diff --git a/.gitignore b/.gitignore index 72f6bf2a..7837009d 100644 --- a/.gitignore +++ b/.gitignore @@ -95,12 +95,18 @@ old-tests/ *.db-corrupt docs/~* files/~* -output/* +output/*.xlsx +output/*.svg SOA Workbench Wishlist.docx NCT01750580_limited.json CLAUDE.md edit-column-collapse.html .claude api_test.py +.scripts +files/pilot_LZZT_narrative_2026MAR10.json +.help +files/NCT01797120.pdf +.mcp.json # End of file diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 00000000..64dddfda --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "cdisc-json-validation"] + path = cdisc-json-validation + url = https://github.com/pendingintent/cdisc-json-validation.git diff --git a/README.md b/README.md index 8ec11809..18feaa69 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,34 @@ This workspace provides a Python package `soa_builder` with APIs to create a Schedule of Activites for Clinical Studies. +## Cloning the repository +This project now includes a submodule for USDM JSON validation with the USDM_API_v4.0.0.json schema. + +In order to clone the repository with the new submodule, use the command: + +```bash +> git clone --recurse-submodules https://github.com/pendingintent/soa-workbench.git +``` + +Once the repository has been cloned locally, in order to ensure the submodule is up-to-date, use the commands: +```bash +> cd cdisc-json-validation +> git pull +# or use the command for updating all registered submodules +> git submodule update --remote +``` + +This will ensure the submodule is always up-to-date. + + ## Installation Recommended: editable install for development. ```bash -python3 -m venv .venv -source .venv/bin/activate -pip install -r requirements.txt -pre-commit install -pre-commit run --all-files +> python3 -m venv .venv +> source .venv/bin/activate +> pip install -r requirements.txt +> pre-commit install +> pre-commit run --all-files ``` ## Start web server @@ -66,22 +86,20 @@ rm -f soa_builder_web_tests.db soa_builder_web_tests.db-wal soa_builder_web_test ## USDM Export Export USDM-compliant JSON for integration with external systems: ```bash - -# Or use the USDM generator scripts directly -python -m usdm.generate_activities --soa-id 1 --output-file activities.json -python -m usdm.generate_encounters --soa-id 1 --output-file encounters.json -python -m usdm.generate_study_epochs --soa-id 1 --output-file epochs.json +# Use the USDM generator scripts directly +python -m usdm.generate_usdm 1 -o study_usdm.json +python -m usdm.generate_activities 1 -o activities.json +python -m usdm.generate_encounters 1 -o encounters.json +python -m usdm.generate_study_epochs 1 -o epochs.json # See src/usdm/ for all generator scripts ``` --- ## Architecture Notes -- **Web UI**: HTMX loaded via CDN; no build step required - **Database**: SQLite with WAL mode (production) or DELETE mode (tests) - **Test Isolation**: Tests use `soa_builder_web_tests.db` (set via `SOA_BUILDER_DB` env var) - **Production Config**: Set `SOA_BUILDER_DB` environment variable for persistent DB path - **USDM Generators**: Python scripts in `src/usdm/` transform database state → USDM JSON artifacts -For detailed architectural patterns, USDM entity relationships, and development workflows, see `.github/copilot-instructions.md`. diff --git a/cdisc-json-validation b/cdisc-json-validation new file mode 160000 index 00000000..4abb841c --- /dev/null +++ b/cdisc-json-validation @@ -0,0 +1 @@ +Subproject commit 4abb841c48f9b701df9aeea0155a1a5e18fa224a diff --git a/docs/BC_WORKFLOW.md b/docs/BC_WORKFLOW.md new file mode 100644 index 00000000..af911a29 --- /dev/null +++ b/docs/BC_WORKFLOW.md @@ -0,0 +1,414 @@ +# Workflow for linking Biomedical Concept with Scheduled Activity Instance + +Assumes that the Activties and Scheduled Activity Instances have been created to form the SOA Matrix. + +![Activities linked with Concepts](../images/image-1.png) + + +## Assign Biomedical Concept to an Activity + +![Add Biomedical Concept from CDISC Library](../images/image-4.png) + +![Activity linked to Biomedical Concepts](../images/image-3.png) + +Hovering the cursor over a Biomedical Concept (BC) will display the C code for the BC. + +![C Code on Hover](../images/image-5.png) + +C25298 is the C Code for Systolic Blood Pressure. + +In the DSS (Data Set Specialization) column, the SDTM DSS values corresponding to the C Code of the Biomedical Concept is automagically mapped in the background. This is done using the CDISC Library API: https://api.library.cdisc.org/api/cosmos/v2/mdr/specializations/datasetspecializations?biomedicalconcept=C25298 + + +Response: + +```JSON +{ + "_links": { + "datasetSpecializations": { + "sdtm": [ + { + "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP", + "title": "Systolic Blood Pressure", + "type": "SDTM Dataset Specialization" + }, + { + "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP_EXT", + "title": "Systolic Blood Pressure Extended", + "type": "SDTM Dataset Specialization" + } + ] + }, + "self": { + "href": "/mdr/specializations/datasetspecializations?biomedicalconcept=C25298", + "title": "Dataset Specializations that specialize a Biomedical Concept", + "type": "Dataset Specializations List" + }, + "parentBiomedicalConcept": { + "href": "/mdr/bc/biomedicalconcepts/C25298", + "title": "Systolic Blood Pressure", + "type": "Biomedical Concept" + } + }, + "name": "Dataset Specializations (latest version)", + "label": "Dataset Specializations List" +} +``` +The `href` attribute has the value **/mdr/specializations/sdtm/datasetspecializations/SYSBP**. This is then used by the application to retrieve the SDTM data set specialization and corresponding data element concepts: https://api.library.cdisc.org/api/cosmos/v2/mdr/specializations/sdtm/datasetspecializations/SYSBP + +Response: + +```JSON +{ + "_links": { + "parentBiomedicalConcept": { + "href": "/mdr/bc/biomedicalconcepts/C25298", + "title": "Systolic Blood Pressure", + "type": "Biomedical Concept" + }, + "parentPackage": { + "href": "/mdr/specializations/sdtm/packages/2025-04-01/datasetspecializations", + "title": "SDTM Dataset Specialization Package Effective 2025-04-01", + "type": "SDTM Dataset Specialization Package" + }, + "self": { + "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP", + "title": "Systolic Blood Pressure", + "type": "SDTM Dataset Specialization" + } + }, + "datasetSpecializationId": "SYSBP", + "domain": "VS", + "shortName": "Systolic Blood Pressure", + "source": "VS.VSTESTCD", + "sdtmigStartVersion": "3-2", + "sdtmigEndVersion": "", + "variables": [ + { + "name": "VSTESTCD", + "isNonStandard": false, + "codelist": { + "conceptId": "C66741", + "submissionValue": "VSTESTCD", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C66741" + }, + "assignedTerm": { + "conceptId": "C25298", + "value": "SYSBP" + }, + "role": "Topic", + "relationship": { + "subject": "VSTESTCD", + "linkingPhrase": "is the code for the value in", + "predicateTerm": "IS_DECODED_BY", + "object": "VSTEST" + }, + "mandatoryVariable": true, + "mandatoryValue": false, + "comparator": "EQ" + }, + { + "name": "VSTEST", + "isNonStandard": false, + "codelist": { + "conceptId": "C67153", + "submissionValue": "VSTEST", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C67153" + }, + "assignedTerm": { + "conceptId": "C25298", + "value": "Systolic Blood Pressure" + }, + "role": "Qualifier", + "relationship": { + "subject": "VSTEST", + "linkingPhrase": "decodes the value in", + "predicateTerm": "DECODES", + "object": "VSTESTCD" + }, + "mandatoryVariable": true, + "mandatoryValue": false + }, + { + "name": "VSORRES", + "dataElementConceptId": "C70856", + "isNonStandard": false, + "role": "Qualifier", + "dataType": "integer", + "length": 3, + "relationship": { + "subject": "VSORRES", + "linkingPhrase": "is the result of the test in", + "predicateTerm": "IS_RESULT_OF", + "object": "VSTESTCD" + }, + "mandatoryVariable": true, + "mandatoryValue": false, + "originType": "Collected", + "originSource": "Investigator", + "vlmTarget": true + }, + { + "name": "VSORRESU", + "dataElementConceptId": "C49669", + "isNonStandard": false, + "codelist": { + "conceptId": "C66770", + "submissionValue": "VSRESU", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C66770" + }, + "assignedTerm": { + "conceptId": "C49670", + "value": "mmHg" + }, + "role": "Qualifier", + "relationship": { + "subject": "VSORRESU", + "linkingPhrase": "is the unit for the value in", + "predicateTerm": "IS_UNIT_FOR", + "object": "VSORRES" + }, + "mandatoryVariable": true, + "mandatoryValue": false, + "vlmTarget": true + }, + { + "name": "VSSTRESC", + "dataElementConceptId": "C70856", + "isNonStandard": false, + "role": "Qualifier", + "dataType": "integer", + "length": 3, + "relationship": { + "subject": "VSSTRESC", + "linkingPhrase": "is the result of the test in", + "predicateTerm": "IS_RESULT_OF", + "object": "VSTESTCD" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "vlmTarget": true + }, + { + "name": "VSSTRESN", + "dataElementConceptId": "C70856", + "isNonStandard": false, + "role": "Qualifier", + "dataType": "integer", + "length": 3, + "relationship": { + "subject": "VSSTRESN", + "linkingPhrase": "is the result of the test in", + "predicateTerm": "IS_RESULT_OF", + "object": "VSTESTCD" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "vlmTarget": true + }, + { + "name": "VSSTRESU", + "dataElementConceptId": "C49669", + "isNonStandard": false, + "codelist": { + "conceptId": "C66770", + "submissionValue": "VSRESU", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C66770" + }, + "assignedTerm": { + "conceptId": "C49670", + "value": "mmHg" + }, + "role": "Qualifier", + "relationship": { + "subject": "VSSTRESU", + "linkingPhrase": "is the unit for the value in", + "predicateTerm": "IS_UNIT_FOR", + "object": "VSSTRESN" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "vlmTarget": true + }, + { + "name": "VSPOS", + "dataElementConceptId": "C62164", + "isNonStandard": false, + "codelist": { + "conceptId": "C71148", + "submissionValue": "POSITION", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C71148" + }, + "valueList": [ + "PRONE", + "SEMI-RECUMBENT", + "SITTING", + "STANDING", + "SUPINE" + ], + "role": "Qualifier", + "relationship": { + "subject": "VSPOS", + "linkingPhrase": "is the subject position during performance of the test in", + "predicateTerm": "IS_SUBJECT_STATE_FOR", + "object": "VSTESTCD" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "comparator": "IN" + }, + { + "name": "VSLOC", + "dataElementConceptId": "C13717", + "isNonStandard": false, + "codelist": { + "conceptId": "C74456", + "submissionValue": "LOC", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C74456" + }, + "valueList": [ + "BRACHIAL ARTERY", + "CAROTID ARTERY", + "DORSALIS PEDIS ARTERY", + "FEMORAL ARTERY", + "FINGER", + "PERIPHERAL ARTERY", + "RADIAL ARTERY" + ], + "role": "Qualifier", + "relationship": { + "subject": "VSLOC", + "linkingPhrase": "specifies the anatomical location of the performance of the test in", + "predicateTerm": "SPECIFIES", + "object": "VSTESTCD" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "comparator": "IN" + }, + { + "name": "VSLAT", + "dataElementConceptId": "C25185", + "isNonStandard": false, + "codelist": { + "conceptId": "C99073", + "submissionValue": "LAT", + "href": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C99073" + }, + "subsetCodelist": "VSLAT_BP", + "valueList": [ + "LEFT", + "RIGHT" + ], + "role": "Qualifier", + "relationship": { + "subject": "VSLAT", + "linkingPhrase": "further specifies the anatomical location in", + "predicateTerm": "SPECIFIES", + "object": "VSLOC" + }, + "mandatoryVariable": false, + "mandatoryValue": false, + "comparator": "IN" + }, + { + "name": "VSDTC", + "dataElementConceptId": "C82515", + "isNonStandard": false, + "role": "Timing", + "relationship": { + "subject": "VSDTC", + "linkingPhrase": "is the date of occurrence for", + "predicateTerm": "IS_TIMING_FOR", + "object": "VSTESTCD" + }, + "mandatoryVariable": true, + "mandatoryValue": false + } + ] +} +``` + +## Assign Biomedical Concept Surrogate to an Activity + +When a Biomedical Concept does not exist in the Library, there is a facility to create a Surrogate Concept to link to an Activity. + +The USDM Implementation Guide describes Biomedical Concept Surrogates as: + +_Surrogate BCs are a +placeholder mechanism for when a BC definition is not available. This allows the name of a test to be specified but +no further detail need be provided. Surrogates can contain a name and description pair for the concept required. A +reference field is also provided to allow for links to reference materials (e.g., a URL for an external resource)._ + +In order to map a Surrogate to an Activity, first create the Surrogate. + +![Define Surrogates](../images/image-6.png) + +Once created, these Surrogates can be added to a Scheduled Activity Instance in the same way as Biomedical Concepts. + +![Surrogate selection box](../images/image-7.png) + +![Choose from list of defined Surrogates](../images/image-8.png) + +![Surrogates linked to Activity](../images/image-10.png) + +These Surrogates are shown in the USDM JSON associated with their Scheduled Activity Instances. + +```JSON +{ + "id": "Activity_8", + "extensionAttributes": [], + "name": "CHEMISTRY LABS", + "label": "Serum Creatinine, Electrolytes (K, Na, Cl, CO2), Ca, BUN, Albumin, Total Protein, Phosphorus, AST (SGOT), ALT (SGPT), Alkaline Phosphatase, Total Bilirubin, Magnesium, Uric Acid.", + "description": "Serum Creatinine, Electrolytes (K, Na, Cl, CO2), Ca, BUN, Albumin, Total Protein, Phosphorus, AST (SGOT), ALT (SGPT), Alkaline Phosphatase, Total Bilirubin, Magnesium, Uric Acid.", + "previousId": "Activity_24", + "nextId": "Activity_25", + "childIds": [], + "definedProcedures": [], + "biomedicalConceptIds": [ + "BiomedicalConcept_18", + "BiomedicalConcept_19", + "BiomedicalConcept_20", + "BiomedicalConcept_21", + "BiomedicalConcept_22", + "BiomedicalConcept_64", + "BiomedicalConcept_65", + "BiomedicalConcept_66", + "BiomedicalConcept_67", + "BiomedicalConcept_68", + "BiomedicalConcept_69", + "BiomedicalConcept_70", + "BiomedicalConcept_71", + "BiomedicalConcept_72" + ], + "bcCategoryIds": [], + "bcSurrogateIds": [ + "BiomedicalConceptSurrogate_1", + "BiomedicalConceptSurrogate_8" + ], + "timelineId": null, + "notes": [], + "instanceType": "Activity" + }, +``` + +```JSON +"bcSurrogates": [ + { + "id": "BiomedicalConceptSurrogate_1", + "extensionAttributes": [], + "name": "Magnesium Measurement", + "label": "Magnesium Measurement (C64840)", + "description": "A quantitative measurement of the amount of magnesium present in a sample.", + "reference": "https://evsexplore.semantics.cancer.gov/evsexplore/concept/ncit/C64840", + "notes": [], + "instanceType": "BiomedicalConceptSurrogate" + }, +``` + +Since there is no C Code associated with the Biomedical Concept Surrogate, there are no corresponding Data Set Specialization defined so there is no automagic mapping as seen with the Library Biomedical Concepts. + + + + + diff --git a/files/NCT01797120_Footnote_1.html b/files/NCT01797120_Footnote_1.html new file mode 100644 index 00000000..28da54c1 --- /dev/null +++ b/files/NCT01797120_Footnote_1.html @@ -0,0 +1,79 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
a:≤ 4 weeks of randomization; if assessments required ≤ 7 days of Cycle 1 Day 1 (C1D1), they do not need to be repeated (includes labs).
b:≤ 7 days prior to the start of C1D1.
c:+/- 72 hour window allowed prior to D1 of each subsequent cycle after the first cycle for scheduled therapy/tests/visits. Delay due to holidays, weekends, +bad weather or other unforeseen circumstances will be permitted.
d:In the event of grade 3 or 4 hematologic toxicity, CBC with differential and platelet count will be obtained every 1-3 days until there is evidence of +hematologic recovery.
e:+/- 72 hours prior to Cycle 2 Day 1 then approximately every 12 weeks during treatment (and more frequently as clinically indicated), and at end of +treatment.
f:All patients should be screened for hepatitis risk factors and any past illnesses of hepatitis B and hepatitis C infection (see Section 7.1.1). All patients with a +positive medical history per Section 7.1.1 need hepatitis testing as noted on above table. It is highly recommended that patients positive for HBV-DNA or +HBsAg are treated prophylactically with an antiviral (e.g., Lamivudine) for 1-2 weeks prior to receiving study drug (see Table 5-3). The antiviral treatment +should continue throughout the entire study period and for at least 4 weeks after the last dose of everolimus.
g:Patients on antiviral prophylaxis treatment or positive HBV antibodies should be tested for HBV-DNA ≤ 7 days prior to the start of C1D1 and +/- 72 hrs prior +to D1 of each subsequent cycle to monitor for reactivation. See Table 5-4 for reactivation instructions.
h:Patients with positive HCV RNA-PCR results at screening and/or a history of past infection (even if treated and considered ‘cured’) should have HCV RNA- +PCR testing performed on ≤ 7 days prior to the start of C1D1 and +/- 72 hrs prior to D1 of each subsequent cycle to monitor for flare. Everolimus must be +discontinued if HCV flare is confirmed according to the guidance in Table 5-5.
i:Tumor measurements may be made using physical examination, CT Scans or MRI. Tumor assessments will be performed every 12 weeks, +/- 1 week +(every 3 months). Imaging will include chest and abdomen. Bone Scans and Brain CT/MRI may be performed as clinically indicated. Scans do not have to be +repeated once disease progression is documented.
j:Adverse events related to fulvestrant and/or everolimus/placebo will be followed for 30 days after the last dose of study therapy (fulvestrant and/or +everolimus/placebo) or until ≤ grade 1 or if the grade is >1, the event must be permanent and stable. Please note- Serious adverse events >30 days after last +dose of fulvestrant and/or everolimus/placebo are not reported unless the event may be related to everolimus/placebo.
k:CBC and chemistry may be used to assess ongoing toxicity but are not required in the Continuation Phase for patients who receive fulvestrant alone. +Patients who continue fulvestrant with everolimus should periodically have CBC, chemistries, fasting glucose, fasting lipids, HBV DNA, HCV RNA-PCR per +labeling guidelines.
l:Study Drug Compliance (Pill Diary) for those patients who receive everolimus in the Continuation Phase.
m:All patients including those that discontinue protocol therapy will be followed for 3 years from the time of randomization. Patients that have not progressed +during the Induction or Continuation Phase will continue to have imaging scans completed every 12 weeks, +/- 1 week (every 3 months) until documented +progression.
n:PFTs with DLCO as medically indicated only, (PFTs are not otherwise required during course of study).
o:Follow every 3 months for disease progression and survival. Initiation of any new systemic therapy will also be documented
\ No newline at end of file diff --git a/files/NCT01797120_Footnote_2.html b/files/NCT01797120_Footnote_2.html new file mode 100644 index 00000000..cb3f82cd --- /dev/null +++ b/files/NCT01797120_Footnote_2.html @@ -0,0 +1,17 @@ + + + + + + + + + + + + + +
*Cycle 1, Day 1 is defined as the first day on which fulvestrant is given in combination with placebo/everolimus (the second fulvestrant dose is given on day 15 +of the first cycle only). Day 1 of each additional cycle is defined as the day in which fulvestrant is given in combination with everolimus/placebo.
