74980452 100644 --- a/client-api_python/generated/docs/CompoundsApi.md +++ b/client-api_python/generated/docs/CompoundsApi.md @@ -5,18 +5,10 @@ All URIs are relative to *http://localhost:8080* Method | HTTP request | Description ------------- | ------------- | ------------- [**add_compounds**](CompoundsApi.md#add_compounds) | **POST** /api/projects/{projectId}/compounds | Import Compounds and its contained features. -[**add_tags_to_compound_experimental**](CompoundsApi.md#add_tags_to_compound_experimental) | **PUT** /api/projects/{projectId}/compounds/tags/{compoundId} | [EXPERIMENTAL] Tags with the same name will be overwritten [**delete_compound**](CompoundsApi.md#delete_compound) | **DELETE** /api/projects/{projectId}/compounds/{compoundId} | Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. [**get_compound**](CompoundsApi.md#get_compound) | **GET** /api/projects/{projectId}/compounds/{compoundId} | Get compound (group of ion identities) with the given identifier from the specified project-space. -[**get_compound_quant_table_experimental**](CompoundsApi.md#get_compound_quant_table_experimental) | **GET** /api/projects/{projectId}/compounds/quant-table | [EXPERIMENTAL] Returns the full quantification table of compounds -[**get_compound_quant_table_row_experimental**](CompoundsApi.md#get_compound_quant_table_row_experimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given compound -[**get_compound_traces_experimental**](CompoundsApi.md#get_compound_traces_experimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/traces | [EXPERIMENTAL] Returns the traces of the given compound [**get_compounds**](CompoundsApi.md#get_compounds) | **GET** /api/projects/{projectId}/compounds | List of all available compounds (group of ion identities) in the given project-space. -[**get_compounds_by_group_experimental**](CompoundsApi.md#get_compounds_by_group_experimental) | **GET** /api/projects/{projectId}/compounds/grouped | [EXPERIMENTAL] Get compounds (group of ion identities) by tag group -[**get_compounds_by_tag_experimental**](CompoundsApi.md#get_compounds_by_tag_experimental) | **GET** /api/projects/{projectId}/compounds/tagged | [EXPERIMENTAL] Get compounds (group of ion identities) by tag [**get_compounds_paged**](CompoundsApi.md#get_compounds_paged) | **GET** /api/projects/{projectId}/compounds/page | Page of available compounds (group of ion identities) in the given project-space. -[**get_tags_for_compound_experimental**](CompoundsApi.md#get_tags_for_compound_experimental) | **GET** /api/projects/{projectId}/compounds/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Compound -[**remove_tag_from_compound_experimental**](CompoundsApi.md#remove_tag_from_compound_experimental) | **DELETE** /api/projects/{projectId}/compounds/tags/{compoundId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space # **add_compounds** @@ -100,80 +92,6 @@ No authorization required [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **add_tags_to_compound_experimental** -> List[Tag] add_tags_to_compound_experimental(project_id, compound_id, tag) - -[EXPERIMENTAL] Tags with the same name will be overwritten - -[EXPERIMENTAL] Tags with the same name will be overwritten. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag import Tag -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to add to. - compound_id = 'compound_id_example' # str | compound (group of ion identities) to add tags to. - tag = [PySirius.Tag()] # List[Tag] | tags to add. - - try: - # [EXPERIMENTAL] Tags with the same name will be overwritten - api_response = api_instance.add_tags_to_compound_experimental(project_id, compound_id, tag) - print("The response of CompoundsApi->add_tags_to_compound_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundsApi->add_tags_to_compound_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to add to. | - **compound_id** | **str**| compound (group of ion identities) to add tags to. | - **tag** | [**List[Tag]**](Tag.md)| tags to add. | - -### Return type - -[**List[Tag]**](Tag.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: application/json - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | the tags that have been added | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - # **delete_compound** > delete_compound(project_id, compound_id) @@ -320,240 +238,6 @@ No authorization required [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_compound_quant_table_experimental** -> QuantTableExperimental get_compound_quant_table_experimental(project_id, type=type) - -[EXPERIMENTAL] Returns the full quantification table of compounds - -[EXPERIMENTAL] Returns the full quantification table of compounds. -
- The quantification table contains a quantification of the features within all - runs they are contained in. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - -### Example - - -```python -import PySirius -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - type = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - - try: - # [EXPERIMENTAL] Returns the full quantification table of compounds - api_response = api_instance.get_compound_quant_table_experimental(project_id, type=type) - print("The response of CompoundsApi->get_compound_quant_table_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundsApi->get_compound_quant_table_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **type** | [**QuantMeasure**](.md)| quantification type. | [optional] - -### Return type - -[**QuantTableExperimental**](QuantTableExperimental.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_compound_quant_table_row_experimental** -> QuantTableExperimental get_compound_quant_table_row_experimental(project_id, compound_id, type=type) - -[EXPERIMENTAL] Returns a single quantification table row for the given compound - -[EXPERIMENTAL] Returns a single quantification table row for the given compound. -
- The quantification table contains a quantification of the feature within all - samples it is contained in. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - -### Example - - -```python -import PySirius -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - compound_id = 'compound_id_example' # str | compound which should be read out - type = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - - try: - # [EXPERIMENTAL] Returns a single quantification table row for the given compound - api_response = api_instance.get_compound_quant_table_row_experimental(project_id, compound_id, type=type) - print("The response of CompoundsApi->get_compound_quant_table_row_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundsApi->get_compound_quant_table_row_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **compound_id** | **str**| compound which should be read out | - **type** | [**QuantMeasure**](.md)| quantification type. | [optional] - -### Return type - -[**QuantTableExperimental**](QuantTableExperimental.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_compound_traces_experimental** -> TraceSetExperimental get_compound_traces_experimental(project_id, compound_id, feature_id=feature_id) - -[EXPERIMENTAL] Returns the traces of the given compound - -[EXPERIMENTAL] Returns the traces of the given compound. -
- A trace consists of m/z and intensity values over the retention - time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, - but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. - However, this also means that all traces can be directly compared against each other, as they all lie in the same - retention time axis. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.* - -### Example - - -```python -import PySirius -from PySirius.models.trace_set_experimental import TraceSetExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - compound_id = 'compound_id_example' # str | compound which intensities should be read out - feature_id = '' # str | (optional) (default to '') - - try: - # [EXPERIMENTAL] Returns the traces of the given compound - api_response = api_instance.get_compound_traces_experimental(project_id, compound_id, feature_id=feature_id) - print("The response of CompoundsApi->get_compound_traces_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundsApi->get_compound_traces_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **compound_id** | **str**| compound which intensities should be read out | - **feature_id** | **str**| | [optional] [default to ''] - -### Return type - -[**TraceSetExperimental**](TraceSetExperimental.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Traces of the given compound. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - # **get_compounds** > List[Compound] get_compounds(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields, opt_fields_features=opt_fields_features) @@ -630,197 +314,6 @@ No authorization required [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_compounds_by_group_experimental** -> PagedModelCompound get_compounds_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) - -[EXPERIMENTAL] Get compounds (group of ion identities) by tag group - -[EXPERIMENTAL] Get compounds (group of ion identities) by tag group. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.compound_opt_field import CompoundOptField -from PySirius.models.paged_model_compound import PagedModelCompound -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - group_name = 'group_name_example' # str | tag group name. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = ["none"] # List[CompoundOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) - - try: - # [EXPERIMENTAL] Get compounds (group of ion identities) by tag group - api_response = api_instance.get_compounds_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of CompoundsApi->get_compounds_by_group_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling CompoundsApi->get_compounds_by_group_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **group_name** | **str**| tag group name. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[CompoundOptField]**](CompoundOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] - -### Return type - -[**PagedModelCompound**](PagedModelCompound.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | tagged compounds (group of ion identities) | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_compounds_by_tag_experimental** -> PagedModelCompound get_compounds_by_tag_experimental(project_id, filter=filter, page=page, size=size, sort=sort, opt_fields=opt_fields) - -[EXPERIMENTAL] Get compounds (group of ion identities) by tag - -[EXPERIMENTAL] Get compounds (group of ion identities) by tag. - -
The filter string must contain one or more clauses. A clause is prefÃxed - by a field name. -
- - Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).
- Tag name based field need to be prefixed with the namespace tags..
- Possible value types of tags are bool, integer, real, text, date, or time - tag value
-
- The format of the date type is yyyy-MM-dd and of the time type is HH\:mm\:ss.
A clause may be:
-tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
- -tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\:00\:00 OR tags.time:[12\:00\:00 TO 14\:00\:00] OR tags.time<10\:00\:00
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.CompoundsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - compound_id = 'compound_id_example' # str | compound (group of ion identities) to delete tag from. - tag_name = 'tag_name_example' # str | name of the tag to delete. - - try: - # [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space - api_instance.remove_tag_from_compound_experimental(project_id, compound_id, tag_name) - except Exception as e: - print("Exception when calling CompoundsApi->remove_tag_from_compound_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **compound_id** | **str**| compound (group of ion identities) to delete tag from. | - **tag_name** | **str**| name of the tag to delete. | - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - diff --git a/client-api_python/generated/docs/FeatureStatisticsApi.md b/client-api_python/generated/docs/FeatureStatisticsApi.md deleted file mode 100644 index 53d15570..00000000 --- a/client-api_python/generated/docs/FeatureStatisticsApi.md +++ /dev/null @@ -1,322 +0,0 @@ -# PySirius.FeatureStatisticsApi - -All URIs are relative to *http://localhost:8080* - -Method | HTTP request | Description -------------- | ------------- | ------------- -[**compute_aligned_feature_fold_changes_experimental**](FeatureStatisticsApi.md#compute_aligned_feature_fold_changes_experimental) | **PUT** /api/projects/{projectId}/aligned-features/statistics/foldchange/compute | [EXPERIMENTAL] Compute the fold change between two groups of runs -[**delete_aligned_feature_fold_changes_experimental**](FeatureStatisticsApi.md#delete_aligned_feature_fold_changes_experimental) | **DELETE** /api/projects/{projectId}/aligned-features/statistics/foldchanges | [EXPERIMENTAL] Delete fold changes -[**get_aligned_feature_fold_change_table_experimental**](FeatureStatisticsApi.md#get_aligned_feature_fold_change_table_experimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table | [EXPERIMENTAL] Get table of all fold changes in the project space -[**get_fold_changes_by_aligned_feature_experimental**](FeatureStatisticsApi.md#get_fold_changes_by_aligned_feature_experimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId} | [EXPERIMENTAL] List all fold changes that are associated with an object - - -# **compute_aligned_feature_fold_changes_experimental** -> Job compute_aligned_feature_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification, opt_fields=opt_fields) - -[EXPERIMENTAL] Compute the fold change between two groups of runs - -[EXPERIMENTAL] Compute the fold change between two groups of runs. -
- The runs need to be tagged and grouped. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.quant_measure import QuantMeasure -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeatureStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to compute the fold change in. - left_group_name = 'left_group_name_example' # str | name of the left tag group. - right_group_name = 'right_group_name_example' # str | name of the right tag group. - aggregation = PySirius.AggregationType() # AggregationType | aggregation type. (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - opt_fields = ["progress"] # List[JobOptField] | job opt fields. (optional) (default to ["progress"]) - - try: - # [EXPERIMENTAL] Compute the fold change between two groups of runs - api_response = api_instance.compute_aligned_feature_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification, opt_fields=opt_fields) - print("The response of FeatureStatisticsApi->compute_aligned_feature_fold_changes_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeatureStatisticsApi->compute_aligned_feature_fold_changes_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to compute the fold change in. | - **left_group_name** | **str**| name of the left tag group. | - **right_group_name** | **str**| name of the right tag group. | - **aggregation** | [**AggregationType**](.md)| aggregation type. | [optional] - **quantification** | [**QuantMeasure**](.md)| quantification type. | [optional] - **opt_fields** | [**List[JobOptField]**](JobOptField.md)| job opt fields. | [optional] [default to ["progress"]] - -### Return type - -[**Job**](Job.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **delete_aligned_feature_fold_changes_experimental** -> delete_aligned_feature_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification) - -[EXPERIMENTAL] Delete fold changes - -[EXPERIMENTAL] Delete fold changes. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeatureStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - left_group_name = 'left_group_name_example' # str | name of the left group. - right_group_name = 'right_group_name_example' # str | name of the right group. - aggregation = PySirius.AggregationType() # AggregationType | (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | (optional) - - try: - # [EXPERIMENTAL] Delete fold changes - api_instance.delete_aligned_feature_fold_changes_experimental(project_id, left_group_name, right_group_name, aggregation=aggregation, quantification=quantification) - except Exception as e: - print("Exception when calling FeatureStatisticsApi->delete_aligned_feature_fold_changes_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **left_group_name** | **str**| name of the left group. | - **right_group_name** | **str**| name of the right group. | - **aggregation** | [**AggregationType**](.md)| | [optional] - **quantification** | [**QuantMeasure**](.md)| | [optional] - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_aligned_feature_fold_change_table_experimental** -> StatisticsTable get_aligned_feature_fold_change_table_experimental(project_id, aggregation=aggregation, quantification=quantification) - -[EXPERIMENTAL] Get table of all fold changes in the project space - -[EXPERIMENTAL] Get table of all fold changes in the project space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.aggregation_type import AggregationType -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.statistics_table import StatisticsTable -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeatureStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aggregation = PySirius.AggregationType() # AggregationType | aggregation type. (optional) - quantification = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - - try: - # [EXPERIMENTAL] Get table of all fold changes in the project space - api_response = api_instance.get_aligned_feature_fold_change_table_experimental(project_id, aggregation=aggregation, quantification=quantification) - print("The response of FeatureStatisticsApi->get_aligned_feature_fold_change_table_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeatureStatisticsApi->get_aligned_feature_fold_change_table_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aggregation** | [**AggregationType**](.md)| aggregation type. | [optional] - **quantification** | [**QuantMeasure**](.md)| quantification type. | [optional] - -### Return type - -[**StatisticsTable**](StatisticsTable.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | table of fold changes. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_fold_changes_by_aligned_feature_experimental** -> List[FoldChange] get_fold_changes_by_aligned_feature_experimental(project_id, object_id) - -[EXPERIMENTAL] List all fold changes that are associated with an object - -[EXPERIMENTAL] List all fold changes that are associated with an object. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.fold_change import FoldChange -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeatureStatisticsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - object_id = 'object_id_example' # str | id of the object the fold changes are assigned to. - - try: - # [EXPERIMENTAL] List all fold changes that are associated with an object - api_response = api_instance.get_fold_changes_by_aligned_feature_experimental(project_id, object_id) - print("The response of FeatureStatisticsApi->get_fold_changes_by_aligned_feature_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeatureStatisticsApi->get_fold_changes_by_aligned_feature_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **object_id** | **str**| id of the object the fold changes are assigned to. | - -### Return type - -[**List[FoldChange]**](FoldChange.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | fold changes | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - diff --git a/client-api_python/generated/docs/FeaturesApi.md b/client-api_python/generated/docs/FeaturesApi.md index a58240a6..473aee9b 100644 --- a/client-api_python/generated/docs/FeaturesApi.md +++ b/client-api_python/generated/docs/FeaturesApi.md @@ -5,24 +5,16 @@ All URIs are relative to *http://localhost:8080* Method | HTTP request | Description ------------- | ------------- | ------------- [**add_aligned_features**](FeaturesApi.md#add_aligned_features) | **POST** /api/projects/{projectId}/aligned-features | Import (aligned) features into the project. -[**add_de_novo_structure_candidate**](FeaturesApi.md#add_de_novo_structure_candidate) | **PUT** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. -[**add_tags_to_aligned_feature_experimental**](FeaturesApi.md#add_tags_to_aligned_feature_experimental) | **PUT** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId} | [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project [**delete_aligned_feature**](FeaturesApi.md#delete_aligned_feature) | **DELETE** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Delete feature (aligned over runs) with the given identifier from the specified project-space. [**delete_aligned_features**](FeaturesApi.md#delete_aligned_features) | **PUT** /api/projects/{projectId}/aligned-features/delete | Delete feature (aligned over runs) with the given identifier from the specified project-space. -[**get_adduct_network_with_merged_traces_experimental**](FeaturesApi.md#get_adduct_network_with_merged_traces_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts | [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network [**get_aligned_feature**](FeaturesApi.md#get_aligned_feature) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Get feature (aligned over runs) with the given identifier from the specified project-space. -[**get_aligned_feature_quality_experimental**](FeaturesApi.md#get_aligned_feature_quality_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report | [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) [**get_aligned_features**](FeaturesApi.md#get_aligned_features) | **GET** /api/projects/{projectId}/aligned-features | Get all available features (aligned over runs) in the given project-space. -[**get_aligned_features_by_group_experimental**](FeaturesApi.md#get_aligned_features_by_group_experimental) | **GET** /api/projects/{projectId}/aligned-features/grouped | [EXPERIMENTAL] Get features (aligned over runs) by tag group -[**get_aligned_features_by_tag_experimental**](FeaturesApi.md#get_aligned_features_by_tag_experimental) | **GET** /api/projects/{projectId}/aligned-features/tagged | [EXPERIMENTAL] Get features (aligned over runs) by tag [**get_aligned_features_paged**](FeaturesApi.md#get_aligned_features_paged) | **GET** /api/projects/{projectId}/aligned-features/page | Get all available features (aligned over runs) in the given project-space. [**get_best_matching_compound_classes**](FeaturesApi.md#get_best_matching_compound_classes) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes | Return Best matching compound classes for given formulaId [**get_canopus_prediction**](FeaturesApi.md#get_canopus_prediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction | All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, -[**get_de_novo_structure_candidates**](FeaturesApi.md#get_de_novo_structure_candidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. [**get_de_novo_structure_candidates_by_formula**](FeaturesApi.md#get_de_novo_structure_candidates_by_formula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. [**get_de_novo_structure_candidates_by_formula_paged**](FeaturesApi.md#get_de_novo_structure_candidates_by_formula_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. [**get_de_novo_structure_candidates_paged**](FeaturesApi.md#get_de_novo_structure_candidates_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. -[**get_feature_quant_table_experimental**](FeaturesApi.md#get_feature_quant_table_experimental) | **GET** /api/projects/{projectId}/aligned-features/quant-table | [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) [**get_fingerprint_prediction**](FeaturesApi.md#get_fingerprint_prediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint | Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) [**get_formula_annotated_ms_ms_data**](FeaturesApi.md#get_formula_annotated_ms_ms_data) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata | Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId [**get_formula_annotated_spectrum**](FeaturesApi.md#get_formula_annotated_spectrum) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum | Returns a fragmentation spectrum (e @@ -33,21 +25,14 @@ Method | HTTP request | Description [**get_isotope_pattern_annotation**](FeaturesApi.md#get_isotope_pattern_annotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern | Returns Isotope pattern information for given formulaId [**get_lipid_annotation**](FeaturesApi.md#get_lipid_annotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation | Returns Lipid annotation (ElGordo) for the given formulaId [**get_ms_data**](FeaturesApi.md#get_ms_data) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data | Mass Spec data (input data) for the given 'alignedFeatureId' . -[**get_quant_table_row_experimental**](FeaturesApi.md#get_quant_table_row_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) [**get_spectral_library_match**](FeaturesApi.md#get_spectral_library_match) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId} | Spectral library match for the given 'alignedFeatureId'. [**get_spectral_library_matches**](FeaturesApi.md#get_spectral_library_matches) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches | List of spectral library matches for the given 'alignedFeatureId'. [**get_spectral_library_matches_paged**](FeaturesApi.md#get_spectral_library_matches_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page | Page of spectral library matches for the given 'alignedFeatureId'. [**get_spectral_library_matches_summary**](FeaturesApi.md#get_spectral_library_matches_summary) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary | Summarize matched reference spectra for the given 'alignedFeatureId'. -[**get_structure_annotated_ms_data_experimental**](FeaturesApi.md#get_structure_annotated_ms_data_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata | [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey -[**get_structure_annotated_spectral_library_match_experimental**](FeaturesApi.md#get_structure_annotated_spectral_library_match_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated | [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations -[**get_structure_annotated_spectrum_experimental**](FeaturesApi.md#get_structure_annotated_spectrum_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum | [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey [**get_structure_candidates**](FeaturesApi.md#get_structure_candidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures | List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. [**get_structure_candidates_by_formula**](FeaturesApi.md#get_structure_candidates_by_formula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures | List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. [**get_structure_candidates_by_formula_paged**](FeaturesApi.md#get_structure_candidates_by_formula_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page | Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. [**get_structure_candidates_paged**](FeaturesApi.md#get_structure_candidates_paged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page | Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. -[**get_tags_for_aligned_features_experimental**](FeaturesApi.md#get_tags_for_aligned_features_experimental) | **GET** /api/projects/{projectId}/aligned-features/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Object -[**get_traces_experimental**](FeaturesApi.md#get_traces_experimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces | [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) -[**remove_tag_from_aligned_feature_experimental**](FeaturesApi.md#remove_tag_from_aligned_feature_experimental) | **DELETE** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space # **add_aligned_features** @@ -128,19 +113,18 @@ No authorization required [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **add_de_novo_structure_candidate** -> List[StructureCandidateFormula] add_de_novo_structure_candidate(project_id, aligned_feature_id, smiles=smiles) +# **delete_aligned_feature** +> delete_aligned_feature(project_id, aligned_feature_id) -[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. +Delete feature (aligned over runs) with the given identifier from the specified project-space. -[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list. +Delete feature (aligned over runs) with the given identifier from the specified project-space. ### Example ```python import PySirius -from PySirius.models.structure_candidate_formula import StructureCandidateFormula from PySirius.rest import ApiException from pprint import pprint @@ -155,17 +139,14 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - smiles = 'none' # str | smiles (optional) (default to 'none') + project_id = 'project_id_example' # str | project-space to delete from. + aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to delete. try: - # [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. - api_response = api_instance.add_de_novo_structure_candidate(project_id, aligned_feature_id, smiles=smiles) - print("The response of FeaturesApi->add_de_novo_structure_candidate:\n") - pprint(api_response) + # Delete feature (aligned over runs) with the given identifier from the specified project-space. + api_instance.delete_aligned_feature(project_id, aligned_feature_id) except Exception as e: - print("Exception when calling FeaturesApi->add_de_novo_structure_candidate: %s\n" % e) + print("Exception when calling FeaturesApi->delete_aligned_feature: %s\n" % e) ``` @@ -175,13 +156,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **smiles** | **str**| smiles | [optional] [default to 'none'] + **project_id** | **str**| project-space to delete from. | + **aligned_feature_id** | **str**| identifier of feature (aligned over runs) to delete. | ### Return type -[**List[StructureCandidateFormula]**](StructureCandidateFormula.md) +void (empty response body) ### Authorization @@ -190,31 +170,28 @@ No authorization required ### HTTP request headers - **Content-Type**: Not defined - - **Accept**: application/json + - **Accept**: Not defined ### HTTP response details | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | StructureCandidate of this feature candidate with specified optional fields. | - | +**200** | OK | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **add_tags_to_aligned_feature_experimental** -> List[Tag] add_tags_to_aligned_feature_experimental(project_id, aligned_feature_id, tag) +# **delete_aligned_features** +> delete_aligned_features(project_id, request_body) -[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project +Delete feature (aligned over runs) with the given identifier from the specified project-space. -[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Delete feature (aligned over runs) with the given identifier from the specified project-space. ### Example ```python import PySirius -from PySirius.models.tag import Tag from PySirius.rest import ApiException from pprint import pprint @@ -229,17 +206,14 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to add to. - aligned_feature_id = 'aligned_feature_id_example' # str | run to add tags to. - tag = [PySirius.Tag()] # List[Tag] | tags to add. + project_id = 'project_id_example' # str | project-space to delete from. + request_body = ['request_body_example'] # List[str] | try: - # [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project - api_response = api_instance.add_tags_to_aligned_feature_experimental(project_id, aligned_feature_id, tag) - print("The response of FeaturesApi->add_tags_to_aligned_feature_experimental:\n") - pprint(api_response) + # Delete feature (aligned over runs) with the given identifier from the specified project-space. + api_instance.delete_aligned_features(project_id, request_body) except Exception as e: - print("Exception when calling FeaturesApi->add_tags_to_aligned_feature_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->delete_aligned_features: %s\n" % e) ``` @@ -249,13 +223,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to add to. | - **aligned_feature_id** | **str**| run to add tags to. | - **tag** | [**List[Tag]**](Tag.md)| tags to add. | + **project_id** | **str**| project-space to delete from. | + **request_body** | [**List[str]**](str.md)| | ### Return type -[**List[Tag]**](Tag.md) +void (empty response body) ### Authorization @@ -264,28 +237,30 @@ No authorization required ### HTTP request headers - **Content-Type**: application/json - - **Accept**: application/json + - **Accept**: Not defined ### HTTP response details | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | the tags that have been added | - | +**200** | OK | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **delete_aligned_feature** -> delete_aligned_feature(project_id, aligned_feature_id) +# **get_aligned_feature** +> AlignedFeature get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -Delete feature (aligned over runs) with the given identifier from the specified project-space. +Get feature (aligned over runs) with the given identifier from the specified project-space. -Delete feature (aligned over runs) with the given identifier from the specified project-space. +Get feature (aligned over runs) with the given identifier from the specified project-space. ### Example ```python import PySirius +from PySirius.models.aligned_feature import AlignedFeature +from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField from PySirius.rest import ApiException from pprint import pprint @@ -300,14 +275,18 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to delete. + project_id = 'project_id_example' # str | project-space to read from. + aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to access. + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # Delete feature (aligned over runs) with the given identifier from the specified project-space. - api_instance.delete_aligned_feature(project_id, aligned_feature_id) + # Get feature (aligned over runs) with the given identifier from the specified project-space. + api_response = api_instance.get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_aligned_feature:\n") + pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->delete_aligned_feature: %s\n" % e) + print("Exception when calling FeaturesApi->get_aligned_feature: %s\n" % e) ``` @@ -317,12 +296,14 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **aligned_feature_id** | **str**| identifier of feature (aligned over runs) to delete. | + **project_id** | **str**| project-space to read from. | + **aligned_feature_id** | **str**| identifier of feature (aligned over runs) to access. | + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -void (empty response body) +[**AlignedFeature**](AlignedFeature.md) ### Authorization @@ -331,28 +312,30 @@ No authorization required ### HTTP request headers - **Content-Type**: Not defined - - **Accept**: Not defined + - **Accept**: application/json ### HTTP response details | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | OK | - | +**200** | AlignedFeature with additional annotations and MS/MS data (if specified). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **delete_aligned_features** -> delete_aligned_features(project_id, request_body) +# **get_aligned_features** +> List[AlignedFeature] get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -Delete feature (aligned over runs) with the given identifier from the specified project-space. +Get all available features (aligned over runs) in the given project-space. -Delete feature (aligned over runs) with the given identifier from the specified project-space. +Get all available features (aligned over runs) in the given project-space. ### Example ```python import PySirius +from PySirius.models.aligned_feature import AlignedFeature +from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField from PySirius.rest import ApiException from pprint import pprint @@ -367,14 +350,17 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - request_body = ['request_body_example'] # List[str] | + project_id = 'project_id_example' # str | project-space to read from. + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # Delete feature (aligned over runs) with the given identifier from the specified project-space. - api_instance.delete_aligned_features(project_id, request_body) + # Get all available features (aligned over runs) in the given project-space. + api_response = api_instance.get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_aligned_features:\n") + pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->delete_aligned_features: %s\n" % e) + print("Exception when calling FeaturesApi->get_aligned_features: %s\n" % e) ``` @@ -384,12 +370,13 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **request_body** | [**List[str]**](str.md)| | + **project_id** | **str**| project-space to read from. | + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -void (empty response body) +[**List[AlignedFeature]**](AlignedFeature.md) ### Authorization @@ -397,32 +384,31 @@ No authorization required ### HTTP request headers - - **Content-Type**: application/json - - **Accept**: Not defined + - **Content-Type**: Not defined + - **Accept**: application/json ### HTTP response details | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | OK | - | +**200** | AlignedFeatures with additional annotations and MS/MS data (if specified). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_adduct_network_with_merged_traces_experimental** -> TraceSetExperimental get_adduct_network_with_merged_traces_experimental(project_id, aligned_feature_id) +# **get_aligned_features_paged** +> PagedModelAlignedFeature get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network +Get all available features (aligned over runs) in the given project-space. -[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Get all available features (aligned over runs) in the given project-space. ### Example ```python import PySirius -from PySirius.models.trace_set_experimental import TraceSetExperimental +from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField +from PySirius.models.paged_model_aligned_feature import PagedModelAlignedFeature from PySirius.rest import ApiException from pprint import pprint @@ -438,15 +424,19 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | one feature that is considered the main feature of the adduct network + page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) + size = 20 # int | The size of the page to be returned (optional) (default to 20) + sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network - api_response = api_instance.get_adduct_network_with_merged_traces_experimental(project_id, aligned_feature_id) - print("The response of FeaturesApi->get_adduct_network_with_merged_traces_experimental:\n") + # Get all available features (aligned over runs) in the given project-space. + api_response = api_instance.get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_aligned_features_paged:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_adduct_network_with_merged_traces_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_aligned_features_paged: %s\n" % e) ``` @@ -457,11 +447,15 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| one feature that is considered the main feature of the adduct network | + **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] + **size** | **int**| The size of the page to be returned | [optional] [default to 20] + **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**TraceSetExperimental**](TraceSetExperimental.md) +[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md) ### Authorization @@ -476,24 +470,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | OK | - | +**200** | AlignedFeatures with additional annotations and MS/MS data (if specified). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_feature** -> AlignedFeature get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) +# **get_best_matching_compound_classes** +> CompoundClasses get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id) -Get feature (aligned over runs) with the given identifier from the specified project-space. +Return Best matching compound classes for given formulaId -Get feature (aligned over runs) with the given identifier from the specified project-space. +Return Best matching compound classes for given formulaId. +
+ Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, ### Example ```python import PySirius -from PySirius.models.aligned_feature import AlignedFeature -from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField +from PySirius.models.compound_classes import CompoundClasses from PySirius.rest import ApiException from pprint import pprint @@ -509,17 +504,16 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to access. - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result try: - # Get feature (aligned over runs) with the given identifier from the specified project-space. - api_response = api_instance.get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_aligned_feature:\n") + # Return Best matching compound classes for given formulaId + api_response = api_instance.get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_best_matching_compound_classes:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_feature: %s\n" % e) + print("Exception when calling FeaturesApi->get_best_matching_compound_classes: %s\n" % e) ``` @@ -530,13 +524,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| identifier of feature (aligned over runs) to access. | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | ### Return type -[**AlignedFeature**](AlignedFeature.md) +[**CompoundClasses**](CompoundClasses.md) ### Authorization @@ -551,27 +544,23 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | AlignedFeature with additional annotations and MS/MS data (if specified). | - | +**200** | Best matching Predicted compound classes | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_feature_quality_experimental** -> AlignedFeatureQualityExperimental get_aligned_feature_quality_experimental(project_id, aligned_feature_id) +# **get_canopus_prediction** +> CanopusPrediction get_canopus_prediction(project_id, aligned_feature_id, formula_id) -[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) +All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, -[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) -
- Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, ### Example ```python import PySirius -from PySirius.models.aligned_feature_quality_experimental import AlignedFeatureQualityExperimental +from PySirius.models.canopus_prediction import CanopusPrediction from PySirius.rest import ApiException from pprint import pprint @@ -587,15 +576,16 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to access. + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result try: - # [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) - api_response = api_instance.get_aligned_feature_quality_experimental(project_id, aligned_feature_id) - print("The response of FeaturesApi->get_aligned_feature_quality_experimental:\n") + # All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, + api_response = api_instance.get_canopus_prediction(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_canopus_prediction:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_feature_quality_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_canopus_prediction: %s\n" % e) ``` @@ -606,11 +596,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| identifier of feature (aligned over runs) to access. | + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | ### Return type -[**AlignedFeatureQualityExperimental**](AlignedFeatureQualityExperimental.md) +[**CanopusPrediction**](CanopusPrediction.md) ### Authorization @@ -625,24 +616,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | AlignedFeatureQuality quality information of the respective feature. | - | +**200** | Predicted compound classes | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_features** -> List[AlignedFeature] get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) +# **get_de_novo_structure_candidates_by_formula** +> List[StructureCandidateScored] get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields) -Get all available features (aligned over runs) in the given project-space. +List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. -Get all available features (aligned over runs) in the given project-space. +List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. + StructureCandidates can be enriched with molecular fingerprint. ### Example ```python import PySirius -from PySirius.models.aligned_feature import AlignedFeature -from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField +from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField +from PySirius.models.structure_candidate_scored import StructureCandidateScored from PySirius.rest import ApiException from pprint import pprint @@ -658,16 +650,17 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result + opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # Get all available features (aligned over runs) in the given project-space. - api_response = api_instance.get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_aligned_features:\n") + # List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + api_response = api_instance.get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields) + print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_features: %s\n" % e) + print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula: %s\n" % e) ``` @@ -678,12 +671,13 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | + **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**List[AlignedFeature]**](AlignedFeature.md) +[**List[StructureCandidateScored]**](StructureCandidateScored.md) ### Authorization @@ -698,26 +692,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | AlignedFeatures with additional annotations and MS/MS data (if specified). | - | +**200** | StructureCandidate of this formula candidate with specified optional fields. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_features_by_group_experimental** -> PagedModelAlignedFeature get_aligned_features_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) +# **get_de_novo_structure_candidates_by_formula_paged** +> PagedModelStructureCandidateScored get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields) -[EXPERIMENTAL] Get features (aligned over runs) by tag group +Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. -[EXPERIMENTAL] Get features (aligned over runs) by tag group. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. + StructureCandidates can be enriched with molecular fingerprint. ### Example ```python import PySirius -from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField -from PySirius.models.paged_model_aligned_feature import PagedModelAlignedFeature +from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored +from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField from PySirius.rest import ApiException from pprint import pprint @@ -732,20 +725,21 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - group_name = 'group_name_example' # str | tag group name. + project_id = 'project_id_example' # str | project-space to read from. + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) size = 20 # int | The size of the page to be returned (optional) (default to 20) sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # [EXPERIMENTAL] Get features (aligned over runs) by tag group - api_response = api_instance.get_aligned_features_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of FeaturesApi->get_aligned_features_by_group_experimental:\n") + # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + api_response = api_instance.get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields) + print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula_paged:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_features_by_group_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula_paged: %s\n" % e) ``` @@ -755,16 +749,17 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **group_name** | **str**| tag group name. | + **project_id** | **str**| project-space to read from. | + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] **size** | **int**| The size of the page to be returned | [optional] [default to 20] **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md) +[**PagedModelStructureCandidateScored**](PagedModelStructureCandidateScored.md) ### Authorization @@ -779,55 +774,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | tagged features (aligned over runs) | - | +**200** | StructureCandidate of this formula candidate with specified optional fields. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_features_by_tag_experimental** -> PagedModelAlignedFeature get_aligned_features_by_tag_experimental(project_id, filter=filter, page=page, size=size, sort=sort, opt_fields=opt_fields) +# **get_de_novo_structure_candidates_paged** +> PagedModelStructureCandidateFormula get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields) -[EXPERIMENTAL] Get features (aligned over runs) by tag +Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. -[EXPERIMENTAL] Get features (aligned over runs) by tag. - -
The filter string must contain one or more clauses. A clause is prefÃxed - by a field name. -
-
- Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).
