diff --git a/.github/workflows/RTest.yml b/.github/workflows/RTest.yml index a8016185..ab00a5c6 100644 --- a/.github/workflows/RTest.yml +++ b/.github/workflows/RTest.yml @@ -29,7 +29,7 @@ jobs: with: cache: false working-directory: ./client-api_r/generated - - name: Install Rsirius + - name: Install RSirius id: rsirius_install run: | install.packages("/home/runner/work/sirius-client-openAPI/sirius-client-openAPI/client-api_r/generated", repos = NULL, type = "source") @@ -62,7 +62,7 @@ jobs: - name: Login to SIRIUS id: login run: | - library(Rsirius) + library(RSirius) var_accept_terms <- TRUE var_account_credentials <- AccountCredentials$new(Sys.getenv('SIRIUS_USER'), Sys.getenv('SIRIUS_PW')) api_instance <- rsirius_api$new() @@ -78,7 +78,7 @@ jobs: - name: Test Actuator API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_actuator_api.R", reporter=multi_reporter) @@ -86,7 +86,7 @@ jobs: - name: Test Info API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_info_api.R", reporter=multi_reporter) @@ -94,7 +94,7 @@ jobs: - name: Test Login and Account API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_login_and_account_api.R", reporter=multi_reporter) @@ -102,7 +102,7 @@ jobs: - name: Test Projects API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_projects_api.R", reporter=multi_reporter) @@ -110,7 +110,7 @@ jobs: - name: Test Compounds API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_compounds_api.R", reporter=multi_reporter) @@ -118,7 +118,7 @@ jobs: - name: Test Databases API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_searchable_databases_api.R", reporter=multi_reporter) @@ -126,7 +126,7 @@ jobs: - name: Test Features API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_features_api.R", reporter=multi_reporter) @@ -134,7 +134,7 @@ jobs: - name: Test Jobs API if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_jobs_api.R", reporter=multi_reporter) @@ -142,8 +142,8 @@ jobs: - name: Test acceptance if: always() && steps.api_start.outcome == 'success' && steps.rsirius_install.outcome == 'success' && steps.login.outcome == 'success' run: | - library(Rsirius) + library(RSirius) library(testthat) multi_reporter = MultiReporter$new(reporters=list(SummaryReporter$new(), FailReporter$new())) test_file("client-api_r/generated/tests/testthat/test_acceptance.R", reporter=multi_reporter) - shell: Rscript {0} \ No newline at end of file + shell: Rscript {0} diff --git a/.updater/config/R/config.json b/.updater/config/R/config.json index f28b9749..45c76429 100644 --- a/.updater/config/R/config.json +++ b/.updater/config/R/config.json @@ -1,5 +1,5 @@ { - "packageName" : "Rsirius", + "packageName" : "RSirius", "generateWrapper": true, "library": "httr2", "hideGenerationTimestamp": true diff --git a/client-api_r/SiriusSDK.R b/client-api_r/SiriusSDK.R index 6fe1a36f..fc1936ef 100644 --- a/client-api_r/SiriusSDK.R +++ b/client-api_r/SiriusSDK.R @@ -32,13 +32,13 @@ SiriusSDK <- R6::R6Class( connect = function(url) { self$host <- url - self$api_client <- Rsirius::ApiClient$new(self$host) - return(Rsirius::rsirius_api$new(self$api_client)) + self$api_client <- RSirius::ApiClient$new(self$host) + return(RSirius::rsirius_api$new(self$api_client)) }, reconnect = function() { if (!is.null(self$api_client) && !is.null(self$process) && self$process$is_alive()) { - return(Rsirius::rsirius_api(self$api_client)) + return(RSirius::rsirius_api(self$api_client)) } cat("Cannot reconnect, api_client and/or process are NULL or process has terminated.\n") return(NULL) @@ -105,8 +105,8 @@ SiriusSDK <- R6::R6Class( # check if connection to API client is possible if (!is.null(self$api_client)) { tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) } }, error = function(e) { message("Found existing API Client, but could not reach API.") @@ -119,8 +119,8 @@ SiriusSDK <- R6::R6Class( sirius_api <- self$connect(self$host) self$api_client <- sirius_api$api_client tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) } }, error = function(e) { message("Found existing port, but could not reach API under this port.") @@ -162,8 +162,8 @@ SiriusSDK <- R6::R6Class( self$api_client <- sirius_api$api_client tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) } }, error = function(e) { message("Created API client from process_id and port, but could not reach API.") @@ -287,7 +287,7 @@ SiriusSDK <- R6::R6Class( shutdown_sirius = function() { if (!is.null(self$process)) { tryCatch({ - Rsirius::ActuatorApi$new(self$api_client)$Shutdown() + RSirius::ActuatorApi$new(self$api_client)$Shutdown() Sys.sleep(3) if (!self$process$is_alive()) { cat("Sirius was shut down successfully\n") diff --git a/client-api_r/generated/.Rbuildignore b/client-api_r/generated/.Rbuildignore index 0df5be23..d0e83e70 100644 --- a/client-api_r/generated/.Rbuildignore +++ b/client-api_r/generated/.Rbuildignore @@ -16,5 +16,5 @@ ^\.openapi-generator$ ^docs$ ^git_push\.sh$ -^Rsirius\.Rcheck$ +^RSirius\.Rcheck$ ^\.\.Rcheck$ diff --git a/client-api_r/generated/DESCRIPTION b/client-api_r/generated/DESCRIPTION index 63240e0c..b7ddcd27 100644 --- a/client-api_r/generated/DESCRIPTION +++ b/client-api_r/generated/DESCRIPTION @@ -1,4 +1,4 @@ -Package: Rsirius +Package: RSirius Title: R Package Client for SIRIUS Nightsky API Version: 6.3.3 Author: person("OpenAPI Generator community", email = "team@openapitools.org", role = c("aut", "cre")) diff --git a/client-api_r/generated/R/SiriusSDK.R b/client-api_r/generated/R/SiriusSDK.R index 6fe1a36f..5ce6ec5f 100644 --- a/client-api_r/generated/R/SiriusSDK.R +++ b/client-api_r/generated/R/SiriusSDK.R @@ -1,434 +1,434 @@ -SiriusSDK <- R6::R6Class( - "SiriusSDK", - public = list( - port = NULL, - host = NULL, - sirius_path = NULL, - projectspace = NULL, - workspace = NULL, - process = NULL, - process_id = NULL, - api_client = NULL, - run_command = NULL, - run_args = NULL, - - reset_sdk_class = function() { - self$port <- NULL - self$host <- NULL - self$sirius_path <- NULL - self$projectspace <- NULL - self$workspace <- NULL - self$process <- NULL - self$process_id <- NULL - self$api_client <- NULL - self$run_command <- NULL - self$run_args <- NULL - }, - - reset_sdk_process = function() { - self$process <- NULL - self$process_id <- NULL - }, - - connect = function(url) { - self$host <- url - self$api_client <- Rsirius::ApiClient$new(self$host) - return(Rsirius::rsirius_api$new(self$api_client)) - }, - - reconnect = function() { - if (!is.null(self$api_client) && !is.null(self$process) && self$process$is_alive()) { - return(Rsirius::rsirius_api(self$api_client)) - } - cat("Cannot reconnect, api_client and/or process are NULL or process has terminated.\n") - return(NULL) - }, - - restart_sirius = function() { - if (!is.null(self$run_command) && !is.null(self$run_args) && !is.null(self$process) && !is.null(self$api_client)) { - if (inherits(self$shutdown_sirius(), "logical")) { - cat("Shutdown seems to have gone wrong, aborting restart...\n") - return(NULL) - } - - self$process <- processx::process$new(command = self$run_command, args = self$run_args) - for (i in 1:60) { - Sys.sleep(1) - tryCatch({ - if (self$process$is_alive()) { - found <- private$cycle_find_sirius_pid_and_port() - if (!found) { - cat("Could not find sirius.port file. Please terminate SIRIUS if needed and try specifying a port\n") - cat("Alternatively, try attaching to a running SIRIUS instance with attach_to_running_sirius()\n") - return(NULL) - } - # connect() sets self$host and self$api_client - host <- paste0('http://localhost:', self$port) - sirius_api <- self$connect(host) - return(sirius_api) - } else { - cat("The SIRIUS process seems to have exited during startup. Please investigate this error.\n") - self$reset_sdk_class() - } - }, error = function(e) { - cat(e$message, "\n") - }) - } - - cat("SIRIUS seems to have problems starting. Resetting SiriusSDK...\n") - self$reset_sdk_class() - return(NULL) - } - cat("Could not attempt REST restart, run_command, run_args, process or api_client are NULL.\n") - return(NULL) - }, - - attach_or_start_sirius = function(headless = NULL) { - sirius_api <- self$attach_to_sirius() - # attachment encountered issue - if (is.logical(sirius_api)) { - return(NULL) - } - # attachment did not encounter issue but also found no SIRIUS - else if (is.null(sirius_api)) { - sirius_api <- self$start_sirius(headless = headless) - } - # attachment successful - else { - message("Attached to running SIRIUS instance.") - } - return(sirius_api) - }, - - attach_to_sirius = function(sirius_major_version = NULL, sirius_port = NULL) { - - # check if connection to API client is possible - if (!is.null(self$api_client)) { - tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) - } - }, error = function(e) { - message("Found existing API Client, but could not reach API.") - }) - } - - # create and check API client from existing port - if (!is.null(self$port)) { - self$host <- paste0('http://localhost:', self$port) - sirius_api <- self$connect(self$host) - self$api_client <- sirius_api$api_client - tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) - } - }, error = function(e) { - message("Found existing port, but could not reach API under this port.") - }) - } - - # if client is not reachable, search for process and kill if necessary - if (!is.null(self$process)) { - if (self$process$is_alive()) { - message("The SIRIUS process still seems to be lingering, but no connection could be made to the API.") - message("Shutting down the process...") - if (inherits(self$shutdown_sirius(), "logical")) { - # before error messages will be done by shutdown function - message("Aborting....") - return(FALSE) - } - message("Process shut down successfully.") - } else { - message("Known process seems to have terminated at some time.") - } - } - - self$reset_sdk_class() - message("SiriusSDK has been reset. Continuing with search for new SIRIUS instance...") - - if (!is.null(sirius_port)) { - self$port <- sirius_port - } else { - found <- private$find_sirius_pid_and_port(sirius_major_version) - if (!found) { - message("No port file matching ~/.sirius/sirius-X.X.port was found.") - message("Please try providing the port.") - return(NULL) - } - } - - self$host <- paste0('http://localhost:', self$port) - sirius_api <- self$connect(self$host) - self$api_client <- sirius_api$api_client - - tryCatch({ - if (Rsirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { - return(Rsirius::rsirius_api$new(self$api_client)) - } - }, error = function(e) { - message("Created API client from process_id and port, but could not reach API.") - }) - - message("Files for SIRIUS process_id and port have been found, but do not belong to an alive API.") - message("Process_id and port files will be deleted and start_sirius will be called.") - private$delete_sirius_pid_and_port(sirius_major_version) - self$reset_sdk_class() - - return(NULL) - }, - - start_sirius = function(sirius_path = NULL, port = NULL, projectspace = NULL, workspace = NULL, forceStart = FALSE, headless = NULL) { - if (!is.null(self$process) && !forceStart) { - cat("Sirius seems to have already been started with PID:", self$process$get_pid(), ".