^End of Induction/End of Treatment should be performed within 30 days of last dose of fulvestrant.
£Continuation Phase: Patients in the Continuation Phase should continue to receive fulvestrant alone (if originally randomized to placebo) or in combination +with everolimus (if originally randomized to everolimus) at the same dose and schedule (+/- 1 week window for scheduled therapy/tests/visits; delays due to +holidays, weekends, bad weather or other unforeseen circumstances will be permitted) until disease progression or unacceptable toxicity.
\ No newline at end of file diff --git a/images/image-1.png b/images/image-1.png new file mode 100644 index 00000000..24b02b02 Binary files /dev/null and b/images/image-1.png differ diff --git a/images/image-10.png b/images/image-10.png new file mode 100644 index 00000000..5ebda170 Binary files /dev/null and b/images/image-10.png differ diff --git a/images/image-2.png b/images/image-2.png new file mode 100644 index 00000000..24b02b02 Binary files /dev/null and b/images/image-2.png differ diff --git a/images/image-3.png b/images/image-3.png new file mode 100644 index 00000000..8a84c994 Binary files /dev/null and b/images/image-3.png differ diff --git a/images/image-4.png b/images/image-4.png new file mode 100644 index 00000000..60b79db6 Binary files /dev/null and b/images/image-4.png differ diff --git a/images/image-5.png b/images/image-5.png new file mode 100644 index 00000000..0023bc91 Binary files /dev/null and b/images/image-5.png differ diff --git a/images/image-6.png b/images/image-6.png new file mode 100644 index 00000000..39eae0d6 Binary files /dev/null and b/images/image-6.png differ diff --git a/images/image-7.png b/images/image-7.png new file mode 100644 index 00000000..ea696d22 Binary files /dev/null and b/images/image-7.png differ diff --git a/images/image-8.png b/images/image-8.png new file mode 100644 index 00000000..c371721c Binary files /dev/null and b/images/image-8.png differ diff --git a/images/image-9.png b/images/image-9.png new file mode 100644 index 00000000..9551b989 Binary files /dev/null and b/images/image-9.png differ diff --git a/images/image.png b/images/image.png new file mode 100644 index 00000000..9ffe703e Binary files /dev/null and b/images/image.png differ diff --git a/output/json/NCT01797120.json b/output/json/NCT01797120.json new file mode 100644 index 00000000..5c41cb2a --- /dev/null +++ b/output/json/NCT01797120.json @@ -0,0 +1,14392 @@ +{ + "study": { + "id": null, + "extensionAttributes": [], + "name": "NCT01797120", + "description": "Post-menopausal women with hormone-receptor positive (HR+) metastatic breast cancer resistant to aromatase inhibitor (AI) therapy will be randomized to receive Fulvestrant (Faslodex) with Everolimus or Fulvestrant (Faslodex) with a placebo (no active ingredients).\r\n\r\nFulvestrant has demonstrated activity when used as first, second, or third line endocrine therapy, making it an attractive therapy for combination with other agents. In addition, it is commonly reserved for use following disease progression on AI therapy.\r\n\r\nEverolimus is an orally administered drug that blocks a signaling pathway called \"mTOR\". \"mTOR\" acts as a regulator for many processes in the body, including cell growth. Blocking this pathway may have an effect on cell growth.\r\n\r\nThe combination of a novel class of agents (mTOR inhibitors) and an established standard treatment for metastatic HR+ breast cancer may potentially increase the clinical benefit by targeting multiple different biological pathways.", + "label": "Phase II - Hormone-receptor positive (HR+) metastatic breast cancer resistant to aromatase inhibitor (AI)", + "versions": [ + { + "id": "StudyVersion_1", + "extensionAttributes": [], + "versionIdentifier": "1", + "rationale": "", + "studyIdentifiers": [ + { + "id": "StudyIdentifier_1", + "extensionAttributes": [], + "text": "NCT01797120", + "scopeId": "", + "instanceType": "StudyIdentifier" + } + ], + "referenceIdentifiers": [], + "studyDesigns": [ + { + "id": "InterventionalStudyDesign_1", + "extensionAttributes": [], + "name": "Study of Fulvestrant +/\u200b- Everolimus in Post-Menopausal, Hormone-Receptor + Metastatic Breast Ca Resistant to AI (PrE0102)", + "label": "Phase II - Hormone-receptor positive (HR+) metastatic breast cancer resistant to aromatase inhibitor (AI)", + "description": "Post-menopausal women with hormone-receptor positive (HR+) metastatic breast cancer resistant to aromatase inhibitor (AI) therapy will be randomized to receive Fulvestrant (Faslodex) with Everolimus or Fulvestrant (Faslodex) with a placebo (no active ingredients).\r\n\r\nFulvestrant has demonstrated activity when used as first, second, or third line endocrine therapy, making it an attractive therapy for combination with other agents. In addition, it is commonly reserved for use following disease progression on AI therapy.\r\n\r\nEverolimus is an orally administered drug that blocks a signaling pathway called \"mTOR\". \"mTOR\" acts as a regulator for many processes in the body, including cell growth. Blocking this pathway may have an effect on cell growth.\r\n\r\nThe combination of a novel class of agents (mTOR inhibitors) and an established standard treatment for metastatic HR+ breast cancer may potentially increase the clinical benefit by targeting multiple different biological pathways.", + "studyType": null, + "studyPhase": null, + "therapeuticAreas": [], + "characteristics": [], + "encounters": [ + { + "id": "Encounter_1", + "extensionAttributes": [], + "name": "PRE-STUDY", + "label": "Pre-Study", + "description": "Occuring before Randomization and Treatment", + "type": { + "id": "Code_485", + "extensionAttributes": [], + "code": "C25716", + "codeSystem": "http://www.cdisc.org", + "codeSystemVersion": "2025-09-26", + "decode": "Visit", + "instanceType": "Code" + }, + "previousId": null, + "nextId": "Encounter_2", + "scheduledAt": "Timing_1", + "environmentSettings": [ + { + "id": "Code_486", + "extensionAttributes": [], + "code": "C211570", + "codeSystem": 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"#/components/schemas/StudyIntervention-Input" + }, + "type": "array", + "title": "Studyinterventions", + "default": [] + }, + "administrableProducts": { + "items": { + "$ref": "#/components/schemas/AdministrableProduct-Input" + }, + "type": "array", + "title": "Administrableproducts", + "default": [] + }, + "medicalDevices": { + "items": { + "$ref": "#/components/schemas/MedicalDevice-Input" + }, + "type": "array", + "title": "Medicaldevices", + "default": [] + }, + "productOrganizationRoles": { + "items": { + "$ref": "#/components/schemas/ProductOrganizationRole-Input" + }, + "type": "array", + "title": "Productorganizationroles", + "default": [] + }, + "biomedicalConcepts": { + "items": { + "$ref": "#/components/schemas/BiomedicalConcept-Input" + }, + "type": "array", + "title": "Biomedicalconcepts", + "default": [] + }, + "bcCategories": { + "items": { + "$ref": "#/components/schemas/BiomedicalConceptCategory-Input" + }, + "type": "array", + "title": "Bccategories", + "default": [] + }, + "bcSurrogates": { + "items": { + "$ref": "#/components/schemas/BiomedicalConceptSurrogate-Input" + }, + "type": "array", + "title": "Bcsurrogates", + "default": [] + }, + "dictionaries": { + "items": { + "$ref": "#/components/schemas/SyntaxTemplateDictionary-Input" + }, + "type": "array", + "title": "Dictionaries", + "default": [] + }, + "conditions": { + "items": { + "$ref": "#/components/schemas/Condition-Input" + }, + "type": "array", + "title": "Conditions", + "default": [] + }, + "notes": { + "items": { + "$ref": "#/components/schemas/CommentAnnotation-Input" + }, + "type": "array", + "title": "Notes", + "default": [] + }, + "instanceType": { + "type": "string", + "enum": [ + "StudyVersion" + ], + "const": "StudyVersion", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "versionIdentifier", + "rationale", + "studyIdentifiers", + "titles", + "instanceType" + ], + "title": "StudyVersion" + }, + "StudyVersion-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "versionIdentifier": { + "type": "string", + "title": "Versionidentifier" + }, + "rationale": { + "type": "string", + "title": "Rationale" + }, + "documentVersionIds": { + "items": { + "type": "string" + }, + "type": "array", + "title": "Documentversionids", + "default": [] + }, + "dateValues": { + "items": { + "$ref": "#/components/schemas/GovernanceDate-Output" + }, + "type": "array", + "title": "Datevalues", + "default": [] + }, + "amendments": { + "items": { + "$ref": "#/components/schemas/StudyAmendment-Output" + }, + "type": "array", + "title": "Amendments", + "default": [] + }, + "businessTherapeuticAreas": { + "items": { + "$ref": "#/components/schemas/Code-Output" + }, + "type": "array", + "title": "Businesstherapeuticareas", + "default": [] + }, + "studyIdentifiers": { + "items": { + "$ref": "#/components/schemas/StudyIdentifier-Output" + }, + "type": "array", + "title": "Studyidentifiers" + }, + "referenceIdentifiers": { + "items": { + "$ref": "#/components/schemas/ReferenceIdentifier-Output" + }, + "type": "array", + "title": "Referenceidentifiers", + "default": [] + }, + "studyDesigns": { + "items": { + "anyOf": [ + { + "$ref": "#/components/schemas/InterventionalStudyDesign-Output" + }, + { + "$ref": "#/components/schemas/ObservationalStudyDesign-Output" + } + ] + }, + "type": "array", + "title": "Studydesigns", + "default": [] + }, + "titles": { + "items": { + "$ref": "#/components/schemas/StudyTitle-Output" + }, + "type": "array", + "title": "Titles" + }, + "eligibilityCriterionItems": { + "items": { + "$ref": "#/components/schemas/EligibilityCriterionItem-Output" + }, + "type": "array", + "title": "Eligibilitycriterionitems", + "default": [] + }, + "narrativeContentItems": { + "items": { + "$ref": "#/components/schemas/NarrativeContentItem-Output" + }, + "type": "array", + "title": "Narrativecontentitems", + "default": [] + }, + "abbreviations": { + "items": { + "$ref": "#/components/schemas/Abbreviation-Output" + }, + "type": "array", + "title": "Abbreviations", + "default": [] + }, + "roles": { + "items": { + "$ref": "#/components/schemas/StudyRole-Output" + }, + "type": "array", + "title": "Roles", + "default": [] + }, + "organizations": { + "items": { + "$ref": "#/components/schemas/Organization-Output" + }, + "type": "array", + "title": "Organizations", + "default": [] + }, + "studyInterventions": { + "items": { + "$ref": "#/components/schemas/StudyIntervention-Output" + }, + "type": "array", + "title": "Studyinterventions", + "default": [] + }, + "administrableProducts": { + "items": { + "$ref": "#/components/schemas/AdministrableProduct-Output" + }, + "type": "array", + "title": "Administrableproducts", + "default": [] + }, + "medicalDevices": { + "items": { + "$ref": "#/components/schemas/MedicalDevice-Output" + }, + "type": "array", + "title": "Medicaldevices", + "default": [] + }, + "productOrganizationRoles": { + "items": { + "$ref": "#/components/schemas/ProductOrganizationRole-Output" + }, + "type": "array", + "title": "Productorganizationroles", + "default": [] + }, + "biomedicalConcepts": { + "items": { + "$ref": "#/components/schemas/BiomedicalConcept-Output" + }, + "type": "array", + "title": "Biomedicalconcepts", + "default": [] + }, + "bcCategories": { + "items": { + "$ref": "#/components/schemas/BiomedicalConceptCategory-Output" + }, + "type": "array", + "title": "Bccategories", + "default": [] + }, + "bcSurrogates": { + "items": { + "$ref": "#/components/schemas/BiomedicalConceptSurrogate-Output" + }, + "type": "array", + "title": "Bcsurrogates", + "default": [] + }, + "dictionaries": { + "items": { + "$ref": "#/components/schemas/SyntaxTemplateDictionary-Output" + }, + "type": "array", + "title": "Dictionaries", + "default": [] + }, + "conditions": { + "items": { + "$ref": "#/components/schemas/Condition-Output" + }, + "type": "array", + "title": "Conditions", + "default": [] + }, + "notes": { + "items": { + "$ref": "#/components/schemas/CommentAnnotation-Output" + }, + "type": "array", + "title": "Notes", + "default": [] + }, + "instanceType": { + "type": "string", + "enum": [ + "StudyVersion" + ], + "const": "StudyVersion", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "versionIdentifier", + "rationale", + "studyIdentifiers", + "titles", + "instanceType" + ], + "title": "StudyVersion" + }, + "SubjectEnrollment-Input": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Input" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "quantity": { + "$ref": "#/components/schemas/Quantity-Input" + }, + "forGeographicScope": { + "anyOf": [ + { + "$ref": "#/components/schemas/GeographicScope-Input" + }, + { + "type": "null" + } + ] + }, + "forStudyCohortId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Forstudycohortid" + }, + "forStudySiteId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Forstudysiteid" + }, + "instanceType": { + "type": "string", + "enum": [ + "SubjectEnrollment" + ], + "const": "SubjectEnrollment", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "quantity", + "instanceType" + ], + "title": "SubjectEnrollment" + }, + "SubjectEnrollment-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "quantity": { + "$ref": "#/components/schemas/Quantity-Output" + }, + "forGeographicScope": { + "anyOf": [ + { + "$ref": "#/components/schemas/GeographicScope-Output" + }, + { + "type": "null" + } + ] + }, + "forStudyCohortId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Forstudycohortid" + }, + "forStudySiteId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Forstudysiteid" + }, + "instanceType": { + "type": "string", + "enum": [ + "SubjectEnrollment" + ], + "const": "SubjectEnrollment", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "quantity", + "instanceType" + ], + "title": "SubjectEnrollment" + }, + "Substance-Input": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Input" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "codes": { + "items": { + "$ref": "#/components/schemas/Code-Input" + }, + "type": "array", + "title": "Codes", + "default": [] + }, + "strengths": { + "items": { + "$ref": "#/components/schemas/Strength-Input" + }, + "type": "array", + "title": "Strengths" + }, + "referenceSubstance": { + "anyOf": [ + { + "$ref": "#/components/schemas/Substance-Input" + }, + { + "type": "null" + } + ] + }, + "instanceType": { + "type": "string", + "enum": [ + "Substance" + ], + "const": "Substance", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "strengths", + "instanceType" + ], + "title": "Substance" + }, + "Substance-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "codes": { + "items": { + "$ref": "#/components/schemas/Code-Output" + }, + "type": "array", + "title": "Codes", + "default": [] + }, + "strengths": { + "items": { + "$ref": "#/components/schemas/Strength-Output" + }, + "type": "array", + "title": "Strengths" + }, + "referenceSubstance": { + "anyOf": [ + { + "$ref": "#/components/schemas/Substance-Output" + }, + { + "type": "null" + } + ] + }, + "instanceType": { + "type": "string", + "enum": [ + "Substance" + ], + "const": "Substance", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "strengths", + "instanceType" + ], + "title": "Substance" + }, + "SyntaxTemplateDictionary-Input": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Input" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "parameterMaps": { + "items": { + "$ref": "#/components/schemas/ParameterMap-Input" + }, + "type": "array", + "title": "Parametermaps" + }, + "instanceType": { + "type": "string", + "enum": [ + "SyntaxTemplateDictionary" + ], + "const": "SyntaxTemplateDictionary", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "parameterMaps", + "instanceType" + ], + "title": "SyntaxTemplateDictionary" + }, + "SyntaxTemplateDictionary-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "parameterMaps": { + "items": { + "$ref": "#/components/schemas/ParameterMap-Output" + }, + "type": "array", + "title": "Parametermaps" + }, + "instanceType": { + "type": "string", + "enum": [ + "SyntaxTemplateDictionary" + ], + "const": "SyntaxTemplateDictionary", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "parameterMaps", + "instanceType" + ], + "title": "SyntaxTemplateDictionary" + }, + "Timing-Input": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Input" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "type": { + "$ref": "#/components/schemas/Code-Input" + }, + "value": { + "type": "string", + "title": "Value" + }, + "valueLabel": { + "type": "string", + "title": "Valuelabel" + }, + "relativeToFrom": { + "$ref": "#/components/schemas/Code-Input" + }, + "relativeFromScheduledInstanceId": { + "type": "string", + "title": "Relativefromscheduledinstanceid" + }, + "relativeToScheduledInstanceId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Relativetoscheduledinstanceid" + }, + "windowLower": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowlower" + }, + "windowUpper": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowupper" + }, + "windowLabel": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowlabel" + }, + "instanceType": { + "type": "string", + "enum": [ + "Timing" + ], + "const": "Timing", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "type", + "value", + "valueLabel", + "relativeToFrom", + "relativeFromScheduledInstanceId", + "instanceType" + ], + "title": "Timing" + }, + "Timing-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "type": { + "$ref": "#/components/schemas/Code-Output" + }, + "value": { + "type": "string", + "title": "Value" + }, + "valueLabel": { + "type": "string", + "title": "Valuelabel" + }, + "relativeToFrom": { + "$ref": "#/components/schemas/Code-Output" + }, + "relativeFromScheduledInstanceId": { + "type": "string", + "title": "Relativefromscheduledinstanceid" + }, + "relativeToScheduledInstanceId": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Relativetoscheduledinstanceid" + }, + "windowLower": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowlower" + }, + "windowUpper": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowupper" + }, + "windowLabel": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Windowlabel" + }, + "instanceType": { + "type": "string", + "enum": [ + "Timing" + ], + "const": "Timing", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "type", + "value", + "valueLabel", + "relativeToFrom", + "relativeFromScheduledInstanceId", + "instanceType" + ], + "title": "Timing" + }, + "TransitionRule-Input": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Input" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "text": { + "type": "string", + "title": "Text" + }, + "instanceType": { + "type": "string", + "enum": [ + "TransitionRule" + ], + "const": "TransitionRule", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "text", + "instanceType" + ], + "title": "TransitionRule" + }, + "TransitionRule-Output": { + "properties": { + "id": { + "type": "string", + "minLength": 1, + "title": "Id" + }, + "extensionAttributes": { + "items": { + "$ref": "#/components/schemas/ExtensionAttribute-Output" + }, + "type": "array", + "title": "Extensionattributes", + "default": [] + }, + "name": { + "type": "string", + "minLength": 1, + "title": "Name" + }, + "label": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Label" + }, + "description": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Description" + }, + "text": { + "type": "string", + "title": "Text" + }, + "instanceType": { + "type": "string", + "enum": [ + "TransitionRule" + ], + "const": "TransitionRule", + "title": "Instancetype" + } + }, + "type": "object", + "required": [ + "id", + "name", + "text", + "instanceType" + ], + "title": "TransitionRule" + }, + "ValidationError": { + "properties": { + "loc": { + "items": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "integer" + } + ] + }, + "type": "array", + "title": "Location" + }, + "msg": { + "type": "string", + "title": "Message" + }, + "type": { + "type": "string", + "title": "Error Type" + } + }, + "type": "object", + "required": [ + "loc", + "msg", + "type" + ], + "title": "ValidationError" + }, + "Wrapper-Input": { + "properties": { + "study": { + "$ref": "#/components/schemas/Study-Input" + }, + "usdmVersion": { + "type": "string", + "title": "Usdmversion" + }, + "systemName": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Systemname" + }, + "systemVersion": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Systemversion" + } + }, + "type": "object", + "required": [ + "study", + "usdmVersion" + ], + "title": "Wrapper" + }, + "Wrapper-Output": { + "properties": { + "study": { + "$ref": "#/components/schemas/Study-Output" + }, + "usdmVersion": { + "type": "string", + "title": "Usdmversion" + }, + "systemName": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Systemname" + }, + "systemVersion": { + "anyOf": [ + { + "type": "string" + }, + { + "type": "null" + } + ], + "title": "Systemversion" + } + }, + "type": "object", + "required": [ + "study", + "usdmVersion" + ], + "title": "Wrapper" + } + } + }, + "tags": [ + { + "name": "Production", + "description": "Routes that form the production specification." + } + ] +} \ No newline at end of file diff --git a/src/soa_builder/web/app.py b/src/soa_builder/web/app.py index 01b73ea4..aeb499eb 100644 --- a/src/soa_builder/web/app.py +++ b/src/soa_builder/web/app.py @@ -7,6 +7,7 @@ from __future__ import annotations import csv +import html as _html import io import json import logging @@ -69,6 +70,13 @@ _migrate_study_cell_add_order_index, _migrate_biomedical_concept_audit, _migrate_backfill_biomedical_concept_codes, + _migrate_add_soa_id_indexes, + _migrate_add_footnote_table, + _migrate_add_footnote_audit_table, + _migrate_matrix_cells_add_superscript, + _migrate_add_bc_surrogate_table, + _migrate_add_activity_surrogate_table, + _migrate_add_bc_surrogate_audit_table, ) from .routers import activities as activities_router from .routers import arms as arms_router @@ -87,6 +95,8 @@ from .routers import tdd as tdd_router from .routers import decision_instances as decision_instances_router from .routers import condition_assignments as condition_assignments_router +from .routers import footnotes as footnotes_router +from .routers import bc_surrogates as bc_surrogates_router from .audit import _record_element_audit @@ -138,6 +148,11 @@ def _configure_logging(): NORMALIZED_ROOT = os.environ.get("SOA_BUILDER_NORMALIZED_ROOT", "normalized") +# Set server listen port +HTTP_LISTEN_PORT = 8000 +HTTP_LISTEN_IP = "0.0.0.0" + + _concept_cache = {"data": None, "fetched_at": 0} _CONCEPT_CACHE_TTL = 60 * 60 # 1 hour TTL # SDTM dataset specializations cache (similar TTL) @@ -199,6 +214,13 @@ def _configure_logging(): _backfill_dataset_date("protocol_terminology", "protocol_terminology_audit") _migrate_biomedical_concept_audit() _migrate_backfill_biomedical_concept_codes() +_migrate_add_soa_id_indexes() +_migrate_add_footnote_table() +_migrate_add_footnote_audit_table() +_migrate_matrix_cells_add_superscript() +_migrate_add_bc_surrogate_table() +_migrate_add_activity_surrogate_table() +_migrate_add_bc_surrogate_audit_table() # Include routers @@ -220,6 +242,10 @@ def _configure_logging(): app.include_router(tdd_router.router) app.include_router(decision_instances_router.router) app.include_router(condition_assignments_router.router) +app.include_router(footnotes_router.router) +app.include_router(footnotes_router.ui_router) +app.include_router(bc_surrogates_router.router) +app.include_router(bc_surrogates_router.ui_router) def _record_visit_audit( @@ -303,72 +329,6 @@ def reorder_visits_api(soa_id: int, order: List[int]): ''' -# API functions for reordering Activities -@app.post("/soa/{soa_id}/activities/reorder", response_class=JSONResponse) -def reorder_activities_api(soa_id: int, order: List[int]): - """JSON reorder endpoint for activities.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - if not order: - raise HTTPException(400, "Order list required") - conn = _connect() - cur = conn.cursor() - cur.execute( - "SELECT id FROM activity WHERE soa_id=? ORDER BY order_index", (soa_id,) - ) - old_order = [r[0] for r in cur.fetchall()] - cur.execute("SELECT id FROM activity WHERE soa_id=?", (soa_id,)) - existing = {r[0] for r in cur.fetchall()} - if set(order) - existing: - conn.close() - raise HTTPException(400, "Order contains invalid activity id") - # Capture before state for audit detail (id -> order_index) - before_rows = { - r[0]: r[1] - for r in cur.execute( - "SELECT id, order_index FROM activity WHERE soa_id=?", (soa_id,) - ).fetchall() - } - for idx, aid in enumerate(order, start=1): - cur.execute("UPDATE activity SET order_index=? WHERE id=?", (idx, aid)) - # Prepare after state mapping prior to UID refresh - after_rows = { - r[0]: r[1] - for r in cur.execute( - "SELECT id, order_index FROM activity WHERE soa_id=?", (soa_id,) - ).fetchall() - } - # Two-phase UID reassignment to avoid UNIQUE constraint collisions during in-place changes - cur.execute( - "UPDATE activity SET activity_uid = 'TMP_' || id WHERE soa_id=?", - (soa_id,), - ) - cur.execute( - "UPDATE activity SET activity_uid = 'Activity_' || order_index WHERE soa_id=?", - (soa_id,), - ) - conn.commit() - conn.close() - _record_reorder_audit(soa_id, "activity", old_order, order) - # Activity-level audit entry capturing each id's order change list - reorder_details = [ - { - "id": aid, - "before_order_index": before_rows.get(aid), - "after_order_index": after_rows.get(aid), - } - for aid in order - ] - _record_activity_audit( - soa_id, - "reorder", - activity_id=None, - before={"old_order": old_order}, - after={"new_order": order, "details": reorder_details}, - ) - return JSONResponse({"ok": True, "old_order": old_order, "new_order": order}) - - def _list_freezes(soa_id: int): conn = _connect() cur = conn.cursor() @@ -1108,12 +1068,13 @@ def _fetch_matrix(soa_id: int): ] cur.execute( """ - SELECT instance_id, activity_id, status FROM matrix_cells WHERE soa_id=? AND instance_id IS NOT NULL + SELECT instance_id, activity_id, status, superscript FROM matrix_cells WHERE soa_id=? AND instance_id IS NOT NULL """, (soa_id,), ) cells = [ - dict(instance_id=r[0], activity_id=r[1], status=r[2]) for r in cur.fetchall() + dict(instance_id=r[0], activity_id=r[1], status=r[2], superscript=r[3]) + for r in cur.fetchall() ] conn.close() return instances, activities, cells @@ -2400,6 +2361,38 @@ def _get_activity_concepts(activity_id: int): return rows +def _get_activity_surrogates(soa_id: int, activity_id: int): + """Return (surrogates, selected_surrogate_list, selected_surrogate_uids) for concepts_cell render.""" + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name, label FROM biomedical_concept_surrogate WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + surrogates = [ + {"id": r[0], "surrogate_uid": r[1], "name": r[2], "label": r[3]} + for r in cur.fetchall() + ] + cur.execute( + "SELECT bcs.id, bcs.surrogate_uid, bcs.name, bcs.label " + "FROM activity_surrogate asr " + "JOIN biomedical_concept_surrogate bcs ON bcs.surrogate_uid=asr.surrogate_uid AND bcs.soa_id=asr.soa_id " + "JOIN activity a ON a.activity_uid=asr.activity_uid AND a.soa_id=asr.soa_id " + "WHERE asr.soa_id=? AND a.id=?", + (soa_id, activity_id), + ) + selected_surrogate_list = [ + {"id": r[0], "surrogate_uid": r[1], "name": r[2], "label": r[3]} + for r in cur.fetchall() + ] + conn.close() + return ( + surrogates, + selected_surrogate_list, + [s["surrogate_uid"] for s in selected_surrogate_list], + ) + + def _lookup_and_save_dss(soa_id: int, activity_id: int, concept_code: str) -> None: """Background task: auto-lookup DSS for a concept via CDISC API and persist.""" import os @@ -3179,6 +3172,9 @@ def ui_add_activity_concept( background_tasks.add_task(_populate_bc_properties_bg, soa_id, activity_id, code) conn.close() selected = _get_activity_concepts(activity_id) + surrogates, selected_surrogate_list, selected_surrogate_uids = ( + _get_activity_surrogates(soa_id, activity_id) + ) html = templates.get_template("concepts_cell.html").render( request=request, soa_id=soa_id, @@ -3186,6 +3182,9 @@ def ui_add_activity_concept( concepts=concepts, selected_codes=[s["code"] for s in selected], selected_list=selected, + surrogates=surrogates, + selected_surrogate_list=selected_surrogate_list, + selected_surrogate_uids=selected_surrogate_uids, edit=False, ) return HTMLResponse(html) @@ -3248,6 +3247,9 @@ def ui_remove_activity_concept( conn.close() concepts = fetch_biomedical_concepts() selected = _get_activity_concepts(activity_id) + surrogates, selected_surrogate_list, selected_surrogate_uids = ( + _get_activity_surrogates(soa_id, activity_id) + ) html = templates.get_template("concepts_cell.html").render( request=request, soa_id=soa_id, @@ -3255,6 +3257,9 @@ def ui_remove_activity_concept( concepts=concepts, selected_codes=[s["code"] for s in selected], selected_list=selected, + surrogates=surrogates, + selected_surrogate_list=selected_surrogate_list, + selected_surrogate_uids=selected_surrogate_uids, edit=False, ) return HTMLResponse(html) @@ -3353,6 +3358,44 @@ def set_cell_instance(soa_id: int, payload: dict): return {"cell_id": cid, "status": status} +def _render_cell_td( + soa_id: int, + instance_id: int, + activity_id: int, + status: str, + superscript: str | None, +) -> str: + """Build the HTML for a matrix cell, including superscript and edit button.""" + soa_id_safe = _html.escape(str(soa_id), quote=True) + instance_id_safe = _html.escape(str(instance_id), quote=True) + activity_id_safe = _html.escape(str(activity_id), quote=True) + + if status == "X": + sup_html = f"{_html.escape(superscript)}" if superscript else "" + edit_btn = ( + f'\u270e' + ) + content = f"X{sup_html}{edit_btn}" + else: + content = "" + + # Build hx-vals as JSON, then HTML-escape for safe embedding in attribute + hx_vals_json = json.dumps( + {"instance_id": instance_id, "activity_id": activity_id}, + separators=(",", ":"), + ) + hx_vals_attr = _html.escape(hx_vals_json, quote=True) + + return ( + f'{content}' + ) + + @app.post("/ui/soa/{soa_id}/toggle_cell_instance", response_class=HTMLResponse) def ui_toggle_cell_instance( request: Request, @@ -3370,16 +3413,11 @@ def ui_toggle_cell_instance( (soa_id, instance_id, activity_id), ) row = cur.fetchone() - if row and row[0] == "X": - cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) - conn.commit() - conn.close() - current = "" - elif row: + if row: cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) conn.commit() conn.close() - current = "" + return HTMLResponse(_render_cell_td(soa_id, instance_id, activity_id, "", None)) else: cur.execute( "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", @@ -3387,9 +3425,9 @@ def ui_toggle_cell_instance( ) conn.commit() conn.close() - current = "X" - cell_html = f'{current}' - return HTMLResponse(cell_html) + return HTMLResponse( + _render_cell_td(soa_id, instance_id, activity_id, "X", None) + ) # API endpoint for exporting the Matrix as XLSX @@ -3445,6 +3483,23 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = conn.close() visits, activities, _cells = _fetch_matrix(soa_id) activity_ids_in_order = [a["id"] for a in activities] + # Fetch BC surrogates per activity + conn_s = _connect() + cur_s = conn_s.cursor() + cur_s.execute( + "SELECT a.id, bcs.surrogate_uid, bcs.name, bcs.label " + "FROM activity_surrogate asr " + "JOIN activity a ON a.activity_uid=asr.activity_uid AND a.soa_id=asr.soa_id " + "JOIN biomedical_concept_surrogate bcs ON bcs.surrogate_uid=asr.surrogate_uid AND bcs.soa_id=asr.soa_id " + "WHERE asr.soa_id=?", + (soa_id,), + ) + surrogates_map: dict = {} + for _aid, _sur_uid, _sur_name, _sur_label in cur_s.fetchall(): + surrogates_map.setdefault(_aid, []).append( + {"surrogate_uid": _sur_uid, "name": _sur_name, "label": _sur_label} + ) + conn_s.close() # Build display strings using EffectiveTitle (override if present) and show code in parentheses concepts_strings = [] concept_titles_strings = [] # For Concept UIDs column, show titles with UIDs @@ -3468,9 +3523,34 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = else: titles_with_uids.append(title) concept_titles_strings.append("; ".join(titles_with_uids)) + surrogates_strings = [] + for aid in activity_ids_in_order: + slist = surrogates_map.get(aid, []) + if not slist: + surrogates_strings.append("") + else: + surrogates_strings.append( + "; ".join( + [ + f"[S] {s['label'] or s['name']} ({s['surrogate_uid']})" + for s in slist + ] + ) + ) + combined_uid_strings = [] + for _i in range(len(activity_ids_in_order)): + _parts = [ + _p for _p in [concept_titles_strings[_i], surrogates_strings[_i]] if _p + ] + combined_uid_strings.append("; ".join(_parts)) if len(concepts_strings) == len(df): df.insert(1, "Concepts", concepts_strings) - df["Concept UIDs"] = concept_titles_strings + df["Concept UIDs"] = combined_uid_strings + if len(surrogates_strings) == len(df): + concepts_col_idx = ( + df.columns.get_loc("Concepts") + 1 if "Concepts" in df.columns else 1 + ) + df.insert(concepts_col_idx, "Surrogates", surrogates_strings) # Build concept mappings sheet data mapping_rows = [] for a in activities: @@ -3511,6 +3591,18 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = "ConceptUID", ], ) + # Build BC surrogate mappings sheet data + surrogate_mapping_rows = [] + for a in activities: + aid = a["id"] + for s in surrogates_map.get(aid, []): + surrogate_mapping_rows.append( + [aid, a["name"], s["surrogate_uid"], s["name"], s["label"]] + ) + surrogate_mapping_df = pd.DataFrame( + surrogate_mapping_rows, + columns=["ActivityID", "ActivityName", "SurrogateUID", "Name", "Label"], + ) # Build rollback audit sheet data (optional) audit_rows = ( _list_rollback_audit(soa_id) if "_list_rollback_audit" in globals() else [] @@ -3670,6 +3762,9 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = with pd.ExcelWriter(bio, engine="openpyxl") as writer: study_df.to_excel(writer, index=False, sheet_name="Study") mapping_df.to_excel(writer, index=False, sheet_name="ConceptMappings") + surrogate_mapping_df.to_excel( + writer, index=False, sheet_name="SurrogateMappings" + ) audit_df.to_excel(writer, index=False, sheet_name="RollbackAudit") if concept_diff_df is not None: concept_diff_df.to_excel(writer, index=False, sheet_name="ConceptDiff") @@ -3711,7 +3806,14 @@ def export_xlsx(soa_id: int, left: Optional[int] = None, right: Optional[int] = # Add concepts columns if len(concepts_strings) == len(df_tl): df_tl.insert(1, "Concepts", concepts_strings) - df_tl["Concept UIDs"] = concept_titles_strings + df_tl["Concept UIDs"] = combined_uid_strings + if len(surrogates_strings) == len(df_tl): + _sur_col_idx = ( + df_tl.columns.get_loc("Concepts") + 1 + if "Concepts" in df_tl.columns + else 1 + ) + df_tl.insert(_sur_col_idx, "Surrogates", surrogates_strings) # Sanitize sheet name (max 31 chars, no special chars) sheet_name = f"SoA - {timeline_name}"[:31] @@ -4037,7 +4139,7 @@ def import_matrix(soa_id: int, payload: MatrixImport): next_order += 1 if has_activity_uid: cols.append("activity_uid") - vals.append(f"Activity_{soa_id}_{next_order}") + vals.append(activities_router._next_activity_uid(cur, soa_id)) cur.execute( f"INSERT INTO activity ({','.join(cols)}) VALUES ({','.join(['?'] * len(vals))})", vals, @@ -4076,17 +4178,6 @@ def _reindex(table: str, soa_id: int): ids = [r[0] for r in cur.fetchall()] for idx, _id in enumerate(ids, start=1): cur.execute(f"UPDATE {table} SET order_index=? WHERE id=?", (idx, _id)) - # Maintain activity_uid after any activity reindex - if table == "activity": - # Two-phase UID refresh to satisfy UNIQUE(soa_id, activity_uid) without transient collisions - cur.execute( - "UPDATE activity SET activity_uid = 'TMP_' || id WHERE soa_id=?", - (soa_id,), - ) - cur.execute( - "UPDATE activity SET activity_uid = 'Activity_' || order_index WHERE soa_id=?", - (soa_id,), - ) conn.commit() conn.close() @@ -4179,7 +4270,7 @@ def ui_add_activity(request: Request, soa_id: int, name: str = Form(...)): order_index = cur.fetchone()[0] + 1 cur.execute( "INSERT INTO activity (soa_id,name,order_index,activity_uid) VALUES (?,?,?,?)", - (soa_id, nm, order_index, f"Activity_{order_index}"), + (soa_id, nm, order_index, activities_router._next_activity_uid(cur, soa_id)), ) aid = cur.lastrowid conn.commit() @@ -4348,6 +4439,9 @@ def ui_edit(request: Request, soa_id: int): activities_page = activities # Build cell lookup cell_map = {(c["instance_id"], c["activity_id"]): c["status"] for c in cells} + superscript_map = { + (c["instance_id"], c["activity_id"]): c.get("superscript") for c in cells + } concepts = fetch_biomedical_concepts() activity_ids = [a["id"] for a in activities_page] activity_concepts = {} @@ -4368,6 +4462,29 @@ def ui_edit(request: Request, soa_id: int): for aid, code, title in cur.fetchall(): activity_concepts.setdefault(aid, []).append({"code": code, "title": title}) conn.close() + # Fetch per-activity surrogate mappings for the matrix view + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT a.id, bcs.id, bcs.surrogate_uid, bcs.name, bcs.label " + "FROM activity_surrogate asr " + "JOIN activity a ON a.activity_uid=asr.activity_uid AND a.soa_id=asr.soa_id " + "JOIN biomedical_concept_surrogate bcs ON bcs.surrogate_uid=asr.surrogate_uid AND bcs.soa_id=asr.soa_id " + "WHERE asr.soa_id=?", + (soa_id,), + ) + activity_surrogates: dict = {} + for row in cur.fetchall(): + aid, sur_id, sur_uid, sur_name, sur_label = row + activity_surrogates.setdefault(aid, []).append( + { + "id": sur_id, + "surrogate_uid": sur_uid, + "name": sur_name, + "label": sur_label, + } + ) + conn.close() concepts_diag = { "count": len(_concept_cache.get("data") or []), "last_status": _concept_cache.get("last_status"), @@ -4642,6 +4759,28 @@ def ui_edit(request: Request, soa_id: int): if not default_timeline and "unassigned" in instances_by_timeline: default_timeline = "unassigned" + # Load footnotes for display below matrix + conn_fn = _connect() + cur_fn = conn_fn.cursor() + cur_fn.execute( + "SELECT id,soa_id,footnote_uid,name,label,description,text,dictionary_uid FROM footnote WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + footnotes = [ + dict( + id=r[0], + soa_id=r[1], + footnote_uid=r[2], + name=r[3], + label=r[4], + description=r[5], + text=r[6], + dictionary_uid=r[7], + ) + for r in cur_fn.fetchall() + ] + conn_fn.close() + instances_crud = instances_router.list_instances(soa_id) encounter_options = get_encounter_id(soa_id) epoch_options = get_epoch_uid(soa_id) @@ -4666,6 +4805,7 @@ def ui_edit(request: Request, soa_id: int): "cell_map": cell_map, "concepts": concepts, "activity_concepts": activity_concepts, + "activity_surrogates": activity_surrogates, "concepts_empty": len(concepts) == 0, "concepts_diag": concepts_diag, "concepts_last_fetch_iso": last_fetch_iso, @@ -4685,6 +4825,8 @@ def ui_edit(request: Request, soa_id: int): "timelines": timelines, "instances_by_timeline": instances_by_timeline, "default_timeline": default_timeline, + "footnotes": footnotes, + "superscript_map": superscript_map, }, ) @@ -5526,6 +5668,9 @@ def ui_set_activity_concepts( ) selected = [{"code": c, "title": t} for c, t in cur.fetchall()] conn.close() + surrogates, selected_surrogate_list, selected_surrogate_uids = ( + _get_activity_surrogates(soa_id, activity_id) + ) html = templates.get_template("concepts_cell.html").render( request=request, soa_id=soa_id, @@ -5533,6 +5678,9 @@ def ui_set_activity_concepts( concepts=concepts, selected_codes=[s["code"] for s in selected], selected_list=selected, + surrogates=surrogates, + selected_surrogate_list=selected_surrogate_list, + selected_surrogate_uids=selected_surrogate_uids, edit=False, ) return HTMLResponse(html) @@ -5570,6 +5718,9 @@ def ui_activity_concepts_cell( ) selected = [{"code": c, "title": t} for c, t in cur.fetchall()] conn.close() + surrogates, selected_surrogate_list, selected_surrogate_uids = ( + _get_activity_surrogates(soa_id, activity_id) + ) return HTMLResponse( templates.get_template("concepts_cell.html").render( request=request, @@ -5578,6 +5729,9 @@ def ui_activity_concepts_cell( concepts=concepts, selected_codes=[s["code"] for s in selected], selected_list=selected, + surrogates=surrogates, + selected_surrogate_list=selected_surrogate_list, + selected_surrogate_uids=selected_surrogate_uids, edit=bool(edit), ) ) @@ -5625,7 +5779,9 @@ def ui_toggle_cell( cur.execute("DELETE FROM matrix_cells WHERE id=?", (row[1],)) conn.commit() conn.close() - current = "" + return HTMLResponse( + _render_cell_td(soa_id, int(instance_id), activity_id, "", None) + ) else: cur.execute( "INSERT INTO matrix_cells (soa_id, instance_id, activity_id, status) VALUES (?,?,?,?)", @@ -5633,12 +5789,9 @@ def ui_toggle_cell( ) conn.commit() conn.close() - current = "X" - cell_html = ( - f'{current}' - ) + return HTMLResponse( + _render_cell_td(soa_id, int(instance_id), activity_id, "X", None) + ) else: # Legacy visit-based toggle if visit_id is None: @@ -5662,6 +5815,7 @@ def ui_toggle_cell( conn.commit() conn.close() current = "X" + # Legacy path: visit-based cells don't have superscript support cell_html = ( f' for superscript inline editing.""" + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT superscript FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, instance_id, activity_id), + ) + row = cur.fetchone() + conn.close() + if not row: + raise HTTPException(404, "Cell not found") + sup_val = _html.escape(row[0] or "", quote=True) + html = ( + f'' + f"X" + f'
' + f'' + f'' + f"
" + f'✕' + f"" + ) + return HTMLResponse(html) + + +@app.post( + "/ui/soa/{soa_id}/cell_superscript/{instance_id}/{activity_id}", + response_class=HTMLResponse, +) +def ui_cell_superscript_save( + request: Request, + soa_id: int, + instance_id: int, + activity_id: int, + superscript: Optional[str] = Form(None), +): + """Save superscript value for a cell and return rendered .""" + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + # Normalise empty string to NULL + sup_val = superscript.strip() if superscript else None + conn = _connect() + cur = conn.cursor() + cur.execute( + "UPDATE matrix_cells SET superscript=? WHERE soa_id=? AND instance_id=? AND activity_id=?", + (sup_val, soa_id, instance_id, activity_id), + ) + # If no rows were updated, the target cell does not exist (or does not belong to this SOA) + if cur.rowcount == 0: + conn.close() + raise HTTPException(404, "Matrix cell not found") + # Read back the actual status and superscript from the database to render an accurate cell + cur.execute( + "SELECT status, superscript FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, instance_id, activity_id), + ) + row = cur.fetchone() + conn.commit() + conn.close() + status = row[0] if row else "" + sup_val_db = row[1] if row else None + return HTMLResponse( + _render_cell_td(soa_id, instance_id, activity_id, status or "", sup_val_db) + ) + + +@app.get( + "/ui/soa/{soa_id}/cell_superscript_view/{instance_id}/{activity_id}", + response_class=HTMLResponse, +) +def ui_cell_superscript_view( + request: Request, + soa_id: int, + instance_id: int, + activity_id: int, +): + """Return rendered (view-mode) — used for cancel.""" + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT status, superscript FROM matrix_cells WHERE soa_id=? AND instance_id=? AND activity_id=?", + (soa_id, instance_id, activity_id), + ) + row = cur.fetchone() + conn.close() + status = row[0] if row else "" + sup_val = row[1] if row else None + return HTMLResponse( + _render_cell_td(soa_id, instance_id, activity_id, status or "", sup_val) + ) + + # UI endpoint for associating a Transition Start Rule with Visit/Encounter (visit.transitionStartRule) @app.post( "/ui/soa/{soa_id}/set_visit_transition_start_rule", response_class=HTMLResponse @@ -6108,6 +6373,17 @@ def load_ddf_terminology( return {"columns": sanitized, "row_count": len(records)} +def _validate_terminology_path(file_path: str, project_root: str) -> str: + safe_root = os.path.realpath(os.path.join(project_root, "files")) + resolved = os.path.realpath(file_path) + if not resolved.startswith(safe_root + os.sep) and resolved != safe_root: + raise HTTPException( + 400, + f"file_path must be within the project files directory. Got: {file_path}", + ) + return resolved + + # UI endpoint to load DDF Terminology @app.post("/admin/load_ddf_terminology") def admin_load_ddf( @@ -6130,7 +6406,7 @@ def admin_load_ddf( ] # If explicit file_path provided, prefer it if file_path: - fp = file_path + fp = _validate_terminology_path(file_path, project_root) else: fp = None for c in candidates: @@ -6716,7 +6992,7 @@ def admin_load_protocol( os.path.join(project_root, "files", "Protocol_Terminology_2025-09-26.xls"), ] if file_path: - fp = file_path + fp = _validate_terminology_path(file_path, project_root) else: fp = None for c in candidates: @@ -7153,1115 +7429,13 @@ def ui_protocol_audit( def main(): import uvicorn - uvicorn.run("soa_builder.web.app:app", host="0.0.0.0", port=8000, reload=True) + uvicorn.run( + "soa_builder.web.app:app", + host=HTTP_LISTEN_IP, + port=HTTP_LISTEN_PORT, + reload=True, + ) if __name__ == "__main__": main() - - -# Deprecated (Moved to routers/epochs.py) -""" -def _record_epoch_audit( - soa_id: int, - action: str, - epoch_id: Optional[int], - before: Optional[dict] = None, - after: Optional[dict] = None, -): - try: - conn = _connect() - cur = conn.cursor() - cur.execute( - "INSERT INTO epoch_audit (soa_id, epoch_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", - ( - soa_id, - epoch_id, - action, - json.dumps(before) if before else None, - json.dumps(after) if after else None, - datetime.now(timezone.utc).isoformat(), - ), - ) - conn.commit() - conn.close() - except Exception as e: # pragma: no cover - logger.warning("Failed recording epoch audit: %s", e) -""" -# Moved to routers/epochs.py -''' -@app.delete("/soa/{soa_id}/epochs/{epoch_id}") -def delete_epoch(soa_id: int, epoch_id: int): - """Delete an Epoch from an SoA.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT 1 FROM epoch WHERE id=? AND soa_id=?", (epoch_id, soa_id)) - if not cur.fetchone(): - conn.close() - raise HTTPException(404, "Epoch not found") - cur.execute( - "SELECT id,name,order_index,epoch_seq,epoch_label,epoch_description FROM epoch WHERE id=?", - (epoch_id,), - ) - b = cur.fetchone() - before = None - if b: - before = { - "id": b[0], - "name": b[1], - "order_index": b[2], - "epoch_seq": b[3], - "epoch_label": b[4], - "epoch_description": b[5], - } - # Include current type in before snapshot - try: - cur.execute("SELECT type FROM epoch WHERE id=?", (epoch_id,)) - tr = cur.fetchone() - if before is not None: - before["type"] = tr[0] if tr else None - except Exception: - pass - # Clear visit epoch references to avoid dangling links - try: - cur.execute( - "UPDATE visit SET epoch_id=NULL WHERE soa_id=? AND epoch_id=?", - (soa_id, epoch_id), - ) - except Exception: - pass - # Delete the epoch row - cur.execute("DELETE FROM epoch WHERE id=?", (epoch_id,)) - conn.commit() - conn.close() - _reindex("epoch", soa_id) - _record_epoch_audit(soa_id, "delete", epoch_id, before=before, after=None) - return {"deleted_epoch_id": epoch_id} -''' - -# # UI endpoint for reordering Epochs <- moved to routers/epochs.py -''' -@app.post("/ui/soa/{soa_id}/reorder_epochs", response_class=HTMLResponse) -def ui_reorder_epochs(request: Request, soa_id: int, order: str = Form("")): - """Form handler to persist new epoch ordering.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - ids = [int(x) for x in order.split(",") if x.strip().isdigit()] - if not ids: - return HTMLResponse("Invalid order", status_code=400) - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT id FROM epoch WHERE soa_id=? ORDER BY order_index", (soa_id,)) - old_order = [r[0] for r in cur.fetchall()] - cur.execute("SELECT id FROM epoch WHERE soa_id=?", (soa_id,)) - existing = {r[0] for r in cur.fetchall()} - if set(ids) - existing: - conn.close() - return HTMLResponse("Order contains invalid epoch id", status_code=400) - for idx, eid in enumerate(ids, start=1): - cur.execute("UPDATE epoch SET order_index=? WHERE id=?", (idx, eid)) - conn.commit() - conn.close() - _record_reorder_audit(soa_id, "epoch", old_order, ids) - - # Also record epoch-specific reorder audit for parity with JSON endpoint - def _epoch_types_snapshot(soa_id_int: int) -> list[dict]: - conn_s = _connect() - cur_s = conn_s.cursor() - cur_s.execute( - "SELECT id,type FROM epoch WHERE soa_id=? ORDER BY order_index", - (soa_id_int,), - ) - rows = cur_s.fetchall() - conn_s.close() - return [{"id": rid, "type": rtype} for rid, rtype in rows] - - _record_epoch_audit( - soa_id, - "reorder", - epoch_id=None, - before={ - "old_order": old_order, - "types": _epoch_types_snapshot(soa_id), - }, - after={"new_order": ids}, - ) - return HTMLResponse("OK") -''' -# UI endpoint for deleting an Epoch <- moved to routers/epochs.py -''' -@app.post("/ui/soa/{soa_id}/delete_epoch", response_class=HTMLResponse) -def ui_delete_epoch(request: Request, soa_id: int, epoch_id: int = Form(...)): - """Form handler to delete an Epoch.""" - delete_epoch(soa_id, epoch_id) - return HTMLResponse( - f"" - ) -''' - -# UI endpoint for reordering Encounters/Visits <- Deprecated -''' -@app.post("/ui/soa/{soa_id}/reorder_visits", response_class=HTMLResponse) -def ui_reorder_visits(request: Request, soa_id: int, order: str = Form("")): - """Persist new visit ordering. 'order' is a comma-separated list of visit IDs in desired order.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - ids = [int(x) for x in order.split(",") if x.strip().isdigit()] - if not ids: - return HTMLResponse("Invalid order", status_code=400) - conn = _connect() - cur = conn.cursor() - # Capture existing order BEFORE modifications - cur.execute("SELECT id FROM visit WHERE soa_id=? ORDER BY order_index", (soa_id,)) - old_order = [r[0] for r in cur.fetchall()] - # Validate membership - cur.execute("SELECT id FROM visit WHERE soa_id=?", (soa_id,)) - existing = {r[0] for r in cur.fetchall()} - if set(ids) - existing: - conn.close() - return HTMLResponse("Order contains invalid visit id", status_code=400) - # Apply new order indices - for idx, vid in enumerate(ids, start=1): - cur.execute("UPDATE visit SET order_index=? WHERE id=?", (idx, vid)) - conn.commit() - conn.close() - _record_reorder_audit(soa_id, "visit", old_order, ids) - return HTMLResponse("OK") -''' -# UI endpoint for updating an Encounter/Visit <- moved to routers/visits.py -''' -@app.post("/ui/soa/{soa_id}/update_visit", response_class=HTMLResponse) -def ui_update_visit( - request: Request, - soa_id: int, - visit_id: int = Form(...), - name: Optional[str] = Form(None), - label: Optional[str] = Form(None), - description: Optional[str] = Form(None), -): - """Form handler to update a Visit's mutable fields (name/label/description).""" - # Build payload with provided fields; blanks should clear values - payload = VisitUpdate( - name=name, - label=label, - description=description, - ) - try: - visits_router.update_visit(soa_id, visit_id, payload) - except Exception: - # Let redirect proceed; detailed errors will appear in API logs - pass - return HTMLResponse( - f"" - ) -''' -# UI code to delete an Encounter/Visit from an SOA <- moved to routers/visits.py -""" -@app.post("/ui/soa/{soa_id}/delete_visit", response_class=HTMLResponse) -def ui_delete_visit(request: Request, soa_id: int, visit_id: int = Form(...)): - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - - try: - # Call through router to avoid stale import bindings - visits_router.delete_visit(soa_id, visit_id) - except HTTPException: - # swallow 404 to keep UX smooth - pass - # If HTMX, use HX-Redirect; else script redirect - if request.headers.get("HX-Request") == "true": - return HTMLResponse("", headers={"HX-Redirect": f"/ui/soa/{int(soa_id)}/edit"}) - return HTMLResponse( - f"" - ) -""" - - -# UI endpoint for associating an Epoch with a Visit/Encounter <- Deprecated (Visits are not directly related to an Epoch) -''' -@app.post("/ui/soa/{soa_id}/set_visit_epoch", response_class=HTMLResponse) -def ui_set_visit_epoch( - request: Request, - soa_id: int, - visit_id: int = Form(...), - epoch_id_raw: str = Form(""), # new field name (blank means clear) - epoch_id: str = Form(""), # legacy field name used by template select -): - """Form handler to associate an Epoch with a Visit/Encounter.