- Tag name based field need to be prefixed with the namespace tags..
- Possible value types of tags are bool, integer, real, text, date, or time - tag value
-
-
The format of the date type is yyyy-MM-dd and of the time type is HH\:mm\:ss.
A clause may be:
-tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
- -tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\:00\:00 OR tags.time:[12\:00\:00 TO 14\:00\:00] OR tags.time<10\:00\:00
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. + StructureCandidates can be enriched with molecular fingerprint. ### Example ```python import PySirius -from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField -from PySirius.models.paged_model_aligned_feature import PagedModelAlignedFeature +from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula +from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField from PySirius.rest import ApiException from pprint import pprint @@ -842,20 +807,20 @@ configuration = PySirius.Configuration( with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project space to get features (aligned over runs) from. - filter = '' # str | tag filter. (optional) (default to '') + project_id = 'project_id_example' # str | project-space to read from. + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) size = 20 # int | The size of the page to be returned (optional) (default to 20) sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = [] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to []) + opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # [EXPERIMENTAL] Get features (aligned over runs) by tag - api_response = api_instance.get_aligned_features_by_tag_experimental(project_id, filter=filter, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of FeaturesApi->get_aligned_features_by_tag_experimental:\n") + # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. + api_response = api_instance.get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields) + print("The response of FeaturesApi->get_de_novo_structure_candidates_paged:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_features_by_tag_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_paged: %s\n" % e) ``` @@ -865,16 +830,16 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project space to get features (aligned over runs) from. | - **filter** | **str**| tag filter. | [optional] [default to ''] + **project_id** | **str**| project-space to read from. | + **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] **size** | **int**| The size of the page to be returned | [optional] [default to 20] **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []] + **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md) +[**PagedModelStructureCandidateFormula**](PagedModelStructureCandidateFormula.md) ### Authorization @@ -889,24 +854,24 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | tagged features (aligned over runs) | - | +**200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_aligned_features_paged** -> PagedModelAlignedFeature get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) +# **get_fingerprint_prediction** +> List[float] get_fingerprint_prediction(project_id, aligned_feature_id, formula_id) -Get all available features (aligned over runs) in the given project-space. +Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) -Get all available features (aligned over runs) in the given project-space. +Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) +
+ This fingerprint is used to perform structure database search and predict compound classes. ### Example ```python import PySirius -from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField -from PySirius.models.paged_model_aligned_feature import PagedModelAlignedFeature from PySirius.rest import ApiException from pprint import pprint @@ -922,19 +887,16 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result try: - # Get all available features (aligned over runs) in the given project-space. - api_response = api_instance.get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_aligned_features_paged:\n") + # Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) + api_response = api_instance.get_fingerprint_prediction(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_fingerprint_prediction:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_aligned_features_paged: %s\n" % e) + print("Exception when calling FeaturesApi->get_fingerprint_prediction: %s\n" % e) ``` @@ -945,15 +907,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[AlignedFeatureOptField]**](AlignedFeatureOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | ### Return type -[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md) +**List[float]** ### Authorization @@ -968,25 +927,27 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | AlignedFeatures with additional annotations and MS/MS data (if specified). | - | +**200** | probabilistic fingerprint predicted by CSI:FingerID | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_best_matching_compound_classes** -> CompoundClasses get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id) +# **get_formula_annotated_ms_ms_data** +> AnnotatedMsMsData get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared) -Return Best matching compound classes for given formulaId +Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId -Return Best matching compound classes for given formulaId. +Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
- Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology, + Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses + for the given formula result identifier + These annotations are only available if a fragmentation tree and the structure candidate are available. ### Example ```python import PySirius -from PySirius.models.compound_classes import CompoundClasses +from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData from PySirius.rest import ApiException from pprint import pprint @@ -1004,14 +965,15 @@ with PySirius.ApiClient(configuration) as api_client: project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. formula_id = 'formula_id_example' # str | identifier of the requested formula result + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) try: - # Return Best matching compound classes for given formulaId - api_response = api_instance.get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_best_matching_compound_classes:\n") + # Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId + api_response = api_instance.get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared) + print("The response of FeaturesApi->get_formula_annotated_ms_ms_data:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_best_matching_compound_classes: %s\n" % e) + print("Exception when calling FeaturesApi->get_formula_annotated_ms_ms_data: %s\n" % e) ``` @@ -1024,10 +986,11 @@ Name | Type | Description | Notes **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | **formula_id** | **str**| identifier of the requested formula result | + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] ### Return type -[**CompoundClasses**](CompoundClasses.md) +[**AnnotatedMsMsData**](AnnotatedMsMsData.md) ### Authorization @@ -1042,23 +1005,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Best matching Predicted compound classes | - | +**200** | Fragmentation spectra annotated with fragment formulas and losses. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_canopus_prediction** -> CanopusPrediction get_canopus_prediction(project_id, aligned_feature_id, formula_id) +# **get_formula_annotated_spectrum** +> AnnotatedSpectrum get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared) -All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, +Returns a fragmentation spectrum (e -All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, +Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier +
+ These annotations are only available if a fragmentation tree is available. ### Example ```python import PySirius -from PySirius.models.canopus_prediction import CanopusPrediction +from PySirius.models.annotated_spectrum import AnnotatedSpectrum from PySirius.rest import ApiException from pprint import pprint @@ -1076,14 +1041,16 @@ with PySirius.ApiClient(configuration) as api_client: project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. formula_id = 'formula_id_example' # str | identifier of the requested formula result + spectrum_index = -1 # int | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) (optional) (default to -1) + search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) try: - # All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, - api_response = api_instance.get_canopus_prediction(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_canopus_prediction:\n") + # Returns a fragmentation spectrum (e + api_response = api_instance.get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared) + print("The response of FeaturesApi->get_formula_annotated_spectrum:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_canopus_prediction: %s\n" % e) + print("Exception when calling FeaturesApi->get_formula_annotated_spectrum: %s\n" % e) ``` @@ -1096,10 +1063,12 @@ Name | Type | Description | Notes **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | **formula_id** | **str**| identifier of the requested formula result | + **spectrum_index** | **int**| index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) | [optional] [default to -1] + **search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] ### Return type -[**CanopusPrediction**](CanopusPrediction.md) +[**AnnotatedSpectrum**](AnnotatedSpectrum.md) ### Authorization @@ -1114,25 +1083,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Predicted compound classes | - | +**200** | Fragmentation spectrum annotated with fragment formulas and losses. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_de_novo_structure_candidates** -> List[StructureCandidateFormula] get_de_novo_structure_candidates(project_id, aligned_feature_id, opt_fields=opt_fields) +# **get_formula_candidate** +> FormulaCandidate get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. +FormulaResultContainers for the given 'formulaId' with minimal information. -List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - StructureCandidates can be enriched with molecular fingerprint. +FormulaResultContainers for the given 'formulaId' with minimal information. + Can be enriched with an optional results overview and formula candidate information. ### Example ```python import PySirius -from PySirius.models.structure_candidate_formula import StructureCandidateFormula -from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField +from PySirius.models.formula_candidate import FormulaCandidate +from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField from PySirius.rest import ApiException from pprint import pprint @@ -1148,16 +1117,18 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - api_response = api_instance.get_de_novo_structure_candidates(project_id, aligned_feature_id, opt_fields=opt_fields) - print("The response of FeaturesApi->get_de_novo_structure_candidates:\n") + # FormulaResultContainers for the given 'formulaId' with minimal information. + api_response = api_instance.get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_formula_candidate:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_de_novo_structure_candidates: %s\n" % e) + print("Exception when calling FeaturesApi->get_formula_candidate: %s\n" % e) ``` @@ -1168,12 +1139,14 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**List[StructureCandidateFormula]**](StructureCandidateFormula.md) +[**FormulaCandidate**](FormulaCandidate.md) ### Authorization @@ -1188,25 +1161,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - | +**200** | FormulaCandidate of this feature (aligned over runs) with. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_de_novo_structure_candidates_by_formula** -> List[StructureCandidateScored] get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields) +# **get_formula_candidates** +> List[FormulaCandidate] get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. +List of FormulaResultContainers available for this feature with minimal information. -List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. - StructureCandidates can be enriched with molecular fingerprint. +List of FormulaResultContainers available for this feature with minimal information. + Can be enriched with an optional results overview. ### Example ```python import PySirius -from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField -from PySirius.models.structure_candidate_scored import StructureCandidateScored +from PySirius.models.formula_candidate import FormulaCandidate +from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField from PySirius.rest import ApiException from pprint import pprint @@ -1223,16 +1196,16 @@ with PySirius.ApiClient(configuration) as api_client: api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - api_response = api_instance.get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields) - print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula:\n") + # List of FormulaResultContainers available for this feature with minimal information. + api_response = api_instance.get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_formula_candidates:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula: %s\n" % e) + print("Exception when calling FeaturesApi->get_formula_candidates: %s\n" % e) ``` @@ -1244,12 +1217,12 @@ Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**List[StructureCandidateScored]**](StructureCandidateScored.md) +[**List[FormulaCandidate]**](FormulaCandidate.md) ### Authorization @@ -1264,25 +1237,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | StructureCandidate of this formula candidate with specified optional fields. | - | +**200** | All FormulaCandidate of this feature with. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_de_novo_structure_candidates_by_formula_paged** -> PagedModelStructureCandidateScored get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields) +# **get_formula_candidates_paged** +> PagedModelFormulaCandidate get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) -Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. +Page of FormulaResultContainers available for this feature with minimal information. -Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. - StructureCandidates can be enriched with molecular fingerprint. +Page of FormulaResultContainers available for this feature with minimal information. + Can be enriched with an optional results overview. ### Example ```python import PySirius -from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored -from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField +from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField +from PySirius.models.paged_model_formula_candidate import PagedModelFormulaCandidate from PySirius.rest import ApiException from pprint import pprint @@ -1299,19 +1272,19 @@ with PySirius.ApiClient(configuration) as api_client: api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) size = 20 # int | The size of the page to be returned (optional) (default to 20) sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) try: - # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - api_response = api_instance.get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula_paged:\n") + # Page of FormulaResultContainers available for this feature with minimal information. + api_response = api_instance.get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) + print("The response of FeaturesApi->get_formula_candidates_paged:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula_paged: %s\n" % e) + print("Exception when calling FeaturesApi->get_formula_candidates_paged: %s\n" % e) ``` @@ -1323,15 +1296,15 @@ Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] **size** | **int**| The size of the page to be returned | [optional] [default to 20] **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] ### Return type -[**PagedModelStructureCandidateScored**](PagedModelStructureCandidateScored.md) +[**PagedModelFormulaCandidate**](PagedModelFormulaCandidate.md) ### Authorization @@ -1346,25 +1319,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | StructureCandidate of this formula candidate with specified optional fields. | - | +**200** | All FormulaCandidate of this feature with. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_de_novo_structure_candidates_paged** -> PagedModelStructureCandidateFormula get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields) +# **get_frag_tree** +> FragmentationTree get_frag_tree(project_id, aligned_feature_id, formula_id) -Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. +Returns fragmentation tree (SIRIUS) for the given formula result identifier -Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. - StructureCandidates can be enriched with molecular fingerprint. +Returns fragmentation tree (SIRIUS) for the given formula result identifier +
+ This tree is used to rank formula candidates (treeScore). ### Example ```python import PySirius -from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula -from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField +from PySirius.models.fragmentation_tree import FragmentationTree from PySirius.rest import ApiException from pprint import pprint @@ -1380,19 +1353,16 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. + formula_id = 'formula_id_example' # str | identifier of the requested formula result try: - # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. - api_response = api_instance.get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of FeaturesApi->get_de_novo_structure_candidates_paged:\n") + # Returns fragmentation tree (SIRIUS) for the given formula result identifier + api_response = api_instance.get_frag_tree(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_frag_tree:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_paged: %s\n" % e) + print("Exception when calling FeaturesApi->get_frag_tree: %s\n" % e) ``` @@ -1403,91 +1373,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[StructureCandidateOptField]**](StructureCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] - -### Return type - -[**PagedModelStructureCandidateFormula**](PagedModelStructureCandidateFormula.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_feature_quant_table_experimental** -> QuantTableExperimental get_feature_quant_table_experimental(project_id, type=type) - -[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) - -[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId). -
- Returns the full quantification table. The quantification table contains a quantities of the features within all - runs they are contained in. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - type = PySirius.QuantMeasure() # QuantMeasure | quantification type. (optional) - - try: - # [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) - api_response = api_instance.get_feature_quant_table_experimental(project_id, type=type) - print("The response of FeaturesApi->get_feature_quant_table_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_feature_quant_table_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **type** | [**QuantMeasure**](.md)| quantification type. | [optional] + **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | + **formula_id** | **str**| identifier of the requested formula result | ### Return type -[**QuantTableExperimental**](QuantTableExperimental.md) +[**FragmentationTree**](FragmentationTree.md) ### Authorization @@ -1502,24 +1393,26 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Quant table if akk feature in this project | - | +**200** | Fragmentation Tree | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_fingerprint_prediction** -> List[float] get_fingerprint_prediction(project_id, aligned_feature_id, formula_id) +# **get_isotope_pattern_annotation** +> IsotopePatternAnnotation get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id) -Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) +Returns Isotope pattern information for given formulaId -Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) +Returns Isotope pattern information for given formulaId
- This fingerprint is used to perform structure database search and predict compound classes. + Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) + for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). ### Example ```python import PySirius +from PySirius.models.isotope_pattern_annotation import IsotopePatternAnnotation from PySirius.rest import ApiException from pprint import pprint @@ -1539,12 +1432,12 @@ with PySirius.ApiClient(configuration) as api_client: formula_id = 'formula_id_example' # str | identifier of the requested formula result try: - # Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) - api_response = api_instance.get_fingerprint_prediction(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_fingerprint_prediction:\n") + # Returns Isotope pattern information for given formulaId + api_response = api_instance.get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_isotope_pattern_annotation:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_fingerprint_prediction: %s\n" % e) + print("Exception when calling FeaturesApi->get_isotope_pattern_annotation: %s\n" % e) ``` @@ -1560,7 +1453,7 @@ Name | Type | Description | Notes ### Return type -**List[float]** +[**IsotopePatternAnnotation**](IsotopePatternAnnotation.md) ### Authorization @@ -1575,27 +1468,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | probabilistic fingerprint predicted by CSI:FingerID | - | +**200** | Isotope pattern information | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_formula_annotated_ms_ms_data** -> AnnotatedMsMsData get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared) +# **get_lipid_annotation** +> LipidAnnotation get_lipid_annotation(project_id, aligned_feature_id, formula_id) -Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId +Returns Lipid annotation (ElGordo) for the given formulaId -Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId. +Returns Lipid annotation (ElGordo) for the given formulaId.
- Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses - for the given formula result identifier - These annotations are only available if a fragmentation tree and the structure candidate are available. + ElGordo lipid annotation runs as part of the SIRIUS formula identification step. ### Example ```python import PySirius -from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData +from PySirius.models.lipid_annotation import LipidAnnotation from PySirius.rest import ApiException from pprint import pprint @@ -1613,15 +1504,14 @@ with PySirius.ApiClient(configuration) as api_client: project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. formula_id = 'formula_id_example' # str | identifier of the requested formula result - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) try: - # Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId - api_response = api_instance.get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared) - print("The response of FeaturesApi->get_formula_annotated_ms_ms_data:\n") + # Returns Lipid annotation (ElGordo) for the given formulaId + api_response = api_instance.get_lipid_annotation(project_id, aligned_feature_id, formula_id) + print("The response of FeaturesApi->get_lipid_annotation:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_formula_annotated_ms_ms_data: %s\n" % e) + print("Exception when calling FeaturesApi->get_lipid_annotation: %s\n" % e) ``` @@ -1634,11 +1524,10 @@ Name | Type | Description | Notes **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | **formula_id** | **str**| identifier of the requested formula result | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] ### Return type -[**AnnotatedMsMsData**](AnnotatedMsMsData.md) +[**LipidAnnotation**](LipidAnnotation.md) ### Authorization @@ -1653,25 +1542,23 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Fragmentation spectra annotated with fragment formulas and losses. | - | +**200** | LipidAnnotation | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_formula_annotated_spectrum** -> AnnotatedSpectrum get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared) +# **get_ms_data** +> MsData get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared) -Returns a fragmentation spectrum (e +Mass Spec data (input data) for the given 'alignedFeatureId' . -Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier -
- These annotations are only available if a fragmentation tree is available. +Mass Spec data (input data) for the given 'alignedFeatureId' . ### Example ```python import PySirius -from PySirius.models.annotated_spectrum import AnnotatedSpectrum +from PySirius.models.ms_data import MsData from PySirius.rest import ApiException from pprint import pprint @@ -1687,18 +1574,16 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - spectrum_index = -1 # int | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) (optional) (default to -1) - search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the Mass Spec data belongs to. + ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) try: - # Returns a fragmentation spectrum (e - api_response = api_instance.get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared) - print("The response of FeaturesApi->get_formula_annotated_spectrum:\n") + # Mass Spec data (input data) for the given 'alignedFeatureId' . + api_response = api_instance.get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared) + print("The response of FeaturesApi->get_ms_data:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_formula_annotated_spectrum: %s\n" % e) + print("Exception when calling FeaturesApi->get_ms_data: %s\n" % e) ``` @@ -1709,14 +1594,12 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - **spectrum_index** | **int**| index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) | [optional] [default to -1] - **search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **aligned_feature_id** | **str**| feature (aligned over runs) the Mass Spec data belongs to. | + **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] ### Return type -[**AnnotatedSpectrum**](AnnotatedSpectrum.md) +[**MsData**](MsData.md) ### Authorization @@ -1731,25 +1614,24 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Fragmentation spectrum annotated with fragment formulas and losses. | - | +**200** | Mass Spec data of this feature (aligned over runs). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_formula_candidate** -> FormulaCandidate get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) +# **get_spectral_library_match** +> SpectralLibraryMatch get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields) -FormulaResultContainers for the given 'formulaId' with minimal information. +Spectral library match for the given 'alignedFeatureId'. -FormulaResultContainers for the given 'formulaId' with minimal information. - Can be enriched with an optional results overview and formula candidate information. +Spectral library match for the given 'alignedFeatureId'. ### Example ```python import PySirius -from PySirius.models.formula_candidate import FormulaCandidate -from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField +from PySirius.models.spectral_library_match import SpectralLibraryMatch +from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField from PySirius.rest import ApiException from pprint import pprint @@ -1765,18 +1647,17 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. + match_id = 'match_id_example' # str | id of the library match to be returned. + opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) try: - # FormulaResultContainers for the given 'formulaId' with minimal information. - api_response = api_instance.get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_formula_candidate:\n") + # Spectral library match for the given 'alignedFeatureId'. + api_response = api_instance.get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields) + print("The response of FeaturesApi->get_spectral_library_match:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_formula_candidate: %s\n" % e) + print("Exception when calling FeaturesApi->get_spectral_library_match: %s\n" % e) ``` @@ -1787,14 +1668,13 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] + **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | + **match_id** | **str**| id of the library match to be returned. | + **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] ### Return type -[**FormulaCandidate**](FormulaCandidate.md) +[**SpectralLibraryMatch**](SpectralLibraryMatch.md) ### Authorization @@ -1809,794 +1689,24 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | FormulaCandidate of this feature (aligned over runs) with. | - | +**200** | Spectral library match with requested mathcId. | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_formula_candidates** -> List[FormulaCandidate] get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) +# **get_spectral_library_matches** +> List[SpectralLibraryMatch] get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) -List of FormulaResultContainers available for this feature with minimal information. +List of spectral library matches for the given 'alignedFeatureId'. -List of FormulaResultContainers available for this feature with minimal information. - Can be enriched with an optional results overview. +List of spectral library matches for the given 'alignedFeatureId'. ### Example ```python import PySirius -from PySirius.models.formula_candidate import FormulaCandidate -from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) - - try: - # List of FormulaResultContainers available for this feature with minimal information. - api_response = api_instance.get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_formula_candidates:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_formula_candidates: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] - -### Return type - -[**List[FormulaCandidate]**](FormulaCandidate.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | All FormulaCandidate of this feature with. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_formula_candidates_paged** -> PagedModelFormulaCandidate get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - -Page of FormulaResultContainers available for this feature with minimal information. - -Page of FormulaResultContainers available for this feature with minimal information. - Can be enriched with an optional results overview. - -### Example - - -```python -import PySirius -from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField -from PySirius.models.paged_model_formula_candidate import PagedModelFormulaCandidate -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) - - try: - # Page of FormulaResultContainers available for this feature with minimal information. - api_response = api_instance.get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields) - print("The response of FeaturesApi->get_formula_candidates_paged:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_formula_candidates_paged: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - **opt_fields** | [**List[FormulaCandidateOptField]**](FormulaCandidateOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] - -### Return type - -[**PagedModelFormulaCandidate**](PagedModelFormulaCandidate.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | All FormulaCandidate of this feature with. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_frag_tree** -> FragmentationTree get_frag_tree(project_id, aligned_feature_id, formula_id) - -Returns fragmentation tree (SIRIUS) for the given formula result identifier - -Returns fragmentation tree (SIRIUS) for the given formula result identifier -
- This tree is used to rank formula candidates (treeScore). - -### Example - - -```python -import PySirius -from PySirius.models.fragmentation_tree import FragmentationTree -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - - try: - # Returns fragmentation tree (SIRIUS) for the given formula result identifier - api_response = api_instance.get_frag_tree(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_frag_tree:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_frag_tree: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - -### Return type - -[**FragmentationTree**](FragmentationTree.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Fragmentation Tree | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_isotope_pattern_annotation** -> IsotopePatternAnnotation get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id) - -Returns Isotope pattern information for given formulaId - -Returns Isotope pattern information for given formulaId -
- Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) - for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore). - -### Example - - -```python -import PySirius -from PySirius.models.isotope_pattern_annotation import IsotopePatternAnnotation -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - - try: - # Returns Isotope pattern information for given formulaId - api_response = api_instance.get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_isotope_pattern_annotation:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_isotope_pattern_annotation: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - -### Return type - -[**IsotopePatternAnnotation**](IsotopePatternAnnotation.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Isotope pattern information | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_lipid_annotation** -> LipidAnnotation get_lipid_annotation(project_id, aligned_feature_id, formula_id) - -Returns Lipid annotation (ElGordo) for the given formulaId - -Returns Lipid annotation (ElGordo) for the given formulaId. -
- ElGordo lipid annotation runs as part of the SIRIUS formula identification step. - -### Example - - -```python -import PySirius -from PySirius.models.lipid_annotation import LipidAnnotation -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - - try: - # Returns Lipid annotation (ElGordo) for the given formulaId - api_response = api_instance.get_lipid_annotation(project_id, aligned_feature_id, formula_id) - print("The response of FeaturesApi->get_lipid_annotation:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_lipid_annotation: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - -### Return type - -[**LipidAnnotation**](LipidAnnotation.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | LipidAnnotation | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_ms_data** -> MsData get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared) - -Mass Spec data (input data) for the given 'alignedFeatureId' . - -Mass Spec data (input data) for the given 'alignedFeatureId' . - -### Example - - -```python -import PySirius -from PySirius.models.ms_data import MsData -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the Mass Spec data belongs to. - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) - - try: - # Mass Spec data (input data) for the given 'alignedFeatureId' . - api_response = api_instance.get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared) - print("The response of FeaturesApi->get_ms_data:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_ms_data: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the Mass Spec data belongs to. | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] - -### Return type - -[**MsData**](MsData.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Mass Spec data of this feature (aligned over runs). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_quant_table_row_experimental** -> QuantTableExperimental get_quant_table_row_experimental(project_id, aligned_feature_id, type=type) - -[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) - -[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId). -
- The quantification table contains a quantity of the feature within all samples it is contained in. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.quant_measure import QuantMeasure -from PySirius.models.quant_table_experimental import QuantTableExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature which quantity should be read out - type = PySirius.QuantMeasure() # QuantMeasure | quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. (optional) - - try: - # [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) - api_response = api_instance.get_quant_table_row_experimental(project_id, aligned_feature_id, type=type) - print("The response of FeaturesApi->get_quant_table_row_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_quant_table_row_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature which quantity should be read out | - **type** | [**QuantMeasure**](.md)| quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. | [optional] - -### Return type - -[**QuantTableExperimental**](QuantTableExperimental.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Quant table row for this feature | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_spectral_library_match** -> SpectralLibraryMatch get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields) - -Spectral library match for the given 'alignedFeatureId'. - -Spectral library match for the given 'alignedFeatureId'. - -### Example - - -```python -import PySirius -from PySirius.models.spectral_library_match import SpectralLibraryMatch -from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - match_id = 'match_id_example' # str | id of the library match to be returned. - opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) - - try: - # Spectral library match for the given 'alignedFeatureId'. - api_response = api_instance.get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields) - print("The response of FeaturesApi->get_spectral_library_match:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_spectral_library_match: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **match_id** | **str**| id of the library match to be returned. | - **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] - -### Return type - -[**SpectralLibraryMatch**](SpectralLibraryMatch.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Spectral library match with requested mathcId. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_spectral_library_matches** -> List[SpectralLibraryMatch] get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) - -List of spectral library matches for the given 'alignedFeatureId'. - -List of spectral library matches for the given 'alignedFeatureId'. - -### Example - - -```python -import PySirius -from PySirius.models.spectral_library_match import SpectralLibraryMatch -from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - min_shared_peaks = 1 # int | (optional) (default to 1) - min_similarity = 0.2 # float | (optional) (default to 0.2) - inchi_key = '' # str | (optional) (default to '') - opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) - - try: - # List of spectral library matches for the given 'alignedFeatureId'. - api_response = api_instance.get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) - print("The response of FeaturesApi->get_spectral_library_matches:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_spectral_library_matches: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **min_shared_peaks** | **int**| | [optional] [default to 1] - **min_similarity** | **float**| | [optional] [default to 0.2] - **inchi_key** | **str**| | [optional] [default to ''] - **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] - -### Return type - -[**List[SpectralLibraryMatch]**](SpectralLibraryMatch.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Spectral library matches of this feature (aligned over runs). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_spectral_library_matches_paged** -> PagedModelSpectralLibraryMatch get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) - -Page of spectral library matches for the given 'alignedFeatureId'. - -Page of spectral library matches for the given 'alignedFeatureId'. - If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. - -### Example - - -```python -import PySirius -from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch -from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - min_shared_peaks = 1 # int | (optional) (default to 1) - min_similarity = 0.2 # float | (optional) (default to 0.2) - inchi_key = '' # str | (optional) (default to '') - opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) - - try: - # Page of spectral library matches for the given 'alignedFeatureId'. - api_response = api_instance.get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) - print("The response of FeaturesApi->get_spectral_library_matches_paged:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_spectral_library_matches_paged: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **min_shared_peaks** | **int**| | [optional] [default to 1] - **min_similarity** | **float**| | [optional] [default to 0.2] - **inchi_key** | **str**| | [optional] [default to ''] - **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] - -### Return type - -[**PagedModelSpectralLibraryMatch**](PagedModelSpectralLibraryMatch.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Spectral library matches of this feature (aligned over runs). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_spectral_library_matches_summary** -> SpectralLibraryMatchSummary get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key) - -Summarize matched reference spectra for the given 'alignedFeatureId'. - -Summarize matched reference spectra for the given 'alignedFeatureId'. - If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. - -### Example - - -```python -import PySirius -from PySirius.models.spectral_library_match_summary import SpectralLibraryMatchSummary +from PySirius.models.spectral_library_match import SpectralLibraryMatch +from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField from PySirius.rest import ApiException from pprint import pprint @@ -2613,99 +1723,18 @@ with PySirius.ApiClient(configuration) as api_client: api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - min_shared_peaks = 1 # int | min threshold of shared peaks. (optional) (default to 1) - min_similarity = 0.2 # float | min spectral similarity threshold. (optional) (default to 0.2) - inchi_key = '' # str | 2D inchi key of the compound in the structure database. (optional) (default to '') - - try: - # Summarize matched reference spectra for the given 'alignedFeatureId'. - api_response = api_instance.get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key) - print("The response of FeaturesApi->get_spectral_library_matches_summary:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_spectral_library_matches_summary: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **min_shared_peaks** | **int**| min threshold of shared peaks. | [optional] [default to 1] - **min_similarity** | **float**| min spectral similarity threshold. | [optional] [default to 0.2] - **inchi_key** | **str**| 2D inchi key of the compound in the structure database. | [optional] [default to ''] - -### Return type - -[**SpectralLibraryMatchSummary**](SpectralLibraryMatchSummary.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_structure_annotated_ms_data_experimental** -> AnnotatedMsMsData get_structure_annotated_ms_data_experimental(project_id, aligned_feature_id, formula_id, inchi_key, ms_data_search_prepared=ms_data_search_prepared) - -[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey - -[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey. -
- Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses - for the given formula result identifier and structure candidate inChIKey. - These annotations are only available if a fragmentation tree and the structure candidate are available. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - inchi_key = 'inchi_key_example' # str | 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation - ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False) + min_shared_peaks = 1 # int | (optional) (default to 1) + min_similarity = 0.2 # float | (optional) (default to 0.2) + inchi_key = '' # str | (optional) (default to '') + opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) try: - # [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey - api_response = api_instance.get_structure_annotated_ms_data_experimental(project_id, aligned_feature_id, formula_id, inchi_key, ms_data_search_prepared=ms_data_search_prepared) - print("The response of FeaturesApi->get_structure_annotated_ms_data_experimental:\n") + # List of spectral library matches for the given 'alignedFeatureId'. + api_response = api_instance.get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) + print("The response of FeaturesApi->get_spectral_library_matches:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_structure_annotated_ms_data_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_spectral_library_matches: %s\n" % e) ``` @@ -2716,14 +1745,15 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - **inchi_key** | **str**| 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation | - **ms_data_search_prepared** | **bool**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] + **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | + **min_shared_peaks** | **int**| | [optional] [default to 1] + **min_similarity** | **float**| | [optional] [default to 0.2] + **inchi_key** | **str**| | [optional] [default to ''] + **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] ### Return type -[**AnnotatedMsMsData**](AnnotatedMsMsData.md) +[**List[SpectralLibraryMatch]**](SpectralLibraryMatch.md) ### Authorization @@ -2738,25 +1768,25 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Fragmentation spectrum annotated with fragments and sub-structures. | - | +**200** | Spectral library matches of this feature (aligned over runs). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_structure_annotated_spectral_library_match_experimental** -> AnnotatedSpectrum get_structure_annotated_spectral_library_match_experimental(project_id, aligned_feature_id, match_id) +# **get_spectral_library_matches_paged** +> PagedModelSpectralLibraryMatch get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) -[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations +Page of spectral library matches for the given 'alignedFeatureId'. -[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Page of spectral library matches for the given 'alignedFeatureId'. + If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key. ### Example ```python import PySirius -from PySirius.models.annotated_spectrum import AnnotatedSpectrum +from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch +from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField from PySirius.rest import ApiException from pprint import pprint @@ -2773,15 +1803,21 @@ with PySirius.ApiClient(configuration) as api_client: api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. - match_id = 'match_id_example' # str | id of the library match to be returned. + page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) + size = 20 # int | The size of the page to be returned (optional) (default to 20) + sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) + min_shared_peaks = 1 # int | (optional) (default to 1) + min_similarity = 0.2 # float | (optional) (default to 0.2) + inchi_key = '' # str | (optional) (default to '') + opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"]) try: - # [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations - api_response = api_instance.get_structure_annotated_spectral_library_match_experimental(project_id, aligned_feature_id, match_id) - print("The response of FeaturesApi->get_structure_annotated_spectral_library_match_experimental:\n") + # Page of spectral library matches for the given 'alignedFeatureId'. + api_response = api_instance.get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields) + print("The response of FeaturesApi->get_spectral_library_matches_paged:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_structure_annotated_spectral_library_match_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_spectral_library_matches_paged: %s\n" % e) ``` @@ -2793,11 +1829,17 @@ Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | - **match_id** | **str**| id of the library match to be returned. | + **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] + **size** | **int**| The size of the page to be returned | [optional] [default to 20] + **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] + **min_shared_peaks** | **int**| | [optional] [default to 1] + **min_similarity** | **float**| | [optional] [default to 0.2] + **inchi_key** | **str**| | [optional] [default to ''] + **opt_fields** | [**List[SpectralLibraryMatchOptField]**](SpectralLibraryMatchOptField.md)| | [optional] [default to ["none"]] ### Return type -[**AnnotatedSpectrum**](AnnotatedSpectrum.md) +[**PagedModelSpectralLibraryMatch**](PagedModelSpectralLibraryMatch.md) ### Authorization @@ -2812,28 +1854,24 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Spectral library match with requested mathcId. | - | +**200** | Spectral library matches of this feature (aligned over runs). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_structure_annotated_spectrum_experimental** -> AnnotatedSpectrum get_structure_annotated_spectrum_experimental(project_id, aligned_feature_id, formula_id, inchi_key, spectrum_index=spectrum_index, search_prepared=search_prepared) +# **get_spectral_library_matches_summary** +> SpectralLibraryMatchSummary get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key) -[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey +Summarize matched reference spectra for the given 'alignedFeatureId'. -[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey -
- Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result - These annotations are only available if a fragmentation tree is available. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. +Summarize matched reference spectra for the given 'alignedFeatureId'. + If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key. ### Example ```python import PySirius -from PySirius.models.annotated_spectrum import AnnotatedSpectrum +from PySirius.models.spectral_library_match_summary import SpectralLibraryMatchSummary from PySirius.rest import ApiException from pprint import pprint @@ -2849,19 +1887,18 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.FeaturesApi(api_client) project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to. - formula_id = 'formula_id_example' # str | identifier of the requested formula result - inchi_key = 'inchi_key_example' # str | 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation - spectrum_index = -1 # int | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) (optional) (default to -1) - search_prepared = False # bool | (optional) (default to False) + aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to. + min_shared_peaks = 1 # int | min threshold of shared peaks. (optional) (default to 1) + min_similarity = 0.2 # float | min spectral similarity threshold. (optional) (default to 0.2) + inchi_key = '' # str | 2D inchi key of the compound in the structure database. (optional) (default to '') try: - # [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey - api_response = api_instance.get_structure_annotated_spectrum_experimental(project_id, aligned_feature_id, formula_id, inchi_key, spectrum_index=spectrum_index, search_prepared=search_prepared) - print("The response of FeaturesApi->get_structure_annotated_spectrum_experimental:\n") + # Summarize matched reference spectra for the given 'alignedFeatureId'. + api_response = api_instance.get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key) + print("The response of FeaturesApi->get_spectral_library_matches_summary:\n") pprint(api_response) except Exception as e: - print("Exception when calling FeaturesApi->get_structure_annotated_spectrum_experimental: %s\n" % e) + print("Exception when calling FeaturesApi->get_spectral_library_matches_summary: %s\n" % e) ``` @@ -2872,15 +1909,14 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature (aligned over runs) the formula result belongs to. | - **formula_id** | **str**| identifier of the requested formula result | - **inchi_key** | **str**| 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation | - **spectrum_index** | **int**| index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) | [optional] [default to -1] - **search_prepared** | **bool**| | [optional] [default to False] + **aligned_feature_id** | **str**| feature (aligned over runs) the structure candidates belong to. | + **min_shared_peaks** | **int**| min threshold of shared peaks. | [optional] [default to 1] + **min_similarity** | **float**| min spectral similarity threshold. | [optional] [default to 0.2] + **inchi_key** | **str**| 2D inchi key of the compound in the structure database. | [optional] [default to ''] ### Return type -[**AnnotatedSpectrum**](AnnotatedSpectrum.md) +[**SpectralLibraryMatchSummary**](SpectralLibraryMatchSummary.md) ### Authorization @@ -2895,7 +1931,7 @@ No authorization required | Status code | Description | Response headers | |-------------|-------------|------------------| -**200** | Fragmentation spectrum annotated with fragments and sub-structures. | - | +**200** | Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs). | - | [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) @@ -3211,226 +2247,3 @@ No authorization required [[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) -# **get_tags_for_aligned_features_experimental** -> List[Tag] get_tags_for_aligned_features_experimental(project_id, object_id) - -[EXPERIMENTAL] Get all tags associated with this Object - -[EXPERIMENTAL] Get all tags associated with this Object - -### Example - - -```python -import PySirius -from PySirius.models.tag import Tag -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to get from. - object_id = 'object_id_example' # str | object to get tags for. - - try: - # [EXPERIMENTAL] Get all tags associated with this Object - api_response = api_instance.get_tags_for_aligned_features_experimental(project_id, object_id) - print("The response of FeaturesApi->get_tags_for_aligned_features_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_tags_for_aligned_features_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to get from. | - **object_id** | **str**| object to get tags for. | - -### Return type - -[**List[Tag]**](Tag.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | the tags of the requested object | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_traces_experimental** -> TraceSetExperimental get_traces_experimental(project_id, aligned_feature_id, include_all=include_all) - -[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) - -[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId). -
- Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention - time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, - but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. - However, this also means that all traces can be directly compared against each other, as they all lie in the same - retention time axis. - By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set, - it also includes samples in which the same trace appears in. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.trace_set_experimental import TraceSetExperimental -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature which intensities should be read out - include_all = False # bool | when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. (optional) (default to False) - - try: - # [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) - api_response = api_instance.get_traces_experimental(project_id, aligned_feature_id, include_all=include_all) - print("The response of FeaturesApi->get_traces_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling FeaturesApi->get_traces_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **aligned_feature_id** | **str**| feature which intensities should be read out | - **include_all** | **bool**| when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. | [optional] [default to False] - -### Return type - -[**TraceSetExperimental**](TraceSetExperimental.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Traces of the given feature. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **remove_tag_from_aligned_feature_experimental** -> remove_tag_from_aligned_feature_experimental(project_id, aligned_feature_id, tag_name) - -[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space - -[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.FeaturesApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) to delete tag from. - tag_name = 'tag_name_example' # str | name of the tag to delete. - - try: - # [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space - api_instance.remove_tag_from_aligned_feature_experimental(project_id, aligned_feature_id, tag_name) - except Exception as e: - print("Exception when calling FeaturesApi->remove_tag_from_aligned_feature_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **aligned_feature_id** | **str**| feature (aligned over runs) to delete tag from. | - **tag_name** | **str**| name of the tag to delete. | - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - diff --git a/client-api_python/generated/docs/FoldChange.md b/client-api_python/generated/docs/FoldChange.md deleted file mode 100644 index 18fe240e..00000000 --- a/client-api_python/generated/docs/FoldChange.md +++ /dev/null @@ -1,35 +0,0 @@ -# FoldChange - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**left_group** | **str** | | [optional] -**right_group** | **str** | | [optional] -**aggregation** | [**AggregationType**](AggregationType.md) | | [optional] -**quantification** | [**QuantMeasure**](QuantMeasure.md) | | [optional] -**quant_type** | [**QuantRowType**](QuantRowType.md) | | -**object_id** | **str** | | -**fold_change** | **float** | | - -## Example - -```python -from PySirius.models.fold_change import FoldChange - -# TODO update the JSON string below -json = "{}" -# create an instance of FoldChange from a JSON string -fold_change_instance = FoldChange.from_json(json) -# print the JSON string representation of the object -print(FoldChange.to_json()) - -# convert the object into a dict -fold_change_dict = fold_change_instance.to_dict() -# create an instance of FoldChange from a dict -fold_change_from_dict = FoldChange.from_dict(fold_change_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/PagedModelRun.md b/client-api_python/generated/docs/PagedModelRun.md deleted file mode 100644 index ea6c0287..00000000 --- a/client-api_python/generated/docs/PagedModelRun.md +++ /dev/null @@ -1,30 +0,0 @@ -# PagedModelRun - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**content** | [**List[Run]**](Run.md) | | [optional] -**page** | [**PageMetadata**](PageMetadata.md) | | [optional] - -## Example - -```python -from PySirius.models.paged_model_run import PagedModelRun - -# TODO update the JSON string below -json = "{}" -# create an instance of PagedModelRun from a JSON string -paged_model_run_instance = PagedModelRun.from_json(json) -# print the JSON string representation of the object -print(PagedModelRun.to_json()) - -# convert the object into a dict -paged_model_run_dict = paged_model_run_instance.to_dict() -# create an instance of PagedModelRun from a dict -paged_model_run_from_dict = PagedModelRun.from_dict(paged_model_run_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/ProjectsApi.md b/client-api_python/generated/docs/ProjectsApi.md index 704f3fce..5280c7db 100644 --- a/client-api_python/generated/docs/ProjectsApi.md +++ b/client-api_python/generated/docs/ProjectsApi.md @@ -527,7 +527,7 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.ProjectsApi(api_client) project_id = 'project_id_example' # str | Project-space to import into. - input_files = None # List[bytearray] | Files to import into project. + input_files = None # List[bytearray] | files to import into project parameters = PySirius.LcmsSubmissionParameters() # LcmsSubmissionParameters | try: @@ -547,7 +547,7 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| Project-space to import into. | - **input_files** | **List[bytearray]**| Files to import into project. | + **input_files** | **List[bytearray]**| files to import into project | **parameters** | [**LcmsSubmissionParameters**](LcmsSubmissionParameters.md)| | ### Return type @@ -602,7 +602,7 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.ProjectsApi(api_client) project_id = 'project_id_example' # str | Project-space to import into. - input_files = None # List[bytearray] | Files to import into project. + input_files = None # List[bytearray] | files to import into project parameters = PySirius.LcmsSubmissionParameters() # LcmsSubmissionParameters | opt_fields = ["progress"] # List[JobOptField] | Set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["progress"]) @@ -623,7 +623,7 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| Project-space to import into. | - **input_files** | **List[bytearray]**| Files to import into project. | + **input_files** | **List[bytearray]**| files to import into project | **parameters** | [**LcmsSubmissionParameters**](LcmsSubmissionParameters.md)| | **opt_fields** | [**List[JobOptField]**](JobOptField.md)| Set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["progress"]] @@ -753,7 +753,7 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.ProjectsApi(api_client) project_id = 'project_id_example' # str | project-space to import into. - input_files = None # List[bytearray] | + input_files = None # List[bytearray] | files to import into project ignore_formulas = False # bool | (optional) (default to False) allow_ms1_only = True # bool | (optional) (default to True) opt_fields = ["progress"] # List[JobOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["progress"]) @@ -775,7 +775,7 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **project_id** | **str**| project-space to import into. | - **input_files** | **List[bytearray]**| | + **input_files** | **List[bytearray]**| files to import into project | **ignore_formulas** | **bool**| | [optional] [default to False] **allow_ms1_only** | **bool**| | [optional] [default to True] **opt_fields** | [**List[JobOptField]**](JobOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["progress"]] diff --git a/client-api_python/generated/docs/QualityItem.md b/client-api_python/generated/docs/QualityItem.md deleted file mode 100644 index b1a302d6..00000000 --- a/client-api_python/generated/docs/QualityItem.md +++ /dev/null @@ -1,31 +0,0 @@ -# QualityItem - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**description** | **str** | | [optional] -**quality** | [**DataQuality**](DataQuality.md) | | [optional] -**weight** | [**QualityWeight**](QualityWeight.md) | | [optional] - -## Example - -```python -from PySirius.models.quality_item import QualityItem - -# TODO update the JSON string below -json = "{}" -# create an instance of QualityItem from a JSON string -quality_item_instance = QualityItem.from_json(json) -# print the JSON string representation of the object -print(QualityItem.to_json()) - -# convert the object into a dict -quality_item_dict = quality_item_instance.to_dict() -# create an instance of QualityItem from a dict -quality_item_from_dict = QualityItem.from_dict(quality_item_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/QualityWeight.md b/client-api_python/generated/docs/QualityWeight.md deleted file mode 100644 index 871cb8d7..00000000 --- a/client-api_python/generated/docs/QualityWeight.md +++ /dev/null @@ -1,14 +0,0 @@ -# QualityWeight - - -## Enum - -* `MINOR` (value: `'MINOR'`) - -* `MAJOR` (value: `'MAJOR'`) - -* `CRITICAL` (value: `'CRITICAL'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/QuantMeasure.md b/client-api_python/generated/docs/QuantMeasure.md deleted file mode 100644 index d12338e9..00000000 --- a/client-api_python/generated/docs/QuantMeasure.md +++ /dev/null @@ -1,12 +0,0 @@ -# QuantMeasure - - -## Enum - -* `APEX_INTENSITY` (value: `'APEX_INTENSITY'`) - -* `AREA_UNDER_CURVE` (value: `'AREA_UNDER_CURVE'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/QuantRowType.md b/client-api_python/generated/docs/QuantRowType.md deleted file mode 100644 index 97a3ab9e..00000000 --- a/client-api_python/generated/docs/QuantRowType.md +++ /dev/null @@ -1,12 +0,0 @@ -# QuantRowType - - -## Enum - -* `FEATURES` (value: `'FEATURES'`) - -* `COMPOUNDS` (value: `'COMPOUNDS'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/QuantTableExperimental.md b/client-api_python/generated/docs/QuantTableExperimental.md deleted file mode 100644 index 6924443d..00000000 --- a/client-api_python/generated/docs/QuantTableExperimental.md +++ /dev/null @@ -1,36 +0,0 @@ -# QuantTableExperimental - -EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**quantification_measure** | [**QuantMeasure**](QuantMeasure.md) | | [optional] -**row_type** | [**QuantRowType**](QuantRowType.md) | | [optional] -**row_ids** | **List[Optional[int]]** | | [optional] -**column_ids** | **List[Optional[int]]** | | [optional] -**row_names** | **List[Optional[str]]** | | [optional] -**column_names** | **List[Optional[str]]** | | [optional] -**values** | **List[List[float]]** | | [optional] - -## Example - -```python -from PySirius.models.quant_table_experimental import QuantTableExperimental - -# TODO update the JSON string below -json = "{}" -# create an instance of QuantTableExperimental from a JSON string -quant_table_experimental_instance = QuantTableExperimental.from_json(json) -# print the JSON string representation of the object -print(QuantTableExperimental.to_json()) - -# convert the object into a dict -quant_table_experimental_dict = quant_table_experimental_instance.to_dict() -# create an instance of QuantTableExperimental from a dict -quant_table_experimental_from_dict = QuantTableExperimental.from_dict(quant_table_experimental_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/Run.md b/client-api_python/generated/docs/Run.md deleted file mode 100644 index ca845a7f..00000000 --- a/client-api_python/generated/docs/Run.md +++ /dev/null @@ -1,36 +0,0 @@ -# Run - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**run_id** | **str** | Identifier | [optional] -**name** | **str** | Informative, human-readable name of this run | [optional] -**source** | **str** | Source location | [optional] -**chromatography** | **str** | | [optional] -**ionization** | **str** | | [optional] -**fragmentation** | **str** | | [optional] -**mass_analyzers** | **List[Optional[str]]** | | [optional] -**tags** | [**Dict[str, Tag]**](Tag.md) | Key: tagName, value: tag | [optional] - -## Example - -```python -from PySirius.models.run import Run - -# TODO update the JSON string below -json = "{}" -# create an instance of Run from a JSON string -run_instance = Run.from_json(json) -# print the JSON string representation of the object -print(Run.to_json()) - -# convert the object into a dict -run_dict = run_instance.to_dict() -# create an instance of Run from a dict -run_from_dict = Run.from_dict(run_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/RunOptField.md b/client-api_python/generated/docs/RunOptField.md deleted file mode 100644 index 8c26389a..00000000 --- a/client-api_python/generated/docs/RunOptField.md +++ /dev/null @@ -1,12 +0,0 @@ -# RunOptField - - -## Enum - -* `NONE` (value: `'none'`) - -* `TAGS` (value: `'tags'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/RunsApi.md b/client-api_python/generated/docs/RunsApi.md deleted file mode 100644 index 06cd6011..00000000 --- a/client-api_python/generated/docs/RunsApi.md +++ /dev/null @@ -1,652 +0,0 @@ -# PySirius.RunsApi - -All URIs are relative to *http://localhost:8080* - -Method | HTTP request | Description -------------- | ------------- | ------------- -[**add_tags_to_run_experimental**](RunsApi.md#add_tags_to_run_experimental) | **PUT** /api/projects/{projectId}/runs/tags/{runId} | [EXPERIMENTAL] Add tags to a run in the project -[**compute_fold_change_for_blank_subtraction**](RunsApi.md#compute_fold_change_for_blank_subtraction) | **PUT** /api/projects/{projectId}/runs/blanksubtract/compute | **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter -[**get_run_experimental**](RunsApi.md#get_run_experimental) | **GET** /api/projects/{projectId}/runs/{runId} | [EXPERIMENTAL] Get run with the given identifier from the specified project-space -[**get_run_page_experimental**](RunsApi.md#get_run_page_experimental) | **GET** /api/projects/{projectId}/runs/page | [EXPERIMENTAL] Get all available runs in the given project-space -[**get_runs_by_group_experimental**](RunsApi.md#get_runs_by_group_experimental) | **GET** /api/projects/{projectId}/runs/grouped | [EXPERIMENTAL] Get runs by tag group -[**get_runs_by_tag_experimental**](RunsApi.md#get_runs_by_tag_experimental) | **GET** /api/projects/{projectId}/runs/tagged | [EXPERIMENTAL] Get runs by tag -[**get_tags_for_run_experimental**](RunsApi.md#get_tags_for_run_experimental) | **GET** /api/projects/{projectId}/runs/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Run -[**remove_tag_from_run_experimental**](RunsApi.md#remove_tag_from_run_experimental) | **DELETE** /api/projects/{projectId}/runs/tags/{runId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space - - -# **add_tags_to_run_experimental** -> List[Tag] add_tags_to_run_experimental(project_id, run_id, tag) - -[EXPERIMENTAL] Add tags to a run in the project - -[EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag import Tag -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to add to. - run_id = 'run_id_example' # str | run to add tags to. - tag = [PySirius.Tag()] # List[Tag] | tags to add. - - try: - # [EXPERIMENTAL] Add tags to a run in the project - api_response = api_instance.add_tags_to_run_experimental(project_id, run_id, tag) - print("The response of RunsApi->add_tags_to_run_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling RunsApi->add_tags_to_run_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to add to. | - **run_id** | **str**| run to add tags to. | - **tag** | [**List[Tag]**](Tag.md)| tags to add. | - -### Return type - -[**List[Tag]**](Tag.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: application/json - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | the tags that have been added | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **compute_fold_change_for_blank_subtraction** -> Job compute_fold_change_for_blank_subtraction(project_id, sample_type_fold_change_request, opt_fields=opt_fields) - -**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter - -**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter. - -
This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
- -### Example - - -```python -import PySirius -from PySirius.models.job import Job -from PySirius.models.job_opt_field import JobOptField -from PySirius.models.sample_type_fold_change_request import SampleTypeFoldChangeRequest -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to compute the fold change in. - sample_type_fold_change_request = PySirius.SampleTypeFoldChangeRequest() # SampleTypeFoldChangeRequest | request with lists of run IDs that are sample, blank, and control runs - opt_fields = ["progress"] # List[JobOptField] | job opt fields. (optional) (default to ["progress"]) - - try: - # **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter - api_response = api_instance.compute_fold_change_for_blank_subtraction(project_id, sample_type_fold_change_request, opt_fields=opt_fields) - print("The response of RunsApi->compute_fold_change_for_blank_subtraction:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling RunsApi->compute_fold_change_for_blank_subtraction: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to compute the fold change in. | - **sample_type_fold_change_request** | [**SampleTypeFoldChangeRequest**](SampleTypeFoldChangeRequest.md)| request with lists of run IDs that are sample, blank, and control runs | - **opt_fields** | [**List[JobOptField]**](JobOptField.md)| job opt fields. | [optional] [default to ["progress"]] - -### Return type - -[**Job**](Job.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: application/json - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_run_experimental** -> Run get_run_experimental(project_id, run_id, opt_fields=opt_fields) - -[EXPERIMENTAL] Get run with the given identifier from the specified project-space - -[EXPERIMENTAL] Get run with the given identifier from the specified project-space. -- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.run import Run -from PySirius.models.run_opt_field import RunOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - run_id = 'run_id_example' # str | identifier of run to access. - opt_fields = [] # List[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to []) - - try: - # [EXPERIMENTAL] Get run with the given identifier from the specified project-space - api_response = api_instance.get_run_experimental(project_id, run_id, opt_fields=opt_fields) - print("The response of RunsApi->get_run_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling RunsApi->get_run_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **run_id** | **str**| identifier of run to access. | - **opt_fields** | [**List[RunOptField]**](RunOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []] - -### Return type - -[**Run**](Run.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Run with tags (if specified). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_run_page_experimental** -> PagedModelRun get_run_page_experimental(project_id, page=page, size=size, sort=sort, opt_fields=opt_fields) - -[EXPERIMENTAL] Get all available runs in the given project-space - -[EXPERIMENTAL] Get all available runs in the given project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.paged_model_run import PagedModelRun -from PySirius.models.run_opt_field import RunOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = [] # List[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to []) - - try: - # [EXPERIMENTAL] Get all available runs in the given project-space - api_response = api_instance.get_run_page_experimental(project_id, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of RunsApi->get_run_page_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling RunsApi->get_run_page_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[RunOptField]**](RunOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []] - -### Return type - -[**PagedModelRun**](PagedModelRun.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Runs with tags (if specified). | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_runs_by_group_experimental** -> PagedModelRun get_runs_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) - -[EXPERIMENTAL] Get runs by tag group - -[EXPERIMENTAL] Get runs by tag group. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.paged_model_run import PagedModelRun -from PySirius.models.run_opt_field import RunOptField -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - group_name = 'group_name_example' # str | tag group name. - page = 0 # int | Zero-based page index (0..N) (optional) (default to 0) - size = 20 # int | The size of the page to be returned (optional) (default to 20) - sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional) - opt_fields = ["none"] # List[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"]) - - try: - # [EXPERIMENTAL] Get runs by tag group - api_response = api_instance.get_runs_by_group_experimental(project_id, group_name, page=page, size=size, sort=sort, opt_fields=opt_fields) - print("The response of RunsApi->get_runs_by_group_experimental:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling RunsApi->get_runs_by_group_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **group_name** | **str**| tag group name. | - **page** | **int**| Zero-based page index (0..N) | [optional] [default to 0] - **size** | **int**| The size of the page to be returned | [optional] [default to 20] - **sort** | [**List[str]**](str.md)| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional] - **opt_fields** | [**List[RunOptField]**](RunOptField.md)| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] - -### Return type - -[**PagedModelRun**](PagedModelRun.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | tagged runs | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_runs_by_tag_experimental** -> PagedModelRun get_runs_by_tag_experimental(project_id, filter=filter, page=page, size=size, sort=sort, opt_fields=opt_fields) - -[EXPERIMENTAL] Get runs by tag - -[EXPERIMENTAL] Get runs by tag. - -
The filter string must contain one or more clauses. A clause is prefÃxed - by a field name. -
- - Currently the only searchable fields are names of tags (tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition).