\n") - cat("Use reconnect() to get a new API instance for your current SIRIUS.\n") - cat("Use shutdown_sirius() and then start_sirius() to restart SIRIUS and get a new API instance.\n") - cat("If you are sure the process is not running anymore, use reset_sdk_process() or reset the complete SDK using reset_sdk_class() before calling start() again.\n") - cat("[NOT RECOMMENDED] Use start with forceStart=TRUE to skip this warning and start a second service.\n") - return(NULL) - } - - self$workspace <- workspace - - if (!is.null(sirius_path)) { - if (!file.exists(sirius_path)) { - cat("Wrong path to executable.\n") - self$reset_sdk_class() - return(NULL) - } - self$sirius_path <- normalizePath(sirius_path) - } else { - if (Sys.getenv("PATH") == "" || !grepl("sirius", Sys.getenv("PATH"))) { - cat("Please provide a path to the sirius executable if not declared in PATH!\n") - self$reset_sdk_class() - return(NULL) - } - cat("Found SIRIUS in PATH! Using this information to start the application.\n") - self$sirius_path <- 'sirius' - } - - if (!is.null(projectspace)) { - if (!file.exists(projectspace)) { - cat("Wrong path to project space.\n") - self$reset_sdk_class() - return(NULL) - } - self$projectspace <- normalizePath(projectspace) - run_args <- c("--output", self$projectspace, "REST", "-s") - } else { - run_args <- c("REST", "-s") - } - - if (!is.null(workspace)) { - if (!file.exists(workspace)) { - cat("Wrong path to workspace\n") - self$reset_sdk_class() - return(NULL) - } - cat("[WARNING] Overwriting workspace location [NOT RECOMMENDED]\n") - self$workspace <- normalizePath(workspace) - run_args <- append(run_args, c("--workspace", workspace), 3) - } - - if (!is.null(port)) { - self$port <- port - run_args <- append(run_args, c("-p", as.character(port))) - } - - if (!is.null(headless) && headless == TRUE) { - run_args <- append(run_args, "--headless") - } else if (!is.null(headless) && headless == FALSE) { - run_args <- append(run_args, "--no-headless") - } - - self$run_command <- self$sirius_path - self$run_args <- run_args - self$process <- processx::process$new(command = self$run_command, args = self$run_args) - self$process_id <- self$process$get_pid() - - if (is.null(port)) { - cat("SIRIUS was started without specifying --port (-p), trying to find the sirius.port file.\n") - if (is.null(workspace)) { - found <- private$cycle_find_sirius_pid_and_port() - } else { - found <- private$cycle_find_sirius_pid_and_port(folder = workspace) - } - if (!found) { - cat("Could not find sirius.port file. Please terminate SIRIUS if needed and try specifying a port\n") - cat("Alternatively, try attaching to a running SIRIUS instance with attach_to_running_sirius()\n") - return(NULL) - } - } - - self$host <- paste0('http://localhost:', self$port) - sirius_api <- self$connect(self$host) - self$api_client <- sirius_api$api_client - - for (i in 1:30) { - Sys.sleep(1) - tryCatch({ - if (self$process$is_alive()) { - if (sirius_api$actuator_api$Health()$status == "UP") { - return(sirius_api) - } - } else { - cat("The SIRIUS process seems to have exited during startup. Please investigate this error.\n") - self$reset_sdk_class() - } - }, error = function(e) { - cat(e$message, "\n") - }) - } - - cat("SIRIUS seems to have problems starting. Resetting SiriusSDK...\n") - self$reset_sdk_class() - return(NULL) - }, - - shutdown_sirius = function() { - if (!is.null(self$process)) { - tryCatch({ - Rsirius::ActuatorApi$new(self$api_client)$Shutdown() - Sys.sleep(3) - if (!self$process$is_alive()) { - cat("Sirius was shut down successfully\n") - self$reset_sdk_process() - return(NULL) - } - }, error = function(e) { - cat("An Exception occurred while trying to gracefully shutdown SIRIUS!\n") - cat(e$message, "\n") - }) - - self$process$interrupt() - Sys.sleep(3) - if (!self$process$is_alive()) { - cat("Sirius process has been terminated.\n") - self$reset_sdk_process() - return(NULL) - } - - self$process$kill() - Sys.sleep(3) - if (!self$process$is_alive()) { - cat("Sirius process has been killed.\n") - self$reset_sdk_process() - return(NULL) - } - - cat("Unable to stop Sirius! - Please manually terminate the process with PID ", self$process$get_pid(), "\n") - cat("After terminating the process, use start_sirius() to start a new instance of SIRIUS.\n") - return(FALSE) - } else if (!is.null(self$process_id)) { - system(paste("kill -SIGTERM", self$process_id)) - Sys.sleep(3) - tryCatch({ - system(paste("kill -0", self$process_id)) - }, error = function(e) { - cat("Sirius process has been terminated.\n") - self$reset_sdk_process() - return(NULL) - }) - - system(paste("kill -SIGKILL", self$process_id)) - Sys.sleep(3) - tryCatch({ - system(paste("kill -0", self$process_id)) - }, error = function(e) { - cat("Sirius process has been killed.\n") - self$reset_sdk_process() - return(NULL) - }) - - cat("Unable to stop Sirius! - Please manually terminate the process with PID ", self$process_id, "\n") - cat("After terminating the process, use start_sirius() to start a new instance of SIRIUS.\n") - return(FALSE) - } else { - cat("There does not seem to be any process or process_id to shut down...\n") - return(FALSE) - } - } - ), - - private = list( - are_all_vars_none = function() { - all_names <- ls(envir = self, all.names = TRUE) - # exclude functions - field_names <- all_names[sapply(all_names, function(name) !is.function(self[[name]]))] - # exclude ".__enclos_env__" - field_names <- field_names[-1] - all(sapply(field_names, function(name) is.null(self[[name]]))) - }, - - find_sirius_pid_and_port = function(sirius_version = NULL) { - result = private$get_sirius_pid_and_port(sirius_version) - if (is.logical(result)) { - return(FALSE) - } - pid_file = result[[1]] - port_file = result[[2]] - pid <- as.integer(readLines(pid_file, warn = FALSE)) - port <- as.integer(readLines(port_file, warn = FALSE)) - - self$process_id <- pid - self$port <- port - - message("Using port ", port, " from file ", port_file) - message("Using PID ", pid, " from file ", pid_file) - return(TRUE) - }, - - delete_sirius_pid_and_port = function(sirius_version = NULL) { - result = private$get_sirius_pid_and_port(sirius_version) - if (is.logical(result)) { - return(FALSE) - } - pid_file = result[[1]] - port_file = result[[2]] - file.remove(pid_file) - file.remove (port_file) - }, - - get_sirius_pid_and_port = function(sirius_version = NULL) { - if (Sys.info()['sysname']=="Windows") { - global_workspace <- file.path(Sys.getenv("USERPROFILE"), ".sirius") - } else { - global_workspace <- path.expand("~/.sirius") - } - - if (is.null(sirius_version) || sirius_version == "None") { - port_pattern_match <- "[0-9]*" - } else { - port_pattern_match <- sirius_version - } - - port_pattern <- file.path(global_workspace, paste0("sirius-", port_pattern_match, ".port")) - port_files <- Sys.glob(port_pattern) - - if (length(port_files) == 0) { - return(FALSE) - } - - if (length(port_files) > 1) { - message("Following sirius port files detected:") - for (f in port_files) { - message(f) - } - } - - port_file <- sort(port_files)[length(port_files)] - pid_file <- sub(".port$", ".pid", port_file) - - return(c(pid_file, port_file)) - }, - - cycle_find_sirius_pid_and_port = function() { - for (i in 1:30) { - Sys.sleep(1) - if (private$find_sirius_pid_and_port()) { - return(TRUE) - } - } - return(FALSE) - } - ) -) +SiriusSDK <- R6::R6Class( + "SiriusSDK", + public = list( + port = NULL, + host = NULL, + sirius_path = NULL, + projectspace = NULL, + workspace = NULL, + process = NULL, + process_id = NULL, + api_client = NULL, + run_command = NULL, + run_args = NULL, + + reset_sdk_class = function() { + self$port <- NULL + self$host <- NULL + self$sirius_path <- NULL + self$projectspace <- NULL + self$workspace <- NULL + self$process <- NULL + self$process_id <- NULL + self$api_client <- NULL + self$run_command <- NULL + self$run_args <- NULL + }, + + reset_sdk_process = function() { + self$process <- NULL + self$process_id <- NULL + }, + + connect = function(url) { + self$host <- url + self$api_client <- RSirius::ApiClient$new(self$host) + return(RSirius::rsirius_api$new(self$api_client)) + }, + + reconnect = function() { + if (!is.null(self$api_client) && !is.null(self$process) && self$process$is_alive()) { + return(RSirius::rsirius_api(self$api_client)) + } + cat("Cannot reconnect, api_client and/or process are NULL or process has terminated.\n") + return(NULL) + }, + + restart_sirius = function() { + if (!is.null(self$run_command) && !is.null(self$run_args) && !is.null(self$process) && !is.null(self$api_client)) { + if (inherits(self$shutdown_sirius(), "logical")) { + cat("Shutdown seems to have gone wrong, aborting restart...\n") + return(NULL) + } + + self$process <- processx::process$new(command = self$run_command, args = self$run_args) + for (i in 1:60) { + Sys.sleep(1) + tryCatch({ + if (self$process$is_alive()) { + found <- private$cycle_find_sirius_pid_and_port() + if (!found) { + cat("Could not find sirius.port file. Please terminate SIRIUS if needed and try specifying a port\n") + cat("Alternatively, try attaching to a running SIRIUS instance with attach_to_running_sirius()\n") + return(NULL) + } + # connect() sets self$host and self$api_client + host <- paste0('http://localhost:', self$port) + sirius_api <- self$connect(host) + return(sirius_api) + } else { + cat("The SIRIUS process seems to have exited during startup. Please investigate this error.\n") + self$reset_sdk_class() + } + }, error = function(e) { + cat(e$message, "\n") + }) + } + + cat("SIRIUS seems to have problems starting. Resetting SiriusSDK...\n") + self$reset_sdk_class() + return(NULL) + } + cat("Could not attempt REST restart, run_command, run_args, process or api_client are NULL.