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - # Determine provided raw value (prefer epoch_id_raw if non-blank) - raw_val = (epoch_id_raw or "").strip() or (epoch_id or "").strip() - parsed_epoch: Optional[int] = None - if raw_val: - if raw_val.isdigit(): - parsed_epoch = int(raw_val) - else: - raise HTTPException(400, "Invalid epoch_id value") - conn = _connect() - cur = conn.cursor() - cur.execute( - "SELECT id,name,label,order_index,epoch_id,encounter_uid,description FROM visit WHERE id=? AND soa_id=?", - (visit_id, soa_id), - ) - row = cur.fetchone() - if not row: - conn.close() - raise HTTPException(404, "Visit not found") - before = { - "id": row[0], - "name": row[1], - "label": row[2], - "order_index": row[3], - "epoch_id": row[4], - "encounter_uid": row[5], - "description": row[6], - } - if parsed_epoch is not None: - cur.execute( - "SELECT 1 FROM epoch WHERE id=? AND soa_id=?", (parsed_epoch, soa_id) - ) - if not cur.fetchone(): - conn.close() - raise HTTPException(400, "Invalid epoch_id for this SOA") - cur.execute("UPDATE visit SET epoch_id=? WHERE id=?", (parsed_epoch, visit_id)) - conn.commit() - """ - logger.info( - "ui_set_visit_epoch updated visit id=%s soa_id=%s epoch_id=%s raw_val='%s' db_path=%s", - visit_id, - soa_id, - parsed_epoch, - raw_val, - DB_PATH, - ) - """ - # Fetch after and record audit - cur.execute( - "SELECT id,name,label,order_index,epoch_id,encounter_uid,description FROM visit WHERE id=? AND soa_id=?", - (visit_id, soa_id), - ) - r = cur.fetchone() - after = { - "id": r[0], - "name": r[1], - "label": r[2], - "order_index": r[3], - "epoch_id": r[4], - "encounter_uid": r[5], - "description": r[6], - } - updated_fields = [ - f for f in ["epoch_id"] if (before.get(f) or None) != (after.get(f) or None) - ] - _record_visit_audit( - soa_id, - "update", - visit_id, - before=before, - after={**after, "updated_fields": updated_fields}, - ) - conn.close() - return HTMLResponse( - f"" - ) -''' -# UI endpoint for adding a new Epoch <- moved to routers/epochs.py -''' -@app.post("/ui/soa/{soa_id}/add_epoch", response_class=HTMLResponse) -def ui_add_epoch( - request: Request, - soa_id: int, - name: str = Form(...), - epoch_label: Optional[str] = Form(None), - epoch_description: Optional[str] = Form(None), - epoch_type_submission_value: Optional[str] = Form(None), -): - """Form handler to add an Epoch.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT COUNT(*) FROM epoch WHERE soa_id=?", (soa_id,)) - order_index = cur.fetchone()[0] + 1 - cur.execute("SELECT MAX(epoch_seq) FROM epoch WHERE soa_id=?", (soa_id,)) - row = cur.fetchone() - next_seq = (row[0] or 0) + 1 - # Optional epoch type mapping via code junction (C99079) using API-only map - epoch_type_submission_value = (epoch_type_submission_value or "").strip() or None - selected_code_uid = None - if epoch_type_submission_value: - try: - from .utils import load_epoch_type_map, get_epoch_parent_package_href_cached - - epoch_map = load_epoch_type_map() - except Exception: - epoch_map = {} - # Invert map to find conceptId by submissionValue - concept_id = None - for cid, sv in (epoch_map or {}).items(): - if sv and sv.strip().lower() == epoch_type_submission_value.strip().lower(): - concept_id = cid - break - if concept_id: - # Create a new Code_N for this conceptId under C99079 (API-only) - code_uid = _get_next_code_uid(cur, soa_id) - try: - parent_href = get_epoch_parent_package_href_cached() or None - except Exception: - parent_href = None - cur.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - code_uid, - parent_href, - "C99079", - concept_id, - ), - ) - selected_code_uid = code_uid - cur.execute( - "INSERT INTO epoch (soa_id,name,order_index,epoch_seq,epoch_label,epoch_description,type) VALUES (?,?,?,?,?,?,?)", - ( - soa_id, - name, - order_index, - next_seq, - (epoch_label or "").strip() or None, - (epoch_description or "").strip() or None, - selected_code_uid, - ), - ) - eid = cur.lastrowid - conn.commit() - conn.close() - _record_epoch_audit( - soa_id, - "create", - eid, - before={"type": None}, - after={ - "id": eid, - "name": name, - "order_index": order_index, - "epoch_seq": next_seq, - "epoch_label": (epoch_label or "").strip() or None, - "epoch_description": (epoch_description or "").strip() or None, - "type": selected_code_uid, - }, - ) - return HTMLResponse( - f"" - ) -''' - -# UI endpoint for updating an Epoch <- moved to routers/epochs.py -''' -@app.post("/ui/soa/{soa_id}/update_epoch", response_class=HTMLResponse) -def ui_update_epoch( - request: Request, - soa_id: int, - epoch_id: int = Form(...), - name: Optional[str] = Form(None), - epoch_label: Optional[str] = Form(None), - epoch_description: Optional[str] = Form(None), - epoch_type_submission_value: Optional[str] = Form(None), -): - """Form handler to update an existing Epoch.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT 1 FROM epoch WHERE id=? AND soa_id=?", (epoch_id, soa_id)) - if not cur.fetchone(): - conn.close() - raise HTTPException(404, "Epoch not found") - conn.close() - # Capture before - conn_b = _connect() - cur_b = conn_b.cursor() - cur_b.execute( - "SELECT id,name,order_index,epoch_seq,epoch_label,epoch_description FROM epoch WHERE id=?", - (epoch_id,), - ) - b = cur_b.fetchone() - conn_b.close() - before = None - if b: - before = { - "id": b[0], - "name": b[1], - "order_index": b[2], - "epoch_seq": b[3], - "epoch_label": b[4], - "epoch_description": b[5], - } - # Include current type in before snapshot for audit - try: - conn_bt = _connect() - cur_bt = conn_bt.cursor() - cur_bt.execute("SELECT type FROM epoch WHERE id=?", (epoch_id,)) - br = cur_bt.fetchone() - conn_bt.close() - if before is not None: - before["type"] = br[0] if br else None - except Exception: - pass - sets = [] - vals: list[Any] = [] - if name is not None: - sets.append("name=?") - vals.append((name or "").strip() or None) - if epoch_label is not None: - sets.append("epoch_label=?") - vals.append((epoch_label or "").strip() or None) - if epoch_description is not None: - sets.append("epoch_description=?") - vals.append((epoch_description or "").strip() or None) - # Handle epoch type mapping via code junction (C99079) using API-only map - epoch_type_submission_value = (epoch_type_submission_value or "").strip() or None - if epoch_type_submission_value is not None: - # If empty string provided, clear type - if epoch_type_submission_value == "": - sets.append("type=?") - vals.append(None) - else: - # Resolve submission value to conceptId via API-only map - try: - from .utils import ( - load_epoch_type_map, - get_epoch_parent_package_href_cached, - ) - - epoch_map = load_epoch_type_map() - except Exception: - epoch_map = {} - concept_id = None - for cid, sv in (epoch_map or {}).items(): - if ( - sv - and sv.strip().lower() - == epoch_type_submission_value.strip().lower() - ): - concept_id = cid - break - selected_code_uid = None - if concept_id: - conn_t = _connect() - cur_t = conn_t.cursor() - # Always create a new Code_N for C99079 selections (no reuse) - code_uid = _get_next_code_uid(cur_t, soa_id) - try: - parent_href = get_epoch_parent_package_href_cached() or None - except Exception: - parent_href = None - cur_t.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - code_uid, - parent_href, - "C99079", - concept_id, - ), - ) - selected_code_uid = code_uid - conn_t.commit() - conn_t.close() - # Persist epoch.type even if concept_id not found will be None - sets.append("type=?") - vals.append(selected_code_uid) - if sets: - conn_u = _connect() - cur_u = conn_u.cursor() - vals.append(epoch_id) - cur_u.execute(f"UPDATE epoch SET {', '.join(sets)} WHERE id=?", vals) - conn_u.commit() - conn_u.close() - conn_a = _connect() - cur_a = conn_a.cursor() - cur_a.execute( - "SELECT id,name,order_index,epoch_seq,epoch_label,epoch_description FROM epoch WHERE id=?", - (epoch_id,), - ) - r = cur_a.fetchone() - conn_a.close() - after_api = { - "id": r[0], - "name": r[1], - "order_index": r[2], - "epoch_seq": r[3], - "epoch_label": r[4], - "epoch_description": r[5], - "type": None, - } - # Fetch type from epoch for audit after snapshot - conn_ta = _connect() - cur_ta = conn_ta.cursor() - cur_ta.execute("SELECT type FROM epoch WHERE id=?", (epoch_id,)) - tr_after = cur_ta.fetchone() - conn_ta.close() - if tr_after: - after_api["type"] = tr_after[0] - _record_epoch_audit( - soa_id, - "update", - epoch_id, - before=before, - after=after_api, - ) - return HTMLResponse( - f"" - ) -''' - -# UI endpoint for creating an Encounter/Visit <- Deprecated (moved to routers/visits.py) -""" -@app.post("/ui/soa/{soa_id}/add_visit", response_class=HTMLResponse) -def ui_add_visit( - request: Request, - soa_id: int, - name: str = Form(...), - label: Optional[str] = Form(None), - epoch_id: Optional[str] = Form(None), - description: Optional[str] = Form(None), -): - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - - # Coerce empty epoch_id from form to None, otherwise to int - parsed_epoch_id: Optional[int] = None - if epoch_id is not None: - eid = str(epoch_id).strip() - if eid: - try: - parsed_epoch_id = int(eid) - except ValueError: - parsed_epoch_id = None - - payload = VisitCreate( - name=name, - label=label, - epoch_id=parsed_epoch_id, - description=description, - ) - # Create the visit via the API helper to ensure audits and ordering - try: - visits_router.add_visit(soa_id, payload) - except Exception: - pass - - return HTMLResponse( - f"" - ) -""" - - -# UI endpoint for adding a new Arm <- Deprecated (moved to routers/arms.py) -''' -@app.post("/ui/soa/{soa_id}/add_arm", response_class=HTMLResponse) -async def ui_add_arm( - request: Request, - soa_id: int, - name: str = Form(...), - label: Optional[str] = Form(None), - description: Optional[str] = Form(None), - element_id: Optional[str] = Form(None), -): - """Form handler to create a new Arm.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - # Accept blank/empty element selection gracefully. The form may submit "" which would 422 with Optional[int]. - eid = int(element_id) if element_id and element_id.strip().isdigit() else None - payload = ArmCreate(name=name, label=label, description=description, element_id=eid) - # Create base arm (function may not return id; fetch if needed) - created = create_arm(soa_id, payload) - # routers.arms.create_arm returns a row dict; extract id - new_arm_id = None - try: - if isinstance(created, dict): - new_arm_id = created.get("id") - elif isinstance(created, int): - new_arm_id = created - except Exception: - new_arm_id = None - if not new_arm_id: - try: - conn_tmp = _connect() - cur_tmp = conn_tmp.cursor() - cur_tmp.execute( - "SELECT id FROM arm WHERE soa_id=? ORDER BY id DESC LIMIT 1", - (soa_id,), - ) - rtmp = cur_tmp.fetchone() - new_arm_id = rtmp[0] if rtmp else None - conn_tmp.close() - except Exception: - new_arm_id = None - if not new_arm_id: - return HTMLResponse( - f"", - status_code=500, - ) - # Read optional type fields with hyphenated names - try: - form_data = await request.form() - arm_type_submission = (form_data.get("arm-type") or "").strip() - data_origin_type_submission = (form_data.get("data-origin-type") or "").strip() - except Exception: - arm_type_submission = "" - data_origin_type_submission = "" - - # If type selections provided, resolve to terminology codes and persist via junction table - if arm_type_submission or data_origin_type_submission: - conn = _connect() - cur = conn.cursor() - logger.info( - "ui_add_arm: received type selections arm-type='%s', data-origin-type='%s' for soa_id=%s arm_id=%s", - arm_type_submission, - data_origin_type_submission, - soa_id, - new_arm_id, - ) - new_type_uid: Optional[str] = None - new_data_origin_uid: Optional[str] = None - if arm_type_submission: - cur.execute( - "SELECT code FROM protocol_terminology WHERE codelist_code='C174222' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", - (arm_type_submission, arm_type_submission), - ) - r = cur.fetchone() - resolved_code = r[0] if r else None - if resolved_code is None: - logger.warning( - "ui_add_arm: unknown arm type submission '%s' for soa_id=%s", - arm_type_submission, - soa_id, - ) - conn.close() - return HTMLResponse( - f"", - status_code=400, - ) - # Create Code_N - new_type_uid = _get_next_code_uid(cur, soa_id) - cur.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - new_type_uid, - "protocol_terminology", - "C174222", - resolved_code, - ), - ) - logger.info( - "ui_add_arm: created code junction %s -> table=%s list=%s code=%s", - new_type_uid, - "protocol_terminology", - "C174222", - resolved_code, - ) - if data_origin_type_submission: - cur.execute( - "SELECT code FROM ddf_terminology WHERE codelist_code='C188727' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", - (data_origin_type_submission, data_origin_type_submission), - ) - r2 = cur.fetchone() - resolved_ddf_code = r2[0] if r2 else None - if resolved_ddf_code is None: - logger.warning( - "ui_add_arm: unknown data origin type submission '%s' for soa_id=%s", - data_origin_type_submission, - soa_id, - ) - conn.close() - # Properly escape the value for safety in HTML/JS context - escaped_selection = json.dumps(data_origin_type_submission) - return HTMLResponse( - f"", - status_code=400, - ) - # Create Code_N (continue numbering) - new_data_origin_uid = _get_next_code_uid(cur, soa_id) - cur.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - new_data_origin_uid, - "ddf_terminology", - "C188727", - resolved_ddf_code, - ), - ) - logger.info( - "ui_add_arm: created code junction %s -> table=%s list=%s code=%s", - new_data_origin_uid, - "ddf_terminology", - "C188727", - resolved_ddf_code, - ) - # Update arm row with new code_uids - if new_type_uid or new_data_origin_uid: - cur.execute( - "UPDATE arm SET type=COALESCE(?, type), data_origin_type=COALESCE(?, data_origin_type) WHERE id=? AND soa_id=?", - (new_type_uid, new_data_origin_uid, new_arm_id, soa_id), - ) - logger.info( - "ui_add_arm: updated arm id=%s set type=%s data_origin_type=%s", - new_arm_id, - new_type_uid, - new_data_origin_uid, - ) - conn.commit() - # routers.arms.create_arm already records a create audit; avoid duplicating here - conn.close() - return HTMLResponse( - f"" - ) -''' - -# UI endpoint for updating an Arm <- Deprecated (moved to routers/arms.py) -''' -@app.post("/ui/soa/{soa_id}/update_arm", response_class=HTMLResponse) -async def ui_update_arm( - request: Request, - soa_id: int, - arm_id: int = Form(...), - name: Optional[str] = Form(None), - label: Optional[str] = Form(None), - description: Optional[str] = Form(None), - element_id: Optional[str] = Form(None), -): - """Form handler to update an existing Arm.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - - # Read raw form to capture field names with hyphens: 'arm-type' and 'data-origin-type' - try: - form_data = await request.form() - arm_type_submission = (form_data.get("arm-type") or "").strip() - data_origin_type_submission = (form_data.get("data-origin-type") or "").strip() - except Exception: - arm_type_submission = "" - data_origin_type_submission = "" - logger.info( - "ui_update_arm: arm_id=%s soa_id=%s incoming arm-type='%s' data-origin-type='%s'", - arm_id, - soa_id, - arm_type_submission, - data_origin_type_submission, - ) - - # Fetch current arm (including existing type code_uid if any) - conn = _connect() - cur = conn.cursor() - cur.execute( - "SELECT id, name, label, description, COALESCE(type,''), COALESCE(data_origin_type,'') FROM arm WHERE id=? AND soa_id=?", - (arm_id, soa_id), - ) - row = cur.fetchone() - if not row: - conn.close() - raise HTTPException(404, "Arm not found") - current_code_uid = row[4] or None - current_data_origin_uid = row[5] or None - # Capture prior code values for audits when code mapping changes without uid change - prior_arm_type_code_value: Optional[str] = None - prior_data_origin_code_value: Optional[str] = None - if current_code_uid: - cur.execute( - "SELECT code FROM code_association WHERE soa_id=? AND code_uid=?", - (soa_id, current_code_uid), - ) - rcv = cur.fetchone() - prior_arm_type_code_value = rcv[0] if rcv else None - if current_data_origin_uid: - cur.execute( - "SELECT code FROM code_association WHERE soa_id=? AND code_uid=?", - (soa_id, current_data_origin_uid), - ) - rdv = cur.fetchone() - prior_data_origin_code_value = rdv[0] if rdv else None - before_state = { - "id": row[0], - "name": row[1], - "label": row[2], - "description": row[3], - "type": current_code_uid, - "data_origin_type": current_data_origin_uid, - } - - # Resolve submission value to protocol terminology code (C174222) - resolved_code: Optional[str] = None - if arm_type_submission: - cur.execute( - "SELECT code FROM protocol_terminology WHERE codelist_code='C174222' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", - (arm_type_submission, arm_type_submission), - ) - r = cur.fetchone() - resolved_code = r[0] if r else None - if resolved_code is None: - logger.warning( - "ui_update_arm: unknown arm type submission '%s' for soa_id=%s arm_id=%s", - arm_type_submission, - soa_id, - arm_id, - ) - conn.close() - return HTMLResponse( - f"", - status_code=400, - ) - - # Maintain code table row with immutable code_uid (Code_N unique per SoA) - new_code_uid = current_code_uid - if resolved_code is not None: - if current_code_uid: - # Update existing junction row for this code_uid - cur.execute( - "UPDATE code_association SET code=?, codelist_code='C174222', codelist_table='protocol_terminology' WHERE soa_id=? AND code_uid=?", - (resolved_code, soa_id, current_code_uid), - ) - logger.info( - "ui_update_arm: updated junction code_uid=%s -> table=%s list=%s code=%s", - current_code_uid, - "protocol_terminology", - "C174222", - resolved_code, - ) - else: - # Create new Code_N within this SoA - new_code_uid = _get_next_code_uid(cur, soa_id) - cur.