- Tag name based field need to be prefixed with the namespace tags..
- Possible value types of tags are bool, integer, real, text, date, or time - tag value
-
- The format of the date type is yyyy-MM-dd and of the time type is HH\:mm\:ss.
A clause may be:
-tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] Clauses may be grouped with brackets ( and ) and / or joined with AND or OR (or && and || )
The syntax allows to build complex filter queries such as:
- -tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\:00\:00 OR tags.time:[12\:00\:00 TO 14\:00\:00] OR tags.time<10\:00\:00
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.RunsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - run_id = 'run_id_example' # str | run to delete tag from. - tag_name = 'tag_name_example' # str | name of the tag to delete. - - try: - # [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space - api_instance.remove_tag_from_run_experimental(project_id, run_id, tag_name) - except Exception as e: - print("Exception when calling RunsApi->remove_tag_from_run_experimental: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **run_id** | **str**| run to delete tag from. | - **tag_name** | **str**| name of the tag to delete. | - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - diff --git a/client-api_python/generated/docs/SampleTypeFoldChangeRequest.md b/client-api_python/generated/docs/SampleTypeFoldChangeRequest.md deleted file mode 100644 index f7481ffc..00000000 --- a/client-api_python/generated/docs/SampleTypeFoldChangeRequest.md +++ /dev/null @@ -1,31 +0,0 @@ -# SampleTypeFoldChangeRequest - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**sample_run_ids** | **List[str]** | | [optional] -**blank_run_ids** | **List[str]** | | [optional] -**control_run_ids** | **List[str]** | | [optional] - -## Example - -```python -from PySirius.models.sample_type_fold_change_request import SampleTypeFoldChangeRequest - -# TODO update the JSON string below -json = "{}" -# create an instance of SampleTypeFoldChangeRequest from a JSON string -sample_type_fold_change_request_instance = SampleTypeFoldChangeRequest.from_json(json) -# print the JSON string representation of the object -print(SampleTypeFoldChangeRequest.to_json()) - -# convert the object into a dict -sample_type_fold_change_request_dict = sample_type_fold_change_request_instance.to_dict() -# create an instance of SampleTypeFoldChangeRequest from a dict -sample_type_fold_change_request_from_dict = SampleTypeFoldChangeRequest.from_dict(sample_type_fold_change_request_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/SearchableDatabasesApi.md b/client-api_python/generated/docs/SearchableDatabasesApi.md index 0c7b7d43..c87bb13f 100644 --- a/client-api_python/generated/docs/SearchableDatabasesApi.md +++ b/client-api_python/generated/docs/SearchableDatabasesApi.md @@ -4,7 +4,7 @@ All URIs are relative to *http://localhost:8080* Method | HTTP request | Description ------------- | ------------- | ------------- -[**add_databases**](SearchableDatabasesApi.md#add_databases) | **POST** /api/databases | DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. +[**add_databases**](SearchableDatabasesApi.md#add_databases) | **POST** /api/databases | [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. [**create_database**](SearchableDatabasesApi.md#create_database) | **POST** /api/databases/{databaseId} | [**get_custom_databases**](SearchableDatabasesApi.md#get_custom_databases) | **GET** /api/databases/custom | [**get_database**](SearchableDatabasesApi.md#get_database) | **GET** /api/databases/{databaseId} | @@ -18,7 +18,7 @@ Method | HTTP request | Description # **add_databases** > List[SearchableDatabase] add_databases(request_body) -DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. +[DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. ### Example @@ -43,7 +43,7 @@ with PySirius.ApiClient(configuration) as api_client: request_body = ['request_body_example'] # List[str] | try: - # DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. + # [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API. api_response = api_instance.add_databases(request_body) print("The response of SearchableDatabasesApi->add_databases:\n") pprint(api_response) @@ -434,7 +434,7 @@ with PySirius.ApiClient(configuration) as api_client: # Create an instance of the API class api_instance = PySirius.SearchableDatabasesApi(api_client) database_id = 'database_id_example' # str | database to import into - input_files = None # List[bytearray] | files to be imported + input_files = None # List[bytearray] | files to import into project buffer_size = 1000 # int | (optional) (default to 1000) bio_transformer_parameters = PySirius.BioTransformerParameters() # BioTransformerParameters | (optional) @@ -455,7 +455,7 @@ with PySirius.ApiClient(configuration) as api_client: Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- **database_id** | **str**| database to import into | - **input_files** | **List[bytearray]**| files to be imported | + **input_files** | **List[bytearray]**| files to import into project | **buffer_size** | **int**| | [optional] [default to 1000] **bio_transformer_parameters** | [**BioTransformerParameters**](BioTransformerParameters.md)| | [optional] diff --git a/client-api_python/generated/docs/StatisticsTable.md b/client-api_python/generated/docs/StatisticsTable.md deleted file mode 100644 index 9d6fbcf2..00000000 --- a/client-api_python/generated/docs/StatisticsTable.md +++ /dev/null @@ -1,37 +0,0 @@ -# StatisticsTable - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**statistics_type** | [**StatisticsType**](StatisticsType.md) | | [optional] -**aggregation_type** | [**AggregationType**](AggregationType.md) | | [optional] -**quantification_measure** | [**QuantMeasure**](QuantMeasure.md) | | [optional] -**row_type** | [**QuantRowType**](QuantRowType.md) | | [optional] -**row_ids** | **List[str]** | | [optional] -**column_names** | **List[str]** | | [optional] -**column_left_groups** | **List[str]** | | [optional] -**column_right_groups** | **List[str]** | | [optional] -**values** | **List[List[float]]** | | [optional] - -## Example - -```python -from PySirius.models.statistics_table import StatisticsTable - -# TODO update the JSON string below -json = "{}" -# create an instance of StatisticsTable from a JSON string -statistics_table_instance = StatisticsTable.from_json(json) -# print the JSON string representation of the object -print(StatisticsTable.to_json()) - -# convert the object into a dict -statistics_table_dict = statistics_table_instance.to_dict() -# create an instance of StatisticsTable from a dict -statistics_table_from_dict = StatisticsTable.from_dict(statistics_table_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/StatisticsType.md b/client-api_python/generated/docs/StatisticsType.md deleted file mode 100644 index 58246e2d..00000000 --- a/client-api_python/generated/docs/StatisticsType.md +++ /dev/null @@ -1,10 +0,0 @@ -# StatisticsType - - -## Enum - -* `FOLD_CHANGE` (value: `'FOLD_CHANGE'`) - -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/TagDefinition.md b/client-api_python/generated/docs/TagDefinition.md deleted file mode 100644 index ec08cad2..00000000 --- a/client-api_python/generated/docs/TagDefinition.md +++ /dev/null @@ -1,36 +0,0 @@ -# TagDefinition - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**tag_name** | **str** | Name of this tag defined by this definition (key) | -**description** | **str** | A human-readable description about the purpose of this tag. | [optional] -**tag_type** | **str** | A simple string based identifier to specify the type/scope/purpose of this tag. | [optional] -**value_type** | [**ValueType**](ValueType.md) | | -**possible_values** | **List[Optional[object]]** | | [optional] -**min_value** | **object** | | [optional] -**max_value** | **object** | | [optional] -**editable** | **bool** | | [optional] - -## Example - -```python -from PySirius.models.tag_definition import TagDefinition - -# TODO update the JSON string below -json = "{}" -# create an instance of TagDefinition from a JSON string -tag_definition_instance = TagDefinition.from_json(json) -# print the JSON string representation of the object -print(TagDefinition.to_json()) - -# convert the object into a dict -tag_definition_dict = tag_definition_instance.to_dict() -# create an instance of TagDefinition from a dict -tag_definition_from_dict = TagDefinition.from_dict(tag_definition_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/TagDefinitionImport.md b/client-api_python/generated/docs/TagDefinitionImport.md deleted file mode 100644 index 72bc45d3..00000000 --- a/client-api_python/generated/docs/TagDefinitionImport.md +++ /dev/null @@ -1,35 +0,0 @@ -# TagDefinitionImport - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**tag_name** | **str** | Name of this tag defined by this definition (key) | -**description** | **str** | A human-readable description about the purpose of this tag. | [optional] -**tag_type** | **str** | A simple string based identifier to specify the type/scope/purpose of this tag. | [optional] -**value_type** | [**ValueType**](ValueType.md) | | -**possible_values** | **List[Optional[object]]** | | [optional] -**min_value** | **object** | | [optional] -**max_value** | **object** | | [optional] - -## Example - -```python -from PySirius.models.tag_definition_import import TagDefinitionImport - -# TODO update the JSON string below -json = "{}" -# create an instance of TagDefinitionImport from a JSON string -tag_definition_import_instance = TagDefinitionImport.from_json(json) -# print the JSON string representation of the object -print(TagDefinitionImport.to_json()) - -# convert the object into a dict -tag_definition_import_dict = tag_definition_import_instance.to_dict() -# create an instance of TagDefinitionImport from a dict -tag_definition_import_from_dict = TagDefinitionImport.from_dict(tag_definition_import_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/TagGroup.md b/client-api_python/generated/docs/TagGroup.md deleted file mode 100644 index 0cd70b7a..00000000 --- a/client-api_python/generated/docs/TagGroup.md +++ /dev/null @@ -1,31 +0,0 @@ -# TagGroup - - -## Properties - -Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- -**group_name** | **str** | Name of this Grouping query. | [optional] -**lucene_query** | **str** | Query used to group the entities in lucene format. | [optional] -**group_type** | **str** | | [optional] - -## Example - -```python -from PySirius.models.tag_group import TagGroup - -# TODO update the JSON string below -json = "{}" -# create an instance of TagGroup from a JSON string -tag_group_instance = TagGroup.from_json(json) -# print the JSON string representation of the object -print(TagGroup.to_json()) - -# convert the object into a dict -tag_group_dict = tag_group_instance.to_dict() -# create an instance of TagGroup from a dict -tag_group_from_dict = TagGroup.from_dict(tag_group_dict) -``` -[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) - - diff --git a/client-api_python/generated/docs/TagsApi.md b/client-api_python/generated/docs/TagsApi.md deleted file mode 100644 index 20337034..00000000 --- a/client-api_python/generated/docs/TagsApi.md +++ /dev/null @@ -1,672 +0,0 @@ -# PySirius.TagsApi - -All URIs are relative to *http://localhost:8080* - -Method | HTTP request | Description -------------- | ------------- | ------------- -[**add_group**](TagsApi.md#add_group) | **POST** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Group tags in the project -[**add_possible_values_to_tag_definition**](TagsApi.md#add_possible_values_to_tag_definition) | **PATCH** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Add a possible value to the tag definition in the project -[**create_tags**](TagsApi.md#create_tags) | **PUT** /api/projects/{projectId}/tags | [EXPERIMENTAL] Add tags to the project -[**delete_group**](TagsApi.md#delete_group) | **DELETE** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space -[**delete_tag**](TagsApi.md#delete_tag) | **DELETE** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space -[**get_group_by_name**](TagsApi.md#get_group_by_name) | **GET** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Get tag group by name in the given project-space -[**get_groups**](TagsApi.md#get_groups) | **GET** /api/projects/{projectId}/groups | [EXPERIMENTAL] Get all tag based groups in the given project-space -[**get_tag**](TagsApi.md#get_tag) | **GET** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Get tag definition by its name in the given project-space -[**get_tags**](TagsApi.md#get_tags) | **GET** /api/projects/{projectId}/tags | [EXPERIMENTAL] Get all tag definitions in the given project-space - - -# **add_group** -> TagGroup add_group(project_id, group_name, filter, type) - -[EXPERIMENTAL] Group tags in the project - -[EXPERIMENTAL] Group tags in the project. The group name must not exist in the project. - -
- See /tagged for filter syntax.
-
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag_definition import TagDefinition -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to add to. - tag_name = 'tag_name_example' # str | the tag definition to add the values to - request_body = None # List[object] | - - try: - # [EXPERIMENTAL] Add a possible value to the tag definition in the project - api_response = api_instance.add_possible_values_to_tag_definition(project_id, tag_name, request_body) - print("The response of TagsApi->add_possible_values_to_tag_definition:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling TagsApi->add_possible_values_to_tag_definition: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to add to. | - **tag_name** | **str**| the tag definition to add the values to | - **request_body** | [**List[object]**](object.md)| | - -### Return type - -[**TagDefinition**](TagDefinition.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: application/json - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | the definitions of the tags that have been added | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **create_tags** -> List[TagDefinition] create_tags(project_id, tag_definition_import) - -[EXPERIMENTAL] Add tags to the project - -[EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag_definition import TagDefinition -from PySirius.models.tag_definition_import import TagDefinitionImport -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to add to. - tag_definition_import = [PySirius.TagDefinitionImport()] # List[TagDefinitionImport] | the tag definitions to be created - - try: - # [EXPERIMENTAL] Add tags to the project - api_response = api_instance.create_tags(project_id, tag_definition_import) - print("The response of TagsApi->create_tags:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling TagsApi->create_tags: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to add to. | - **tag_definition_import** | [**List[TagDefinitionImport]**](TagDefinitionImport.md)| the tag definitions to be created | - -### Return type - -[**List[TagDefinition]**](TagDefinition.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: application/json - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | the definitions of the tags that have been created | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **delete_group** -> delete_group(project_id, group_name) - -[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space - -[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - group_name = 'group_name_example' # str | name of group to delete. - - try: - # [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space - api_instance.delete_group(project_id, group_name) - except Exception as e: - print("Exception when calling TagsApi->delete_group: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **group_name** | **str**| name of group to delete. | - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **delete_tag** -> delete_tag(project_id, tag_name) - -[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space - -[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space. -
- This will also remove all tags belonging to this definition from every tagged entity. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to delete from. - tag_name = 'tag_name_example' # str | name of the tag definition to delete. - - try: - # [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space - api_instance.delete_tag(project_id, tag_name) - except Exception as e: - print("Exception when calling TagsApi->delete_tag: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to delete from. | - **tag_name** | **str**| name of the tag definition to delete. | - -### Return type - -void (empty response body) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: Not defined - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | OK | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_group_by_name** -> TagGroup get_group_by_name(project_id, group_name) - -[EXPERIMENTAL] Get tag group by name in the given project-space - -[EXPERIMENTAL] Get tag group by name in the given project-space. -- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag_group import TagGroup -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - group_name = 'group_name_example' # str | name of the group - - try: - # [EXPERIMENTAL] Get tag group by name in the given project-space - api_response = api_instance.get_group_by_name(project_id, group_name) - print("The response of TagsApi->get_group_by_name:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling TagsApi->get_group_by_name: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **group_name** | **str**| name of the group | - -### Return type - -[**TagGroup**](TagGroup.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Tag group. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_groups** -> List[TagGroup] get_groups(project_id, group_type=group_type) - -[EXPERIMENTAL] Get all tag based groups in the given project-space - -[EXPERIMENTAL] Get all tag based groups in the given project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag_group import TagGroup -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - group_type = 'group_type_example' # str | type of the group (optional) - - try: - # [EXPERIMENTAL] Get all tag based groups in the given project-space - api_response = api_instance.get_groups(project_id, group_type=group_type) - print("The response of TagsApi->get_groups:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling TagsApi->get_groups: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **group_type** | **str**| type of the group | [optional] - -### Return type - -[**List[TagGroup]**](TagGroup.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Groups. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_tag** -> TagDefinition get_tag(project_id, tag_name) - -[EXPERIMENTAL] Get tag definition by its name in the given project-space - -[EXPERIMENTAL] Get tag definition by its name in the given project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. - -### Example - - -```python -import PySirius -from PySirius.models.tag_definition import TagDefinition -from PySirius.rest import ApiException -from pprint import pprint - -# Defining the host is optional and defaults to http://localhost:8080 -# See configuration.py for a list of all supported configuration parameters. -configuration = PySirius.Configuration( - host = "http://localhost:8080" -) - - -# Enter a context with an instance of the API client -with PySirius.ApiClient(configuration) as api_client: - # Create an instance of the API class - api_instance = PySirius.TagsApi(api_client) - project_id = 'project_id_example' # str | project-space to read from. - tag_name = 'tag_name_example' # str | name of the tag - - try: - # [EXPERIMENTAL] Get tag definition by its name in the given project-space - api_response = api_instance.get_tag(project_id, tag_name) - print("The response of TagsApi->get_tag:\n") - pprint(api_response) - except Exception as e: - print("Exception when calling TagsApi->get_tag: %s\n" % e) -``` - - - -### Parameters - - -Name | Type | Description | Notes -------------- | ------------- | ------------- | ------------- - **project_id** | **str**| project-space to read from. | - **tag_name** | **str**| name of the tag | - -### Return type - -[**TagDefinition**](TagDefinition.md) - -### Authorization - -No authorization required - -### HTTP request headers - - - **Content-Type**: Not defined - - **Accept**: application/json - -### HTTP response details - -| Status code | Description | Response headers | -|-------------|-------------|------------------| -**200** | Tag definition. | - | - -[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md) - -# **get_tags** -> List[TagDefinition] get_tags(project_id, tag_type=tag_type) - -[EXPERIMENTAL] Get all tag definitions in the given project-space - -[EXPERIMENTAL] Get all tag definitions in the given project-space. -
- [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-
-
-```python
-import PySirius
-from PySirius.models.tag_definition import TagDefinition
-from PySirius.rest import ApiException
-from pprint import pprint
-
-# Defining the host is optional and defaults to http://localhost:8080
-# See configuration.py for a list of all supported configuration parameters.
-configuration = PySirius.Configuration(
- host = "http://localhost:8080"
-)
-
-
-# Enter a context with an instance of the API client
-with PySirius.ApiClient(configuration) as api_client:
- # Create an instance of the API class
- api_instance = PySirius.TagsApi(api_client)
- project_id = 'project_id_example' # str | project-space to read from.
- tag_type = 'tag_type_example' # str | scope of the tag (optional) (optional)
-
- try:
- # [EXPERIMENTAL] Get all tag definitions in the given project-space
- api_response = api_instance.get_tags(project_id, tag_type=tag_type)
- print("The response of TagsApi->get_tags:\n")
- pprint(api_response)
- except Exception as e:
- print("Exception when calling TagsApi->get_tags: %s\n" % e)
-```
-
-
-
-### Parameters
-
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **str**| project-space to read from. |
- **tag_type** | **str**| scope of the tag (optional) | [optional]
-
-### Return type
-
-[**List[TagDefinition]**](TagDefinition.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-**200** | Tag definitions. | - |
-
-[[Back to top]](#) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to Model list]](../README.md#documentation-for-models) [[Back to README]](../README.md)
-
diff --git a/client-api_python/generated/docs/TraceAnnotationExperimental.md b/client-api_python/generated/docs/TraceAnnotationExperimental.md
deleted file mode 100644
index 74fd2470..00000000
--- a/client-api_python/generated/docs/TraceAnnotationExperimental.md
+++ /dev/null
@@ -1,34 +0,0 @@
-# TraceAnnotationExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**type** | [**TraceAnnotationTypeExperimental**](TraceAnnotationTypeExperimental.md) | | [optional]
-**description** | **str** | | [optional]
-**index** | **int** | | [optional]
-**var_from** | **int** | | [optional]
-**to** | **int** | | [optional]
-
-## Example
-
-```python
-from PySirius.models.trace_annotation_experimental import TraceAnnotationExperimental
-
-# TODO update the JSON string below
-json = "{}"
-# create an instance of TraceAnnotationExperimental from a JSON string
-trace_annotation_experimental_instance = TraceAnnotationExperimental.from_json(json)
-# print the JSON string representation of the object
-print(TraceAnnotationExperimental.to_json())
-
-# convert the object into a dict
-trace_annotation_experimental_dict = trace_annotation_experimental_instance.to_dict()
-# create an instance of TraceAnnotationExperimental from a dict
-trace_annotation_experimental_from_dict = TraceAnnotationExperimental.from_dict(trace_annotation_experimental_dict)
-```
-[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
-
-
diff --git a/client-api_python/generated/docs/TraceAnnotationTypeExperimental.md b/client-api_python/generated/docs/TraceAnnotationTypeExperimental.md
deleted file mode 100644
index 959c51f7..00000000
--- a/client-api_python/generated/docs/TraceAnnotationTypeExperimental.md
+++ /dev/null
@@ -1,13 +0,0 @@
-# TraceAnnotationTypeExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Enum
-
-* `FEATURE` (value: `'FEATURE'`)
-
-* `MS2` (value: `'MS2'`)
-
-[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
-
-
diff --git a/client-api_python/generated/docs/TraceExperimental.md b/client-api_python/generated/docs/TraceExperimental.md
deleted file mode 100644
index cf20876a..00000000
--- a/client-api_python/generated/docs/TraceExperimental.md
+++ /dev/null
@@ -1,40 +0,0 @@
-# TraceExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**id** | **str** | | [optional]
-**sample_id** | **str** | | [optional]
-**sample_name** | **str** | | [optional]
-**label** | **str** | | [optional]
-**color** | **str** | | [optional]
-**intensities** | **List[float]** | | [optional]
-**annotations** | [**List[TraceAnnotationExperimental]**](TraceAnnotationExperimental.md) | | [optional]
-**mz** | **float** | | [optional]
-**merged** | **bool** | | [optional]
-**normalization_factor** | **float** | Traces are stored with raw intensity values. The normalization factor maps them to relative intensities, such that traces from different samples can be compared. | [optional]
-**noise_level** | **float** | The noise level is estimated from the median noise in the surrounding scans. It can be used to calculate signal-to-noise ratios. | [optional]
-
-## Example
-
-```python
-from PySirius.models.trace_experimental import TraceExperimental
-
-# TODO update the JSON string below
-json = "{}"
-# create an instance of TraceExperimental from a JSON string
-trace_experimental_instance = TraceExperimental.from_json(json)
-# print the JSON string representation of the object
-print(TraceExperimental.to_json())
-
-# convert the object into a dict
-trace_experimental_dict = trace_experimental_instance.to_dict()
-# create an instance of TraceExperimental from a dict
-trace_experimental_from_dict = TraceExperimental.from_dict(trace_experimental_dict)
-```
-[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
-
-
diff --git a/client-api_python/generated/docs/TraceSetExperimental.md b/client-api_python/generated/docs/TraceSetExperimental.md
deleted file mode 100644
index ab464527..00000000
--- a/client-api_python/generated/docs/TraceSetExperimental.md
+++ /dev/null
@@ -1,34 +0,0 @@
-# TraceSetExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**adduct_network** | [**AdductNetworkExperimental**](AdductNetworkExperimental.md) | | [optional]
-**sample_id** | **str** | | [optional]
-**sample_name** | **str** | | [optional]
-**axes** | [**Axes**](Axes.md) | | [optional]
-**traces** | [**List[TraceExperimental]**](TraceExperimental.md) | | [optional]
-
-## Example
-
-```python
-from PySirius.models.trace_set_experimental import TraceSetExperimental
-
-# TODO update the JSON string below
-json = "{}"
-# create an instance of TraceSetExperimental from a JSON string
-trace_set_experimental_instance = TraceSetExperimental.from_json(json)
-# print the JSON string representation of the object
-print(TraceSetExperimental.to_json())
-
-# convert the object into a dict
-trace_set_experimental_dict = trace_set_experimental_instance.to_dict()
-# create an instance of TraceSetExperimental from a dict
-trace_set_experimental_from_dict = TraceSetExperimental.from_dict(trace_set_experimental_dict)
-```
-[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
-
-
diff --git a/client-api_python/generated/docs/ValueType.md b/client-api_python/generated/docs/ValueType.md
deleted file mode 100644
index 15337e4a..00000000
--- a/client-api_python/generated/docs/ValueType.md
+++ /dev/null
@@ -1,22 +0,0 @@
-# ValueType
-
-
-## Enum
-
-* `NONE` (value: `'NONE'`)
-
-* `BOOLEAN` (value: `'BOOLEAN'`)
-
-* `INTEGER` (value: `'INTEGER'`)
-
-* `REAL` (value: `'REAL'`)
-
-* `TEXT` (value: `'TEXT'`)
-
-* `DATE` (value: `'DATE'`)
-
-* `TIME` (value: `'TIME'`)
-
-[[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md)
-
-
diff --git a/client-api_python/generated/pyproject.toml b/client-api_python/generated/pyproject.toml
index 2ec574d1..eea7472a 100644
--- a/client-api_python/generated/pyproject.toml
+++ b/client-api_python/generated/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "PySirius"
-version = "6.3.3"
+version = "6.3.4"
description = "SIRIUS Nightsky API"
authors = [
{name = "OpenAPI Generator Community",email = "team@openapitools.org"},
diff --git a/client-api_python/generated/setup.py b/client-api_python/generated/setup.py
index 64f83a34..7eba6f39 100644
--- a/client-api_python/generated/setup.py
+++ b/client-api_python/generated/setup.py
@@ -19,7 +19,7 @@
# prerequisite: setuptools
# http://pypi.python.org/pypi/setuptools
NAME = "PySirius"
-VERSION = "6.3.3"
+VERSION = "6.3.4"
PYTHON_REQUIRES = ">= 3.9"
REQUIRES = [
"urllib3 >= 2.1.0, < 3.0.0",
diff --git a/client-api_python/generated/test/test_features_api.py b/client-api_python/generated/test/test_features_api.py
index 54e0e2ca..62460fe7 100644
--- a/client-api_python/generated/test/test_features_api.py
+++ b/client-api_python/generated/test/test_features_api.py
@@ -179,15 +179,6 @@ def test_get_canopus_prediction(self) -> None:
response = self.api.features().get_canopus_prediction(self.project_id, self.aligned_feature_id, self.formula_id)
self.assertIsInstance(response, CanopusPrediction)
- def test_get_de_novo_structure_candidates(self) -> None:
- """Test case for get_de_novo_structure_candidates
-
- List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
- """
- response = self.api.features().get_de_novo_structure_candidates(self.project_id, self.aligned_feature_id)
- self.assertIsInstance(response, list)
- self.assertIsInstance(response[0], StructureCandidateFormula)
-
def test_get_de_novo_structure_candidates_by_formula(self) -> None:
"""Test case for get_de_novo_structure_candidates_by_formula
diff --git a/client-api_r/generated/.openapi-generator/FILES b/client-api_r/generated/.openapi-generator/FILES
index 0ff976a6..ce373421 100644
--- a/client-api_r/generated/.openapi-generator/FILES
+++ b/client-api_r/generated/.openapi-generator/FILES
@@ -6,18 +6,13 @@ NAMESPACE
R/account_credentials.R
R/account_info.R
R/actuator_api.R
-R/adduct_edge_experimental.R
-R/adduct_network_experimental.R
-R/adduct_node_experimental.R
R/aligned_feature.R
-R/aligned_feature_quality_experimental.R
R/allowed_features.R
R/annotated_ms_ms_data.R
R/annotated_peak.R
R/annotated_spectrum.R
R/api_client.R
R/api_response.R
-R/axes.R
R/background_computations_state_event.R
R/basic_spectrum.R
R/binary_fingerprint.R
@@ -25,12 +20,10 @@ R/bio_transformer_parameters.R
R/bio_transformer_sequence_step.R
R/canopus.R
R/canopus_prediction.R
-R/category.R
R/compound.R
R/compound_class.R
R/compound_classes.R
R/compound_import.R
-R/compound_statistics_api.R
R/compounds_api.R
R/computed_subtools.R
R/connection_check.R
@@ -42,10 +35,8 @@ R/db_link.R
R/deviation.R
R/feature_annotations.R
R/feature_import.R
-R/feature_statistics_api.R
R/features_api.R
R/fingerprint_prediction.R
-R/fold_change.R
R/formula_candidate.R
R/fragment_node.R
R/fragmentation_tree.R
@@ -71,7 +62,6 @@ R/paged_model_aligned_feature.R
R/paged_model_compound.R
R/paged_model_formula_candidate.R
R/paged_model_job.R
-R/paged_model_run.R
R/paged_model_spectral_library_match.R
R/paged_model_structure_candidate_formula.R
R/paged_model_structure_candidate_scored.R
@@ -81,13 +71,7 @@ R/peak_pair.R
R/project_change_event.R
R/project_info.R
R/projects_api.R
-R/quality_item.R
-R/quant_table_experimental.R
R/rsirius_api.R
-R/run.R
-R/run_opt_field.R
-R/runs_api.R
-R/sample_type_fold_change_request.R
R/searchable_database.R
R/searchable_database_parameters.R
R/searchable_databases_api.R
@@ -99,7 +83,6 @@ R/spectral_library_match.R
R/spectral_library_match_summary.R
R/spectral_library_search.R
R/spectrum_annotation.R
-R/statistics_table.R
R/stored_job_submission.R
R/structure_candidate.R
R/structure_candidate_formula.R
@@ -108,15 +91,8 @@ R/structure_db_search.R
R/subscription.R
R/subscription_consumables.R
R/tag.R
-R/tag_definition.R
-R/tag_definition_import.R
-R/tag_group.R
-R/tags_api.R
R/term.R
R/timeout.R
-R/trace_annotation_experimental.R
-R/trace_experimental.R
-R/trace_set_experimental.R
R/use_heuristic.R
R/web_server_namespace.R
R/zodiac.R
@@ -128,16 +104,11 @@ README.md
docs/AccountCredentials.md
docs/AccountInfo.md
docs/ActuatorApi.md
-docs/AdductEdgeExperimental.md
-docs/AdductNetworkExperimental.md
-docs/AdductNodeExperimental.md
docs/AlignedFeature.md
-docs/AlignedFeatureQualityExperimental.md
docs/AllowedFeatures.md
docs/AnnotatedMsMsData.md
docs/AnnotatedPeak.md
docs/AnnotatedSpectrum.md
-docs/Axes.md
docs/BackgroundComputationsStateEvent.md
docs/BasicSpectrum.md
docs/BinaryFingerprint.md
@@ -145,12 +116,10 @@ docs/BioTransformerParameters.md
docs/BioTransformerSequenceStep.md
docs/Canopus.md
docs/CanopusPrediction.md
-docs/Category.md
docs/Compound.md
docs/CompoundClass.md
docs/CompoundClasses.md
docs/CompoundImport.md
-docs/CompoundStatisticsApi.md
docs/CompoundsApi.md
docs/ComputedSubtools.md
docs/ConnectionCheck.md
@@ -162,10 +131,8 @@ docs/DataImportEvent.md
docs/Deviation.md
docs/FeatureAnnotations.md
docs/FeatureImport.md
-docs/FeatureStatisticsApi.md
docs/FeaturesApi.md
docs/FingerprintPrediction.md
-docs/FoldChange.md
docs/FormulaCandidate.md
docs/FragmentNode.md
docs/FragmentationTree.md
@@ -191,7 +158,6 @@ docs/PagedModelAlignedFeature.md
docs/PagedModelCompound.md
docs/PagedModelFormulaCandidate.md
docs/PagedModelJob.md
-docs/PagedModelRun.md
docs/PagedModelSpectralLibraryMatch.md
docs/PagedModelStructureCandidateFormula.md
docs/PagedModelStructureCandidateScored.md
@@ -201,12 +167,6 @@ docs/PeakPair.md
docs/ProjectChangeEvent.md
docs/ProjectInfo.md
docs/ProjectsApi.md
-docs/QualityItem.md
-docs/QuantTableExperimental.md
-docs/Run.md
-docs/RunOptField.md
-docs/RunsApi.md
-docs/SampleTypeFoldChangeRequest.md
docs/SearchableDatabase.md
docs/SearchableDatabaseParameters.md
docs/SearchableDatabasesApi.md
@@ -218,7 +178,6 @@ docs/SpectralLibraryMatch.md
docs/SpectralLibraryMatchSummary.md
docs/SpectralLibrarySearch.md
docs/SpectrumAnnotation.md
-docs/StatisticsTable.md
docs/StoredJobSubmission.md
docs/StructureCandidate.md
docs/StructureCandidateFormula.md
@@ -227,15 +186,8 @@ docs/StructureDbSearch.md
docs/Subscription.md
docs/SubscriptionConsumables.md
docs/Tag.md
-docs/TagDefinition.md
-docs/TagDefinitionImport.md
-docs/TagGroup.md
-docs/TagsApi.md
docs/Term.md
docs/Timeout.md
-docs/TraceAnnotationExperimental.md
-docs/TraceExperimental.md
-docs/TraceSetExperimental.md
docs/UseHeuristic.md
docs/WebServerNamespace.md
docs/Zodiac.md
diff --git a/client-api_r/generated/DESCRIPTION b/client-api_r/generated/DESCRIPTION
index b7ddcd27..985480a4 100644
--- a/client-api_r/generated/DESCRIPTION
+++ b/client-api_r/generated/DESCRIPTION
@@ -1,6 +1,6 @@
Package: RSirius
Title: R Package Client for SIRIUS Nightsky API
-Version: 6.3.3
+Version: 6.3.4
Author: person("OpenAPI Generator community", email = "team@openapitools.org", role = c("aut", "cre"))
Maintainer: OpenAPI Generator community The runs need to be tagged and grouped. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Compute the fold change between two groups of runs
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to compute the fold change in.