\n") + return(NULL) + }, + + attach_or_start_sirius = function(headless = NULL) { + sirius_api <- self$attach_to_sirius() + # attachment encountered issue + if (is.logical(sirius_api)) { + return(NULL) + } + # attachment did not encounter issue but also found no SIRIUS + else if (is.null(sirius_api)) { + sirius_api <- self$start_sirius(headless = headless) + } + # attachment successful + else { + message("Attached to running SIRIUS instance.") + } + return(sirius_api) + }, + + attach_to_sirius = function(sirius_major_version = NULL, sirius_port = NULL) { + + # check if connection to API client is possible + if (!is.null(self$api_client)) { + tryCatch({ + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) + } + }, error = function(e) { + message("Found existing API Client, but could not reach API.") + }) + } + + # create and check API client from existing port + if (!is.null(self$port)) { + self$host <- paste0('http://localhost:', self$port) + sirius_api <- self$connect(self$host) + self$api_client <- sirius_api$api_client + tryCatch({ + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) + } + }, error = function(e) { + message("Found existing port, but could not reach API under this port.") + }) + } + + # if client is not reachable, search for process and kill if necessary + if (!is.null(self$process)) { + if (self$process$is_alive()) { + message("The SIRIUS process still seems to be lingering, but no connection could be made to the API.") + message("Shutting down the process...") + if (inherits(self$shutdown_sirius(), "logical")) { + # before error messages will be done by shutdown function + message("Aborting....") + return(FALSE) + } + message("Process shut down successfully.") + } else { + message("Known process seems to have terminated at some time.") + } + } + + self$reset_sdk_class() + message("SiriusSDK has been reset. Continuing with search for new SIRIUS instance...") + + if (!is.null(sirius_port)) { + self$port <- sirius_port + } else { + found <- private$find_sirius_pid_and_port(sirius_major_version) + if (!found) { + message("No port file matching ~/.sirius/sirius-X.X.port was found.") + message("Please try providing the port.") + return(NULL) + } + } + + self$host <- paste0('http://localhost:', self$port) + sirius_api <- self$connect(self$host) + self$api_client <- sirius_api$api_client + + tryCatch({ + if (RSirius::ActuatorApi$new(self$api_client)$Health()$status == "UP") { + return(RSirius::rsirius_api$new(self$api_client)) + } + }, error = function(e) { + message("Created API client from process_id and port, but could not reach API.") + }) + + message("Files for SIRIUS process_id and port have been found, but do not belong to an alive API.") + message("Process_id and port files will be deleted and start_sirius will be called.") + private$delete_sirius_pid_and_port(sirius_major_version) + self$reset_sdk_class() + + return(NULL) + }, + + start_sirius = function(sirius_path = NULL, port = NULL, projectspace = NULL, workspace = NULL, forceStart = FALSE, headless = NULL) { + if (!is.null(self$process) && !forceStart) { + cat("Sirius seems to have already been started with PID:", self$process$get_pid(), ".\n") + cat("Use reconnect() to get a new API instance for your current SIRIUS.\n") + cat("Use shutdown_sirius() and then start_sirius() to restart SIRIUS and get a new API instance.\n") + cat("If you are sure the process is not running anymore, use reset_sdk_process() or reset the complete SDK using reset_sdk_class() before calling start() again.\n") + cat("[NOT RECOMMENDED] Use start with forceStart=TRUE to skip this warning and start a second service.\n") + return(NULL) + } + + self$workspace <- workspace + + if (!is.null(sirius_path)) { + if (!file.exists(sirius_path)) { + cat("Wrong path to executable.\n") + self$reset_sdk_class() + return(NULL) + } + self$sirius_path <- normalizePath(sirius_path) + } else { + if (Sys.getenv("PATH") == "" || !grepl("sirius", Sys.getenv("PATH"))) { + cat("Please provide a path to the sirius executable if not declared in PATH!\n") + self$reset_sdk_class() + return(NULL) + } + cat("Found SIRIUS in PATH! Using this information to start the application.\n") + self$sirius_path <- 'sirius' + } + + if (!is.null(projectspace)) { + if (!file.exists(projectspace)) { + cat("Wrong path to project space.\n") + self$reset_sdk_class() + return(NULL) + } + self$projectspace <- normalizePath(projectspace) + run_args <- c("--output", self$projectspace, "REST", "-s") + } else { + run_args <- c("REST", "-s") + } + + if (!is.null(workspace)) { + if (!file.exists(workspace)) { + cat("Wrong path to workspace\n") + self$reset_sdk_class() + return(NULL) + } + cat("[WARNING] Overwriting workspace location [NOT RECOMMENDED]\n") + self$workspace <- normalizePath(workspace) + run_args <- append(run_args, c("--workspace", workspace), 3) + } + + if (!is.null(port)) { + self$port <- port + run_args <- append(run_args, c("-p", as.character(port))) + } + + if (!is.null(headless) && headless == TRUE) { + run_args <- append(run_args, "--headless") + } else if (!is.null(headless) && headless == FALSE) { + run_args <- append(run_args, "--no-headless") + } + + self$run_command <- self$sirius_path + self$run_args <- run_args + self$process <- processx::process$new(command = self$run_command, args = self$run_args) + self$process_id <- self$process$get_pid() + + if (is.null(port)) { + cat("SIRIUS was started without specifying --port (-p), trying to find the sirius.port file.\n") + if (is.null(workspace)) { + found <- private$cycle_find_sirius_pid_and_port() + } else { + found <- private$cycle_find_sirius_pid_and_port(folder = workspace) + } + if (!found) { + cat("Could not find sirius.port file. Please terminate SIRIUS if needed and try specifying a port\n") + cat("Alternatively, try attaching to a running SIRIUS instance with attach_to_running_sirius()\n") + return(NULL) + } + } + + self$host <- paste0('http://localhost:', self$port) + sirius_api <- self$connect(self$host) + self$api_client <- sirius_api$api_client + + for (i in 1:30) { + Sys.sleep(1) + tryCatch({ + if (self$process$is_alive()) { + if (sirius_api$actuator_api$Health()$status == "UP") { + return(sirius_api) + } + } else { + cat("The SIRIUS process seems to have exited during startup. Please investigate this error.\n") + self$reset_sdk_class() + } + }, error = function(e) { + cat(e$message, "\n") + }) + } + + cat("SIRIUS seems to have problems starting. Resetting SiriusSDK...\n") + self$reset_sdk_class() + return(NULL) + }, + + shutdown_sirius = function() { + if (!is.null(self$process)) { + tryCatch({ + RSirius::ActuatorApi$new(self$api_client)$Shutdown() + Sys.sleep(3) + if (!self$process$is_alive()) { + cat("Sirius was shut down successfully\n") + self$reset_sdk_process() + return(NULL) + } + }, error = function(e) { + cat("An Exception occurred while trying to gracefully shutdown SIRIUS!\n") + cat(e$message, "\n") + }) + + self$process$interrupt() + Sys.sleep(3) + if (!self$process$is_alive()) { + cat("Sirius process has been terminated.\n") + self$reset_sdk_process() + return(NULL) + } + + self$process$kill() + Sys.sleep(3) + if (!self$process$is_alive()) { + cat("Sirius process has been killed.\n") + self$reset_sdk_process() + return(NULL) + } + + cat("Unable to stop Sirius! - Please manually terminate the process with PID ", self$process$get_pid(), "\n") + cat("After terminating the process, use start_sirius() to start a new instance of SIRIUS.\n") + return(FALSE) + } else if (!is.null(self$process_id)) { + system(paste("kill -SIGTERM", self$process_id)) + Sys.sleep(3) + tryCatch({ + system(paste("kill -0", self$process_id)) + }, error = function(e) { + cat("Sirius process has been terminated.\n") + self$reset_sdk_process() + return(NULL) + }) + + system(paste("kill -SIGKILL", self$process_id)) + Sys.sleep(3) + tryCatch({ + system(paste("kill -0", self$process_id)) + }, error = function(e) { + cat("Sirius process has been killed.\n") + self$reset_sdk_process() + return(NULL) + }) + + cat("Unable to stop Sirius! - Please manually terminate the process with PID ", self$process_id, "\n") + cat("After terminating the process, use start_sirius() to start a new instance of SIRIUS.\n") + return(FALSE) + } else { + cat("There does not seem to be any process or process_id to shut down...\n") + return(FALSE) + } + } + ), + + private = list( + are_all_vars_none = function() { + all_names <- ls(envir = self, all.names = TRUE) + # exclude functions + field_names <- all_names[sapply(all_names, function(name) !is.function(self[[name]]))] + # exclude ".__enclos_env__" + field_names <- field_names[-1] + all(sapply(field_names, function(name) is.null(self[[name]]))) + }, + + find_sirius_pid_and_port = function(sirius_version = NULL) { + result = private$get_sirius_pid_and_port(sirius_version) + if (is.logical(result)) { + return(FALSE) + } + pid_file = result[[1]] + port_file = result[[2]] + pid <- as.integer(readLines(pid_file, warn = FALSE)) + port <- as.integer(readLines(port_file, warn = FALSE)) + + self$process_id <- pid + self$port <- port + + message("Using port ", port, " from file ", port_file) + message("Using PID ", pid, " from file ", pid_file) + return(TRUE) + }, + + delete_sirius_pid_and_port = function(sirius_version = NULL) { + result = private$get_sirius_pid_and_port(sirius_version) + if (is.logical(result)) { + return(FALSE) + } + pid_file = result[[1]] + port_file = result[[2]] + file.remove(pid_file) + file.remove (port_file) + }, + + get_sirius_pid_and_port = function(sirius_version = NULL) { + if (Sys.info()['sysname']=="Windows") { + global_workspace <- file.path(Sys.getenv("USERPROFILE"), ".sirius") + } else { + global_workspace <- path.expand("~/.sirius") + } + + if (is.null(sirius_version) || sirius_version == "None") { + port_pattern_match <- "[0-9]*" + } else { + port_pattern_match <- sirius_version + } + + port_pattern <- file.path(global_workspace, paste0("sirius-", port_pattern_match, ".port")) + port_files <- Sys.glob(port_pattern) + + if (length(port_files) == 0) { + return(FALSE) + } + + if (length(port_files) > 1) { + message("Following sirius port files detected:") + for (f in port_files) { + message(f) + } + } + + port_file <- sort(port_files)[length(port_files)] + pid_file <- sub(".port$", ".pid", port_file) + + return(c(pid_file, port_file)) + }, + + cycle_find_sirius_pid_and_port = function() { + for (i in 1:30) { + Sys.sleep(1) + if (private$find_sirius_pid_and_port()) { + return(TRUE) + } + } + return(FALSE) + } + ) +) diff --git a/client-api_r/generated/R/account_info.R b/client-api_r/generated/R/account_info.R index dd6ad56c..1871c94b 100644 --- a/client-api_r/generated/R/account_info.R +++ b/client-api_r/generated/R/account_info.R @@ -152,7 +152,7 @@ AccountInfo <- R6::R6Class( self$`gravatarURL` <- this_object$`gravatarURL` } if (!is.null(this_object$`subscriptions`)) { - self$`subscriptions` <- ApiClient$new()$deserializeObj(this_object$`subscriptions`, "array[Subscription]", loadNamespace("Rsirius")) + self$`subscriptions` <- ApiClient$new()$deserializeObj(this_object$`subscriptions`, "array[Subscription]", loadNamespace("RSirius")) } if (!is.null(this_object$`activeSubscriptionId`)) { self$`activeSubscriptionId` <- this_object$`activeSubscriptionId` @@ -182,7 +182,7 @@ AccountInfo <- R6::R6Class( self$`username` <- this_object$`username` self$`userEmail` <- this_object$`userEmail` self$`gravatarURL` <- this_object$`gravatarURL` - self$`subscriptions` <- ApiClient$new()$deserializeObj(this_object$`subscriptions`, "array[Subscription]", loadNamespace("Rsirius")) + self$`subscriptions` <- ApiClient$new()$deserializeObj(this_object$`subscriptions`, "array[Subscription]", loadNamespace("RSirius")) self$`activeSubscriptionId` <- this_object$`activeSubscriptionId` self }, diff --git a/client-api_r/generated/R/actuator_api.R b/client-api_r/generated/R/actuator_api.R index c313aa25..0492ee98 100644 --- a/client-api_r/generated/R/actuator_api.R +++ b/client-api_r/generated/R/actuator_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### Health #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Actuator web endpoint 'health' #' api_instance <- rsirius_api$new() @@ -28,7 +28,7 @@ #' #' #################### Shutdown #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Actuator web endpoint 'shutdown' #' api_instance <- rsirius_api$new() @@ -148,7 +148,7 @@ ActuatorApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "object", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "object", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/adduct_network_experimental.R b/client-api_r/generated/R/adduct_network_experimental.R index 92936697..fc8ef068 100644 --- a/client-api_r/generated/R/adduct_network_experimental.R +++ b/client-api_r/generated/R/adduct_network_experimental.R @@ -87,10 +87,10 @@ AdductNetworkExperimental <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`nodes`)) { - self$`nodes` <- ApiClient$new()$deserializeObj(this_object$`nodes`, "array[AdductNodeExperimental]", loadNamespace("Rsirius")) + self$`nodes` <- ApiClient$new()$deserializeObj(this_object$`nodes`, "array[AdductNodeExperimental]", loadNamespace("RSirius")) } if (!is.null(this_object$`edges`)) { - self$`edges` <- ApiClient$new()$deserializeObj(this_object$`edges`, "array[AdductEdgeExperimental]", loadNamespace("Rsirius")) + self$`edges` <- ApiClient$new()$deserializeObj(this_object$`edges`, "array[AdductEdgeExperimental]", loadNamespace("RSirius")) } self }, @@ -113,8 +113,8 @@ AdductNetworkExperimental <- R6::R6Class( #' @return the instance of AdductNetworkExperimental fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`nodes` <- ApiClient$new()$deserializeObj(this_object$`nodes`, "array[AdductNodeExperimental]", loadNamespace("Rsirius")) - self$`edges` <- ApiClient$new()$deserializeObj(this_object$`edges`, "array[AdductEdgeExperimental]", loadNamespace("Rsirius")) + self$`nodes` <- ApiClient$new()$deserializeObj(this_object$`nodes`, "array[AdductNodeExperimental]", loadNamespace("RSirius")) + self$`edges` <- ApiClient$new()$deserializeObj(this_object$`edges`, "array[AdductEdgeExperimental]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/adduct_node_experimental.R b/client-api_r/generated/R/adduct_node_experimental.R index 4d77aa17..b2f86c8b 100644 --- a/client-api_r/generated/R/adduct_node_experimental.R +++ b/client-api_r/generated/R/adduct_node_experimental.R @@ -107,7 +107,7 @@ AdductNodeExperimental <- R6::R6Class( self$`mz` <- this_object$`mz` } if (!is.null(this_object$`adductAnnotations`)) { - self$`adductAnnotations` <- ApiClient$new()$deserializeObj(this_object$`adductAnnotations`, "map(numeric)", loadNamespace("Rsirius")) + self$`adductAnnotations` <- ApiClient$new()$deserializeObj(this_object$`adductAnnotations`, "map(numeric)", loadNamespace("RSirius")) } self }, @@ -132,7 +132,7 @@ AdductNodeExperimental <- R6::R6Class( this_object <- jsonlite::fromJSON(input_json) self$`alignedFeatureId` <- this_object$`alignedFeatureId` self$`mz` <- this_object$`mz` - self$`adductAnnotations` <- ApiClient$new()$deserializeObj(this_object$`adductAnnotations`, "map(numeric)", loadNamespace("Rsirius")) + self$`adductAnnotations` <- ApiClient$new()$deserializeObj(this_object$`adductAnnotations`, "map(numeric)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/aligned_feature.R b/client-api_r/generated/R/aligned_feature.R index 9c36aee4..e7e0a8b5 100644 --- a/client-api_r/generated/R/aligned_feature.R +++ b/client-api_r/generated/R/aligned_feature.R @@ -324,7 +324,7 @@ AlignedFeature <- R6::R6Class( self$`charge` <- this_object$`charge` } if (!is.null(this_object$`detectedAdducts`)) { - self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("Rsirius")) + self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("RSirius")) if (!identical(self$`detectedAdducts`, unique(self$`detectedAdducts`))) { stop("Error! Items in `detectedAdducts` are not unique.") } @@ -374,7 +374,7 @@ AlignedFeature <- R6::R6Class( self$`computedTools` <- `computedtools_object` } if (!is.null(this_object$`tags`)) { - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) } self }, @@ -403,7 +403,7 @@ AlignedFeature <- R6::R6Class( self$`externalFeatureId` <- this_object$`externalFeatureId` self$`ionMass` <- this_object$`ionMass` self$`charge` <- this_object$`charge` - self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("Rsirius")) + self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("RSirius")) if (!identical(self$`detectedAdducts`, unique(self$`detectedAdducts`))) { stop("Error! Items in `detectedAdducts` are not unique.") } @@ -421,7 +421,7 @@ AlignedFeature <- R6::R6Class( self$`topAnnotationsDeNovo` <- FeatureAnnotations$new()$fromJSON(jsonlite::toJSON(this_object$`topAnnotationsDeNovo`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`computing` <- this_object$`computing` self$`computedTools` <- ComputedSubtools$new()$fromJSON(jsonlite::toJSON(this_object$`computedTools`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/aligned_feature_quality_experimental.R b/client-api_r/generated/R/aligned_feature_quality_experimental.R index e986237b..50cc5f52 100644 --- a/client-api_r/generated/R/aligned_feature_quality_experimental.R +++ b/client-api_r/generated/R/aligned_feature_quality_experimental.R @@ -113,7 +113,7 @@ AlignedFeatureQualityExperimental <- R6::R6Class( self$`overallQuality` <- this_object$`overallQuality` } if (!is.null(this_object$`categories`)) { - self$`categories` <- ApiClient$new()$deserializeObj(this_object$`categories`, "map(Category)", loadNamespace("Rsirius")) + self$`categories` <- ApiClient$new()$deserializeObj(this_object$`categories`, "map(Category)", loadNamespace("RSirius")) } self }, @@ -141,7 +141,7 @@ AlignedFeatureQualityExperimental <- R6::R6Class( stop(paste("Error! \"", this_object$`overallQuality`, "\" cannot be assigned to `overallQuality`. Must be \"NOT_APPLICABLE\", \"LOWEST\", \"BAD\", \"DECENT\", \"GOOD\".", sep = "")) } self$`overallQuality` <- this_object$`overallQuality` - self$`categories` <- ApiClient$new()$deserializeObj(this_object$`categories`, "map(Category)", loadNamespace("Rsirius")) + self$`categories` <- ApiClient$new()$deserializeObj(this_object$`categories`, "map(Category)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/annotated_ms_ms_data.R b/client-api_r/generated/R/annotated_ms_ms_data.R index 98a443c7..38629d48 100644 --- a/client-api_r/generated/R/annotated_ms_ms_data.R +++ b/client-api_r/generated/R/annotated_ms_ms_data.R @@ -91,7 +91,7 @@ AnnotatedMsMsData <- R6::R6Class( self$`mergedMs2` <- `mergedms2_object` } if (!is.null(this_object$`ms2Spectra`)) { - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[AnnotatedSpectrum]", loadNamespace("Rsirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[AnnotatedSpectrum]", loadNamespace("RSirius")) } self }, @@ -115,7 +115,7 @@ AnnotatedMsMsData <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`mergedMs2` <- AnnotatedSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`mergedMs2`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[AnnotatedSpectrum]", loadNamespace("Rsirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[AnnotatedSpectrum]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/annotated_spectrum.R b/client-api_r/generated/R/annotated_spectrum.R index c2ba2539..b97e12d1 100644 --- a/client-api_r/generated/R/annotated_spectrum.R +++ b/client-api_r/generated/R/annotated_spectrum.R @@ -279,7 +279,7 @@ AnnotatedSpectrum <- R6::R6Class( self$`precursorPeak` <- `precursorpeak_object` } if (!is.null(this_object$`peaks`)) { - self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[AnnotatedPeak]", loadNamespace("Rsirius")) + self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[AnnotatedPeak]", loadNamespace("RSirius")) } if (!is.null(this_object$`absIntensityFactor`)) { self$`absIntensityFactor` <- this_object$`absIntensityFactor` @@ -330,7 +330,7 @@ AnnotatedSpectrum <- R6::R6Class( self$`scanNumber` <- this_object$`scanNumber` self$`cosineQuery` <- this_object$`cosineQuery` self$`precursorPeak` <- SimplePeak$new()$fromJSON(jsonlite::toJSON(this_object$`precursorPeak`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[AnnotatedPeak]", loadNamespace("Rsirius")) + self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[AnnotatedPeak]", loadNamespace("RSirius")) self$`absIntensityFactor` <- this_object$`absIntensityFactor` self$`maxNormFactor` <- this_object$`maxNormFactor` self$`sumNormFactor` <- this_object$`sumNormFactor` diff --git a/client-api_r/generated/R/api_client.R b/client-api_r/generated/R/api_client.R index 4257ae14..349426be 100644 --- a/client-api_r/generated/R/api_client.R +++ b/client-api_r/generated/R/api_client.R @@ -4,418 +4,418 @@ #' #' The version of the OpenAPI document: 3.1 #' Generated by: https://openapi-generator.tech -#' -#' ApiClient Class -#' -#' Generic API client for OpenAPI client library builds. -#' OpenAPI generic API client. This client handles the client- -#' server communication, and is invariant across implementations. Specifics of -#' the methods and models for each application are generated from the OpenAPI Generator -#' templates. -#' -#' NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). -#' Ref: https://openapi-generator.tech -#' Do not edit the class manually. -#' -#' @docType class -#' @title ApiClient -#' @description ApiClient Class -#' @format An \code{R6Class} generator object -#' @field base_path Base url -#' @field user_agent Default user agent -#' @field default_headers Default headers -#' @field username Username for HTTP basic authentication -#' @field password Password for HTTP basic authentication -#' @field api_keys API keys -#' @field bearer_token Bearer token -#' @field timeout Default timeout in seconds -#' @field retry_status_codes vector of status codes to retry -#' @field max_retry_attempts maximum number of retries for the status codes -#' @export -ApiClient <- R6::R6Class( - "ApiClient", - public = list( - # base path of all requests - base_path = "http://localhost:8080", - # user agent in the HTTP request - user_agent = "OpenAPI-Generator/6.3.3/r", - # default headers in the HTTP request - default_headers = NULL, - # username (HTTP basic authentication) - username = NULL, - # password (HTTP basic authentication) - password = NULL, - # API keys - api_keys = NULL, - # Bearer token - bearer_token = NULL, - # Time Out (seconds) - timeout = NULL, - # Vector of status codes to retry - retry_status_codes = NULL, - # Maximum number of retry attempts for the retry status codes - max_retry_attempts = NULL, - #' Initialize a new ApiClient. - #' - #' @description - #' Initialize a new ApiClient. - #' - #' @param base_path Base path. - #' @param user_agent User agent. - #' @param default_headers Default headers. - #' @param username User name. - #' @param password Password. - #' @param api_keys API keys. - #' @param access_token Access token. - #' @param bearer_token Bearer token. - #' @param timeout Timeout. - #' @param retry_status_codes Status codes for retry. - #' @param max_retry_attempts Maxmium number of retry. - #' @export - initialize = function(base_path = NULL, user_agent = NULL, - default_headers = NULL, - username = NULL, password = NULL, api_keys = NULL, - access_token = NULL, bearer_token = NULL, timeout = NULL, - retry_status_codes = NULL, max_retry_attempts = NULL) { - if (!is.null(base_path)) { - self$base_path <- base_path - } - - if (!is.null(default_headers)) { - self$default_headers <- default_headers - } - - if (!is.null(username)) { - self$username <- username - } - - if (!is.null(password)) { - self$password <- password - } - - if (!is.null(access_token)) { - self$access_token <- access_token - } - - if (!is.null(bearer_token)) { - self$bearer_token <- bearer_token - } - - if (!is.null(api_keys)) { - self$api_keys <- api_keys - } else { - self$api_keys <- list() - } - - if (!is.null(user_agent)) { - self$`user_agent` <- user_agent - } - - if (!is.null(timeout)) { - self$timeout <- timeout - } - - if (!is.null(retry_status_codes)) { - self$retry_status_codes <- retry_status_codes - } - - if (!is.null(max_retry_attempts)) { - self$max_retry_attempts <- max_retry_attempts - } - }, - #' Prepare to make an API call with the retry logic. - #' - #' @description - #' Prepare to make an API call with the retry logic. - #' - #' @param url URL. - #' @param method HTTP method. - #' @param query_params The query parameters. - #' @param header_params The header parameters. - #' @param form_params The form parameters. - #' @param file_params The form parameters to upload files. - #' @param accepts The HTTP accept headers. - #' @param content_types The HTTP content-type headers. - #' @param body The HTTP request body. - #' @param is_oauth True if the endpoints required OAuth authentication. - #' @param oauth_scopes OAuth scopes. - #' @param stream_callback Callback function to process the data stream. - #' @param ... Other optional arguments. - #' @return HTTP response - #' @export - CallApi = function(url, method, query_params, header_params, form_params, - file_params, accepts, content_types, body, - is_oauth = FALSE, oauth_scopes = NULL, stream_callback = NULL, ...) { - - # set the URL - req <- request(url) - - resp <- self$Execute(req, method, query_params, header_params, form_params, - file_params, accepts, content_types, body, is_oauth = is_oauth, - oauth_scopes = oauth_scopes, stream_callback = stream_callback, ...) - }, - #' Make an API call - #' - #' @description - #' Make an API call - #' - #' @param req httr2 request. - #' @param method HTTP method. - #' @param query_params The query parameters. - #' @param header_params The header parameters. - #' @param form_params The form parameters. - #' @param file_params The form parameters for uploading files. - #' @param accepts The HTTP accept headers. - #' @param content_types The HTTP content-type headers. - #' @param body The HTTP request body. - #' @param is_oauth True if the endpoints required OAuth authentication. - #' @param oauth_scopes OAuth scopes. - #' @param stream_callback Callback function to process data stream. - #' @param ... Other optional arguments. - #' @return HTTP response - #' @export - Execute = function(req, method, query_params, header_params, form_params, - file_params, accepts, content_types, body, - is_oauth = FALSE, oauth_scopes = NULL, stream_callback = NULL, ...) { - - ## add headers - req <- req %>% req_headers(!!!header_params) - - ## add default headers - req <- req %>% req_headers(!!!self$default_headers) - - # set HTTP accept header - accept <- self$select_header(accepts) - if (!is.null(accept)) { - req <- req %>% req_headers("Accept" = accept) - } - - # set HTTP content-type header - content_type <- self$select_header(content_types) - if (!is.null(content_type)) { - req <- req %>% req_headers("Content-Type" = content_type) - } - - ## add query parameters - for (query_param in names(query_params)) { - if (typeof(query_params[[query_param]]) == "list") { - # for explode, e.g. a=1,a=2,a=3 - req <- req %>% req_url_query(!!!query_params[[query_param]]) - } else { # for non-explode, e.g. a=1,2,3 - tmp <- list() - tmp[[query_param]] <- query_params[[query_param]] - req <- req %>% req_url_query(!!!tmp) - } - } - - # has file upload? - if (!is.null(file_params) && length(file_params) != 0) { - # Create multipart body data - multipart_data <- list() - - # Add form parameters first - if (!is.null(form_params) && length(form_params) != 0) { - for (param_name in names(form_params)) { - param_value <- form_params[[param_name]] - is_json <- tryCatch({ - jsonlite::validate(param_value) - }, error = function(e) { - FALSE - }) - - if (is_json) { - multipart_data[[param_name]] <- curl::form_data(param_value, type = "application/json") - } else { - multipart_data[[param_name]] <- param_value - } - } - } - - # Add file parameters - handle multiple files with same name - for (param_name in names(file_params)) { - param_value <- file_params[[param_name]] - - if (is.list(param_value) && length(param_value) > 1) { - # Multiple files with same parameter name - for (i in seq_along(param_value)) { - multipart_data[[length(multipart_data) + 1]] <- param_value[[i]] - names(multipart_data)[length(multipart_data)] <- param_name - } - } else { - # Single file - multipart_data[[param_name]] <- param_value[[1]] - } - } - req <- req %>% req_body_multipart(!!!multipart_data) - } else { # no file upload - # add form parameters via req_body_form - if (!is.null(form_params) && length(form_params) != 0) { - req <- req %>% req_body_form(!!!form_params) - } - } - - # add body parameters - if (!is.null(body)) { - req <- req %>% req_body_raw(body) - } - - # set timeout - if (!is.null(self$timeout)) { - req <- req %>% req_timeout(self$timeout) - } - - # set retry - if (!is.null(self$max_retry_attempts)) { - req <- req %>% retry_max_tries(self$timeout) - req <- req %>% retry_max_seconds(self$timeout) - } - - # set user agent - if (!is.null(self$user_agent)) { - req <- req %>% req_user_agent(self$user_agent) - } - - # set HTTP verb - req <- req %>% req_method(method) - - # stream data - if (typeof(stream_callback) == "closure") { - req %>% req_stream(stream_callback) - } else { - # perform the HTTP request - resp <- req %>% - req_error(is_error = function(resp) FALSE) %>% - req_perform() - - # return ApiResponse - api_response <- ApiResponse$new() - api_response$status_code <- resp %>% resp_status() - api_response$status_code_desc <- resp %>% resp_status_desc() - if (length(resp$body) == 0) { - api_response$response <- NULL - } else { - api_response$response <- resp %>% resp_body_raw() - } - api_response$headers <- resp %>% resp_headers() - - api_response - } - }, - #' Deserialize the content of API response to the given type. - #' - #' @description - #' Deserialize the content of API response to the given type. - #' - #' @param raw_response Raw response. - #' @param return_type R return type. - #' @param pkg_env Package environment. - #' @return Deserialized object. - #' @export - deserialize = function(raw_response, return_type, pkg_env) { - # jsonlite fails with URLs as strings, pass them raw - if (grepl('^(http|https)://', raw_response)) { - resp_obj <- raw_response - } else { - resp_obj <- jsonlite::fromJSON(raw_response) - } - self$deserializeObj(resp_obj, return_type, pkg_env) - }, - #' Deserialize the response from jsonlite object based on the given type. - #' - #' @description - #' Deserialize the response from jsonlite object based on the given type. - #' by handling complex and nested types by iterating recursively - #' Example return_types will be like "array[integer]", "map(Pet)", "array[map(Tag)]", etc. - #' - #' @param obj Response object. - #' @param return_type R return type. - #' @param pkg_env Package environment. - #' @return Deserialized object. - #' @export - deserializeObj = function(obj, return_type, pkg_env) { - return_obj <- NULL - primitive_types <- c("character", "numeric", "integer", "logical", "complex") - - # To handle the "map" type - if (startsWith(return_type, "map(")) { - inner_return_type <- regmatches(return_type, - regexec(pattern = "map\\((.*)\\)", return_type))[[1]][2] - return_obj <- lapply(names(obj), function(name) { - self$deserializeObj(obj[[name]], inner_return_type, pkg_env) - }) - names(return_obj) <- names(obj) - } else if (startsWith(return_type, "array[")) { - # To handle the "array" type - inner_return_type <- regmatches(return_type, - regexec(pattern = "array\\[(.*)\\]", return_type))[[1]][2] - if (c(inner_return_type) %in% primitive_types) { - return_obj <- vector("list", length = length(obj)) - if (length(obj) > 0) { - for (row in 1:length(obj)) { - return_obj[[row]] <- self$deserializeObj(obj[row], inner_return_type, pkg_env) - } - } - } else { - if (!is.null(nrow(obj))) { - return_obj <- vector("list", length = nrow(obj)) - if (nrow(obj) > 0) { - for (row in 1:nrow(obj)) { - return_obj[[row]] <- self$deserializeObj(obj[row, , drop = FALSE], - inner_return_type, pkg_env) - } - } - } - } - } else if (exists(return_type, pkg_env) && !