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - new_code_uid, - "protocol_terminology", - "C174222", - resolved_code, - ), - ) - logger.info( - "ui_update_arm: created junction code_uid=%s -> table=%s list=%s code=%s", - new_code_uid, - "protocol_terminology", - "C174222", - resolved_code, - ) - - # Resolve Data Origin Type submission value to DDF terminology code (C188727) - resolved_ddf_code: Optional[str] = None - new_data_origin_uid = current_data_origin_uid - if data_origin_type_submission: - cur.execute( - "SELECT code FROM ddf_terminology WHERE codelist_code='C188727' AND (cdisc_submission_value=? OR LOWER(TRIM(cdisc_submission_value))=LOWER(TRIM(?)))", - (data_origin_type_submission, data_origin_type_submission), - ) - r2 = cur.fetchone() - resolved_ddf_code = r2[0] if r2 else None - if resolved_ddf_code is None: - logger.warning( - "ui_update_arm: unknown data origin type submission '%s' for soa_id=%s arm_id=%s", - data_origin_type_submission, - soa_id, - arm_id, - ) - conn.close() - return HTMLResponse( - f"", - status_code=400, - ) - # Maintain/Upsert immutable Code_N for DDF mapping - if current_data_origin_uid: - cur.execute( - "UPDATE code_association SET code=?, codelist_code='C188727', codelist_table='ddf_terminology' WHERE soa_id=? AND code_uid=?", - (resolved_ddf_code, soa_id, current_data_origin_uid), - ) - new_data_origin_uid = current_data_origin_uid - logger.info( - "ui_update_arm: updated junction code_uid=%s -> table=%s list=%s code=%s", - current_data_origin_uid, - "ddf_terminology", - "C188727", - resolved_ddf_code, - ) - else: - # Create new Code_N, ensuring unique across this SoA - new_data_origin_uid = _get_next_code_uid(cur, soa_id) - cur.execute( - "INSERT INTO code_association (soa_id, code_uid, codelist_table, codelist_code, code) VALUES (?,?,?,?,?)", - ( - soa_id, - new_data_origin_uid, - "ddf_terminology", - "C188727", - resolved_ddf_code, - ), - ) - logger.info( - "ui_update_arm: created junction code_uid=%s -> table=%s list=%s code=%s", - new_data_origin_uid, - "ddf_terminology", - "C188727", - resolved_ddf_code, - ) - - # Apply arm field updates (including setting type to code_uid if resolved) - new_name = name if name is not None else row[1] - new_label = label if label is not None else row[2] - new_desc = description if description is not None else row[3] - cur.execute( - "UPDATE arm SET name=?, label=?, description=?, type=?, data_origin_type=? WHERE id=? AND soa_id=?", - ( - new_name, - new_label, - new_desc, - new_code_uid, - new_data_origin_uid, - arm_id, - soa_id, - ), - ) - logger.info( - "ui_update_arm: applied UPDATE arm id=%s set name='%s' label='%s' type=%s data_origin_type=%s", - arm_id, - new_name, - new_label, - new_code_uid, - new_data_origin_uid, - ) - conn.commit() - # Capture post-update code_association values - post_arm_type_code_value: Optional[str] = None - post_data_origin_code_value: Optional[str] = None - if new_code_uid: - cur.execute( - "SELECT code FROM code_association WHERE soa_id=? AND code_uid=?", - (soa_id, new_code_uid), - ) - rav = cur.fetchone() - post_arm_type_code_value = rav[0] if rav else None - if new_data_origin_uid: - cur.execute( - "SELECT code FROM code_association WHERE soa_id=? AND code_uid=?", - (soa_id, new_data_origin_uid), - ) - rdv2 = cur.fetchone() - post_data_origin_code_value = rdv2[0] if rdv2 else None - after_state = { - "id": arm_id, - "name": new_name, - "label": new_label, - "description": new_desc, - "type": new_code_uid, - "data_origin_type": new_data_origin_uid, - "type_code": post_arm_type_code_value, - "data_origin_type_code": post_data_origin_code_value, - } - # Record audit if any relevant fields or underlying code mappings changed - if ( - before_state["type"] != after_state["type"] - or before_state["data_origin_type"] != after_state["data_origin_type"] - or prior_arm_type_code_value != post_arm_type_code_value - or prior_data_origin_code_value != post_data_origin_code_value - or before_state["name"] != after_state["name"] - or before_state["label"] != after_state["label"] - or before_state["description"] != after_state["description"] - ): - try: - _record_arm_audit( - soa_id, - "update", - arm_id=arm_id, - before=before_state, - after=after_state, - ) - except Exception: - pass - else: - logger.info( - "ui_update_arm: no-op update detected for arm_id=%s (no field or code changes)", - arm_id, - ) - conn.close() - return HTMLResponse( - f"" - ) -''' - -# UI endpoint for deleting an Arm <- Deprecated (moved to routers/arms.py) -""" -@app.post("/ui/soa/{soa_id}/delete_arm", response_class=HTMLResponse) -def ui_delete_arm(request: Request, soa_id: int, arm_id: int = Form(...)): - delete_arm(soa_id, arm_id) - return HTMLResponse( - f"" - ) -""" - -# UI endpoint for reordering Arms <- Deprecated (no longer needed) -''' -@app.post("/ui/soa/{soa_id}/reorder_arms", response_class=HTMLResponse) -def ui_reorder_arms(request: Request, soa_id: int, order: str = Form("")): - """Form handler to reorder existing Arms.""" - if not soa_exists(soa_id): - raise HTTPException(404, "SOA not found") - ids = [int(x) for x in order.split(",") if x.strip().isdigit()] - if not ids: - return HTMLResponse("Invalid order", status_code=400) - conn = _connect() - cur = conn.cursor() - cur.execute("SELECT id FROM arm WHERE soa_id=? ORDER BY order_index", (soa_id,)) - old_order = [r[0] for r in cur.fetchall()] - cur.execute("SELECT id FROM arm WHERE soa_id=?", (soa_id,)) - existing = {r[0] for r in cur.fetchall()} - if set(ids) - existing: - conn.close() - return HTMLResponse("Order contains invalid arm id", status_code=400) - for idx, aid in enumerate(ids, start=1): - cur.execute("UPDATE arm SET order_index=? WHERE id=?", (idx, aid)) - conn.commit() - conn.close() - _record_reorder_audit(soa_id, "arm", old_order, ids) - _record_arm_audit( - soa_id, - "reorder", - arm_id=None, - before={"old_order": old_order}, - after={"new_order": ids}, - ) - return HTMLResponse("OK") -''' -# Deprecated (new definition in arms.py) -""" -def _record_arm_audit( - soa_id: int, - action: str, - arm_id: Optional[int], - before: Optional[dict] = None, - after: Optional[dict] = None, -): - try: - conn = _connect() - cur = conn.cursor() - cur.execute( - "INSERT INTO arm_audit (soa_id, arm_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", - ( - soa_id, - arm_id, - action, - json.dumps(before) if before else None, - json.dumps(after) if after else None, - datetime.now(timezone.utc).isoformat(), - ), - ) - conn.commit() - conn.close() - except Exception as e: # pragma: no cover - logger.warning("Failed recording arm audit: %s", e) -""" diff --git a/src/soa_builder/web/audit.py b/src/soa_builder/web/audit.py index e0835f6c..a45a7db1 100644 --- a/src/soa_builder/web/audit.py +++ b/src/soa_builder/web/audit.py @@ -45,18 +45,6 @@ def _record_element_audit( try: conn = _connect() cur = conn.cursor() - # Ensure table exists (defensive for migrated databases) - cur.execute( - """CREATE TABLE IF NOT EXISTS element_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - element_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO element_audit (soa_id, element_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", ( @@ -163,18 +151,6 @@ def _record_study_cell_audit( try: conn = _connect() cur = conn.cursor() - # Ensure table exists (defensive for migrated databases) - cur.execute( - """CREATE TABLE IF NOT EXISTS study_cell_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - study_cell_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO study_cell_audit (soa_id, study_cell_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", ( @@ -256,18 +232,6 @@ def _record_instance_audit( try: conn = _connect() cur = conn.cursor() - # Ensure table exists defensively - cur.execute( - """CREATE TABLE IF NOT EXISTS instance_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - instance_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO instance_audit (soa_id, instance_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", ( @@ -295,17 +259,6 @@ def _record_decision_instance_audit( try: conn = _connect() cur = conn.cursor() - cur.execute( - """CREATE TABLE IF NOT EXISTS decision_instance_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - decision_instance_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO decision_instance_audit (soa_id, decision_instance_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", ( @@ -333,17 +286,6 @@ def _record_condition_assignment_audit( try: conn = _connect() cur = conn.cursor() - cur.execute( - """CREATE TABLE IF NOT EXISTS condition_assignment_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - condition_assignment_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO condition_assignment_audit (soa_id, condition_assignment_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", ( @@ -403,17 +345,6 @@ def _record_biomedical_concept_audit( if own_conn: conn = _connect() cur = conn.cursor() - cur.execute( - """CREATE TABLE IF NOT EXISTS biomedical_concept_audit ( - id INTEGER PRIMARY KEY AUTOINCREMENT, - soa_id INTEGER NOT NULL, - biomedical_concept_id INTEGER, - action TEXT NOT NULL, - before_json TEXT, - after_json TEXT, - performed_at TEXT NOT NULL - )""" - ) cur.execute( "INSERT INTO biomedical_concept_audit" " (soa_id, biomedical_concept_id, action, before_json, after_json, performed_at)" @@ -432,3 +363,59 @@ def _record_biomedical_concept_audit( conn.close() except Exception as e: logger.warning("Failed recording biomedical_concept audit: %s", e) + + +def _record_bc_surrogate_audit( + soa_id: int, + action: str, + surrogate_id: Optional[int], + before: Optional[Dict[str, Any]] = None, + after: Optional[Dict[str, Any]] = None, +): + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + "INSERT INTO biomedical_concept_surrogate_audit" + " (soa_id, surrogate_id, action, before_json, after_json, performed_at)" + " VALUES (?,?,?,?,?,?)", + ( + soa_id, + surrogate_id, + action, + json.dumps(before) if before else None, + json.dumps(after) if after else None, + datetime.now(timezone.utc).isoformat(), + ), + ) + conn.commit() + conn.close() + except Exception as e: + logger.warning("Failed recording bc_surrogate audit: %s", e) + + +def _record_footnote_audit( + soa_id: int, + action: str, + footnote_id: Optional[int], + before: Optional[Dict[str, Any]] = None, + after: Optional[Dict[str, Any]] = None, +): + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + "INSERT INTO footnote_audit (soa_id, footnote_id, action, before_json, after_json, performed_at) VALUES (?,?,?,?,?,?)", + ( + soa_id, + footnote_id, + action, + json.dumps(before) if before else None, + json.dumps(after) if after else None, + datetime.now(timezone.utc).isoformat(), + ), + ) + conn.commit() + conn.close() + except Exception as e: + logger.warning("Failed recording footnote audit: %s", e) diff --git a/src/soa_builder/web/db.py b/src/soa_builder/web/db.py index 17fc22c3..6061237f 100644 --- a/src/soa_builder/web/db.py +++ b/src/soa_builder/web/db.py @@ -48,6 +48,10 @@ def _connect(): conn.execute("PRAGMA journal_mode=WAL") conn.execute("PRAGMA synchronous=NORMAL") conn.execute("PRAGMA busy_timeout=3000") - except Exception: - pass + except Exception as e: + import logging + + logging.getLogger("soa_builder.db").warning( + "PRAGMA configuration failed on %s: %s", db_path, e + ) return conn diff --git a/src/soa_builder/web/initialize_database.py b/src/soa_builder/web/initialize_database.py index de5ff084..d886d40c 100644 --- a/src/soa_builder/web/initialize_database.py +++ b/src/soa_builder/web/initialize_database.py @@ -352,6 +352,21 @@ def _init_db(): )""" ) + # The footnote table (created until full incorporation of SyntaxTemplates) + cur.execute( + """CREATE TABLE IF NOT EXISTS footnote ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INT, + footnote_uid TEXT NOT NULL, + name TEXT NOT NULL, + label TEXT, + description TEXT, + text TEXT, + dictionary_uid TEXT, + UNIQUE(soa_id, footnote_uid) + )""" + ) + # AUDIT TABLES FOR TRACKING ALL CHANGES TO ENTITIES # Element audit table capturing create/update/delete operations diff --git a/src/soa_builder/web/migrate_database.py b/src/soa_builder/web/migrate_database.py index 71c678ed..6a0df9c6 100644 --- a/src/soa_builder/web/migrate_database.py +++ b/src/soa_builder/web/migrate_database.py @@ -1122,3 +1122,165 @@ def _migrate_biomedical_concept_property_add_uid(): conn.close() except Exception as e: logger.warning("_migrate_biomedical_concept_property_add_uid: %s", e) + + +def _migrate_add_soa_id_indexes(): + """Add standalone soa_id indexes on high-traffic tables. + + The existing UNIQUE constraints cover (soa_id, uid) lookups, but bare + WHERE soa_id=? list queries do full table scans without a leading index. + These indexes cover the ~259 soa_id filter sites in the codebase. + """ + try: + conn = _connect() + cur = conn.cursor() + indexes = [ + ("idx_activity_soa", "activity", "soa_id"), + ("idx_visit_soa", "visit", "soa_id"), + ("idx_matrix_cells_soa", "matrix_cells", "soa_id"), + ("idx_activity_concept_soa", "activity_concept", "soa_id"), + ("idx_instances_soa", "instances", "soa_id"), + ("idx_timing_soa", "timing", "soa_id"), + ] + created = [] + for idx_name, table, col in indexes: + cur.execute(f"CREATE INDEX IF NOT EXISTS {idx_name} ON {table}({col})") + created.append(idx_name) + conn.commit() + conn.close() + logger.info("_migrate_add_soa_id_indexes: ensured indexes %s", created) + except Exception as e: + logger.warning("_migrate_add_soa_id_indexes: %s", e) + + +def _migrate_add_footnote_table(): + """Add the database table footnote""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + """CREATE TABLE IF NOT EXISTS footnote ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INT, + footnote_uid TEXT NOT NULL, + name TEXT NOT NULL, + label TEXT, + description TEXT, + text TEXT, + dictionary_uid TEXT, + UNIQUE(soa_id, footnote_uid) + )""" + ) + conn.commit() + conn.close() + logger.info("_migrate_add_footnote_table created footnote table") + except Exception as e: + logger.warning("_migrate_add_footnote_table failed: %s", e) + + +def _migrate_add_footnote_audit_table(): + """Create footnote_audit table for tracking create/update/delete operations.""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + """CREATE TABLE IF NOT EXISTS footnote_audit ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INTEGER NOT NULL, + footnote_id INTEGER, + action TEXT NOT NULL, + before_json TEXT, + after_json TEXT, + performed_at TEXT NOT NULL + )""" + ) + conn.commit() + conn.close() + logger.info("_migrate_add_footnote_audit_table created footnote_audit table") + except Exception as e: + logger.warning("_migrate_add_footnote_audit_table failed: %s", e) + + +def _migrate_matrix_cells_add_superscript(): + """Add superscript TEXT column to matrix_cells if missing.""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute("PRAGMA table_info(matrix_cells)") + if "superscript" not in {r[1] for r in cur.fetchall()}: + cur.execute("ALTER TABLE matrix_cells ADD COLUMN superscript TEXT") + conn.commit() + logger.info("Added superscript column to matrix_cells") + conn.close() + except Exception as e: + logger.warning("matrix_cells superscript migration failed: %s", e) + + +def _migrate_add_bc_surrogate_table(): + """Create biomedical_concept_surrogate table if missing.""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + """CREATE TABLE IF NOT EXISTS biomedical_concept_surrogate ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INT NOT NULL, + surrogate_uid TEXT NOT NULL, + name TEXT NOT NULL, + label TEXT, + description TEXT, + reference TEXT, + UNIQUE(surrogate_uid, soa_id) + )""" + ) + conn.commit() + conn.close() + logger.info( + "_migrate_add_bc_surrogate_table: biomedical_concept_surrogate ready" + ) + except Exception as e: + logger.warning("_migrate_add_bc_surrogate_table failed: %s", e) + + +def _migrate_add_activity_surrogate_table(): + """Create activity_surrogate junction table if missing.""