-var_left_group_name <- "left_group_name_example" # character | name of the left tag group.
-var_right_group_name <- "right_group_name_example" # character | name of the right tag group.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-var_opt_fields <- c("none") # array[character] | job opt fields. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$ComputeCompoundFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$compound_statistics_api$ComputeCompoundFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to compute the fold change in. |
- **left_group_name** | **character**| name of the left tag group. |
- **right_group_name** | **character**| name of the right tag group. |
- **aggregation** | Enum [AVG, MIN, MAX] | aggregation type. | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_INTENSITY"]
- **opt_fields** | Enum [none, command, progress, affectedIds] | job opt fields. | [optional] [default to ["progress"]]
-
-### Return type
-
-[**Job**](Job.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **DeleteCompoundFoldChangesExperimental**
-> DeleteCompoundFoldChangesExperimental(project_id, left_group_name, right_group_name, aggregation = "AVG", quantification = "APEX_INTENSITY")
-
-[EXPERIMENTAL] Delete fold changes
-
-[EXPERIMENTAL] Delete fold changes. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete fold changes
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_left_group_name <- "left_group_name_example" # character | name of the left group.
-var_right_group_name <- "right_group_name_example" # character | name of the right group.
-var_aggregation <- "AVG" # character | (Optional)
-var_quantification <- "APEX_INTENSITY" # character | (Optional)
-
-api_instance <- rsirius_api$new()
-api_instance$compound_statistics_api$DeleteCompoundFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **left_group_name** | **character**| name of the left group. |
- **right_group_name** | **character**| name of the right group. |
- **aggregation** | Enum [AVG, MIN, MAX] | | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | | [optional] [default to "APEX_INTENSITY"]
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **GetCompoundFoldChangeTableExperimental**
-> StatisticsTable GetCompoundFoldChangeTableExperimental(project_id, aggregation = "AVG", quantification = "APEX_INTENSITY")
-
-[EXPERIMENTAL] Get table of all fold changes in the project space
-
-[EXPERIMENTAL] Get table of all fold changes in the project space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get table of all fold changes in the project space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetCompoundFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantificationdata_file = "result.txt")
-result <- api_instance$compound_statistics_api$GetCompoundFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantification)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aggregation** | Enum [AVG, MIN, MAX] | aggregation type. | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_INTENSITY"]
-
-### Return type
-
-[**StatisticsTable**](StatisticsTable.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | table of fold changes. | - |
-
-# **GetFoldChangesByCompoundExperimental**
-> array[FoldChange] GetFoldChangesByCompoundExperimental(project_id, object_id)
-
-[EXPERIMENTAL] List all fold changes that are associated with an object
-
-[EXPERIMENTAL] List all fold changes that are associated with an object. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] List all fold changes that are associated with an object
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetFoldChangesByCompoundExperimental(var_project_id, var_object_iddata_file = "result.txt")
-result <- api_instance$compound_statistics_api$GetFoldChangesByCompoundExperimental(var_project_id, var_object_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **object_id** | **character**| id of the object the fold changes are assigned to. |
-
-### Return type
-
-[**array[FoldChange]**](FoldChange.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | fold changes | - |
-
diff --git a/client-api_r/generated/docs/CompoundsApi.md b/client-api_r/generated/docs/CompoundsApi.md
index e1703d0c..e8a7dd8a 100644
--- a/client-api_r/generated/docs/CompoundsApi.md
+++ b/client-api_r/generated/docs/CompoundsApi.md
@@ -5,18 +5,10 @@ All URIs are relative to *http://localhost:8080*
Method | HTTP request | Description
------------- | ------------- | -------------
[**AddCompounds**](CompoundsApi.md#AddCompounds) | **POST** /api/projects/{projectId}/compounds | Import Compounds and its contained features.
-[**AddTagsToCompoundExperimental**](CompoundsApi.md#AddTagsToCompoundExperimental) | **PUT** /api/projects/{projectId}/compounds/tags/{compoundId} | [EXPERIMENTAL] Tags with the same name will be overwritten
[**DeleteCompound**](CompoundsApi.md#DeleteCompound) | **DELETE** /api/projects/{projectId}/compounds/{compoundId} | Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space.
[**GetCompound**](CompoundsApi.md#GetCompound) | **GET** /api/projects/{projectId}/compounds/{compoundId} | Get compound (group of ion identities) with the given identifier from the specified project-space.
-[**GetCompoundQuantTableExperimental**](CompoundsApi.md#GetCompoundQuantTableExperimental) | **GET** /api/projects/{projectId}/compounds/quant-table | [EXPERIMENTAL] Returns the full quantification table of compounds
-[**GetCompoundQuantTableRowExperimental**](CompoundsApi.md#GetCompoundQuantTableRowExperimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given compound
-[**GetCompoundTracesExperimental**](CompoundsApi.md#GetCompoundTracesExperimental) | **GET** /api/projects/{projectId}/compounds/{compoundId}/traces | [EXPERIMENTAL] Returns the traces of the given compound
[**GetCompounds**](CompoundsApi.md#GetCompounds) | **GET** /api/projects/{projectId}/compounds | List of all available compounds (group of ion identities) in the given project-space.
-[**GetCompoundsByGroupExperimental**](CompoundsApi.md#GetCompoundsByGroupExperimental) | **GET** /api/projects/{projectId}/compounds/grouped | [EXPERIMENTAL] Get compounds (group of ion identities) by tag group
-[**GetCompoundsByTagExperimental**](CompoundsApi.md#GetCompoundsByTagExperimental) | **GET** /api/projects/{projectId}/compounds/tagged | [EXPERIMENTAL] Get compounds (group of ion identities) by tag
[**GetCompoundsPaged**](CompoundsApi.md#GetCompoundsPaged) | **GET** /api/projects/{projectId}/compounds/page | Page of available compounds (group of ion identities) in the given project-space.
-[**GetTagsForCompoundExperimental**](CompoundsApi.md#GetTagsForCompoundExperimental) | **GET** /api/projects/{projectId}/compounds/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Compound
-[**RemoveTagFromCompoundExperimental**](CompoundsApi.md#RemoveTagFromCompoundExperimental) | **DELETE** /api/projects/{projectId}/compounds/tags/{compoundId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space
# **AddCompounds**
@@ -74,57 +66,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | the Compounds that have been imported with specified optional fields | - |
-# **AddTagsToCompoundExperimental**
-> array[Tag] AddTagsToCompoundExperimental(project_id, compound_id, tag)
-
-[EXPERIMENTAL] Tags with the same name will be overwritten
-
-[EXPERIMENTAL] Tags with the same name will be overwritten. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Tags with the same name will be overwritten
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to add to.
-var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to add tags to.
-var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$AddTagsToCompoundExperimental(var_project_id, var_compound_id, var_tagdata_file = "result.txt")
-result <- api_instance$compounds_api$AddTagsToCompoundExperimental(var_project_id, var_compound_id, var_tag)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to add to. |
- **compound_id** | **character**| compound (group of ion identities) to add tags to. |
- **tag** | list( [**Tag**](Tag.md) )| tags to add. |
-
-### Return type
-
-[**array[Tag]**](Tag.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: application/json
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the tags that have been added | - |
-
# **DeleteCompound**
> DeleteCompound(project_id, compound_id)
@@ -226,157 +167,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | Compounds with additional optional fields (if specified). | - |
-# **GetCompoundQuantTableExperimental**
-> QuantTableExperimental GetCompoundQuantTableExperimental(project_id, type = "APEX_HEIGHT")
-
-[EXPERIMENTAL] Returns the full quantification table of compounds
-
-[EXPERIMENTAL] Returns the full quantification table of compounds. The quantification table contains a quantification of the features within all runs they are contained in. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns the full quantification table of compounds
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_type <- "APEX_HEIGHT" # character | quantification type. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetCompoundQuantTableExperimental(var_project_id, type = var_typedata_file = "result.txt")
-result <- api_instance$compounds_api$GetCompoundQuantTableExperimental(var_project_id, type = var_type)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **type** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_HEIGHT"]
-
-### Return type
-
-[**QuantTableExperimental**](QuantTableExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **GetCompoundQuantTableRowExperimental**
-> QuantTableExperimental GetCompoundQuantTableRowExperimental(project_id, compound_id, type = "APEX_HEIGHT")
-
-[EXPERIMENTAL] Returns a single quantification table row for the given compound
-
-[EXPERIMENTAL] Returns a single quantification table row for the given compound. The quantification table contains a quantification of the feature within all samples it is contained in. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns a single quantification table row for the given compound
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_compound_id <- "compound_id_example" # character | compound which should be read out
-var_type <- "APEX_HEIGHT" # character | quantification type. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetCompoundQuantTableRowExperimental(var_project_id, var_compound_id, type = var_typedata_file = "result.txt")
-result <- api_instance$compounds_api$GetCompoundQuantTableRowExperimental(var_project_id, var_compound_id, type = var_type)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **compound_id** | **character**| compound which should be read out |
- **type** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_HEIGHT"]
-
-### Return type
-
-[**QuantTableExperimental**](QuantTableExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **GetCompoundTracesExperimental**
-> TraceSetExperimental GetCompoundTracesExperimental(project_id, compound_id, feature_id = "")
-
-[EXPERIMENTAL] Returns the traces of the given compound
-
-[EXPERIMENTAL] Returns the traces of the given compound. A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.*
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns the traces of the given compound
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_compound_id <- "compound_id_example" # character | compound which intensities should be read out
-var_feature_id <- "" # character | (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetCompoundTracesExperimental(var_project_id, var_compound_id, feature_id = var_feature_iddata_file = "result.txt")
-result <- api_instance$compounds_api$GetCompoundTracesExperimental(var_project_id, var_compound_id, feature_id = var_feature_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **compound_id** | **character**| compound which intensities should be read out |
- **feature_id** | **character**| | [optional] [default to ""]
-
-### Return type
-
-[**TraceSetExperimental**](TraceSetExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Traces of the given compound. | - |
-
# **GetCompounds**
> array[Compound] GetCompounds(project_id, ms_data_search_prepared = FALSE, opt_fields = ["none"], opt_fields_features = ["none"])
@@ -430,120 +220,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | Compounds with additional optional fields (if specified). | - |
-# **GetCompoundsByGroupExperimental**
-> PagedModelCompound GetCompoundsByGroupExperimental(project_id, group_name, page = 0, size = 20, sort = var.sort, opt_fields = ["none"])
-
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag group
-
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag group. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get compounds (group of ion identities) by tag group
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_group_name <- "group_name_example" # character | tag group name.
-var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
-var_size <- 20 # integer | The size of the page to be returned (Optional)
-var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
-var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetCompoundsByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$compounds_api$GetCompoundsByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **group_name** | **character**| tag group name. |
- **page** | **integer**| Zero-based page index (0..N) | [optional] [default to 0]
- **size** | **integer**| The size of the page to be returned | [optional] [default to 20]
- **sort** | list( **character** )| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional]
- **opt_fields** | Enum [none, consensusAnnotations, consensusAnnotationsDeNovo, customAnnotations, tags] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]]
-
-### Return type
-
-[**PagedModelCompound**](PagedModelCompound.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | tagged compounds (group of ion identities) | - |
-
-# **GetCompoundsByTagExperimental**
-> PagedModelCompound GetCompoundsByTagExperimental(project_id, filter = "", page = 0, size = 20, sort = var.sort, opt_fields = [])
-
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag
-
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag. The filter string must contain one or more clauses. A clause is prefÃxed by a field name. The format of the date type is A clause may be: Clauses may be grouped with brackets The syntax allows to build complex filter queries such as: [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to delete tag from.
-var_tag_name <- "tag_name_example" # character | name of the tag to delete.
-
-api_instance <- rsirius_api$new()
-api_instance$compounds_api$RemoveTagFromCompoundExperimental(var_project_id, var_compound_id, var_tag_name)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **compound_id** | **character**| compound (group of ion identities) to delete tag from. |
- **tag_name** | **character**| name of the tag to delete. |
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
diff --git a/client-api_r/generated/docs/FeatureStatisticsApi.md b/client-api_r/generated/docs/FeatureStatisticsApi.md
deleted file mode 100644
index e057f74b..00000000
--- a/client-api_r/generated/docs/FeatureStatisticsApi.md
+++ /dev/null
@@ -1,221 +0,0 @@
-# FeatureStatisticsApi
-
-All URIs are relative to *http://localhost:8080*
-
-Method | HTTP request | Description
-------------- | ------------- | -------------
-[**ComputeAlignedFeatureFoldChangesExperimental**](FeatureStatisticsApi.md#ComputeAlignedFeatureFoldChangesExperimental) | **PUT** /api/projects/{projectId}/aligned-features/statistics/foldchange/compute | [EXPERIMENTAL] Compute the fold change between two groups of runs
-[**DeleteAlignedFeatureFoldChangesExperimental**](FeatureStatisticsApi.md#DeleteAlignedFeatureFoldChangesExperimental) | **DELETE** /api/projects/{projectId}/aligned-features/statistics/foldchanges | [EXPERIMENTAL] Delete fold changes
-[**GetAlignedFeatureFoldChangeTableExperimental**](FeatureStatisticsApi.md#GetAlignedFeatureFoldChangeTableExperimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/stats-table | [EXPERIMENTAL] Get table of all fold changes in the project space
-[**GetFoldChangesByAlignedFeatureExperimental**](FeatureStatisticsApi.md#GetFoldChangesByAlignedFeatureExperimental) | **GET** /api/projects/{projectId}/aligned-features/statistics/foldchanges/{objectId} | [EXPERIMENTAL] List all fold changes that are associated with an object
-
-
-# **ComputeAlignedFeatureFoldChangesExperimental**
-> Job ComputeAlignedFeatureFoldChangesExperimental(project_id, left_group_name, right_group_name, aggregation = "AVG", quantification = "APEX_INTENSITY", opt_fields = ["progress"])
-
-[EXPERIMENTAL] Compute the fold change between two groups of runs
-
-[EXPERIMENTAL] Compute the fold change between two groups of runs. The runs need to be tagged and grouped. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Compute the fold change between two groups of runs
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to compute the fold change in.
-var_left_group_name <- "left_group_name_example" # character | name of the left tag group.
-var_right_group_name <- "right_group_name_example" # character | name of the right tag group.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-var_opt_fields <- c("none") # array[character] | job opt fields. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$ComputeAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$feature_statistics_api$ComputeAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to compute the fold change in. |
- **left_group_name** | **character**| name of the left tag group. |
- **right_group_name** | **character**| name of the right tag group. |
- **aggregation** | Enum [AVG, MIN, MAX] | aggregation type. | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_INTENSITY"]
- **opt_fields** | Enum [none, command, progress, affectedIds] | job opt fields. | [optional] [default to ["progress"]]
-
-### Return type
-
-[**Job**](Job.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **DeleteAlignedFeatureFoldChangesExperimental**
-> DeleteAlignedFeatureFoldChangesExperimental(project_id, left_group_name, right_group_name, aggregation = "AVG", quantification = "APEX_INTENSITY")
-
-[EXPERIMENTAL] Delete fold changes
-
-[EXPERIMENTAL] Delete fold changes. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete fold changes
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_left_group_name <- "left_group_name_example" # character | name of the left group.
-var_right_group_name <- "right_group_name_example" # character | name of the right group.
-var_aggregation <- "AVG" # character | (Optional)
-var_quantification <- "APEX_INTENSITY" # character | (Optional)
-
-api_instance <- rsirius_api$new()
-api_instance$feature_statistics_api$DeleteAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **left_group_name** | **character**| name of the left group. |
- **right_group_name** | **character**| name of the right group. |
- **aggregation** | Enum [AVG, MIN, MAX] | | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | | [optional] [default to "APEX_INTENSITY"]
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **GetAlignedFeatureFoldChangeTableExperimental**
-> StatisticsTable GetAlignedFeatureFoldChangeTableExperimental(project_id, aggregation = "AVG", quantification = "APEX_INTENSITY")
-
-[EXPERIMENTAL] Get table of all fold changes in the project space
-
-[EXPERIMENTAL] Get table of all fold changes in the project space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get table of all fold changes in the project space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAlignedFeatureFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantificationdata_file = "result.txt")
-result <- api_instance$feature_statistics_api$GetAlignedFeatureFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantification)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aggregation** | Enum [AVG, MIN, MAX] | aggregation type. | [optional] [default to "AVG"]
- **quantification** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_INTENSITY"]
-
-### Return type
-
-[**StatisticsTable**](StatisticsTable.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | table of fold changes. | - |
-
-# **GetFoldChangesByAlignedFeatureExperimental**
-> array[FoldChange] GetFoldChangesByAlignedFeatureExperimental(project_id, object_id)
-
-[EXPERIMENTAL] List all fold changes that are associated with an object
-
-[EXPERIMENTAL] List all fold changes that are associated with an object. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] List all fold changes that are associated with an object
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetFoldChangesByAlignedFeatureExperimental(var_project_id, var_object_iddata_file = "result.txt")
-result <- api_instance$feature_statistics_api$GetFoldChangesByAlignedFeatureExperimental(var_project_id, var_object_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **object_id** | **character**| id of the object the fold changes are assigned to. |
-
-### Return type
-
-[**array[FoldChange]**](FoldChange.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | fold changes | - |
-
diff --git a/client-api_r/generated/docs/FeaturesApi.md b/client-api_r/generated/docs/FeaturesApi.md
index 0e0c184c..074c76f1 100644
--- a/client-api_r/generated/docs/FeaturesApi.md
+++ b/client-api_r/generated/docs/FeaturesApi.md
@@ -5,24 +5,16 @@ All URIs are relative to *http://localhost:8080*
Method | HTTP request | Description
------------- | ------------- | -------------
[**AddAlignedFeatures**](FeaturesApi.md#AddAlignedFeatures) | **POST** /api/projects/{projectId}/aligned-features | Import (aligned) features into the project.
-[**AddDeNovoStructureCandidate**](FeaturesApi.md#AddDeNovoStructureCandidate) | **PUT** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.
-[**AddTagsToAlignedFeatureExperimental**](FeaturesApi.md#AddTagsToAlignedFeatureExperimental) | **PUT** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId} | [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project
[**DeleteAlignedFeature**](FeaturesApi.md#DeleteAlignedFeature) | **DELETE** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Delete feature (aligned over runs) with the given identifier from the specified project-space.
[**DeleteAlignedFeatures**](FeaturesApi.md#DeleteAlignedFeatures) | **PUT** /api/projects/{projectId}/aligned-features/delete | Delete feature (aligned over runs) with the given identifier from the specified project-space.
-[**GetAdductNetworkWithMergedTracesExperimental**](FeaturesApi.md#GetAdductNetworkWithMergedTracesExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/adducts | [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network
[**GetAlignedFeature**](FeaturesApi.md#GetAlignedFeature) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Get feature (aligned over runs) with the given identifier from the specified project-space.
-[**GetAlignedFeatureQualityExperimental**](FeaturesApi.md#GetAlignedFeatureQualityExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quality-report | [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
[**GetAlignedFeatures**](FeaturesApi.md#GetAlignedFeatures) | **GET** /api/projects/{projectId}/aligned-features | Get all available features (aligned over runs) in the given project-space.
-[**GetAlignedFeaturesByGroupExperimental**](FeaturesApi.md#GetAlignedFeaturesByGroupExperimental) | **GET** /api/projects/{projectId}/aligned-features/grouped | [EXPERIMENTAL] Get features (aligned over runs) by tag group
-[**GetAlignedFeaturesByTagExperimental**](FeaturesApi.md#GetAlignedFeaturesByTagExperimental) | **GET** /api/projects/{projectId}/aligned-features/tagged | [EXPERIMENTAL] Get features (aligned over runs) by tag
[**GetAlignedFeaturesPaged**](FeaturesApi.md#GetAlignedFeaturesPaged) | **GET** /api/projects/{projectId}/aligned-features/page | Get all available features (aligned over runs) in the given project-space.
[**GetBestMatchingCompoundClasses**](FeaturesApi.md#GetBestMatchingCompoundClasses) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes | Return Best matching compound classes for given formulaId
[**GetCanopusPrediction**](FeaturesApi.md#GetCanopusPrediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction | All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
-[**GetDeNovoStructureCandidates**](FeaturesApi.md#GetDeNovoStructureCandidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
[**GetDeNovoStructureCandidatesByFormula**](FeaturesApi.md#GetDeNovoStructureCandidatesByFormula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
[**GetDeNovoStructureCandidatesByFormulaPaged**](FeaturesApi.md#GetDeNovoStructureCandidatesByFormulaPaged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
[**GetDeNovoStructureCandidatesPaged**](FeaturesApi.md#GetDeNovoStructureCandidatesPaged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
-[**GetFeatureQuantTableExperimental**](FeaturesApi.md#GetFeatureQuantTableExperimental) | **GET** /api/projects/{projectId}/aligned-features/quant-table | [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)
[**GetFingerprintPrediction**](FeaturesApi.md#GetFingerprintPrediction) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint | Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
[**GetFormulaAnnotatedMsMsData**](FeaturesApi.md#GetFormulaAnnotatedMsMsData) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata | Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
[**GetFormulaAnnotatedSpectrum**](FeaturesApi.md#GetFormulaAnnotatedSpectrum) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum | Returns a fragmentation spectrum (e
@@ -33,21 +25,14 @@ Method | HTTP request | Description
[**GetIsotopePatternAnnotation**](FeaturesApi.md#GetIsotopePatternAnnotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern | Returns Isotope pattern information for given formulaId
[**GetLipidAnnotation**](FeaturesApi.md#GetLipidAnnotation) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation | Returns Lipid annotation (ElGordo) for the given formulaId
[**GetMsData**](FeaturesApi.md#GetMsData) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data | Mass Spec data (input data) for the given 'alignedFeatureId' .
-[**GetQuantTableRowExperimental**](FeaturesApi.md#GetQuantTableRowExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/quant-table-row | [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)
[**GetSpectralLibraryMatch**](FeaturesApi.md#GetSpectralLibraryMatch) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId} | Spectral library match for the given 'alignedFeatureId'.
[**GetSpectralLibraryMatches**](FeaturesApi.md#GetSpectralLibraryMatches) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches | List of spectral library matches for the given 'alignedFeatureId'.
[**GetSpectralLibraryMatchesPaged**](FeaturesApi.md#GetSpectralLibraryMatchesPaged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page | Page of spectral library matches for the given 'alignedFeatureId'.
[**GetSpectralLibraryMatchesSummary**](FeaturesApi.md#GetSpectralLibraryMatchesSummary) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary | Summarize matched reference spectra for the given 'alignedFeatureId'.