(c(return_type) %in% primitive_types)) { - # To handle model objects which are not array or map containers (e.g. Pet) - return_type <- get(return_type, envir = as.environment(pkg_env)) - return_obj <- return_type$new() - # check if discriminator is defined - if (!is.null(return_obj$`_discriminator_property_name`)) { - data_type <- return_obj$`_discriminator_property_name` - # use discriminator mapping if provided - if (!is.null(return_obj$`_discriminator_mapping_name`)) { - data_type <- (return_obj$`_discriminator_mapping_name`)[[obj[[data_type]]]] - } else { - # no mapping provided, use the value directly - data_type <- obj[[data_type]] - } - # create an object of the mapped type (e.g. Cat) - return_type <- get(data_type, envir = as.environment(pkg_env)) - return_obj <- return_type$new() - } - return_obj$fromJSON( - jsonlite::toJSON(obj, digits = NA, auto_unbox = TRUE, null = 'null') - ) - } else { - # To handle primitive type - return_obj <- obj - } - return_obj - }, - #' Return a property header (for accept or content-type). - #' - #' @description - #' Return a property header (for accept or content-type). If JSON-related MIME is found, - #' return it. Otherwise, return the first one, if any. - #' - #' @param headers A list of headers - #' @return A header (e.g. 'application/json') - #' @export - select_header = function(headers) { - if (length(headers) == 0) { - return(invisible(NULL)) - } else { - for (header in headers) { - if (str_detect(header, "(?i)^(application/json|[^;/ \t]+/[^;/ \t]+[+]json)[ \t]*(;.*)?$")) { - # return JSON-related MIME - return(header) - } - } - - # not json mime type, simply return the first one - return(headers[[1]]) - } - } - ) -) +#' +#' ApiClient Class +#' +#' Generic API client for OpenAPI client library builds. +#' OpenAPI generic API client. This client handles the client- +#' server communication, and is invariant across implementations. Specifics of +#' the methods and models for each application are generated from the OpenAPI Generator +#' templates. +#' +#' NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). +#' Ref: https://openapi-generator.tech +#' Do not edit the class manually. +#' +#' @docType class +#' @title ApiClient +#' @description ApiClient Class +#' @format An \code{R6Class} generator object +#' @field base_path Base url +#' @field user_agent Default user agent +#' @field default_headers Default headers +#' @field username Username for HTTP basic authentication +#' @field password Password for HTTP basic authentication +#' @field api_keys API keys +#' @field bearer_token Bearer token +#' @field timeout Default timeout in seconds +#' @field retry_status_codes vector of status codes to retry +#' @field max_retry_attempts maximum number of retries for the status codes +#' @export +ApiClient <- R6::R6Class( + "ApiClient", + public = list( + # base path of all requests + base_path = "http://localhost:8080", + # user agent in the HTTP request + user_agent = "OpenAPI-Generator/6.3.3/r", + # default headers in the HTTP request + default_headers = NULL, + # username (HTTP basic authentication) + username = NULL, + # password (HTTP basic authentication) + password = NULL, + # API keys + api_keys = NULL, + # Bearer token + bearer_token = NULL, + # Time Out (seconds) + timeout = NULL, + # Vector of status codes to retry + retry_status_codes = NULL, + # Maximum number of retry attempts for the retry status codes + max_retry_attempts = NULL, + #' Initialize a new ApiClient. + #' + #' @description + #' Initialize a new ApiClient. + #' + #' @param base_path Base path. + #' @param user_agent User agent. + #' @param default_headers Default headers. + #' @param username User name. + #' @param password Password. + #' @param api_keys API keys. + #' @param access_token Access token. + #' @param bearer_token Bearer token. + #' @param timeout Timeout. + #' @param retry_status_codes Status codes for retry. + #' @param max_retry_attempts Maxmium number of retry. + #' @export + initialize = function(base_path = NULL, user_agent = NULL, + default_headers = NULL, + username = NULL, password = NULL, api_keys = NULL, + access_token = NULL, bearer_token = NULL, timeout = NULL, + retry_status_codes = NULL, max_retry_attempts = NULL) { + if (!is.null(base_path)) { + self$base_path <- base_path + } + + if (!is.null(default_headers)) { + self$default_headers <- default_headers + } + + if (!is.null(username)) { + self$username <- username + } + + if (!is.null(password)) { + self$password <- password + } + + if (!is.null(access_token)) { + self$access_token <- access_token + } + + if (!is.null(bearer_token)) { + self$bearer_token <- bearer_token + } + + if (!is.null(api_keys)) { + self$api_keys <- api_keys + } else { + self$api_keys <- list() + } + + if (!is.null(user_agent)) { + self$`user_agent` <- user_agent + } + + if (!is.null(timeout)) { + self$timeout <- timeout + } + + if (!is.null(retry_status_codes)) { + self$retry_status_codes <- retry_status_codes + } + + if (!is.null(max_retry_attempts)) { + self$max_retry_attempts <- max_retry_attempts + } + }, + #' Prepare to make an API call with the retry logic. + #' + #' @description + #' Prepare to make an API call with the retry logic. + #' + #' @param url URL. + #' @param method HTTP method. + #' @param query_params The query parameters. + #' @param header_params The header parameters. + #' @param form_params The form parameters. + #' @param file_params The form parameters to upload files. + #' @param accepts The HTTP accept headers. + #' @param content_types The HTTP content-type headers. + #' @param body The HTTP request body. + #' @param is_oauth True if the endpoints required OAuth authentication. + #' @param oauth_scopes OAuth scopes. + #' @param stream_callback Callback function to process the data stream. + #' @param ... Other optional arguments. + #' @return HTTP response + #' @export + CallApi = function(url, method, query_params, header_params, form_params, + file_params, accepts, content_types, body, + is_oauth = FALSE, oauth_scopes = NULL, stream_callback = NULL, ...) { + + # set the URL + req <- request(url) + + resp <- self$Execute(req, method, query_params, header_params, form_params, + file_params, accepts, content_types, body, is_oauth = is_oauth, + oauth_scopes = oauth_scopes, stream_callback = stream_callback, ...) + }, + #' Make an API call + #' + #' @description + #' Make an API call + #' + #' @param req httr2 request. + #' @param method HTTP method. + #' @param query_params The query parameters. + #' @param header_params The header parameters. + #' @param form_params The form parameters. + #' @param file_params The form parameters for uploading files. + #' @param accepts The HTTP accept headers. + #' @param content_types The HTTP content-type headers. + #' @param body The HTTP request body. + #' @param is_oauth True if the endpoints required OAuth authentication. + #' @param oauth_scopes OAuth scopes. + #' @param stream_callback Callback function to process data stream. + #' @param ... Other optional arguments. + #' @return HTTP response + #' @export + Execute = function(req, method, query_params, header_params, form_params, + file_params, accepts, content_types, body, + is_oauth = FALSE, oauth_scopes = NULL, stream_callback = NULL, ...) { + + ## add headers + req <- req %>% req_headers(!!!header_params) + + ## add default headers + req <- req %>% req_headers(!!!self$default_headers) + + # set HTTP accept header + accept <- self$select_header(accepts) + if (!is.null(accept)) { + req <- req %>% req_headers("Accept" = accept) + } + + # set HTTP content-type header + content_type <- self$select_header(content_types) + if (!is.null(content_type)) { + req <- req %>% req_headers("Content-Type" = content_type) + } + + ## add query parameters + for (query_param in names(query_params)) { + if (typeof(query_params[[query_param]]) == "list") { + # for explode, e.g. a=1,a=2,a=3 + req <- req %>% req_url_query(!!!query_params[[query_param]]) + } else { # for non-explode, e.g. a=1,2,3 + tmp <- list() + tmp[[query_param]] <- query_params[[query_param]] + req <- req %>% req_url_query(!!!tmp) + } + } + + # has file upload? + if (!is.null(file_params) && length(file_params) != 0) { + # Create multipart body data + multipart_data <- list() + + # Add form parameters first + if (!is.null(form_params) && length(form_params) != 0) { + for (param_name in names(form_params)) { + param_value <- form_params[[param_name]] + is_json <- tryCatch({ + jsonlite::validate(param_value) + }, error = function(e) { + FALSE + }) + + if (is_json) { + multipart_data[[param_name]] <- curl::form_data(param_value, type = "application/json") + } else { + multipart_data[[param_name]] <- param_value + } + } + } + + # Add file parameters - handle multiple files with same name + for (param_name in names(file_params)) { + param_value <- file_params[[param_name]] + + if (is.list(param_value) && length(param_value) > 1) { + # Multiple files with same parameter name + for (i in seq_along(param_value)) { + multipart_data[[length(multipart_data) + 1]] <- param_value[[i]] + names(multipart_data)[length(multipart_data)] <- param_name + } + } else { + # Single file + multipart_data[[param_name]] <- param_value[[1]] + } + } + req <- req %>% req_body_multipart(!!!multipart_data) + } else { # no file upload + # add form parameters via req_body_form + if (!is.null(form_params) && length(form_params) != 0) { + req <- req %>% req_body_form(!!!form_params) + } + } + + # add body parameters + if (!is.null(body)) { + req <- req %>% req_body_raw(body) + } + + # set timeout + if (!is.null(self$timeout)) { + req <- req %>% req_timeout(self$timeout) + } + + # set retry + if (!is.null(self$max_retry_attempts)) { + req <- req %>% retry_max_tries(self$timeout) + req <- req %>% retry_max_seconds(self$timeout) + } + + # set user agent + if (!is.null(self$user_agent)) { + req <- req %>% req_user_agent(self$user_agent) + } + + # set HTTP verb + req <- req %>% req_method(method) + + # stream data + if (typeof(stream_callback) == "closure") { + req %>% req_stream(stream_callback) + } else { + # perform the HTTP request + resp <- req %>% + req_error(is_error = function(resp) FALSE) %>% + req_perform() + + # return ApiResponse + api_response <- ApiResponse$new() + api_response$status_code <- resp %>% resp_status() + api_response$status_code_desc <- resp %>% resp_status_desc() + if (length(resp$body) == 0) { + api_response$response <- NULL + } else { + api_response$response <- resp %>% resp_body_raw() + } + api_response$headers <- resp %>% resp_headers() + + api_response + } + }, + #' Deserialize the content of API response to the given type. + #' + #' @description + #' Deserialize the content of API response to the given type. + #' + #' @param raw_response Raw response. + #' @param return_type R return type. + #' @param pkg_env Package environment. + #' @return Deserialized object. + #' @export + deserialize = function(raw_response, return_type, pkg_env) { + # jsonlite fails with URLs as strings, pass them raw + if (grepl('^(http|https)://', raw_response)) { + resp_obj <- raw_response + } else { + resp_obj <- jsonlite::fromJSON(raw_response) + } + self$deserializeObj(resp_obj, return_type, pkg_env) + }, + #' Deserialize the response from jsonlite object based on the given type. + #' + #' @description + #' Deserialize the response from jsonlite object based on the given type. + #' by handling complex and nested types by iterating recursively + #' Example return_types will be like "array[integer]", "map(Pet)", "array[map(Tag)]", etc. + #' + #' @param obj Response object. + #' @param return_type R return type. + #' @param pkg_env Package environment. + #' @return Deserialized object. + #' @export + deserializeObj = function(obj, return_type, pkg_env) { + return_obj <- NULL + primitive_types <- c("character", "numeric", "integer", "logical", "complex") + + # To handle the "map" type + if (startsWith(return_type, "map(")) { + inner_return_type <- regmatches(return_type, + regexec(pattern = "map\\((.