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + """CREATE TABLE IF NOT EXISTS activity_surrogate ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INT NOT NULL, + activity_uid TEXT NOT NULL, + surrogate_uid TEXT NOT NULL, + UNIQUE(soa_id, activity_uid, surrogate_uid) + )""" + ) + conn.commit() + conn.close() + logger.info("_migrate_add_activity_surrogate_table: activity_surrogate ready") + except Exception as e: + logger.warning("_migrate_add_activity_surrogate_table failed: %s", e) + + +def _migrate_add_bc_surrogate_audit_table(): + """Create biomedical_concept_surrogate_audit table if missing.""" + try: + conn = _connect() + cur = conn.cursor() + cur.execute( + """CREATE TABLE IF NOT EXISTS biomedical_concept_surrogate_audit ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + soa_id INTEGER NOT NULL, + surrogate_id INTEGER, + action TEXT NOT NULL, + before_json TEXT, + after_json TEXT, + performed_at TEXT NOT NULL + )""" + ) + conn.commit() + conn.close() + logger.info("_migrate_add_bc_surrogate_audit_table: audit table ready") + except Exception as e: + logger.warning("_migrate_add_bc_surrogate_audit_table failed: %s", e) diff --git a/src/soa_builder/web/routers/activities.py b/src/soa_builder/web/routers/activities.py index 48d675ce..7f7bef17 100644 --- a/src/soa_builder/web/routers/activities.py +++ b/src/soa_builder/web/routers/activities.py @@ -6,7 +6,7 @@ import time from typing import List -from fastapi import APIRouter, BackgroundTasks, HTTPException, Request, Form +from fastapi import APIRouter, BackgroundTasks, Body, HTTPException, Request, Form from fastapi.responses import JSONResponse, HTMLResponse, RedirectResponse from fastapi.templating import Jinja2Templates @@ -137,6 +137,41 @@ def get_activity(soa_id: int, activity_id: int): } +def _next_activity_uid(cur, soa_id: int) -> str: + """Return the next Activity_N UID, never reusing a deleted one. + + Scans both the live table and the audit trail so deleted UIDs are + never recycled — matching the pattern used by _next_study_cell_uid. + """ + max_n = 0 + cur.execute("SELECT activity_uid FROM activity WHERE soa_id=?", (soa_id,)) + for (uid,) in cur.fetchall(): + if isinstance(uid, str) and uid.startswith("Activity_"): + try: + n = int(uid.split("_")[-1]) + if n > max_n: + max_n = n + except (ValueError, IndexError): + pass + cur.execute( + "SELECT before_json, after_json FROM activity_audit WHERE soa_id=?", + (soa_id,), + ) + for before_raw, after_raw in cur.fetchall(): + for raw in (before_raw, after_raw): + if not raw: + continue + try: + uid = json.loads(raw).get("activity_uid", "") + if isinstance(uid, str) and uid.startswith("Activity_"): + n = int(uid.split("_")[-1]) + if n > max_n: + max_n = n + except Exception: + pass + return f"Activity_{max_n + 1}" + + @router.post("/activities", response_class=JSONResponse) def add_activity(soa_id: int, payload: ActivityCreate): if not soa_exists(soa_id): @@ -148,8 +183,7 @@ def add_activity(soa_id: int, payload: ActivityCreate): "SELECT COALESCE(MAX(order_index),0) FROM activity WHERE soa_id=?", (soa_id,) ) order_index = (cur.fetchone() or [0])[0] + 1 - # Compute activity_uid from order_index (keeps list stable after inserts) - activity_uid = f"Activity_{order_index}" + activity_uid = _next_activity_uid(cur, soa_id) name = (payload.name or "").strip() label = (payload.label or "").strip() or None @@ -313,7 +347,7 @@ def ui_update_activity( @router.post("/activities/reorder", response_class=JSONResponse) -def reorder_activities_api(soa_id: int, order: List[int]): +def reorder_activities_api(soa_id: int, order: List[int] = Body(..., embed=True)): if not soa_exists(soa_id): raise HTTPException(404, "SOA not found") if not order: @@ -355,14 +389,6 @@ def reorder_activities_api(soa_id: int, order: List[int]): ).fetchall() } - # Reassign activity_uid from order_index - cur.execute( - "UPDATE activity SET activity_uid='TMP_' || id WHERE soa_id=?", (soa_id,) - ) - cur.execute( - "UPDATE activity SET activity_uid='Activity_' || order_index WHERE soa_id=?", - (soa_id,), - ) conn.commit() conn.close() @@ -411,7 +437,7 @@ def add_activities_bulk(soa_id: int, payload: BulkActivities): order_index += 1 cur.execute( "INSERT INTO activity (soa_id,name,order_index,activity_uid) VALUES (?,?,?,?)", - (soa_id, name, order_index, f"Activity_{order_index}"), + (soa_id, name, order_index, _next_activity_uid(cur, soa_id)), ) added.append(name) existing.add(lname) @@ -554,7 +580,7 @@ def set_activity_concepts( def _reindex_activities(soa_id: int): - """Re-number order_index and activity_uid after a delete.""" + """Re-number order_index after a delete. activity_uid is immutable and never changed.""" conn = _connect() cur = conn.cursor() cur.execute( @@ -563,13 +589,6 @@ def _reindex_activities(soa_id: int): ids = [r[0] for r in cur.fetchall()] for idx, _id in enumerate(ids, start=1): cur.execute("UPDATE activity SET order_index=? WHERE id=?", (idx, _id)) - cur.execute( - "UPDATE activity SET activity_uid = 'TMP_' || id WHERE soa_id=?", (soa_id,) - ) - cur.execute( - "UPDATE activity SET activity_uid = 'Activity_' || order_index WHERE soa_id=?", - (soa_id,), - ) conn.commit() conn.close() @@ -648,8 +667,46 @@ def ui_list_activities(request: Request, soa_id: int): concepts = _app_fetch_concepts() sdtm_specializations = _app_fetch_dss() + # Fetch surrogates for this SOA conn = _connect() cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name, label, description, reference FROM biomedical_concept_surrogate WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + surrogates = [ + { + "id": r[0], + "surrogate_uid": r[1], + "name": r[2], + "label": r[3], + "description": r[4], + "reference": r[5], + } + for r in cur.fetchall() + ] + + # Per-activity surrogate mappings: activity_id -> [surrogate dicts] + cur.execute( + "SELECT a.id, bcs.id, bcs.surrogate_uid, bcs.name, bcs.label " + "FROM activity_surrogate asr " + "JOIN activity a ON a.activity_uid=asr.activity_uid AND a.soa_id=asr.soa_id " + "JOIN biomedical_concept_surrogate bcs ON bcs.surrogate_uid=asr.surrogate_uid AND bcs.soa_id=asr.soa_id " + "WHERE asr.soa_id=?", + (soa_id,), + ) + activity_surrogates: dict = {} + for row in cur.fetchall(): + activity_id, sur_id, sur_uid, sur_name, sur_label = row + activity_surrogates.setdefault(activity_id, []).append( + { + "id": sur_id, + "surrogate_uid": sur_uid, + "name": sur_name, + "label": sur_label, + } + ) + cur.execute( "SELECT study_id, study_label, study_description, name, created_at FROM soa WHERE id=?", (soa_id,), @@ -668,6 +725,8 @@ def ui_list_activities(request: Request, soa_id: int): "activity_concepts": activity_concepts, "concepts": concepts, "sdtm_specializations": sdtm_specializations, + "surrogates": surrogates, + "activity_surrogates": activity_surrogates, "study_id": study_id, "study_label": study_label, "study_description": study_description, diff --git a/src/soa_builder/web/routers/bc_surrogates.py b/src/soa_builder/web/routers/bc_surrogates.py new file mode 100644 index 00000000..f07c8e9e --- /dev/null +++ b/src/soa_builder/web/routers/bc_surrogates.py @@ -0,0 +1,631 @@ +import json +import logging +import os +from typing import Optional + +from fastapi import APIRouter, Form, HTTPException, Request +from fastapi.responses import HTMLResponse, JSONResponse, RedirectResponse +from fastapi.templating import Jinja2Templates + +from ..audit import _record_bc_surrogate_audit +from ..db import _connect +from ..schemas import BCSurrogateCreate, BCSurrogateUpdate +from ..utils import soa_exists + +router = APIRouter() +ui_router = APIRouter() +logger = logging.getLogger("soa_builder.web.routers.bc_surrogates") +templates = Jinja2Templates( + directory=os.path.join(os.path.dirname(__file__), "..", "templates") +) + + +def _nz(v: Optional[str]) -> Optional[str]: + """Return None for blank strings, otherwise the stripped value.""" + if v is None: + return None + v = v.strip() + return v if v else None + + +def _next_surrogate_uid(cur, soa_id: int) -> str: + """Generate next BiomedicalConceptSurrogate_N UID (monotonic, never reuses). + + Scans both the live table and the audit trail so deleted UIDs are never recycled. + """ + prefix = "BiomedicalConceptSurrogate_" + max_n = 0 + + cur.execute( + "SELECT surrogate_uid FROM biomedical_concept_surrogate WHERE soa_id=?", + (soa_id,), + ) + for (uid,) in cur.fetchall(): + if isinstance(uid, str) and uid.startswith(prefix): + try: + n = int(uid[len(prefix) :]) + if n > max_n: + max_n = n + except (ValueError, IndexError): + pass + + cur.execute( + "SELECT before_json, after_json FROM biomedical_concept_surrogate_audit WHERE soa_id=?", + (soa_id,), + ) + for before_raw, after_raw in cur.fetchall(): + for raw in (before_raw, after_raw): + if not raw: + continue + try: + uid = json.loads(raw).get("surrogate_uid", "") + if isinstance(uid, str) and uid.startswith(prefix): + n = int(uid[len(prefix) :]) + if n > max_n: + max_n = n + except Exception: + pass + + return f"{prefix}{max_n + 1}" + + +# --------------------------------------------------------------------------- +# API — list +# --------------------------------------------------------------------------- + + +@router.get( + "/soa/{soa_id}/bc-surrogates", response_class=JSONResponse, response_model=None +) +def list_bc_surrogates(soa_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name, label, description, reference " + "FROM biomedical_concept_surrogate WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + rows = [ + { + "id": r[0], + "surrogate_uid": r[1], + "name": r[2], + "label": r[3], + "description": r[4], + "reference": r[5], + } + for r in cur.fetchall() + ] + conn.close() + return rows + + +# --------------------------------------------------------------------------- +# API — create +# --------------------------------------------------------------------------- + + +@router.post( + "/soa/{soa_id}/bc-surrogates", response_class=JSONResponse, response_model=None +) +def create_bc_surrogate(soa_id: int, payload: BCSurrogateCreate): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + name = (payload.name or "").strip() + if not name: + raise HTTPException(400, "Surrogate name required") + + conn = _connect() + cur = conn.cursor() + uid = _next_surrogate_uid(cur, soa_id) + cur.execute( + "INSERT INTO biomedical_concept_surrogate (soa_id, surrogate_uid, name, label, description, reference) VALUES (?,?,?,?,?,?)", + ( + soa_id, + uid, + name, + _nz(payload.label), + _nz(payload.description), + _nz(payload.reference), + ), + ) + surrogate_id = cur.lastrowid + conn.commit() + conn.close() + after = { + "id": surrogate_id, + "surrogate_uid": uid, + "name": name, + "label": _nz(payload.label), + "description": _nz(payload.description), + "reference": _nz(payload.reference), + } + _record_bc_surrogate_audit(soa_id, "create", surrogate_id, before=None, after=after) + return after + + +# --------------------------------------------------------------------------- +# API — update +# --------------------------------------------------------------------------- + + +@router.patch( + "/soa/{soa_id}/bc-surrogates/{surrogate_id}", + response_class=JSONResponse, + response_model=None, +) +def update_bc_surrogate(soa_id: int, surrogate_id: int, payload: BCSurrogateUpdate): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name, label, description, reference " + "FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Surrogate not found") + before = { + "id": row[0], + "surrogate_uid": row[1], + "name": row[2], + "label": row[3], + "description": row[4], + "reference": row[5], + } + + new_name = _nz(payload.name) if payload.name is not None else before["name"] + new_label = _nz(payload.label) if payload.label is not None else before["label"] + new_desc = ( + _nz(payload.description) + if payload.description is not None + else before["description"] + ) + new_ref = ( + _nz(payload.reference) if payload.reference is not None else before["reference"] + ) + + cur.execute( + "UPDATE biomedical_concept_surrogate SET name=?, label=?, description=?, reference=? WHERE id=? AND soa_id=?", + (new_name, new_label, new_desc, new_ref, surrogate_id, soa_id), + ) + conn.commit() + conn.close() + after = { + **before, + "name": new_name, + "label": new_label, + "description": new_desc, + "reference": new_ref, + } + _record_bc_surrogate_audit( + soa_id, "update", surrogate_id, before=before, after=after + ) + return after + + +# --------------------------------------------------------------------------- +# API — delete +# --------------------------------------------------------------------------- + + +@router.delete( + "/soa/{soa_id}/bc-surrogates/{surrogate_id}", + response_class=JSONResponse, + response_model=None, +) +def delete_bc_surrogate(soa_id: int, surrogate_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Surrogate not found") + before = {"id": row[0], "surrogate_uid": row[1], "name": row[2]} + # Remove activity links first + cur.execute( + "DELETE FROM activity_surrogate WHERE soa_id=? AND surrogate_uid=?", + (soa_id, row[1]), + ) + cur.execute( + "DELETE FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + conn.commit() + conn.close() + _record_bc_surrogate_audit( + soa_id, "delete", surrogate_id, before=before, after=None + ) + return {"deleted": True, "id": surrogate_id} + + +# --------------------------------------------------------------------------- +# API — link / unlink surrogate ↔ activity +# --------------------------------------------------------------------------- + + +@router.post( + "/soa/{soa_id}/activities/{activity_id}/bc-surrogates/{surrogate_id}", + response_class=JSONResponse, + response_model=None, +) +def link_surrogate_to_activity(soa_id: int, activity_id: int, surrogate_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT activity_uid FROM activity WHERE id=? AND soa_id=?", + (activity_id, soa_id), + ) + act_row = cur.fetchone() + if not act_row: + conn.close() + raise HTTPException(404, "Activity not found") + activity_uid = act_row[0] + + cur.execute( + "SELECT surrogate_uid FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + sur_row = cur.fetchone() + if not sur_row: + conn.close() + raise HTTPException(404, "Surrogate not found") + surrogate_uid = sur_row[0] + + cur.execute( + "INSERT OR IGNORE INTO activity_surrogate (soa_id, activity_uid, surrogate_uid) VALUES (?,?,?)", + (soa_id, activity_uid, surrogate_uid), + ) + conn.commit() + conn.close() + return { + "linked": True, + "activity_uid": activity_uid, + "surrogate_uid": surrogate_uid, + } + + +@router.delete( + "/soa/{soa_id}/activities/{activity_id}/bc-surrogates/{surrogate_id}", + response_class=JSONResponse, + response_model=None, +) +def unlink_surrogate_from_activity(soa_id: int, activity_id: int, surrogate_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT activity_uid FROM activity WHERE id=? AND soa_id=?", + (activity_id, soa_id), + ) + act_row = cur.fetchone() + if not act_row: + conn.close() + raise HTTPException(404, "Activity not found") + activity_uid = act_row[0] + + cur.execute( + "SELECT surrogate_uid FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + sur_row = cur.fetchone() + if not sur_row: + conn.close() + raise HTTPException(404, "Surrogate not found") + surrogate_uid = sur_row[0] + + cur.execute( + "DELETE FROM activity_surrogate WHERE soa_id=? AND activity_uid=? AND surrogate_uid=?", + (soa_id, activity_uid, surrogate_uid), + ) + conn.commit() + conn.close() + return { + "unlinked": True, + "activity_uid": activity_uid, + "surrogate_uid": surrogate_uid, + } + + +# --------------------------------------------------------------------------- +# UI — create / update / delete (form POST → redirect) +# --------------------------------------------------------------------------- + + +@ui_router.post("/ui/soa/{soa_id}/bc-surrogates/create", response_class=HTMLResponse) +def ui_create_bc_surrogate( + request: Request, + soa_id: int, + name: str = Form(...), + label: str = Form(""), + description: str = Form(""), + reference: str = Form(""), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + name = name.strip() + if not name: + raise HTTPException(400, "Surrogate name required") + + conn = _connect() + cur = conn.cursor() + uid = _next_surrogate_uid(cur, soa_id) + cur.execute( + "INSERT INTO biomedical_concept_surrogate (soa_id, surrogate_uid, name, label, description, reference) VALUES (?,?,?,?,?,?)", + (soa_id, uid, name, _nz(label), _nz(description), _nz(reference)), + ) + surrogate_id = cur.lastrowid + conn.commit() + conn.close() + _record_bc_surrogate_audit( + soa_id, + "create", + surrogate_id, + before=None, + after={ + "surrogate_uid": uid, + "name": name, + "label": _nz(label), + "description": _nz(description), + "reference": _nz(reference), + }, + ) + return RedirectResponse(f"/ui/soa/{soa_id}/activities", status_code=303) + + +@ui_router.post( + "/ui/soa/{soa_id}/bc-surrogates/{surrogate_id}/update", response_class=HTMLResponse +) +def ui_update_bc_surrogate( + request: Request, + soa_id: int, + surrogate_id: int, + name: str = Form(...), + label: str = Form(""), + description: str = Form(""), + reference: str = Form(""), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name, label, description, reference " + "FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Surrogate not found") + before = { + "id": row[0], + "surrogate_uid": row[1], + "name": row[2], + "label": row[3], + "description": row[4], + "reference": row[5], + } + + new_name = name.strip() or before["name"] + new_label = _nz(label) + new_desc = _nz(description) + new_ref = _nz(reference) + cur.execute( + "UPDATE biomedical_concept_surrogate SET name=?, label=?, description=?, reference=? WHERE id=? AND soa_id=?", + (new_name, new_label, new_desc, new_ref, surrogate_id, soa_id), + ) + conn.commit() + conn.close() + after = { + **before, + "name": new_name, + "label": new_label, + "description": new_desc, + "reference": new_ref, + } + _record_bc_surrogate_audit( + soa_id, "update", surrogate_id, before=before, after=after + ) + return RedirectResponse(f"/ui/soa/{soa_id}/activities", status_code=303) + + +@ui_router.post( + "/ui/soa/{soa_id}/bc-surrogates/{surrogate_id}/delete", response_class=HTMLResponse +) +def ui_delete_bc_surrogate(request: Request, soa_id: int, surrogate_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id, surrogate_uid, name FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Surrogate not found") + before = {"id": row[0], "surrogate_uid": row[1], "name": row[2]} + cur.execute( + "DELETE FROM activity_surrogate WHERE soa_id=? AND surrogate_uid=?", + (soa_id, row[1]), + ) + cur.execute( + "DELETE FROM biomedical_concept_surrogate WHERE id=? AND soa_id=?", + (surrogate_id, soa_id), + ) + conn.commit() + conn.close() + _record_bc_surrogate_audit( + soa_id, "delete", surrogate_id, before=before, after=None + ) + return RedirectResponse(f"/ui/soa/{soa_id}/activities", status_code=303) + + +# --------------------------------------------------------------------------- +# UI — HTMX add/remove surrogate link on activity (returns concepts_cell partial) +# --------------------------------------------------------------------------- + + +def _render_concepts_cell(request: Request, soa_id: int, activity_id: int): + """Re-render the concepts_cell partial after a surrogate link/unlink.""" + conn = _connect() + cur = conn.cursor() + + # Fetch activity uid + cur.execute( + "SELECT activity_uid FROM activity WHERE id=? AND soa_id=?", + (activity_id, soa_id), + ) + act_row = cur.fetchone() + if not act_row: + conn.close() + raise HTTPException(404, "Activity not found") + activity_uid = act_row[0] + + # Fetch linked BC concepts + cur.execute( + "SELECT concept_code, concept_title FROM activity_concept WHERE activity_id=? AND soa_id=?", + (activity_id, soa_id), + ) + selected_list = [ + {"code": r[0], "title": r[1], "dss_title": "", "dss_href": ""} + for r in cur.fetchall() + ] + selected_codes = [c["code"] for c in selected_list] + + # Fetch linked surrogates + cur.execute( + "SELECT bcs.id, bcs.surrogate_uid, bcs.name, bcs.label " + "FROM activity_surrogate asr " + "JOIN biomedical_concept_surrogate bcs ON bcs.surrogate_uid=asr.surrogate_uid AND bcs.soa_id=asr.soa_id " + "WHERE asr.activity_uid=? AND asr.soa_id=?", + (activity_uid, soa_id), + ) + selected_surrogate_list = [ + {"id": r[0], "surrogate_uid": r[1], "name": r[2], "label": r[3]} + for r in cur.fetchall() + ] + selected_surrogate_uids = [s["surrogate_uid"] for s in selected_surrogate_list] + + # Fetch all surrogates for this SOA (for the dropdown) + cur.execute( + "SELECT id, surrogate_uid, name, label FROM biomedical_concept_surrogate WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + surrogates = [ + {"id": r[0], "surrogate_uid": r[1], "name": r[2], "label": r[3]} + for r in cur.fetchall() + ] + conn.close() + + # Fetch BC concepts list (for the dropdown) + from ..app import fetch_biomedical_concepts as _app_fetch_concepts + + concepts = _app_fetch_concepts() + + return templates.TemplateResponse( + request, + "concepts_cell.html", + { + "request": request, + "soa_id": soa_id, + "activity_id": activity_id, + "selected_list": selected_list, + "selected_codes": selected_codes, + "selected_surrogate_list": selected_surrogate_list, + "selected_surrogate_uids": selected_surrogate_uids, + "concepts": concepts, + "surrogates": surrogates, + "edit": False, + }, + ) + + +@ui_router.post( + "/ui/soa/{soa_id}/activity/{activity_id}/bc-surrogates/add", + response_class=HTMLResponse, +) +def ui_add_surrogate_to_activity( + request: Request, + soa_id: int, + activity_id: int, + surrogate_uid: str = Form(...), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT activity_uid FROM activity WHERE id=? AND soa_id=?", + (activity_id, soa_id), + ) + act_row = cur.fetchone() + if not act_row: + conn.close() + raise HTTPException(404, "Activity not found") + activity_uid = act_row[0] + + cur.execute( + "SELECT id FROM biomedical_concept_surrogate WHERE surrogate_uid=? AND soa_id=?", + (surrogate_uid, soa_id), + ) + if not cur.fetchone(): + conn.close() + raise HTTPException(404, "Surrogate not found") + + cur.execute( + "INSERT OR IGNORE INTO activity_surrogate (soa_id, activity_uid, surrogate_uid) VALUES (?,?,?)", + (soa_id, activity_uid, surrogate_uid), + ) + conn.commit() + conn.close() + return _render_concepts_cell(request, soa_id, activity_id) + + +@ui_router.post( + "/ui/soa/{soa_id}/activity/{activity_id}/bc-surrogates/remove", + response_class=HTMLResponse, +) +def ui_remove_surrogate_from_activity( + request: Request, + soa_id: int, + activity_id: int, + surrogate_uid: str = Form(...), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT activity_uid FROM activity WHERE id=? AND soa_id=?", + (activity_id, soa_id), + ) + act_row = cur.fetchone() + if not act_row: + conn.close() + raise HTTPException(404, "Activity not found") + activity_uid = act_row[0] + + cur.execute( + "DELETE FROM activity_surrogate WHERE soa_id=? AND activity_uid=? AND surrogate_uid=?", + (soa_id, activity_uid, surrogate_uid), + ) + conn.commit() + conn.close() + return _render_concepts_cell(request, soa_id, activity_id) diff --git a/src/soa_builder/web/routers/footnotes.py b/src/soa_builder/web/routers/footnotes.py new file mode 100644 index 00000000..32aaf85f --- /dev/null +++ b/src/soa_builder/web/routers/footnotes.py @@ -0,0 +1,260 @@ +import logging + +from fastapi import APIRouter, Form, HTTPException, Request +from fastapi.responses import HTMLResponse, JSONResponse, RedirectResponse + +from ..audit import _record_footnote_audit +from ..db import _connect +from ..schemas import FootnoteCreate, FootnoteUpdate +from ..utils import soa_exists + +router = APIRouter(prefix="/soa/{soa_id}") +ui_router = APIRouter() +logger = logging.getLogger("soa_builder.web.routers.footnotes") + + +def _next_footnote_uid(soa_id: int) -> str: + """Return next Footnote_N UID, never reusing deleted UIDs.""" + conn = _connect() + cur = conn.cursor() + cur.execute("SELECT MAX(id) FROM footnote WHERE soa_id=?", (soa_id,)) + row = cur.fetchone() + live_max = row[0] or 0 + cur.execute("SELECT MAX(footnote_id) FROM footnote_audit WHERE soa_id=?", (soa_id,)) + row = cur.fetchone() + audit_max = row[0] or 0 + conn.close() + return f"Footnote_{max(live_max, audit_max) + 1}" + + +def _row_to_dict(row) -> dict: + keys = [ + "id", + "soa_id", + "footnote_uid", + "name", + "label", + "description", + "text", + "dictionary_uid", + ] + return dict(zip(keys, row)) + + +# --------------------------------------------------------------------------- +# JSON API endpoints +# --------------------------------------------------------------------------- + + +@router.get("/footnotes", response_class=JSONResponse) +def list_footnotes(soa_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id,soa_id,footnote_uid,name,label,description,text,dictionary_uid FROM footnote WHERE soa_id=? ORDER BY id", + (soa_id,), + ) + rows = [_row_to_dict(r) for r in cur.fetchall()] + conn.close() + return JSONResponse(rows) + + +@router.post("/footnotes", response_class=JSONResponse) +def create_footnote(soa_id: int, body: FootnoteCreate): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + uid = _next_footnote_uid(soa_id) + conn = _connect() + cur = conn.cursor() + cur.execute( + "INSERT INTO footnote (soa_id, footnote_uid, name, label, description, text, dictionary_uid) VALUES (?,?,?,?,?,?,?)", + ( + soa_id, + uid, + body.name, + body.label or None, + body.description or None, + body.text or None, + body.dictionary_uid or None, + ), + ) + conn.commit() + footnote_id = cur.lastrowid + after = { + "footnote_uid": uid, + "name": body.name, + "label": body.label, + "description": body.description, + "text": body.text, + "dictionary_uid": body.dictionary_uid, + } + conn.close() + _record_footnote_audit(soa_id, "create", footnote_id, before=None, after=after) + return JSONResponse( + {"id": footnote_id, "footnote_uid": uid, **after}, status_code=201 + ) + + +@router.patch("/footnotes/{footnote_id}", response_class=JSONResponse) +def update_footnote( + soa_id: int, + footnote_id: int, + body: FootnoteUpdate, +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id,soa_id,footnote_uid,name,label,description,text,dictionary_uid FROM footnote WHERE id=? AND soa_id=?", + (footnote_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Footnote not found") + before = _row_to_dict(row) + new_name = body.name if body.name is not None else before["name"] + new_label = body.label if body.label is not None else before["label"] + new_desc = ( + body.description if body.description is not None else before["description"] + ) + new_text = body.text if body.text is not None else before["text"] + new_dict_uid = ( + body.dictionary_uid + if body.dictionary_uid is not None + else before["dictionary_uid"] + ) + cur.execute( + "UPDATE footnote SET name=?, label=?, description=?, text=?, dictionary_uid=? WHERE id=? AND soa_id=?", + ( + new_name, + new_label or None, + new_desc or None, + new_text or None, + new_dict_uid or None, + footnote_id, + soa_id, + ), + ) + conn.commit() + conn.close() + after = { + **before, + "name": new_name, + "label": new_label, + "description": new_desc, + "text": new_text, + "dictionary_uid": new_dict_uid, + } + _record_footnote_audit(soa_id, "update", footnote_id, before=before, after=after) + return JSONResponse(after) + + +@router.delete("/footnotes/{footnote_id}", response_class=JSONResponse) +def delete_footnote(soa_id: int, footnote_id: int): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + conn = _connect() + cur = conn.cursor() + cur.execute( + "SELECT id,soa_id,footnote_uid,name,label,description,text,dictionary_uid FROM footnote WHERE id=? AND soa_id=?", + (footnote_id, soa_id), + ) + row = cur.fetchone() + if not row: + conn.close() + raise HTTPException(404, "Footnote not found") + before = _row_to_dict(row) + cur.execute("DELETE FROM footnote WHERE id=? AND soa_id=?", (footnote_id, soa_id)) + conn.commit() + conn.close() + _record_footnote_audit(soa_id, "delete", footnote_id, before=before, after=None) + return JSONResponse({"deleted": footnote_id}) + + +# --------------------------------------------------------------------------- +# UI form endpoints +# --------------------------------------------------------------------------- + + +@ui_router.post("/ui/soa/{soa_id}/footnotes/create", response_class=HTMLResponse) +def ui_create_footnote( + request: Request, + soa_id: int, + name: str = Form(...), + label: str | None = Form(None), + description: str | None = Form(None), + text: str | None = Form(None), + dictionary_uid: str | None = Form(None), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + create_footnote( + soa_id, + FootnoteCreate( + name=name, + label=label, + description=description, + text=text, + dictionary_uid=dictionary_uid, + ), + ) + redirect_url = f"/ui/soa/{soa_id}/edit" + if request.headers.get("HX-Request") == "true": + return HTMLResponse("", headers={"HX-Redirect": redirect_url}) + + return RedirectResponse(redirect_url, status_code=303) + + +@ui_router.post( + "/ui/soa/{soa_id}/footnotes/{footnote_id}/update", response_class=HTMLResponse +) +def ui_update_footnote( + request: Request, + soa_id: int, + footnote_id: int, + name: str | None = Form(None), + label: str | None = Form(None), + description: str | None = Form(None), + text: str | None = Form(None), + dictionary_uid: str | None = Form(None), +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + update_footnote( + soa_id, + footnote_id, + FootnoteUpdate( + name=name, + label=label, + description=description, + text=text, + dictionary_uid=dictionary_uid, + ), + ) + redirect_url = f"/ui/soa/{soa_id}/edit" + if request.headers.get("HX-Request") == "true": + return HTMLResponse("", headers={"HX-Redirect": redirect_url}) + + return RedirectResponse(redirect_url, status_code=303) + + +@ui_router.post( + "/ui/soa/{soa_id}/footnotes/{footnote_id}/delete", response_class=HTMLResponse +) +def ui_delete_footnote( + request: Request, + soa_id: int, + footnote_id: int, +): + if not soa_exists(soa_id): + raise HTTPException(404, "SOA not found") + delete_footnote(soa_id, footnote_id) + redirect_url = f"/ui/soa/{soa_id}/edit" + if request.headers.get("HX-Request") == "true": + return HTMLResponse("", headers={"HX-Redirect": redirect_url}) + + return RedirectResponse(redirect_url, status_code=303) diff --git a/src/soa_builder/web/routers/freezes.py b/src/soa_builder/web/routers/freezes.py index 839738e2..62704520 100644 --- a/src/soa_builder/web/routers/freezes.py +++ b/src/soa_builder/web/routers/freezes.py @@ -1,14 +1,13 @@ import json import logging import os -import sqlite3 from fastapi import APIRouter, Form, HTTPException, Request from fastapi.responses import HTMLResponse, JSONResponse from fastapi.templating import Jinja2Templates +from ..db import _connect from ..utils import soa_exists -DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db") TEMPLATES_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "templates") templates = Jinja2Templates(directory=TEMPLATES_DIR) @@ -16,10 +15,6 @@ logger = logging.getLogger("soa_builder.web.routers.freezes") -def _connect(): - return sqlite3.connect(DB_PATH) - - # Removed local _soa_exists; using shared utils.soa_exists diff --git a/src/soa_builder/web/routers/rollback.py b/src/soa_builder/web/routers/rollback.py index 01a3d509..1a6f66a5 100644 --- a/src/soa_builder/web/routers/rollback.py +++ b/src/soa_builder/web/routers/rollback.py @@ -9,7 +9,6 @@ from ..utils import soa_exists -DB_PATH = os.environ.get("SOA_BUILDER_DB", "soa_builder_web.db") TEMPLATES_DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "templates") templates = Jinja2Templates(directory=TEMPLATES_DIR) diff --git a/src/soa_builder/web/routers/visits.py b/src/soa_builder/web/routers/visits.py index f40dcd21..aa4f059e 100644 --- a/src/soa_builder/web/routers/visits.py +++ b/src/soa_builder/web/routers/visits.py @@ -457,7 +457,6 @@ def update_visit(soa_id: int, visit_id: int, payload: VisitUpdate): soa_id, ), ) - conn.commit() if new_environmental_value is not None: if not env_code_uid: @@ -498,8 +497,6 @@ def update_visit(soa_id: int, visit_id: int, payload: VisitUpdate): (env_code_uid, visit_id, soa_id), ) - conn.commit() - if new_contact_mode is not None: if not contact_mode_code_uid: contact_mode_code_uid = _get_next_code_uid(cur, soa_id) @@ -539,7 +536,7 @@ def update_visit(soa_id: int, visit_id: int, payload: VisitUpdate): (contact_mode_code_uid, visit_id, soa_id), ) - conn.commit() + conn.commit() cur.execute( """ @@ -643,6 +640,7 @@ def delete_visit(soa_id: int, visit_id: int): ) row = cur.fetchone() if not row: + conn.close() raise HTTPException(404, f"Encounter id={int(visit_id)} not found") before = { diff --git a/src/soa_builder/web/schemas.py b/src/soa_builder/web/schemas.py index 1e0095c7..75002d09 100644 --- a/src/soa_builder/web/schemas.py +++ b/src/soa_builder/web/schemas.py @@ -339,3 +339,33 @@ class ConditionAssignmentUpdate(BaseModel): condition: Optional[str] = None decision_instance_uid: Optional[str] = None condition_target_uid: Optional[str] = None + + +class BCSurrogateCreate(BaseModel): + name: str + label: Optional[str] = None + description: Optional[str] = None + reference: Optional[str] = None + + +class BCSurrogateUpdate(BaseModel): + name: Optional[str] = None + label: Optional[str] = None + description: Optional[str] = None + reference: Optional[str] = None + + +class FootnoteCreate(BaseModel): + name: str + label: Optional[str] = None + description: Optional[str] = None + text: Optional[str] = None + dictionary_uid: Optional[str] = None + + +class FootnoteUpdate(BaseModel): + name: Optional[str] = None + label: Optional[str] = None + description: Optional[str] = None + text: Optional[str] = None + dictionary_uid: Optional[str] = None diff --git a/src/soa_builder/web/templates/activities.html b/src/soa_builder/web/templates/activities.html index 98ef8d11..9daefef4 100644 --- a/src/soa_builder/web/templates/activities.html +++ b/src/soa_builder/web/templates/activities.html @@ -61,7 +61,7 @@

Activities for Study: {% if study_label %}{{ study_label }}{% else %}{{ stud {% for a in activities %} -
+ {{ a.activity_uid }} @@ -73,6 +73,8 @@

Activities for Study: {% if study_label %}{{ study_label }}{% else %}{{ stud {% set concepts_list = activity_concepts.get(a.id, []) %} {% set selected_list = concepts_list %} {% set selected_codes = concepts_list | map(attribute='code') | list %} + {% set selected_surrogate_list = activity_surrogates.get(a.id, []) %} + {% set selected_surrogate_uids = selected_surrogate_list | map(attribute='surrogate_uid') | list %} {% set activity_id = a.id %} {% include 'concepts_cell.html' %} {% set activity_id = a.id %} @@ -94,6 +96,70 @@

Activities for Study: {% if study_label %}{{ study_label }}{% else %}{{ stud {% endfor %} +
+

Biomedical Concept Surrogates

+

+ Add named placeholders for concepts not yet available in the CDISC Library. + Once a CDISC Biomedical Concept is assigned, remove the surrogate. +

+ +
+ +
+ + +
+
+ + +
+
+ + +
+
+ + +
+ + +
+ +{% if surrogates %} + + + + + + + + + + + {% for s in surrogates %} + + + + + + + + + + + + {% endfor %} +
UIDNameLabelDescriptionReferenceSaveDelete
{{ s.surrogate_uid }} + + +
+ +
+
+{% else %} +

No surrogates defined yet.

+{% endif %} +