-[**GetStructureAnnotatedMsDataExperimental**](FeaturesApi.md#GetStructureAnnotatedMsDataExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-msmsdata | [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey
-[**GetStructureAnnotatedSpectralLibraryMatchExperimental**](FeaturesApi.md#GetStructureAnnotatedSpectralLibraryMatchExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId}/annotated | [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations
-[**GetStructureAnnotatedSpectrumExperimental**](FeaturesApi.md#GetStructureAnnotatedSpectrumExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/structures/{inchiKey}/annotated-spectrum | [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
[**GetStructureCandidates**](FeaturesApi.md#GetStructureCandidates) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures | List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
[**GetStructureCandidatesByFormula**](FeaturesApi.md#GetStructureCandidatesByFormula) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures | List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
[**GetStructureCandidatesByFormulaPaged**](FeaturesApi.md#GetStructureCandidatesByFormulaPaged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page | Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
[**GetStructureCandidatesPaged**](FeaturesApi.md#GetStructureCandidatesPaged) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page | Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
-[**GetTagsForAlignedFeaturesExperimental**](FeaturesApi.md#GetTagsForAlignedFeaturesExperimental) | **GET** /api/projects/{projectId}/aligned-features/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Object
-[**GetTracesExperimental**](FeaturesApi.md#GetTracesExperimental) | **GET** /api/projects/{projectId}/aligned-features/{alignedFeatureId}/traces | [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)
-[**RemoveTagFromAlignedFeatureExperimental**](FeaturesApi.md#RemoveTagFromAlignedFeatureExperimental) | **DELETE** /api/projects/{projectId}/aligned-features/tags/{alignedFeatureId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space
# **AddAlignedFeatures**
@@ -103,108 +88,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | the Features that have been imported with specified optional fields | - |
-# **AddDeNovoStructureCandidate**
-> array[StructureCandidateFormula] AddDeNovoStructureCandidate(project_id, aligned_feature_id, smiles = "none")
-
-[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.
-
-[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. This starts a scoring job to incorporate the structures in the de novo results list.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to.
-var_smiles <- "none" # character | smiles (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$AddDeNovoStructureCandidate(var_project_id, var_aligned_feature_id, smiles = var_smilesdata_file = "result.txt")
-result <- api_instance$features_api$AddDeNovoStructureCandidate(var_project_id, var_aligned_feature_id, smiles = var_smiles)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the structure candidates belong to. |
- **smiles** | **character**| smiles | [optional] [default to "none"]
-
-### Return type
-
-[**array[StructureCandidateFormula]**](StructureCandidateFormula.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | StructureCandidate of this feature candidate with specified optional fields. | - |
-
-# **AddTagsToAlignedFeatureExperimental**
-> array[Tag] AddTagsToAlignedFeatureExperimental(project_id, aligned_feature_id, tag)
-
-[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project
-
-[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project. Tags with the same name will be overwritten. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to add to.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | run to add tags to.
-var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$AddTagsToAlignedFeatureExperimental(var_project_id, var_aligned_feature_id, var_tagdata_file = "result.txt")
-result <- api_instance$features_api$AddTagsToAlignedFeatureExperimental(var_project_id, var_aligned_feature_id, var_tag)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to add to. |
- **aligned_feature_id** | **character**| run to add tags to. |
- **tag** | list( [**Tag**](Tag.md) )| tags to add. |
-
-### Return type
-
-[**array[Tag]**](Tag.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: application/json
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the tags that have been added | - |
-
# **DeleteAlignedFeature**
> DeleteAlignedFeature(project_id, aligned_feature_id)
@@ -297,55 +180,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | OK | - |
-# **GetAdductNetworkWithMergedTracesExperimental**
-> TraceSetExperimental GetAdductNetworkWithMergedTracesExperimental(project_id, aligned_feature_id)
-
-[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network
-
-[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | one feature that is considered the main feature of the adduct network
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAdductNetworkWithMergedTracesExperimental(var_project_id, var_aligned_feature_iddata_file = "result.txt")
-result <- api_instance$features_api$GetAdductNetworkWithMergedTracesExperimental(var_project_id, var_aligned_feature_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| one feature that is considered the main feature of the adduct network |
-
-### Return type
-
-[**TraceSetExperimental**](TraceSetExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
# **GetAlignedFeature**
> AlignedFeature GetAlignedFeature(project_id, aligned_feature_id, ms_data_search_prepared = FALSE, opt_fields = ["none"])
@@ -399,55 +233,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | AlignedFeature with additional annotations and MS/MS data (if specified). | - |
-# **GetAlignedFeatureQualityExperimental**
-> AlignedFeatureQualityExperimental GetAlignedFeatureQualityExperimental(project_id, aligned_feature_id)
-
-[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
-
-[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) Get data quality information for feature (aligned over runs) with the given identifier from the specified project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to access.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAlignedFeatureQualityExperimental(var_project_id, var_aligned_feature_iddata_file = "result.txt")
-result <- api_instance$features_api$GetAlignedFeatureQualityExperimental(var_project_id, var_aligned_feature_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| identifier of feature (aligned over runs) to access. |
-
-### Return type
-
-[**AlignedFeatureQualityExperimental**](AlignedFeatureQualityExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | AlignedFeatureQuality quality information of the respective feature. | - |
-
# **GetAlignedFeatures**
> array[AlignedFeature] GetAlignedFeatures(project_id, ms_data_search_prepared = FALSE, opt_fields = ["none"])
@@ -499,120 +284,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | AlignedFeatures with additional annotations and MS/MS data (if specified). | - |
-# **GetAlignedFeaturesByGroupExperimental**
-> PagedModelAlignedFeature GetAlignedFeaturesByGroupExperimental(project_id, group_name, page = 0, size = 20, sort = var.sort, opt_fields = ["none"])
-
-[EXPERIMENTAL] Get features (aligned over runs) by tag group
-
-[EXPERIMENTAL] Get features (aligned over runs) by tag group. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get features (aligned over runs) by tag group
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_group_name <- "group_name_example" # character | tag group name.
-var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
-var_size <- 20 # integer | The size of the page to be returned (Optional)
-var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
-var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAlignedFeaturesByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$features_api$GetAlignedFeaturesByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **group_name** | **character**| tag group name. |
- **page** | **integer**| Zero-based page index (0..N) | [optional] [default to 0]
- **size** | **integer**| The size of the page to be returned | [optional] [default to 20]
- **sort** | list( **character** )| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional]
- **opt_fields** | Enum [none, msData, topAnnotationsSummary, topAnnotations, topAnnotationsDeNovo, computedTools, tags] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]]
-
-### Return type
-
-[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | tagged features (aligned over runs) | - |
-
-# **GetAlignedFeaturesByTagExperimental**
-> PagedModelAlignedFeature GetAlignedFeaturesByTagExperimental(project_id, filter = "", page = 0, size = 20, sort = var.sort, opt_fields = [])
-
-[EXPERIMENTAL] Get features (aligned over runs) by tag
-
-[EXPERIMENTAL] Get features (aligned over runs) by tag. The filter string must contain one or more clauses. A clause is prefÃxed by a field name. Currently the only searchable fields are names of tags ( The format of the date type is A clause may be: Clauses may be grouped with brackets The syntax allows to build complex filter queries such as: [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get features (aligned over runs) by tag
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project space to get features (aligned over runs) from.
-var_filter <- "" # character | tag filter. (Optional)
-var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
-var_size <- 20 # integer | The size of the page to be returned (Optional)
-var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
-var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAlignedFeaturesByTagExperimental(var_project_id, filter = var_filter, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$features_api$GetAlignedFeaturesByTagExperimental(var_project_id, filter = var_filter, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project space to get features (aligned over runs) from. |
- **filter** | **character**| tag filter. | [optional] [default to ""]
- **page** | **integer**| Zero-based page index (0..N) | [optional] [default to 0]
- **size** | **integer**| The size of the page to be returned | [optional] [default to 20]
- **sort** | list( **character** )| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional]
- **opt_fields** | Enum [none, msData, topAnnotationsSummary, topAnnotations, topAnnotationsDeNovo, computedTools, tags] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []]
-
-### Return type
-
-[**PagedModelAlignedFeature**](PagedModelAlignedFeature.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | tagged features (aligned over runs) | - |
-
# **GetAlignedFeaturesPaged**
> PagedModelAlignedFeature GetAlignedFeaturesPaged(project_id, page = 0, size = 20, sort = var.sort, ms_data_search_prepared = FALSE, opt_fields = ["none"])
@@ -772,57 +443,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | Predicted compound classes | - |
-# **GetDeNovoStructureCandidates**
-> array[StructureCandidateFormula] GetDeNovoStructureCandidates(project_id, aligned_feature_id, opt_fields = ["none"])
-
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
-
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
-
-### Example
-```R
-library(RSirius)
-
-# List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to.
-var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetDeNovoStructureCandidates(var_project_id, var_aligned_feature_id, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$features_api$GetDeNovoStructureCandidates(var_project_id, var_aligned_feature_id, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the structure candidates belong to. |
- **opt_fields** | Enum [none, fingerprint, dbLinks, libraryMatches, structureSvg] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]]
-
-### Return type
-
-[**array[StructureCandidateFormula]**](StructureCandidateFormula.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
-
# **GetDeNovoStructureCandidatesByFormula**
> array[StructureCandidateScored] GetDeNovoStructureCandidatesByFormula(project_id, aligned_feature_id, formula_id, opt_fields = ["none"])
@@ -992,55 +612,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
-# **GetFeatureQuantTableExperimental**
-> QuantTableExperimental GetFeatureQuantTableExperimental(project_id, type = "APEX_HEIGHT")
-
-[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)
-
-[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId). Returns the full quantification table. The quantification table contains a quantities of the features within all runs they are contained in. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_type <- "APEX_HEIGHT" # character | quantification type. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetFeatureQuantTableExperimental(var_project_id, type = var_typedata_file = "result.txt")
-result <- api_instance$features_api$GetFeatureQuantTableExperimental(var_project_id, type = var_type)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **type** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. | [optional] [default to "APEX_HEIGHT"]
-
-### Return type
-
-[**QuantTableExperimental**](QuantTableExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Quant table if akk feature in this project | - |
-
# **GetFingerprintPrediction**
> array[numeric] GetFingerprintPrediction(project_id, aligned_feature_id, formula_id)
@@ -1525,74 +1096,23 @@ No authorization required
Mass Spec data (input data) for the given 'alignedFeatureId' .
-Mass Spec data (input data) for the given 'alignedFeatureId' .
-
-### Example
-```R
-library(RSirius)
-
-# Mass Spec data (input data) for the given 'alignedFeatureId' .
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the Mass Spec data belongs to.
-var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetMsData(var_project_id, var_aligned_feature_id, ms_data_search_prepared = var_ms_data_search_prepareddata_file = "result.txt")
-result <- api_instance$features_api$GetMsData(var_project_id, var_aligned_feature_id, ms_data_search_prepared = var_ms_data_search_prepared)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the Mass Spec data belongs to. |
- **ms_data_search_prepared** | **character**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to FALSE]
-
-### Return type
-
-[**MsData**](MsData.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Mass Spec data of this feature (aligned over runs). | - |
-
-# **GetQuantTableRowExperimental**
-> QuantTableExperimental GetQuantTableRowExperimental(project_id, aligned_feature_id, type = "APEX_HEIGHT")
-
-[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)
-
-[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId). The quantification table contains a quantity of the feature within all samples it is contained in. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
+Mass Spec data (input data) for the given 'alignedFeatureId' .
### Example
```R
library(RSirius)
-# [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)
+# Mass Spec data (input data) for the given 'alignedFeatureId' .
#
# prepare function argument(s)
var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which quantity should be read out
-var_type <- "APEX_HEIGHT" # character | quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. (Optional)
+var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the Mass Spec data belongs to.
+var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional)
api_instance <- rsirius_api$new()
# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetQuantTableRowExperimental(var_project_id, var_aligned_feature_id, type = var_typedata_file = "result.txt")
-result <- api_instance$features_api$GetQuantTableRowExperimental(var_project_id, var_aligned_feature_id, type = var_type)
+# result <- api_instance$GetMsData(var_project_id, var_aligned_feature_id, ms_data_search_prepared = var_ms_data_search_prepareddata_file = "result.txt")
+result <- api_instance$features_api$GetMsData(var_project_id, var_aligned_feature_id, ms_data_search_prepared = var_ms_data_search_prepared)
dput(result)
```
@@ -1601,12 +1121,12 @@ dput(result)
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
**project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature which quantity should be read out |
- **type** | Enum [APEX_INTENSITY, AREA_UNDER_CURVE] | quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. | [optional] [default to "APEX_HEIGHT"]
+ **aligned_feature_id** | **character**| feature (aligned over runs) the Mass Spec data belongs to. |
+ **ms_data_search_prepared** | **character**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to FALSE]
### Return type
-[**QuantTableExperimental**](QuantTableExperimental.md)
+[**MsData**](MsData.md)
### Authorization
@@ -1620,7 +1140,7 @@ No authorization required
### HTTP response details
| Status code | Description | Response headers |
|-------------|-------------|------------------|
-| **200** | Quant table row for this feature | - |
+| **200** | Mass Spec data of this feature (aligned over runs). | - |
# **GetSpectralLibraryMatch**
> SpectralLibraryMatch GetSpectralLibraryMatch(project_id, aligned_feature_id, match_id, opt_fields = ["none"])
@@ -1850,169 +1370,6 @@ No authorization required
|-------------|-------------|------------------|
| **200** | Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs). | - |
-# **GetStructureAnnotatedMsDataExperimental**
-> AnnotatedMsMsData GetStructureAnnotatedMsDataExperimental(project_id, aligned_feature_id, formula_id, inchi_key, ms_data_search_prepared = FALSE)
-
-[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey
-
-[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey. Returns MS/MS Data (Merged MS/MS and list of measured MS/MS ) which are annotated with fragments and losses for the given formula result identifier and structure candidate inChIKey. These annotations are only available if a fragmentation tree and the structure candidate are available. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to.
-var_formula_id <- "formula_id_example" # character | identifier of the requested formula result
-var_inchi_key <- "inchi_key_example" # character | 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation
-var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetStructureAnnotatedMsDataExperimental(var_project_id, var_aligned_feature_id, var_formula_id, var_inchi_key, ms_data_search_prepared = var_ms_data_search_prepareddata_file = "result.txt")
-result <- api_instance$features_api$GetStructureAnnotatedMsDataExperimental(var_project_id, var_aligned_feature_id, var_formula_id, var_inchi_key, ms_data_search_prepared = var_ms_data_search_prepared)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the formula result belongs to. |
- **formula_id** | **character**| identifier of the requested formula result |
- **inchi_key** | **character**| 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation |
- **ms_data_search_prepared** | **character**| Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to FALSE]
-
-### Return type
-
-[**AnnotatedMsMsData**](AnnotatedMsMsData.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Fragmentation spectrum annotated with fragments and sub-structures. | - |
-
-# **GetStructureAnnotatedSpectralLibraryMatchExperimental**
-> AnnotatedSpectrum GetStructureAnnotatedSpectralLibraryMatchExperimental(project_id, aligned_feature_id, match_id)
-
-[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations
-
-[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to.
-var_match_id <- "match_id_example" # character | id of the library match to be returned.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetStructureAnnotatedSpectralLibraryMatchExperimental(var_project_id, var_aligned_feature_id, var_match_iddata_file = "result.txt")
-result <- api_instance$features_api$GetStructureAnnotatedSpectralLibraryMatchExperimental(var_project_id, var_aligned_feature_id, var_match_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the structure candidates belong to. |
- **match_id** | **character**| id of the library match to be returned. |
-
-### Return type
-
-[**AnnotatedSpectrum**](AnnotatedSpectrum.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Spectral library match with requested mathcId. | - |
-
-# **GetStructureAnnotatedSpectrumExperimental**
-> AnnotatedSpectrum GetStructureAnnotatedSpectrumExperimental(project_id, aligned_feature_id, formula_id, inchi_key, spectrum_index = -1, search_prepared = FALSE)
-
-[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
-
-[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the selected formula result These annotations are only available if a fragmentation tree is available. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to.
-var_formula_id <- "formula_id_example" # character | identifier of the requested formula result
-var_inchi_key <- "inchi_key_example" # character | 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation
-var_spectrum_index <- -1 # integer | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) (Optional)
-var_search_prepared <- FALSE # character | (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetStructureAnnotatedSpectrumExperimental(var_project_id, var_aligned_feature_id, var_formula_id, var_inchi_key, spectrum_index = var_spectrum_index, search_prepared = var_search_prepareddata_file = "result.txt")
-result <- api_instance$features_api$GetStructureAnnotatedSpectrumExperimental(var_project_id, var_aligned_feature_id, var_formula_id, var_inchi_key, spectrum_index = var_spectrum_index, search_prepared = var_search_prepared)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) the formula result belongs to. |
- **formula_id** | **character**| identifier of the requested formula result |
- **inchi_key** | **character**| 2d InChIKey of the structure candidate to be used to annotate the spectrum annotation |
- **spectrum_index** | **integer**| index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) | [optional] [default to -1]
- **search_prepared** | **character**| | [optional] [default to FALSE]
-
-### Return type
-
-[**AnnotatedSpectrum**](AnnotatedSpectrum.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Fragmentation spectrum annotated with fragments and sub-structures. | - |
-
# **GetStructureCandidates**
> array[StructureCandidateFormula] GetStructureCandidates(project_id, aligned_feature_id, opt_fields = ["none"])
@@ -2233,151 +1590,3 @@ No authorization required
|-------------|-------------|------------------|
| **200** | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
-# **GetTagsForAlignedFeaturesExperimental**
-> array[Tag] GetTagsForAlignedFeaturesExperimental(project_id, object_id)
-
-[EXPERIMENTAL] Get all tags associated with this Object
-
-[EXPERIMENTAL] Get all tags associated with this Object
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get all tags associated with this Object
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to get from.
-var_object_id <- "object_id_example" # character | object to get tags for.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetTagsForAlignedFeaturesExperimental(var_project_id, var_object_iddata_file = "result.txt")
-result <- api_instance$features_api$GetTagsForAlignedFeaturesExperimental(var_project_id, var_object_id)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to get from. |
- **object_id** | **character**| object to get tags for. |
-
-### Return type
-
-[**array[Tag]**](Tag.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the tags of the requested object | - |
-
-# **GetTracesExperimental**
-> TraceSetExperimental GetTracesExperimental(project_id, aligned_feature_id, include_all = FALSE)
-
-[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)
-
-[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId). Returns the traces of the given feature. A trace consists of m/z and intensity values over the retention time axis. All the returned traces are 'projected', which means they refer not to the original retention time axis, but to a recalibrated axis. This means the data points in the trace are not exactly the same as in the raw data. However, this also means that all traces can be directly compared against each other, as they all lie in the same retention time axis. By default, this method only returns traces of samples the aligned feature appears in. When includeAll is set, it also includes samples in which the same trace appears in. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which intensities should be read out
-var_include_all <- FALSE # character | when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetTracesExperimental(var_project_id, var_aligned_feature_id, include_all = var_include_alldata_file = "result.txt")
-result <- api_instance$features_api$GetTracesExperimental(var_project_id, var_aligned_feature_id, include_all = var_include_all)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **aligned_feature_id** | **character**| feature which intensities should be read out |
- **include_all** | **character**| when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. | [optional] [default to FALSE]
-
-### Return type
-
-[**TraceSetExperimental**](TraceSetExperimental.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Traces of the given feature. | - |
-
-# **RemoveTagFromAlignedFeatureExperimental**
-> RemoveTagFromAlignedFeatureExperimental(project_id, aligned_feature_id, tag_name)
-
-[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space
-
-[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) to delete tag from.
-var_tag_name <- "tag_name_example" # character | name of the tag to delete.
-
-api_instance <- rsirius_api$new()
-api_instance$features_api$RemoveTagFromAlignedFeatureExperimental(var_project_id, var_aligned_feature_id, var_tag_name)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **aligned_feature_id** | **character**| feature (aligned over runs) to delete tag from. |
- **tag_name** | **character**| name of the tag to delete. |
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
diff --git a/client-api_r/generated/docs/FoldChange.md b/client-api_r/generated/docs/FoldChange.md
deleted file mode 100644
index 02ef1381..00000000
--- a/client-api_r/generated/docs/FoldChange.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# RSirius::FoldChange
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**leftGroup** | **character** | | [optional]
-**rightGroup** | **character** | | [optional]
-**aggregation** | **character** | | [optional] [Enum: [AVG, MIN, MAX]]
-**quantification** | **character** | | [optional] [Enum: [APEX_INTENSITY, AREA_UNDER_CURVE]]
-**quantType** | **character** | | [Enum: [FEATURES, COMPOUNDS]]
-**objectId** | **character** | |
-**foldChange** | **numeric** | |
-
-
diff --git a/client-api_r/generated/docs/PagedModelRun.md b/client-api_r/generated/docs/PagedModelRun.md
deleted file mode 100644
index a467c744..00000000
--- a/client-api_r/generated/docs/PagedModelRun.md
+++ /dev/null
@@ -1,10 +0,0 @@
-# RSirius::PagedModelRun
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**content** | [**array[Run]**](Run.md) | | [optional]
-**page** | [**PageMetadata**](PageMetadata.md) | | [optional]
-
-
diff --git a/client-api_r/generated/docs/ProjectsApi.md b/client-api_r/generated/docs/ProjectsApi.md
index 75b0baa5..090ccdd5 100644
--- a/client-api_r/generated/docs/ProjectsApi.md
+++ b/client-api_r/generated/docs/ProjectsApi.md
@@ -362,7 +362,7 @@ library(RSirius)
#
# prepare function argument(s)
var_project_id <- "project_id_example" # character | Project-space to import into.
-var_input_files <- c(123) # array[data.frame] | Files to import into project.
+var_input_files <- c(123) # array[data.frame] | files to import into project
var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters |
api_instance <- rsirius_api$new()
@@ -377,7 +377,7 @@ dput(result)
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
**project_id** | **character**| Project-space to import into. |
- **input_files** | list( **data.frame** )| Files to import into project. |
+ **input_files** | list( **data.frame** )| files to import into project |
**parameters** | [**LcmsSubmissionParameters**](LcmsSubmissionParameters.md)| |
### Return type
@@ -413,7 +413,7 @@ library(RSirius)
#
# prepare function argument(s)
var_project_id <- "project_id_example" # character | Project-space to import into.
-var_input_files <- c(123) # array[data.frame] | Files to import into project.
+var_input_files <- c(123) # array[data.frame] | files to import into project
var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters |
var_opt_fields <- c("none") # array[character] | Set of optional fields to be included. Use 'none' only to override defaults. (Optional)
@@ -429,7 +429,7 @@ dput(result)
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
**project_id** | **character**| Project-space to import into. |
- **input_files** | list( **data.frame** )| Files to import into project. |
+ **input_files** | list( **data.frame** )| files to import into project |
**parameters** | [**LcmsSubmissionParameters**](LcmsSubmissionParameters.md)| |
**opt_fields** | Enum [none, command, progress, affectedIds] | Set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["progress"]]
@@ -519,7 +519,7 @@ library(RSirius)
#
# prepare function argument(s)
var_project_id <- "project_id_example" # character | project-space to import into.
-var_input_files <- c(123) # array[data.frame] |
+var_input_files <- c(123) # array[data.frame] | files to import into project
var_ignore_formulas <- FALSE # character | (Optional)
var_allow_ms1_only <- TRUE # character | (Optional)
var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
@@ -536,7 +536,7 @@ dput(result)
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
**project_id** | **character**| project-space to import into. |
- **input_files** | list( **data.frame** )| |
+ **input_files** | list( **data.frame** )| files to import into project |
**ignore_formulas** | **character**| | [optional] [default to FALSE]
**allow_ms1_only** | **character**| | [optional] [default to TRUE]
**opt_fields** | Enum [none, command, progress, affectedIds] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["progress"]]
diff --git a/client-api_r/generated/docs/QualityItem.md b/client-api_r/generated/docs/QualityItem.md
deleted file mode 100644
index 15784b99..00000000
--- a/client-api_r/generated/docs/QualityItem.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# RSirius::QualityItem
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**description** | **character** | | [optional]
-**quality** | **character** | | [optional] [Enum: [NOT_APPLICABLE, LOWEST, BAD, DECENT, GOOD]]
-**weight** | **character** | | [optional] [Enum: [MINOR, MAJOR, CRITICAL]]
-
-
diff --git a/client-api_r/generated/docs/QuantTableExperimental.md b/client-api_r/generated/docs/QuantTableExperimental.md
deleted file mode 100644
index 3dc57383..00000000
--- a/client-api_r/generated/docs/QuantTableExperimental.md
+++ /dev/null
@@ -1,16 +0,0 @@
-# RSirius::QuantTableExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**quantificationMeasure** | **character** | | [optional] [Enum: [APEX_INTENSITY, AREA_UNDER_CURVE]]
-**rowType** | **character** | | [optional] [Enum: [FEATURES, COMPOUNDS]]
-**rowIds** | **array[integer]** | | [optional]
-**columnIds** | **array[integer]** | | [optional]
-**rowNames** | **array[character]** | | [optional]
-**columnNames** | **array[character]** | | [optional]
-**values** | [**array[array[numeric]]**](array.md) | | [optional]
-
-
diff --git a/client-api_r/generated/docs/Run.md b/client-api_r/generated/docs/Run.md
deleted file mode 100644
index a645dab4..00000000
--- a/client-api_r/generated/docs/Run.md
+++ /dev/null
@@ -1,16 +0,0 @@
-# RSirius::Run
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**runId** | **character** | Identifier | [optional]
-**name** | **character** | Informative, human-readable name of this run | [optional]
-**source** | **character** | Source location | [optional]
-**chromatography** | **character** | | [optional]
-**ionization** | **character** | | [optional]
-**fragmentation** | **character** | | [optional]
-**massAnalyzers** | **array[character]** | | [optional]
-**tags** | [**map(Tag)**](Tag.md) | Key: tagName, value: tag | [optional]
-
-
diff --git a/client-api_r/generated/docs/RunOptField.md b/client-api_r/generated/docs/RunOptField.md
deleted file mode 100644
index 46fc9215..00000000
--- a/client-api_r/generated/docs/RunOptField.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# RSirius::RunOptField
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-
-
diff --git a/client-api_r/generated/docs/RunsApi.md b/client-api_r/generated/docs/RunsApi.md
deleted file mode 100644
index 2cfbbcf2..00000000
--- a/client-api_r/generated/docs/RunsApi.md
+++ /dev/null
@@ -1,435 +0,0 @@
-# RunsApi
-
-All URIs are relative to *http://localhost:8080*
-
-Method | HTTP request | Description
-------------- | ------------- | -------------
-[**AddTagsToRunExperimental**](RunsApi.md#AddTagsToRunExperimental) | **PUT** /api/projects/{projectId}/runs/tags/{runId} | [EXPERIMENTAL] Add tags to a run in the project
-[**ComputeFoldChangeForBlankSubtraction**](RunsApi.md#ComputeFoldChangeForBlankSubtraction) | **PUT** /api/projects/{projectId}/runs/blanksubtract/compute | **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter
-[**GetRunExperimental**](RunsApi.md#GetRunExperimental) | **GET** /api/projects/{projectId}/runs/{runId} | [EXPERIMENTAL] Get run with the given identifier from the specified project-space
-[**GetRunPageExperimental**](RunsApi.md#GetRunPageExperimental) | **GET** /api/projects/{projectId}/runs/page | [EXPERIMENTAL] Get all available runs in the given project-space
-[**GetRunsByGroupExperimental**](RunsApi.md#GetRunsByGroupExperimental) | **GET** /api/projects/{projectId}/runs/grouped | [EXPERIMENTAL] Get runs by tag group
-[**GetRunsByTagExperimental**](RunsApi.md#GetRunsByTagExperimental) | **GET** /api/projects/{projectId}/runs/tagged | [EXPERIMENTAL] Get runs by tag
-[**GetTagsForRunExperimental**](RunsApi.md#GetTagsForRunExperimental) | **GET** /api/projects/{projectId}/runs/tags/{objectId} | [EXPERIMENTAL] Get all tags associated with this Run
-[**RemoveTagFromRunExperimental**](RunsApi.md#RemoveTagFromRunExperimental) | **DELETE** /api/projects/{projectId}/runs/tags/{runId}/{tagName} | [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space
-
-
-# **AddTagsToRunExperimental**
-> array[Tag] AddTagsToRunExperimental(project_id, run_id, tag)
-
-[EXPERIMENTAL] Add tags to a run in the project
-
-[EXPERIMENTAL] Add tags to a run in the project. Tags with the same name will be overwritten. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Add tags to a run in the project
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to add to.
-var_run_id <- "run_id_example" # character | run to add tags to.
-var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add.
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$AddTagsToRunExperimental(var_project_id, var_run_id, var_tagdata_file = "result.txt")
-result <- api_instance$runs_api$AddTagsToRunExperimental(var_project_id, var_run_id, var_tag)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to add to. |
- **run_id** | **character**| run to add tags to. |
- **tag** | list( [**Tag**](Tag.md) )| tags to add. |
-
-### Return type
-
-[**array[Tag]**](Tag.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: application/json
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the tags that have been added | - |
-
-# **ComputeFoldChangeForBlankSubtraction**
-> Job ComputeFoldChangeForBlankSubtraction(project_id, sample_type_fold_change_request, opt_fields = ["progress"])
-
-**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter
-
-**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter. This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get run with the given identifier from the specified project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_run_id <- "run_id_example" # character | identifier of run to access.
-var_opt_fields <- c(RunOptField$new()) # array[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetRunExperimental(var_project_id, var_run_id, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$runs_api$GetRunExperimental(var_project_id, var_run_id, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **run_id** | **character**| identifier of run to access. |
- **opt_fields** | list( [**RunOptField**](RunOptField.md) )| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []]
-
-### Return type
-
-[**Run**](Run.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Run with tags (if specified). | - |
-
-# **GetRunPageExperimental**
-> PagedModelRun GetRunPageExperimental(project_id, page = 0, size = 20, sort = var.sort, opt_fields = [])
-
-[EXPERIMENTAL] Get all available runs in the given project-space
-
-[EXPERIMENTAL] Get all available runs in the given project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get all available runs in the given project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
-var_size <- 20 # integer | The size of the page to be returned (Optional)
-var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
-var_opt_fields <- c(RunOptField$new()) # array[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetRunPageExperimental(var_project_id, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$runs_api$GetRunPageExperimental(var_project_id, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **page** | **integer**| Zero-based page index (0..N) | [optional] [default to 0]
- **size** | **integer**| The size of the page to be returned | [optional] [default to 20]
- **sort** | list( **character** )| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional]
- **opt_fields** | list( [**RunOptField**](RunOptField.md) )| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to []]
-
-### Return type
-
-[**PagedModelRun**](PagedModelRun.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Runs with tags (if specified). | - |
-
-# **GetRunsByGroupExperimental**
-> PagedModelRun GetRunsByGroupExperimental(project_id, group_name, page = 0, size = 20, sort = var.sort, opt_fields = ["none"])
-
-[EXPERIMENTAL] Get runs by tag group
-
-[EXPERIMENTAL] Get runs by tag group. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get runs by tag group
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_group_name <- "group_name_example" # character | tag group name.
-var_page <- 0 # integer | Zero-based page index (0..N) (Optional)
-var_size <- 20 # integer | The size of the page to be returned (Optional)
-var_sort <- c("inner_example") # array[character] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (Optional)
-var_opt_fields <- c(RunOptField$new()) # array[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetRunsByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$runs_api$GetRunsByGroupExperimental(var_project_id, var_group_name, page = var_page, size = var_size, sort = var_sort, opt_fields = var_opt_fields)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **group_name** | **character**| tag group name. |
- **page** | **integer**| Zero-based page index (0..N) | [optional] [default to 0]
- **size** | **integer**| The size of the page to be returned | [optional] [default to 20]
- **sort** | list( **character** )| Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. | [optional]
- **opt_fields** | list( [**RunOptField**](RunOptField.md) )| set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]]
-
-### Return type
-
-[**PagedModelRun**](PagedModelRun.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | tagged runs | - |
-
-# **GetRunsByTagExperimental**
-> PagedModelRun GetRunsByTagExperimental(project_id, filter = "", page = 0, size = 20, sort = var.sort, opt_fields = [])
-
-[EXPERIMENTAL] Get runs by tag
-
-[EXPERIMENTAL] Get runs by tag. The filter string must contain one or more clauses. A clause is prefÃxed by a field name. The format of the date type is A clause may be: Clauses may be grouped with brackets The syntax allows to build complex filter queries such as: [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_run_id <- "run_id_example" # character | run to delete tag from.
-var_tag_name <- "tag_name_example" # character | name of the tag to delete.
-
-api_instance <- rsirius_api$new()
-api_instance$runs_api$RemoveTagFromRunExperimental(var_project_id, var_run_id, var_tag_name)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **run_id** | **character**| run to delete tag from. |
- **tag_name** | **character**| name of the tag to delete. |
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
diff --git a/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md b/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md
deleted file mode 100644
index b970f32c..00000000
--- a/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# RSirius::SampleTypeFoldChangeRequest
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**sampleRunIds** | **array[character]** | | [optional]
-**blankRunIds** | **array[character]** | | [optional]
-**controlRunIds** | **array[character]** | | [optional]
-
-
diff --git a/client-api_r/generated/docs/SearchableDatabasesApi.md b/client-api_r/generated/docs/SearchableDatabasesApi.md
index 5fc68684..70546745 100644
--- a/client-api_r/generated/docs/SearchableDatabasesApi.md
+++ b/client-api_r/generated/docs/SearchableDatabasesApi.md
@@ -4,7 +4,7 @@ All URIs are relative to *http://localhost:8080*
Method | HTTP request | Description
------------- | ------------- | -------------
-[**AddDatabases**](SearchableDatabasesApi.md#AddDatabases) | **POST** /api/databases | DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API.
+[**AddDatabases**](SearchableDatabasesApi.md#AddDatabases) | **POST** /api/databases | [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API.
[**CreateDatabase**](SearchableDatabasesApi.md#CreateDatabase) | **POST** /api/databases/{databaseId} |
[**GetCustomDatabases**](SearchableDatabasesApi.md#GetCustomDatabases) | **GET** /api/databases/custom |
[**GetDatabase**](SearchableDatabasesApi.md#GetDatabase) | **GET** /api/databases/{databaseId} |
@@ -18,13 +18,13 @@ Method | HTTP request | Description
# **AddDatabases**
> array[SearchableDatabase] AddDatabases(request_body)
-DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API.
+[DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API.
### Example
```R
library(RSirius)
-# DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API.
+# [DEPRECATED] This endpoint is based on local file paths and will likely be replaced in future versions of this API.
#
# prepare function argument(s)
var_request_body <- c("property_example") # array[character] |
@@ -298,7 +298,7 @@ library(RSirius)
#
# prepare function argument(s)
var_database_id <- "database_id_example" # character | database to import into
-var_input_files <- c(123) # array[data.frame] | files to be imported
+var_input_files <- c(123) # array[data.frame] | files to import into project
var_buffer_size <- 1000 # integer | (Optional)
var_bio_transformer_parameters <- BioTransformerParameters$new("RULE_BASED", "BT_RULE_BASED", c(BioTransformerSequenceStep$new("PHASE_1_CYP450", 123)), "useDB_example") # BioTransformerParameters | (Optional)
@@ -314,7 +314,7 @@ dput(result)
Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
**database_id** | **character**| database to import into |
- **input_files** | list( **data.frame** )| files to be imported |
+ **input_files** | list( **data.frame** )| files to import into project |
**buffer_size** | **integer**| | [optional] [default to 1000]
**bio_transformer_parameters** | [**BioTransformerParameters**](BioTransformerParameters.md)| | [optional]
diff --git a/client-api_r/generated/docs/StatisticsTable.md b/client-api_r/generated/docs/StatisticsTable.md
deleted file mode 100644
index eba0c44a..00000000
--- a/client-api_r/generated/docs/StatisticsTable.md
+++ /dev/null
@@ -1,17 +0,0 @@
-# RSirius::StatisticsTable
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**statisticsType** | **character** | | [optional] [Enum: [FOLD_CHANGE]]
-**aggregationType** | **character** | | [optional] [Enum: [AVG, MIN, MAX]]
-**quantificationMeasure** | **character** | | [optional] [Enum: [APEX_INTENSITY, AREA_UNDER_CURVE]]
-**rowType** | **character** | | [optional] [Enum: [FEATURES, COMPOUNDS]]
-**rowIds** | **array[character]** | | [optional]
-**columnNames** | **array[character]** | | [optional]
-**columnLeftGroups** | **array[character]** | | [optional]
-**columnRightGroups** | **array[character]** | | [optional]
-**values** | [**array[array[numeric]]**](array.md) | | [optional]
-
-
diff --git a/client-api_r/generated/docs/TagDefinition.md b/client-api_r/generated/docs/TagDefinition.md
deleted file mode 100644
index 53ab3538..00000000
--- a/client-api_r/generated/docs/TagDefinition.md
+++ /dev/null
@@ -1,16 +0,0 @@
-# RSirius::TagDefinition
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**tagName** | **character** | Name of this tag defined by this definition (key) |
-**description** | **character** | A human-readable description about the purpose of this tag. | [optional]
-**tagType** | **character** | A simple string based identifier to specify the type/scope/purpose of this tag. | [optional]
-**valueType** | **character** | | [Enum: [NONE, BOOLEAN, INTEGER, REAL, TEXT, DATE, TIME]]
-**possibleValues** | **array[object]** | | [optional]
-**minValue** | **object** | | [optional]
-**maxValue** | **object** | | [optional]
-**editable** | **character** | | [optional]
-
-
diff --git a/client-api_r/generated/docs/TagDefinitionImport.md b/client-api_r/generated/docs/TagDefinitionImport.md
deleted file mode 100644
index f7541234..00000000
--- a/client-api_r/generated/docs/TagDefinitionImport.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# RSirius::TagDefinitionImport
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**tagName** | **character** | Name of this tag defined by this definition (key) |
-**description** | **character** | A human-readable description about the purpose of this tag. | [optional]
-**tagType** | **character** | A simple string based identifier to specify the type/scope/purpose of this tag. | [optional]
-**valueType** | **character** | | [Enum: [NONE, BOOLEAN, INTEGER, REAL, TEXT, DATE, TIME]]
-**possibleValues** | **array[object]** | | [optional]
-**minValue** | **object** | | [optional]
-**maxValue** | **object** | | [optional]
-
-
diff --git a/client-api_r/generated/docs/TagGroup.md b/client-api_r/generated/docs/TagGroup.md
deleted file mode 100644
index 1554e828..00000000
--- a/client-api_r/generated/docs/TagGroup.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# RSirius::TagGroup
-
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**groupName** | **character** | Name of this Grouping query. | [optional]
-**luceneQuery** | **character** | Query used to group the entities in lucene format. | [optional]
-**groupType** | **character** | | [optional]
-
-
diff --git a/client-api_r/generated/docs/TagsApi.md b/client-api_r/generated/docs/TagsApi.md
deleted file mode 100644
index 1b86b8e3..00000000
--- a/client-api_r/generated/docs/TagsApi.md
+++ /dev/null
@@ -1,458 +0,0 @@
-# TagsApi
-
-All URIs are relative to *http://localhost:8080*
-
-Method | HTTP request | Description
-------------- | ------------- | -------------
-[**AddGroup**](TagsApi.md#AddGroup) | **POST** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Group tags in the project
-[**AddPossibleValuesToTagDefinition**](TagsApi.md#AddPossibleValuesToTagDefinition) | **PATCH** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Add a possible value to the tag definition in the project
-[**CreateTags**](TagsApi.md#CreateTags) | **PUT** /api/projects/{projectId}/tags | [EXPERIMENTAL] Add tags to the project
-[**DeleteGroup**](TagsApi.md#DeleteGroup) | **DELETE** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space
-[**DeleteTag**](TagsApi.md#DeleteTag) | **DELETE** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space
-[**GetGroupByName**](TagsApi.md#GetGroupByName) | **GET** /api/projects/{projectId}/groups/{groupName} | [EXPERIMENTAL] Get tag group by name in the given project-space
-[**GetGroups**](TagsApi.md#GetGroups) | **GET** /api/projects/{projectId}/groups | [EXPERIMENTAL] Get all tag based groups in the given project-space
-[**GetTag**](TagsApi.md#GetTag) | **GET** /api/projects/{projectId}/tags/{tagName} | [EXPERIMENTAL] Get tag definition by its name in the given project-space
-[**GetTags**](TagsApi.md#GetTags) | **GET** /api/projects/{projectId}/tags | [EXPERIMENTAL] Get all tag definitions in the given project-space
-
-
-# **AddGroup**
-> TagGroup AddGroup(project_id, group_name, filter, type)
-
-[EXPERIMENTAL] Group tags in the project
-
-[EXPERIMENTAL] Group tags in the project. The group name must not exist in the project. See [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Add a possible value to the tag definition in the project
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to add to.
-var_tag_name <- "tag_name_example" # character | the tag definition to add the values to
-var_request_body <- c(123) # array[object] |
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$AddPossibleValuesToTagDefinition(var_project_id, var_tag_name, var_request_bodydata_file = "result.txt")
-result <- api_instance$tags_api$AddPossibleValuesToTagDefinition(var_project_id, var_tag_name, var_request_body)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to add to. |
- **tag_name** | **character**| the tag definition to add the values to |
- **request_body** | list( **object** )| |
-
-### Return type
-
-[**TagDefinition**](TagDefinition.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: application/json
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the definitions of the tags that have been added | - |
-
-# **CreateTags**
-> array[TagDefinition] CreateTags(project_id, tag_definition_import)
-
-[EXPERIMENTAL] Add tags to the project
-
-[EXPERIMENTAL] Add tags to the project. Tag names must not exist in the project. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Add tags to the project
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to add to.
-var_tag_definition_import <- c(TagDefinitionImport$new("tagName_example", "NONE", "description_example", "tagType_example", c(123), 123, 123)) # array[TagDefinitionImport] | the tag definitions to be created
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$CreateTags(var_project_id, var_tag_definition_importdata_file = "result.txt")
-result <- api_instance$tags_api$CreateTags(var_project_id, var_tag_definition_import)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to add to. |
- **tag_definition_import** | list( [**TagDefinitionImport**](TagDefinitionImport.md) )| the tag definitions to be created |
-
-### Return type
-
-[**array[TagDefinition]**](TagDefinition.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: application/json
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | the definitions of the tags that have been created | - |
-
-# **DeleteGroup**
-> DeleteGroup(project_id, group_name)
-
-[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space
-
-[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_group_name <- "group_name_example" # character | name of group to delete.
-
-api_instance <- rsirius_api$new()
-api_instance$tags_api$DeleteGroup(var_project_id, var_group_name)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to delete from. |
- **group_name** | **character**| name of group to delete. |
-
-### Return type
-
-void (empty response body)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: Not defined
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | OK | - |
-
-# **DeleteTag**
-> DeleteTag(project_id, tag_name)
-
-[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space
-
-[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space. This will also remove all tags belonging to this definition from every tagged entity. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get tag group by name in the given project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_group_name <- "group_name_example" # character | name of the group
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetGroupByName(var_project_id, var_group_namedata_file = "result.txt")
-result <- api_instance$tags_api$GetGroupByName(var_project_id, var_group_name)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **group_name** | **character**| name of the group |
-
-### Return type
-
-[**TagGroup**](TagGroup.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Tag group. | - |
-
-# **GetGroups**
-> array[TagGroup] GetGroups(project_id, group_type = var.group_type)
-
-[EXPERIMENTAL] Get all tag based groups in the given project-space
-
-[EXPERIMENTAL] Get all tag based groups in the given project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get all tag based groups in the given project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_group_type <- "group_type_example" # character | type of the group (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetGroups(var_project_id, group_type = var_group_typedata_file = "result.txt")
-result <- api_instance$tags_api$GetGroups(var_project_id, group_type = var_group_type)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **group_type** | **character**| type of the group | [optional]
-
-### Return type
-
-[**array[TagGroup]**](TagGroup.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Groups. | - |
-
-# **GetTag**
-> TagDefinition GetTag(project_id, tag_name)
-
-[EXPERIMENTAL] Get tag definition by its name in the given project-space
-
-[EXPERIMENTAL] Get tag definition by its name in the given project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get tag definition by its name in the given project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_tag_name <- "tag_name_example" # character | name of the tag
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetTag(var_project_id, var_tag_namedata_file = "result.txt")
-result <- api_instance$tags_api$GetTag(var_project_id, var_tag_name)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **tag_name** | **character**| name of the tag |
-
-### Return type
-
-[**TagDefinition**](TagDefinition.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Tag definition. | - |
-
-# **GetTags**
-> array[TagDefinition] GetTags(project_id, tag_type = var.tag_type)
-
-[EXPERIMENTAL] Get all tag definitions in the given project-space
-
-[EXPERIMENTAL] Get all tag definitions in the given project-space. [EXPERIMENTAL] This endpoint is experimental and not part of the stable API specification. This endpoint can change at any time, even in minor updates.
-
-### Example
-```R
-library(RSirius)
-
-# [EXPERIMENTAL] Get all tag definitions in the given project-space
-#
-# prepare function argument(s)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_tag_type <- "tag_type_example" # character | scope of the tag (optional) (Optional)
-
-api_instance <- rsirius_api$new()
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetTags(var_project_id, tag_type = var_tag_typedata_file = "result.txt")
-result <- api_instance$tags_api$GetTags(var_project_id, tag_type = var_tag_type)
-dput(result)
-```
-
-### Parameters
-
-Name | Type | Description | Notes
-------------- | ------------- | ------------- | -------------
- **project_id** | **character**| project-space to read from. |
- **tag_type** | **character**| scope of the tag (optional) | [optional]
-
-### Return type
-
-[**array[TagDefinition]**](TagDefinition.md)
-
-### Authorization
-
-No authorization required
-
-### HTTP request headers
-
- - **Content-Type**: Not defined
- - **Accept**: application/json
-
-### HTTP response details
-| Status code | Description | Response headers |
-|-------------|-------------|------------------|
-| **200** | Tag definitions. | - |
-
diff --git a/client-api_r/generated/docs/TraceAnnotationExperimental.md b/client-api_r/generated/docs/TraceAnnotationExperimental.md
deleted file mode 100644
index 128cdca0..00000000
--- a/client-api_r/generated/docs/TraceAnnotationExperimental.md
+++ /dev/null
@@ -1,14 +0,0 @@
-# RSirius::TraceAnnotationExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**type** | **character** | EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. | [optional] [Enum: [FEATURE, MS2]]
-**description** | **character** | | [optional]
-**index** | **integer** | | [optional]
-**from** | **integer** | | [optional]
-**to** | **integer** | | [optional]
-
-
diff --git a/client-api_r/generated/docs/TraceExperimental.md b/client-api_r/generated/docs/TraceExperimental.md
deleted file mode 100644
index e684d77a..00000000
--- a/client-api_r/generated/docs/TraceExperimental.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# RSirius::TraceExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**id** | **character** | | [optional]
-**sampleId** | **character** | | [optional]
-**sampleName** | **character** | | [optional]
-**label** | **character** | | [optional]
-**color** | **character** | | [optional]
-**intensities** | **array[numeric]** | | [optional]
-**annotations** | [**array[TraceAnnotationExperimental]**](TraceAnnotationExperimental.md) | | [optional]
-**mz** | **numeric** | | [optional]
-**merged** | **character** | | [optional]
-**normalizationFactor** | **numeric** | Traces are stored with raw intensity values. The normalization factor maps them to relative intensities, such that traces from different samples can be compared. | [optional]
-**noiseLevel** | **numeric** | The noise level is estimated from the median noise in the surrounding scans. It can be used to calculate signal-to-noise ratios. | [optional]
-
-
diff --git a/client-api_r/generated/docs/TraceSetExperimental.md b/client-api_r/generated/docs/TraceSetExperimental.md
deleted file mode 100644
index 19cc3cbf..00000000
--- a/client-api_r/generated/docs/TraceSetExperimental.md
+++ /dev/null
@@ -1,14 +0,0 @@
-# RSirius::TraceSetExperimental
-
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-## Properties
-Name | Type | Description | Notes
------------- | ------------- | ------------- | -------------
-**adductNetwork** | [**AdductNetworkExperimental**](AdductNetworkExperimental.md) | | [optional]
-**sampleId** | **character** | | [optional]
-**sampleName** | **character** | | [optional]
-**axes** | [**Axes**](Axes.md) | | [optional]
-**traces** | [**array[TraceExperimental]**](TraceExperimental.md) | | [optional]
-
-
diff --git a/client-api_r/generated/man/AdductEdgeExperimental.Rd b/client-api_r/generated/man/AdductEdgeExperimental.Rd
deleted file mode 100644
index 2913165e..00000000
--- a/client-api_r/generated/man/AdductEdgeExperimental.Rd
+++ /dev/null
@@ -1,314 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/adduct_edge_experimental.R
-\docType{class}
-\name{AdductEdgeExperimental}
-\alias{AdductEdgeExperimental}
-\title{AdductEdgeExperimental}
-\format{
-An \code{R6Class} generator object
-}
-\description{
-EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable.
-
-AdductEdgeExperimental Class
-}
-\details{
-Create a new AdductEdgeExperimental
-}
-\examples{
-
-## ------------------------------------------------
-## Method `AdductEdgeExperimental$toList`
-## ------------------------------------------------
-
-# convert array of AdductEdgeExperimental (x) to a data frame
-\dontrun{
-library(purrr)
-library(tibble)
-df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
-df
-}
-}
-\section{Public fields}{
-\if{html}{\out{Supported filter syntax
tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] ( and ) and / or joined with AND or OR (or && and || )Example
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00 Supported filter syntax
tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] ( and ) and / or joined with AND or OR (or && and || )Example
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00 Supported filter syntax
tagName) followed by a clause that is valued for the value type of the tag (See TagDefinition). Tag name based field need to be prefixed with the namespace tags.. Possible value types of tags are bool, integer, real, text, date, or time - tag value yyyy-MM-dd and of the time type is HH\\:mm\\:ss.
tags.MyTagA:sampletags.MyTagA:"Some Text"tags.MyTagA:/[mb]oat/tags.MyTagB<3[ and ] ) or (semi-)closed range (indiced by { and }), e.g. tags.MyTagB:[* TO 3] ( and ) and / or joined with AND or OR (or && and || )Example
tags.city:"new york" AND tags.ATextTag:/[mb]oat/ AND tags.count:[1 TO *] OR tags.realNumberTag<=3.2 OR tags.MyDateTag:2024-01-01 OR tags.MyDateTag:[2023-10-01 TO 2023-12-24] OR tags.MyDateTag<2022-01-01 OR tags.time:12\\:00\\:00 OR tags.time:[12\\:00\\:00 TO 14\\:00\\:00] OR tags.time<10\\:00\\:00 /tagged for filter syntax.
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new AdductEdgeExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert AdductEdgeExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of AdductEdgeExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of AdductEdgeExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to AdductEdgeExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductEdgeExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new AdductNetworkExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert AdductNetworkExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of AdductNetworkExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of AdductNetworkExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to AdductNetworkExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNetworkExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new AdductNodeExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert AdductNodeExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of AdductNodeExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of AdductNodeExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to AdductNodeExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AdductNodeExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new AlignedFeatureQualityExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert AlignedFeatureQualityExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of AlignedFeatureQualityExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of AlignedFeatureQualityExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to AlignedFeatureQualityExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-AlignedFeatureQualityExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new Axes class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert Axes to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of Axes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of Axes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to Axes and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Axes-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new Category class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert Category to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of Category
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of Category
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to Category and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Category-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new CompoundStatisticsApi.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-ComputeCompoundFoldChangesExperimental}{}}}
-\subsection{Method \code{ComputeCompoundFoldChangesExperimental()}}{
-[EXPERIMENTAL] Compute the fold change between two groups of runs
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-ComputeCompoundFoldChangesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{ComputeCompoundFoldChangesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Compute the fold change between two groups of runs
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-DeleteCompoundFoldChangesExperimental}{}}}
-\subsection{Method \code{DeleteCompoundFoldChangesExperimental()}}{
-[EXPERIMENTAL] Delete fold changes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-DeleteCompoundFoldChangesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{DeleteCompoundFoldChangesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Delete fold changes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-GetCompoundFoldChangeTableExperimental}{}}}
-\subsection{Method \code{GetCompoundFoldChangeTableExperimental()}}{
-[EXPERIMENTAL] Get table of all fold changes in the project space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-GetCompoundFoldChangeTableExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundFoldChangeTableExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get table of all fold changes in the project space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-GetFoldChangesByCompoundExperimental}{}}}
-\subsection{Method \code{GetFoldChangesByCompoundExperimental()}}{
-[EXPERIMENTAL] List all fold changes that are associated with an object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-GetFoldChangesByCompoundExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetFoldChangesByCompoundExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] List all fold changes that are associated with an object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundStatisticsApi-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-AddTagsToCompoundExperimental}{}}}
-\subsection{Method \code{AddTagsToCompoundExperimental()}}{
-[EXPERIMENTAL] Tags with the same name will be overwritten
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-AddTagsToCompoundExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{AddTagsToCompoundExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Tags with the same name will be overwritten
-\subsection{Usage}{
-\if{html}{\out{
}}
\if{html}{\out{}}
\if{latex}{\out{\hypertarget{method-CompoundsApi-DeleteCompound}{}}}
\subsection{Method \code{DeleteCompound()}}{
@@ -570,204 +357,6 @@ API response (Compound) with additional information such as HTTP status code, he
}
}
\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundQuantTableExperimental}{}}}
-\subsection{Method \code{GetCompoundQuantTableExperimental()}}{
-[EXPERIMENTAL] Returns the full quantification table of compounds
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundQuantTableExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundQuantTableExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns the full quantification table of compounds
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundQuantTableRowExperimental}{}}}
-\subsection{Method \code{GetCompoundQuantTableRowExperimental()}}{
-[EXPERIMENTAL] Returns a single quantification table row for the given compound
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundQuantTableRowExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundQuantTableRowExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns a single quantification table row for the given compound
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundTracesExperimental}{}}}
-\subsection{Method \code{GetCompoundTracesExperimental()}}{
-[EXPERIMENTAL] Returns the traces of the given compound
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundTracesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundTracesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns the traces of the given compound
-\subsection{Usage}{
-\if{html}{\out{
}}
\if{html}{\out{}}
\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompounds}{}}}
\subsection{Method \code{GetCompounds()}}{
@@ -842,178 +431,6 @@ API response (array[Compound]) with additional information such as HTTP status c
}
}
\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundsByGroupExperimental}{}}}
-\subsection{Method \code{GetCompoundsByGroupExperimental()}}{
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag group
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundsByGroupExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundsByGroupExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag group
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundsByTagExperimental}{}}}
-\subsection{Method \code{GetCompoundsByTagExperimental()}}{
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundsByTagExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetCompoundsByTagExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get compounds (group of ion identities) by tag
-\subsection{Usage}{
-\if{html}{\out{
}}
\if{html}{\out{}}
\if{latex}{\out{\hypertarget{method-CompoundsApi-GetCompoundsPaged}{}}}
\subsection{Method \code{GetCompoundsPaged()}}{
@@ -1106,130 +523,6 @@ API response (PagedModelCompound) with additional information such as HTTP statu
}
}
\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetTagsForCompoundExperimental}{}}}
-\subsection{Method \code{GetTagsForCompoundExperimental()}}{
-[EXPERIMENTAL] Get all tags associated with this Compound
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-GetTagsForCompoundExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetTagsForCompoundExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get all tags associated with this Compound
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-RemoveTagFromCompoundExperimental}{}}}
-\subsection{Method \code{RemoveTagFromCompoundExperimental()}}{
-[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-CompoundsApi-RemoveTagFromCompoundExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{RemoveTagFromCompoundExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
\if{html}{\out{}}
\if{latex}{\out{\hypertarget{method-CompoundsApi-clone}{}}}
\subsection{Method \code{clone()}}{
diff --git a/client-api_r/generated/man/FeatureStatisticsApi.Rd b/client-api_r/generated/man/FeatureStatisticsApi.Rd
deleted file mode 100644
index dfac66ae..00000000
--- a/client-api_r/generated/man/FeatureStatisticsApi.Rd
+++ /dev/null
@@ -1,436 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/feature_statistics_api.R
-\docType{class}
-\name{FeatureStatisticsApi}
-\alias{FeatureStatisticsApi}
-\title{FeatureStatistics operations}
-\format{
-An \code{R6Class} generator object
-}
-\description{
-FeatureStatisticsApi
-}
-\details{
-SIRIUS Nightsky API
-
-REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6
-
-The version of the OpenAPI document: 3.1
-Generated by: https://openapi-generator.tech
-}
-\examples{
-\dontrun{
-#################### ComputeAlignedFeatureFoldChangesExperimental ####################
-
-library(RSirius)
-var_project_id <- "project_id_example" # character | project-space to compute the fold change in.
-var_left_group_name <- "left_group_name_example" # character | name of the left tag group.
-var_right_group_name <- "right_group_name_example" # character | name of the right tag group.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-var_opt_fields <- c("none") # array[character] | job opt fields. (Optional)
-
-#[EXPERIMENTAL] Compute the fold change between two groups of runs
-api_instance <- rsirius_api$new()
-
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$ComputeAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fieldsdata_file = "result.txt")
-result <- api_instance$feature_statistics_api$ComputeAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification, opt_fields = var_opt_fields)
-dput(result)
-
-
-#################### DeleteAlignedFeatureFoldChangesExperimental ####################
-
-library(RSirius)
-var_project_id <- "project_id_example" # character | project-space to delete from.
-var_left_group_name <- "left_group_name_example" # character | name of the left group.
-var_right_group_name <- "right_group_name_example" # character | name of the right group.
-var_aggregation <- "AVG" # character | (Optional)
-var_quantification <- "APEX_INTENSITY" # character | (Optional)
-
-#[EXPERIMENTAL] Delete fold changes
-api_instance <- rsirius_api$new()
-
-api_instance$feature_statistics_api$DeleteAlignedFeatureFoldChangesExperimental(var_project_id, var_left_group_name, var_right_group_name, aggregation = var_aggregation, quantification = var_quantification)
-
-
-#################### GetAlignedFeatureFoldChangeTableExperimental ####################
-
-library(RSirius)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_aggregation <- "AVG" # character | aggregation type. (Optional)
-var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional)
-
-#[EXPERIMENTAL] Get table of all fold changes in the project space
-api_instance <- rsirius_api$new()
-
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetAlignedFeatureFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantificationdata_file = "result.txt")
-result <- api_instance$feature_statistics_api$GetAlignedFeatureFoldChangeTableExperimental(var_project_id, aggregation = var_aggregation, quantification = var_quantification)
-dput(result)
-
-
-#################### GetFoldChangesByAlignedFeatureExperimental ####################
-
-library(RSirius)
-var_project_id <- "project_id_example" # character | project-space to read from.
-var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to.
-
-#[EXPERIMENTAL] List all fold changes that are associated with an object
-api_instance <- rsirius_api$new()
-
-# to save the result into a file, simply add the optional `data_file` parameter, e.g.
-# result <- api_instance$GetFoldChangesByAlignedFeatureExperimental(var_project_id, var_object_iddata_file = "result.txt")
-result <- api_instance$feature_statistics_api$GetFoldChangesByAlignedFeatureExperimental(var_project_id, var_object_id)
-dput(result)
-
-
-}
-}
-\section{Public fields}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new FeatureStatisticsApi.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-ComputeAlignedFeatureFoldChangesExperimental}{}}}
-\subsection{Method \code{ComputeAlignedFeatureFoldChangesExperimental()}}{
-[EXPERIMENTAL] Compute the fold change between two groups of runs
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-ComputeAlignedFeatureFoldChangesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{ComputeAlignedFeatureFoldChangesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Compute the fold change between two groups of runs
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-DeleteAlignedFeatureFoldChangesExperimental}{}}}
-\subsection{Method \code{DeleteAlignedFeatureFoldChangesExperimental()}}{
-[EXPERIMENTAL] Delete fold changes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-DeleteAlignedFeatureFoldChangesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{DeleteAlignedFeatureFoldChangesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Delete fold changes
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-GetAlignedFeatureFoldChangeTableExperimental}{}}}
-\subsection{Method \code{GetAlignedFeatureFoldChangeTableExperimental()}}{
-[EXPERIMENTAL] Get table of all fold changes in the project space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-GetAlignedFeatureFoldChangeTableExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeatureFoldChangeTableExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get table of all fold changes in the project space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-GetFoldChangesByAlignedFeatureExperimental}{}}}
-\subsection{Method \code{GetFoldChangesByAlignedFeatureExperimental()}}{
-[EXPERIMENTAL] List all fold changes that are associated with an object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-GetFoldChangesByAlignedFeatureExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetFoldChangesByAlignedFeatureExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] List all fold changes that are associated with an object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeatureStatisticsApi-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-AddDeNovoStructureCandidate}{}}}
-\subsection{Method \code{AddDeNovoStructureCandidate()}}{
-[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeature}{}}}
+\subsection{Method \code{DeleteAlignedFeature()}}{
+Delete feature (aligned over runs) with the given identifier from the specified project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-AddDeNovoStructureCandidateWithHttpInfo}{}}}
-\subsection{Method \code{AddDeNovoStructureCandidateWithHttpInfo()}}{
-[EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeatureWithHttpInfo}{}}}
+\subsection{Method \code{DeleteAlignedFeatureWithHttpInfo()}}{
+Delete feature (aligned over runs) with the given identifier from the specified project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-AddTagsToAlignedFeatureExperimental}{}}}
-\subsection{Method \code{AddTagsToAlignedFeatureExperimental()}}{
-[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeatures}{}}}
+\subsection{Method \code{DeleteAlignedFeatures()}}{
+Delete feature (aligned over runs) with the given identifier from the specified project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeaturesWithHttpInfo}{}}}
+\subsection{Method \code{DeleteAlignedFeaturesWithHttpInfo()}}{
+Delete feature (aligned over runs) with the given identifier from the specified project-space.
+\subsection{Usage}{
+\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-AddTagsToAlignedFeatureExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{AddTagsToAlignedFeatureExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeature}{}}}
+\subsection{Method \code{GetAlignedFeature()}}{
+Get feature (aligned over runs) with the given identifier from the specified project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeature}{}}}
-\subsection{Method \code{DeleteAlignedFeature()}}{
-Delete feature (aligned over runs) with the given identifier from the specified project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatureWithHttpInfo}{}}}
+\subsection{Method \code{GetAlignedFeatureWithHttpInfo()}}{
+Get feature (aligned over runs) with the given identifier from the specified project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeatureWithHttpInfo}{}}}
-\subsection{Method \code{DeleteAlignedFeatureWithHttpInfo()}}{
-Delete feature (aligned over runs) with the given identifier from the specified project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatures}{}}}
+\subsection{Method \code{GetAlignedFeatures()}}{
+Get all available features (aligned over runs) in the given project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeatures}{}}}
-\subsection{Method \code{DeleteAlignedFeatures()}}{
-Delete feature (aligned over runs) with the given identifier from the specified project-space.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-DeleteAlignedFeaturesWithHttpInfo}{}}}
-\subsection{Method \code{DeleteAlignedFeaturesWithHttpInfo()}}{
-Delete feature (aligned over runs) with the given identifier from the specified project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesWithHttpInfo}{}}}
+\subsection{Method \code{GetAlignedFeaturesWithHttpInfo()}}{
+Get all available features (aligned over runs) in the given project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAdductNetworkWithMergedTracesExperimental}{}}}
-\subsection{Method \code{GetAdductNetworkWithMergedTracesExperimental()}}{
-[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesPaged}{}}}
+\subsection{Method \code{GetAlignedFeaturesPaged()}}{
+Get all available features (aligned over runs) in the given project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAdductNetworkWithMergedTracesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetAdductNetworkWithMergedTracesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesPagedWithHttpInfo}{}}}
+\subsection{Method \code{GetAlignedFeaturesPagedWithHttpInfo()}}{
+Get all available features (aligned over runs) in the given project-space.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeature}{}}}
-\subsection{Method \code{GetAlignedFeature()}}{
-Get feature (aligned over runs) with the given identifier from the specified project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetBestMatchingCompoundClasses}{}}}
+\subsection{Method \code{GetBestMatchingCompoundClasses()}}{
+Return Best matching compound classes for given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatureWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeatureWithHttpInfo()}}{
-Get feature (aligned over runs) with the given identifier from the specified project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetBestMatchingCompoundClassesWithHttpInfo}{}}}
+\subsection{Method \code{GetBestMatchingCompoundClassesWithHttpInfo()}}{
+Return Best matching compound classes for given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatureQualityExperimental}{}}}
-\subsection{Method \code{GetAlignedFeatureQualityExperimental()}}{
-[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetCanopusPrediction}{}}}
+\subsection{Method \code{GetCanopusPrediction()}}{
+All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatureQualityExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeatureQualityExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId)
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetCanopusPredictionWithHttpInfo}{}}}
+\subsection{Method \code{GetCanopusPredictionWithHttpInfo()}}{
+All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeatures}{}}}
-\subsection{Method \code{GetAlignedFeatures()}}{
-Get all available features (aligned over runs) in the given project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormula}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesByFormula()}}{
+List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeaturesWithHttpInfo()}}{
-Get all available features (aligned over runs) in the given project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaWithHttpInfo}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaWithHttpInfo()}}{
+List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesByGroupExperimental}{}}}
-\subsection{Method \code{GetAlignedFeaturesByGroupExperimental()}}{
-[EXPERIMENTAL] Get features (aligned over runs) by tag group
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaPaged}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaPaged()}}{
+Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesByGroupExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeaturesByGroupExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get features (aligned over runs) by tag group
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaPagedWithHttpInfo}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaPagedWithHttpInfo()}}{
+Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesByTagExperimental}{}}}
-\subsection{Method \code{GetAlignedFeaturesByTagExperimental()}}{
-[EXPERIMENTAL] Get features (aligned over runs) by tag
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesPaged}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesPaged()}}{
+Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesByTagExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeaturesByTagExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get features (aligned over runs) by tag
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesPagedWithHttpInfo}{}}}
+\subsection{Method \code{GetDeNovoStructureCandidatesPagedWithHttpInfo()}}{
+Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesPaged}{}}}
-\subsection{Method \code{GetAlignedFeaturesPaged()}}{
-Get all available features (aligned over runs) in the given project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFingerprintPrediction}{}}}
+\subsection{Method \code{GetFingerprintPrediction()}}{
+Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetAlignedFeaturesPagedWithHttpInfo}{}}}
-\subsection{Method \code{GetAlignedFeaturesPagedWithHttpInfo()}}{
-Get all available features (aligned over runs) in the given project-space.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFingerprintPredictionWithHttpInfo}{}}}
+\subsection{Method \code{GetFingerprintPredictionWithHttpInfo()}}{
+Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetBestMatchingCompoundClasses}{}}}
-\subsection{Method \code{GetBestMatchingCompoundClasses()}}{
-Return Best matching compound classes for given formulaId
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedMsMsData}{}}}
+\subsection{Method \code{GetFormulaAnnotatedMsMsData()}}{
+Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetBestMatchingCompoundClassesWithHttpInfo}{}}}
-\subsection{Method \code{GetBestMatchingCompoundClassesWithHttpInfo()}}{
-Return Best matching compound classes for given formulaId
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedMsMsDataWithHttpInfo}{}}}
+\subsection{Method \code{GetFormulaAnnotatedMsMsDataWithHttpInfo()}}{
+Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetCanopusPrediction}{}}}
-\subsection{Method \code{GetCanopusPrediction()}}{
-All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedSpectrum}{}}}
+\subsection{Method \code{GetFormulaAnnotatedSpectrum()}}{
+Returns a fragmentation spectrum (e
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetCanopusPredictionWithHttpInfo}{}}}
-\subsection{Method \code{GetCanopusPredictionWithHttpInfo()}}{
-All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedSpectrumWithHttpInfo}{}}}
+\subsection{Method \code{GetFormulaAnnotatedSpectrumWithHttpInfo()}}{
+Returns a fragmentation spectrum (e
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidates}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidates()}}{
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidate}{}}}
+\subsection{Method \code{GetFormulaCandidate()}}{
+FormulaResultContainers for the given 'formulaId' with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesWithHttpInfo}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesWithHttpInfo()}}{
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidateWithHttpInfo}{}}}
+\subsection{Method \code{GetFormulaCandidateWithHttpInfo()}}{
+FormulaResultContainers for the given 'formulaId' with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormula}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesByFormula()}}{
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidates}{}}}
+\subsection{Method \code{GetFormulaCandidates()}}{
+List of FormulaResultContainers available for this feature with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaWithHttpInfo}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaWithHttpInfo()}}{
-List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesWithHttpInfo}{}}}
+\subsection{Method \code{GetFormulaCandidatesWithHttpInfo()}}{
+List of FormulaResultContainers available for this feature with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaPaged}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaPaged()}}{
-Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesPaged}{}}}
+\subsection{Method \code{GetFormulaCandidatesPaged()}}{
+Page of FormulaResultContainers available for this feature with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesByFormulaPagedWithHttpInfo}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesByFormulaPagedWithHttpInfo()}}{
-Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesPagedWithHttpInfo}{}}}
+\subsection{Method \code{GetFormulaCandidatesPagedWithHttpInfo()}}{
+Page of FormulaResultContainers available for this feature with minimal information.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesPaged}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesPaged()}}{
-Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFragTree}{}}}
+\subsection{Method \code{GetFragTree()}}{
+Returns fragmentation tree (SIRIUS) for the given formula result identifier
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetDeNovoStructureCandidatesPagedWithHttpInfo}{}}}
-\subsection{Method \code{GetDeNovoStructureCandidatesPagedWithHttpInfo()}}{
-Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFragTreeWithHttpInfo}{}}}
+\subsection{Method \code{GetFragTreeWithHttpInfo()}}{
+Returns fragmentation tree (SIRIUS) for the given formula result identifier
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFeatureQuantTableExperimental}{}}}
-\subsection{Method \code{GetFeatureQuantTableExperimental()}}{
-[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetIsotopePatternAnnotation}{}}}
+\subsection{Method \code{GetIsotopePatternAnnotation()}}{
+Returns Isotope pattern information for given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFeatureQuantTableExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetFeatureQuantTableExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFingerprintPrediction}{}}}
-\subsection{Method \code{GetFingerprintPrediction()}}{
-Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetIsotopePatternAnnotationWithHttpInfo}{}}}
+\subsection{Method \code{GetIsotopePatternAnnotationWithHttpInfo()}}{
+Returns Isotope pattern information for given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFingerprintPredictionWithHttpInfo}{}}}
-\subsection{Method \code{GetFingerprintPredictionWithHttpInfo()}}{
-Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetLipidAnnotation}{}}}
+\subsection{Method \code{GetLipidAnnotation()}}{
+Returns Lipid annotation (ElGordo) for the given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedMsMsData}{}}}
-\subsection{Method \code{GetFormulaAnnotatedMsMsData()}}{
-Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetLipidAnnotationWithHttpInfo}{}}}
+\subsection{Method \code{GetLipidAnnotationWithHttpInfo()}}{
+Returns Lipid annotation (ElGordo) for the given formulaId
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedMsMsDataWithHttpInfo}{}}}
-\subsection{Method \code{GetFormulaAnnotatedMsMsDataWithHttpInfo()}}{
-Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetMsData}{}}}
+\subsection{Method \code{GetMsData()}}{
+Mass Spec data (input data) for the given 'alignedFeatureId' .
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedSpectrum}{}}}
-\subsection{Method \code{GetFormulaAnnotatedSpectrum()}}{
-Returns a fragmentation spectrum (e
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetMsDataWithHttpInfo}{}}}
+\subsection{Method \code{GetMsDataWithHttpInfo()}}{
+Mass Spec data (input data) for the given 'alignedFeatureId' .
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaAnnotatedSpectrumWithHttpInfo}{}}}
-\subsection{Method \code{GetFormulaAnnotatedSpectrumWithHttpInfo()}}{
-Returns a fragmentation spectrum (e
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatch}{}}}
+\subsection{Method \code{GetSpectralLibraryMatch()}}{
+Spectral library match for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidate}{}}}
-\subsection{Method \code{GetFormulaCandidate()}}{
-FormulaResultContainers for the given 'formulaId' with minimal information.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchWithHttpInfo}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchWithHttpInfo()}}{
+Spectral library match for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidateWithHttpInfo}{}}}
-\subsection{Method \code{GetFormulaCandidateWithHttpInfo()}}{
-FormulaResultContainers for the given 'formulaId' with minimal information.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatches}{}}}
+\subsection{Method \code{GetSpectralLibraryMatches()}}{
+List of spectral library matches for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidates}{}}}
-\subsection{Method \code{GetFormulaCandidates()}}{
-List of FormulaResultContainers available for this feature with minimal information.
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesWithHttpInfo}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchesWithHttpInfo()}}{
+List of spectral library matches for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesWithHttpInfo}{}}}
-\subsection{Method \code{GetFormulaCandidatesWithHttpInfo()}}{
-List of FormulaResultContainers available for this feature with minimal information.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesPaged}{}}}
-\subsection{Method \code{GetFormulaCandidatesPaged()}}{
-Page of FormulaResultContainers available for this feature with minimal information.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFormulaCandidatesPagedWithHttpInfo}{}}}
-\subsection{Method \code{GetFormulaCandidatesPagedWithHttpInfo()}}{
-Page of FormulaResultContainers available for this feature with minimal information.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFragTree}{}}}
-\subsection{Method \code{GetFragTree()}}{
-Returns fragmentation tree (SIRIUS) for the given formula result identifier
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetFragTreeWithHttpInfo}{}}}
-\subsection{Method \code{GetFragTreeWithHttpInfo()}}{
-Returns fragmentation tree (SIRIUS) for the given formula result identifier
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetIsotopePatternAnnotation}{}}}
-\subsection{Method \code{GetIsotopePatternAnnotation()}}{
-Returns Isotope pattern information for given formulaId
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetIsotopePatternAnnotationWithHttpInfo}{}}}
-\subsection{Method \code{GetIsotopePatternAnnotationWithHttpInfo()}}{
-Returns Isotope pattern information for given formulaId
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetLipidAnnotation}{}}}
-\subsection{Method \code{GetLipidAnnotation()}}{
-Returns Lipid annotation (ElGordo) for the given formulaId
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetLipidAnnotationWithHttpInfo}{}}}
-\subsection{Method \code{GetLipidAnnotationWithHttpInfo()}}{
-Returns Lipid annotation (ElGordo) for the given formulaId
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetMsData}{}}}
-\subsection{Method \code{GetMsData()}}{
-Mass Spec data (input data) for the given 'alignedFeatureId' .
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetMsDataWithHttpInfo}{}}}
-\subsection{Method \code{GetMsDataWithHttpInfo()}}{
-Mass Spec data (input data) for the given 'alignedFeatureId' .
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetQuantTableRowExperimental}{}}}
-\subsection{Method \code{GetQuantTableRowExperimental()}}{
-[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetQuantTableRowExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetQuantTableRowExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatch}{}}}
-\subsection{Method \code{GetSpectralLibraryMatch()}}{
-Spectral library match for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchWithHttpInfo}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchWithHttpInfo()}}{
-Spectral library match for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatches}{}}}
-\subsection{Method \code{GetSpectralLibraryMatches()}}{
-List of spectral library matches for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesWithHttpInfo}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchesWithHttpInfo()}}{
-List of spectral library matches for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesPaged}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchesPaged()}}{
-Page of spectral library matches for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesPagedWithHttpInfo}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchesPagedWithHttpInfo()}}{
-Page of spectral library matches for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesSummary}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchesSummary()}}{
-Summarize matched reference spectra for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesSummaryWithHttpInfo}{}}}
-\subsection{Method \code{GetSpectralLibraryMatchesSummaryWithHttpInfo()}}{
-Summarize matched reference spectra for the given 'alignedFeatureId'.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedMsDataExperimental}{}}}
-\subsection{Method \code{GetStructureAnnotatedMsDataExperimental()}}{
-[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedMsDataExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetStructureAnnotatedMsDataExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedSpectralLibraryMatchExperimental}{}}}
-\subsection{Method \code{GetStructureAnnotatedSpectralLibraryMatchExperimental()}}{
-[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesPaged}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchesPaged()}}{
+Page of spectral library matches for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedSpectralLibraryMatchExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetStructureAnnotatedSpectralLibraryMatchExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesPagedWithHttpInfo}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchesPagedWithHttpInfo()}}{
+Page of spectral library matches for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedSpectrumExperimental}{}}}
-\subsection{Method \code{GetStructureAnnotatedSpectrumExperimental()}}{
-[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesSummary}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchesSummary()}}{
+Summarize matched reference spectra for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetStructureAnnotatedSpectrumExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetStructureAnnotatedSpectrumExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-FeaturesApi-GetSpectralLibraryMatchesSummaryWithHttpInfo}{}}}
+\subsection{Method \code{GetSpectralLibraryMatchesSummaryWithHttpInfo()}}{
+Summarize matched reference spectra for the given 'alignedFeatureId'.
\subsection{Usage}{
-\if{html}{\out{
}}
@@ -3943,198 +2805,6 @@ API response (PagedModelStructureCandidateFormula) with additional information s
}
}
\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetTagsForAlignedFeaturesExperimental}{}}}
-\subsection{Method \code{GetTagsForAlignedFeaturesExperimental()}}{
-[EXPERIMENTAL] Get all tags associated with this Object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetTagsForAlignedFeaturesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetTagsForAlignedFeaturesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get all tags associated with this Object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetTracesExperimental}{}}}
-\subsection{Method \code{GetTracesExperimental()}}{
-[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-GetTracesExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetTracesExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-RemoveTagFromAlignedFeatureExperimental}{}}}
-\subsection{Method \code{RemoveTagFromAlignedFeatureExperimental()}}{
-[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FeaturesApi-RemoveTagFromAlignedFeatureExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{RemoveTagFromAlignedFeatureExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
\if{html}{\out{}}
\if{latex}{\out{\hypertarget{method-FeaturesApi-clone}{}}}
\subsection{Method \code{clone()}}{
diff --git a/client-api_r/generated/man/FoldChange.Rd b/client-api_r/generated/man/FoldChange.Rd
deleted file mode 100644
index 59c34004..00000000
--- a/client-api_r/generated/man/FoldChange.Rd
+++ /dev/null
@@ -1,304 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fold_change.R
-\docType{class}
-\name{FoldChange}
-\alias{FoldChange}
-\title{FoldChange}
-\format{
-An \code{R6Class} generator object
-}
-\description{
-FoldChange Class
-
-FoldChange Class
-}
-\details{
-Create a new FoldChange
-}
-\examples{
-
-## ------------------------------------------------
-## Method `FoldChange$toList`
-## ------------------------------------------------
-
-# convert array of FoldChange (x) to a data frame
-\dontrun{
-library(purrr)
-library(tibble)
-df <- x |> map(\(y)y$toList()) |> map(as_tibble) |> list_rbind()
-df
-}
-}
-\section{Public fields}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new FoldChange class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert FoldChange to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of FoldChange
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of FoldChange
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to FoldChange and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-FoldChange-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new PagedModelRun class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert PagedModelRun to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of PagedModelRun
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of PagedModelRun
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to PagedModelRun and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-PagedModelRun-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new QualityItem class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert QualityItem to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of QualityItem
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of QualityItem
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to QualityItem and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QualityItem-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new QuantTableExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert QuantTableExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of QuantTableExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of QuantTableExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to QuantTableExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-QuantTableExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new Run class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert Run to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of Run
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of Run
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to Run and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-Run-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new RunOptField class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of RunOptField
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of RunOptField
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunOptField-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new RunsApi.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-AddTagsToRunExperimental}{}}}
-\subsection{Method \code{AddTagsToRunExperimental()}}{
-[EXPERIMENTAL] Add tags to a run in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-AddTagsToRunExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{AddTagsToRunExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Add tags to a run in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-ComputeFoldChangeForBlankSubtraction}{}}}
-\subsection{Method \code{ComputeFoldChangeForBlankSubtraction()}}{
-**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-ComputeFoldChangeForBlankSubtractionWithHttpInfo}{}}}
-\subsection{Method \code{ComputeFoldChangeForBlankSubtractionWithHttpInfo()}}{
-**EXPERIMENTAL** Compute the fold changes that are required for the fold change filter
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunExperimental}{}}}
-\subsection{Method \code{GetRunExperimental()}}{
-[EXPERIMENTAL] Get run with the given identifier from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetRunExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get run with the given identifier from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunPageExperimental}{}}}
-\subsection{Method \code{GetRunPageExperimental()}}{
-[EXPERIMENTAL] Get all available runs in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunPageExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetRunPageExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get all available runs in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunsByGroupExperimental}{}}}
-\subsection{Method \code{GetRunsByGroupExperimental()}}{
-[EXPERIMENTAL] Get runs by tag group
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunsByGroupExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetRunsByGroupExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get runs by tag group
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunsByTagExperimental}{}}}
-\subsection{Method \code{GetRunsByTagExperimental()}}{
-[EXPERIMENTAL] Get runs by tag
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetRunsByTagExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetRunsByTagExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get runs by tag
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetTagsForRunExperimental}{}}}
-\subsection{Method \code{GetTagsForRunExperimental()}}{
-[EXPERIMENTAL] Get all tags associated with this Run
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-GetTagsForRunExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{GetTagsForRunExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Get all tags associated with this Run
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-RemoveTagFromRunExperimental}{}}}
-\subsection{Method \code{RemoveTagFromRunExperimental()}}{
-[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-RemoveTagFromRunExperimentalWithHttpInfo}{}}}
-\subsection{Method \code{RemoveTagFromRunExperimentalWithHttpInfo()}}{
-[EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-RunsApi-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new SampleTypeFoldChangeRequest class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert SampleTypeFoldChangeRequest to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of SampleTypeFoldChangeRequest
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of SampleTypeFoldChangeRequest
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to SampleTypeFoldChangeRequest and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-SampleTypeFoldChangeRequest-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new StatisticsTable class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert StatisticsTable to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of StatisticsTable
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of StatisticsTable
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to StatisticsTable and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-StatisticsTable-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TagDefinition class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TagDefinition to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TagDefinition
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TagDefinition
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TagDefinition and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinition-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TagDefinitionImport class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TagDefinitionImport to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TagDefinitionImport
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TagDefinitionImport
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TagDefinitionImport and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagDefinitionImport-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TagGroup class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TagGroup to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TagGroup
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TagGroup
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TagGroup and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagGroup-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TagsApi.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-AddGroup}{}}}
-\subsection{Method \code{AddGroup()}}{
-[EXPERIMENTAL] Group tags in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-AddGroupWithHttpInfo}{}}}
-\subsection{Method \code{AddGroupWithHttpInfo()}}{
-[EXPERIMENTAL] Group tags in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-AddPossibleValuesToTagDefinition}{}}}
-\subsection{Method \code{AddPossibleValuesToTagDefinition()}}{
-[EXPERIMENTAL] Add a possible value to the tag definition in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-AddPossibleValuesToTagDefinitionWithHttpInfo}{}}}
-\subsection{Method \code{AddPossibleValuesToTagDefinitionWithHttpInfo()}}{
-[EXPERIMENTAL] Add a possible value to the tag definition in the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-CreateTags}{}}}
-\subsection{Method \code{CreateTags()}}{
-[EXPERIMENTAL] Add tags to the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-CreateTagsWithHttpInfo}{}}}
-\subsection{Method \code{CreateTagsWithHttpInfo()}}{
-[EXPERIMENTAL] Add tags to the project
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-DeleteGroup}{}}}
-\subsection{Method \code{DeleteGroup()}}{
-[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-DeleteGroupWithHttpInfo}{}}}
-\subsection{Method \code{DeleteGroupWithHttpInfo()}}{
-[EXPERIMENTAL] Delete tag groups with the given name from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-DeleteTag}{}}}
-\subsection{Method \code{DeleteTag()}}{
-[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-DeleteTagWithHttpInfo}{}}}
-\subsection{Method \code{DeleteTagWithHttpInfo()}}{
-[EXPERIMENTAL] Delete tag definition with the given name from the specified project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetGroupByName}{}}}
-\subsection{Method \code{GetGroupByName()}}{
-[EXPERIMENTAL] Get tag group by name in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetGroupByNameWithHttpInfo}{}}}
-\subsection{Method \code{GetGroupByNameWithHttpInfo()}}{
-[EXPERIMENTAL] Get tag group by name in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetGroups}{}}}
-\subsection{Method \code{GetGroups()}}{
-[EXPERIMENTAL] Get all tag based groups in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetGroupsWithHttpInfo}{}}}
-\subsection{Method \code{GetGroupsWithHttpInfo()}}{
-[EXPERIMENTAL] Get all tag based groups in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetTag}{}}}
-\subsection{Method \code{GetTag()}}{
-[EXPERIMENTAL] Get tag definition by its name in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetTagWithHttpInfo}{}}}
-\subsection{Method \code{GetTagWithHttpInfo()}}{
-[EXPERIMENTAL] Get tag definition by its name in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetTags}{}}}
-\subsection{Method \code{GetTags()}}{
-[EXPERIMENTAL] Get all tag definitions in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-GetTagsWithHttpInfo}{}}}
-\subsection{Method \code{GetTagsWithHttpInfo()}}{
-[EXPERIMENTAL] Get all tag definitions in the given project-space
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TagsApi-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TraceAnnotationExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TraceAnnotationExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TraceAnnotationExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TraceAnnotationExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TraceAnnotationExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceAnnotationExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TraceExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TraceExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TraceExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TraceExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TraceExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-new}{}}}
-\subsection{Method \code{new()}}{
-Initialize a new TraceSetExperimental class.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-toJSON}{}}}
-\subsection{Method \code{toJSON()}}{
-Convert to an R object. This method is deprecated. Use `toSimpleType()` instead.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-toList}{}}}
-\subsection{Method \code{toList()}}{
-Convert to a List
-
-Convert the R6 object to a list to work more easily with other tooling.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-toSimpleType}{}}}
-\subsection{Method \code{toSimpleType()}}{
-Convert TraceSetExperimental to a base R type
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-fromJSON}{}}}
-\subsection{Method \code{fromJSON()}}{
-Deserialize JSON string into an instance of TraceSetExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-toJSONString}{}}}
-\subsection{Method \code{toJSONString()}}{
-To JSON String
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-fromJSONString}{}}}
-\subsection{Method \code{fromJSONString()}}{
-Deserialize JSON string into an instance of TraceSetExperimental
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-validateJSON}{}}}
-\subsection{Method \code{validateJSON()}}{
-Validate JSON input with respect to TraceSetExperimental and throw an exception if invalid
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-toString}{}}}
-\subsection{Method \code{toString()}}{
-To string (JSON format)
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-isValid}{}}}
-\subsection{Method \code{isValid()}}{
-Return true if the values in all fields are valid.
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-getInvalidFields}{}}}
-\subsection{Method \code{getInvalidFields()}}{
-Return a list of invalid fields (if any).
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-print}{}}}
-\subsection{Method \code{print()}}{
-Print the object
-\subsection{Usage}{
-\if{html}{\out{
}}
-\if{html}{\out{}}
-\if{latex}{\out{\hypertarget{method-TraceSetExperimental-clone}{}}}
-\subsection{Method \code{clone()}}{
-The objects of this class are cloneable with this method.
-\subsection{Usage}{
-\if{html}{\out{