*)\\)", return_type))[[1]][2] + return_obj <- lapply(names(obj), function(name) { + self$deserializeObj(obj[[name]], inner_return_type, pkg_env) + }) + names(return_obj) <- names(obj) + } else if (startsWith(return_type, "array[")) { + # To handle the "array" type + inner_return_type <- regmatches(return_type, + regexec(pattern = "array\\[(.*)\\]", return_type))[[1]][2] + if (c(inner_return_type) %in% primitive_types) { + return_obj <- vector("list", length = length(obj)) + if (length(obj) > 0) { + for (row in 1:length(obj)) { + return_obj[[row]] <- self$deserializeObj(obj[row], inner_return_type, pkg_env) + } + } + } else { + if (!is.null(nrow(obj))) { + return_obj <- vector("list", length = nrow(obj)) + if (nrow(obj) > 0) { + for (row in 1:nrow(obj)) { + return_obj[[row]] <- self$deserializeObj(obj[row, , drop = FALSE], + inner_return_type, pkg_env) + } + } + } + } + } else if (exists(return_type, pkg_env) && !(c(return_type) %in% primitive_types)) { + # To handle model objects which are not array or map containers (e.g. Pet) + return_type <- get(return_type, envir = as.environment(pkg_env)) + return_obj <- return_type$new() + # check if discriminator is defined + if (!is.null(return_obj$`_discriminator_property_name`)) { + data_type <- return_obj$`_discriminator_property_name` + # use discriminator mapping if provided + if (!is.null(return_obj$`_discriminator_mapping_name`)) { + data_type <- (return_obj$`_discriminator_mapping_name`)[[obj[[data_type]]]] + } else { + # no mapping provided, use the value directly + data_type <- obj[[data_type]] + } + # create an object of the mapped type (e.g. Cat) + return_type <- get(data_type, envir = as.environment(pkg_env)) + return_obj <- return_type$new() + } + return_obj$fromJSON( + jsonlite::toJSON(obj, digits = NA, auto_unbox = TRUE, null = 'null') + ) + } else { + # To handle primitive type + return_obj <- obj + } + return_obj + }, + #' Return a property header (for accept or content-type). + #' + #' @description + #' Return a property header (for accept or content-type). If JSON-related MIME is found, + #' return it. Otherwise, return the first one, if any. + #' + #' @param headers A list of headers + #' @return A header (e.g. 'application/json') + #' @export + select_header = function(headers) { + if (length(headers) == 0) { + return(invisible(NULL)) + } else { + for (header in headers) { + if (str_detect(header, "(?i)^(application/json|[^;/ \t]+/[^;/ \t]+[+]json)[ \t]*(;.*)?$")) { + # return JSON-related MIME + return(header) + } + } + + # not json mime type, simply return the first one + return(headers[[1]]) + } + } + ) +) diff --git a/client-api_r/generated/R/axes.R b/client-api_r/generated/R/axes.R index cc82cdac..2b553970 100644 --- a/client-api_r/generated/R/axes.R +++ b/client-api_r/generated/R/axes.R @@ -99,13 +99,13 @@ Axes <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`scanNumber`)) { - self$`scanNumber` <- ApiClient$new()$deserializeObj(this_object$`scanNumber`, "array[integer]", loadNamespace("Rsirius")) + self$`scanNumber` <- ApiClient$new()$deserializeObj(this_object$`scanNumber`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`scanIds`)) { - self$`scanIds` <- ApiClient$new()$deserializeObj(this_object$`scanIds`, "array[character]", loadNamespace("Rsirius")) + self$`scanIds` <- ApiClient$new()$deserializeObj(this_object$`scanIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`retentionTimeInSeconds`)) { - self$`retentionTimeInSeconds` <- ApiClient$new()$deserializeObj(this_object$`retentionTimeInSeconds`, "array[numeric]", loadNamespace("Rsirius")) + self$`retentionTimeInSeconds` <- ApiClient$new()$deserializeObj(this_object$`retentionTimeInSeconds`, "array[numeric]", loadNamespace("RSirius")) } self }, @@ -128,9 +128,9 @@ Axes <- R6::R6Class( #' @return the instance of Axes fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`scanNumber` <- ApiClient$new()$deserializeObj(this_object$`scanNumber`, "array[integer]", loadNamespace("Rsirius")) - self$`scanIds` <- ApiClient$new()$deserializeObj(this_object$`scanIds`, "array[character]", loadNamespace("Rsirius")) - self$`retentionTimeInSeconds` <- ApiClient$new()$deserializeObj(this_object$`retentionTimeInSeconds`, "array[numeric]", loadNamespace("Rsirius")) + self$`scanNumber` <- ApiClient$new()$deserializeObj(this_object$`scanNumber`, "array[integer]", loadNamespace("RSirius")) + self$`scanIds` <- ApiClient$new()$deserializeObj(this_object$`scanIds`, "array[character]", loadNamespace("RSirius")) + self$`retentionTimeInSeconds` <- ApiClient$new()$deserializeObj(this_object$`retentionTimeInSeconds`, "array[numeric]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/background_computations_state_event.R b/client-api_r/generated/R/background_computations_state_event.R index ad688b82..44746f23 100644 --- a/client-api_r/generated/R/background_computations_state_event.R +++ b/client-api_r/generated/R/background_computations_state_event.R @@ -114,7 +114,7 @@ BackgroundComputationsStateEvent <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`affectedJobs`)) { - self$`affectedJobs` <- ApiClient$new()$deserializeObj(this_object$`affectedJobs`, "array[Job]", loadNamespace("Rsirius")) + self$`affectedJobs` <- ApiClient$new()$deserializeObj(this_object$`affectedJobs`, "array[Job]", loadNamespace("RSirius")) } if (!is.null(this_object$`numberOfJobs`)) { self$`numberOfJobs` <- this_object$`numberOfJobs` @@ -146,7 +146,7 @@ BackgroundComputationsStateEvent <- R6::R6Class( #' @return the instance of BackgroundComputationsStateEvent fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`affectedJobs` <- ApiClient$new()$deserializeObj(this_object$`affectedJobs`, "array[Job]", loadNamespace("Rsirius")) + self$`affectedJobs` <- ApiClient$new()$deserializeObj(this_object$`affectedJobs`, "array[Job]", loadNamespace("RSirius")) self$`numberOfJobs` <- this_object$`numberOfJobs` self$`numberOfRunningJobs` <- this_object$`numberOfRunningJobs` self$`numberOfFinishedJobs` <- this_object$`numberOfFinishedJobs` diff --git a/client-api_r/generated/R/basic_spectrum.R b/client-api_r/generated/R/basic_spectrum.R index f187da6d..c3ca83be 100644 --- a/client-api_r/generated/R/basic_spectrum.R +++ b/client-api_r/generated/R/basic_spectrum.R @@ -268,7 +268,7 @@ BasicSpectrum <- R6::R6Class( self$`precursorPeak` <- `precursorpeak_object` } if (!is.null(this_object$`peaks`)) { - self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[SimplePeak]", loadNamespace("Rsirius")) + self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[SimplePeak]", loadNamespace("RSirius")) } if (!is.null(this_object$`absIntensityFactor`)) { self$`absIntensityFactor` <- this_object$`absIntensityFactor` @@ -314,7 +314,7 @@ BasicSpectrum <- R6::R6Class( self$`scanNumber` <- this_object$`scanNumber` self$`cosineQuery` <- this_object$`cosineQuery` self$`precursorPeak` <- SimplePeak$new()$fromJSON(jsonlite::toJSON(this_object$`precursorPeak`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[SimplePeak]", loadNamespace("Rsirius")) + self$`peaks` <- ApiClient$new()$deserializeObj(this_object$`peaks`, "array[SimplePeak]", loadNamespace("RSirius")) self$`absIntensityFactor` <- this_object$`absIntensityFactor` self$`maxNormFactor` <- this_object$`maxNormFactor` self$`sumNormFactor` <- this_object$`sumNormFactor` diff --git a/client-api_r/generated/R/binary_fingerprint.R b/client-api_r/generated/R/binary_fingerprint.R index 58e952e3..c4c6117b 100644 --- a/client-api_r/generated/R/binary_fingerprint.R +++ b/client-api_r/generated/R/binary_fingerprint.R @@ -88,7 +88,7 @@ BinaryFingerprint <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`bitsSet`)) { - self$`bitsSet` <- ApiClient$new()$deserializeObj(this_object$`bitsSet`, "array[integer]", loadNamespace("Rsirius")) + self$`bitsSet` <- ApiClient$new()$deserializeObj(this_object$`bitsSet`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`length`)) { self$`length` <- this_object$`length` @@ -114,7 +114,7 @@ BinaryFingerprint <- R6::R6Class( #' @return the instance of BinaryFingerprint fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`bitsSet` <- ApiClient$new()$deserializeObj(this_object$`bitsSet`, "array[integer]", loadNamespace("Rsirius")) + self$`bitsSet` <- ApiClient$new()$deserializeObj(this_object$`bitsSet`, "array[integer]", loadNamespace("RSirius")) self$`length` <- this_object$`length` self }, diff --git a/client-api_r/generated/R/bio_transformer_parameters.R b/client-api_r/generated/R/bio_transformer_parameters.R index d7cdde6b..d767cd61 100644 --- a/client-api_r/generated/R/bio_transformer_parameters.R +++ b/client-api_r/generated/R/bio_transformer_parameters.R @@ -135,7 +135,7 @@ BioTransformerParameters <- R6::R6Class( self$`useDB` <- this_object$`useDB` } if (!is.null(this_object$`bioTransformerSequenceSteps`)) { - self$`bioTransformerSequenceSteps` <- ApiClient$new()$deserializeObj(this_object$`bioTransformerSequenceSteps`, "array[BioTransformerSequenceStep]", loadNamespace("Rsirius")) + self$`bioTransformerSequenceSteps` <- ApiClient$new()$deserializeObj(this_object$`bioTransformerSequenceSteps`, "array[BioTransformerSequenceStep]", loadNamespace("RSirius")) } self }, @@ -167,7 +167,7 @@ BioTransformerParameters <- R6::R6Class( } self$`p2Mode` <- this_object$`p2Mode` self$`useDB` <- this_object$`useDB` - self$`bioTransformerSequenceSteps` <- ApiClient$new()$deserializeObj(this_object$`bioTransformerSequenceSteps`, "array[BioTransformerSequenceStep]", loadNamespace("Rsirius")) + self$`bioTransformerSequenceSteps` <- ApiClient$new()$deserializeObj(this_object$`bioTransformerSequenceSteps`, "array[BioTransformerSequenceStep]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/canopus_prediction.R b/client-api_r/generated/R/canopus_prediction.R index 1e5c1a5a..0b587baf 100644 --- a/client-api_r/generated/R/canopus_prediction.R +++ b/client-api_r/generated/R/canopus_prediction.R @@ -87,10 +87,10 @@ CanopusPrediction <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`classyFireClasses`)) { - self$`classyFireClasses` <- ApiClient$new()$deserializeObj(this_object$`classyFireClasses`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`classyFireClasses` <- ApiClient$new()$deserializeObj(this_object$`classyFireClasses`, "array[CompoundClass]", loadNamespace("RSirius")) } if (!is.null(this_object$`npcClasses`)) { - self$`npcClasses` <- ApiClient$new()$deserializeObj(this_object$`npcClasses`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`npcClasses` <- ApiClient$new()$deserializeObj(this_object$`npcClasses`, "array[CompoundClass]", loadNamespace("RSirius")) } self }, @@ -113,8 +113,8 @@ CanopusPrediction <- R6::R6Class( #' @return the instance of CanopusPrediction fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`classyFireClasses` <- ApiClient$new()$deserializeObj(this_object$`classyFireClasses`, "array[CompoundClass]", loadNamespace("Rsirius")) - self$`npcClasses` <- ApiClient$new()$deserializeObj(this_object$`npcClasses`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`classyFireClasses` <- ApiClient$new()$deserializeObj(this_object$`classyFireClasses`, "array[CompoundClass]", loadNamespace("RSirius")) + self$`npcClasses` <- ApiClient$new()$deserializeObj(this_object$`npcClasses`, "array[CompoundClass]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/category.R b/client-api_r/generated/R/category.R index 89ce12c3..19ecba5f 100644 --- a/client-api_r/generated/R/category.R +++ b/client-api_r/generated/R/category.R @@ -113,7 +113,7 @@ Category <- R6::R6Class( self$`overallQuality` <- this_object$`overallQuality` } if (!is.null(this_object$`items`)) { - self$`items` <- ApiClient$new()$deserializeObj(this_object$`items`, "array[QualityItem]", loadNamespace("Rsirius")) + self$`items` <- ApiClient$new()$deserializeObj(this_object$`items`, "array[QualityItem]", loadNamespace("RSirius")) } self }, @@ -141,7 +141,7 @@ Category <- R6::R6Class( stop(paste("Error! \"", this_object$`overallQuality`, "\" cannot be assigned to `overallQuality`. Must be \"NOT_APPLICABLE\", \"LOWEST\", \"BAD\", \"DECENT\", \"GOOD\".", sep = "")) } self$`overallQuality` <- this_object$`overallQuality` - self$`items` <- ApiClient$new()$deserializeObj(this_object$`items`, "array[QualityItem]", loadNamespace("Rsirius")) + self$`items` <- ApiClient$new()$deserializeObj(this_object$`items`, "array[QualityItem]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/compound.R b/client-api_r/generated/R/compound.R index 112e4d67..747d6f0d 100644 --- a/client-api_r/generated/R/compound.R +++ b/client-api_r/generated/R/compound.R @@ -200,7 +200,7 @@ Compound <- R6::R6Class( self$`neutralMass` <- this_object$`neutralMass` } if (!is.null(this_object$`features`)) { - self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[AlignedFeature]", loadNamespace("Rsirius")) + self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[AlignedFeature]", loadNamespace("RSirius")) } if (!is.null(this_object$`consensusAnnotations`)) { `consensusannotations_object` <- ConsensusAnnotationsCSI$new() @@ -218,7 +218,7 @@ Compound <- R6::R6Class( self$`customAnnotations` <- `customannotations_object` } if (!is.null(this_object$`tags`)) { - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) } self }, @@ -246,11 +246,11 @@ Compound <- R6::R6Class( self$`rtStartSeconds` <- this_object$`rtStartSeconds` self$`rtEndSeconds` <- this_object$`rtEndSeconds` self$`neutralMass` <- this_object$`neutralMass` - self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[AlignedFeature]", loadNamespace("Rsirius")) + self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[AlignedFeature]", loadNamespace("RSirius")) self$`consensusAnnotations` <- ConsensusAnnotationsCSI$new()$fromJSON(jsonlite::toJSON(this_object$`consensusAnnotations`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`consensusAnnotationsDeNovo` <- ConsensusAnnotationsDeNovo$new()$fromJSON(jsonlite::toJSON(this_object$`consensusAnnotationsDeNovo`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`customAnnotations` <- ConsensusAnnotationsCSI$new()$fromJSON(jsonlite::toJSON(this_object$`customAnnotations`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/compound_classes.R b/client-api_r/generated/R/compound_classes.R index c80ecdb4..5043b3f2 100644 --- a/client-api_r/generated/R/compound_classes.R +++ b/client-api_r/generated/R/compound_classes.R @@ -135,10 +135,10 @@ CompoundClasses <- R6::R6Class( self$`npcClass` <- `npcclass_object` } if (!is.null(this_object$`classyFireLineage`)) { - self$`classyFireLineage` <- ApiClient$new()$deserializeObj(this_object$`classyFireLineage`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`classyFireLineage` <- ApiClient$new()$deserializeObj(this_object$`classyFireLineage`, "array[CompoundClass]", loadNamespace("RSirius")) } if (!is.null(this_object$`classyFireAlternatives`)) { - self$`classyFireAlternatives` <- ApiClient$new()$deserializeObj(this_object$`classyFireAlternatives`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`classyFireAlternatives` <- ApiClient$new()$deserializeObj(this_object$`classyFireAlternatives`, "array[CompoundClass]", loadNamespace("RSirius")) } self }, @@ -164,8 +164,8 @@ CompoundClasses <- R6::R6Class( self$`npcPathway` <- CompoundClass$new()$fromJSON(jsonlite::toJSON(this_object$`npcPathway`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`npcSuperclass` <- CompoundClass$new()$fromJSON(jsonlite::toJSON(this_object$`npcSuperclass`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`npcClass` <- CompoundClass$new()$fromJSON(jsonlite::toJSON(this_object$`npcClass`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`classyFireLineage` <- ApiClient$new()$deserializeObj(this_object$`classyFireLineage`, "array[CompoundClass]", loadNamespace("Rsirius")) - self$`classyFireAlternatives` <- ApiClient$new()$deserializeObj(this_object$`classyFireAlternatives`, "array[CompoundClass]", loadNamespace("Rsirius")) + self$`classyFireLineage` <- ApiClient$new()$deserializeObj(this_object$`classyFireLineage`, "array[CompoundClass]", loadNamespace("RSirius")) + self$`classyFireAlternatives` <- ApiClient$new()$deserializeObj(this_object$`classyFireAlternatives`, "array[CompoundClass]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/compound_import.R b/client-api_r/generated/R/compound_import.R index 977d048c..487a2d68 100644 --- a/client-api_r/generated/R/compound_import.R +++ b/client-api_r/generated/R/compound_import.R @@ -91,7 +91,7 @@ CompoundImport <- R6::R6Class( self$`name` <- this_object$`name` } if (!is.null(this_object$`features`)) { - self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[FeatureImport]", loadNamespace("Rsirius")) + self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[FeatureImport]", loadNamespace("RSirius")) } self }, @@ -115,7 +115,7 @@ CompoundImport <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`name` <- this_object$`name` - self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[FeatureImport]", loadNamespace("Rsirius")) + self$`features` <- ApiClient$new()$deserializeObj(this_object$`features`, "array[FeatureImport]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/compound_statistics_api.R b/client-api_r/generated/R/compound_statistics_api.R index 742937ee..f9dc5c8e 100644 --- a/client-api_r/generated/R/compound_statistics_api.R +++ b/client-api_r/generated/R/compound_statistics_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### ComputeCompoundFoldChangesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to compute the fold change in. #' var_left_group_name <- "left_group_name_example" # character | name of the left tag group. #' var_right_group_name <- "right_group_name_example" # character | name of the right tag group. @@ -34,7 +34,7 @@ #' #' #################### DeleteCompoundFoldChangesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_left_group_name <- "left_group_name_example" # character | name of the left group. #' var_right_group_name <- "right_group_name_example" # character | name of the right group. @@ -49,7 +49,7 @@ #' #' #################### GetCompoundFoldChangeTableExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aggregation <- "AVG" # character | aggregation type. (Optional) #' var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional) @@ -65,7 +65,7 @@ #' #' #################### GetFoldChangesByCompoundExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to. #' @@ -247,7 +247,7 @@ CompoundStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -501,7 +501,7 @@ CompoundStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "StatisticsTable", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "StatisticsTable", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -634,7 +634,7 @@ CompoundStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[FoldChange]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[FoldChange]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/compounds_api.R b/client-api_r/generated/R/compounds_api.R index a72c6b36..222ed229 100644 --- a/client-api_r/generated/R/compounds_api.R +++ b/client-api_r/generated/R/compounds_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### AddCompounds #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to import into. #' var_compound_import <- c(CompoundImport$new(c(FeatureImport$new(123, 123, "name_example", "externalFeatureId_example", c("detectedAdducts_example"), 123, 123, 123, "NOT_APPLICABLE", BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)))), "name_example")) # array[CompoundImport] | the compound data to be imported #' var_profile <- "profile_example" # character | profile describing the instrument used to measure the data. Used to merge spectra. (Optional) @@ -33,7 +33,7 @@ #' #' #################### AddTagsToCompoundExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to add tags to. #' var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -49,7 +49,7 @@ #' #' #################### DeleteCompound #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_compound_id <- "compound_id_example" # character | identifier of the compound to delete. #' @@ -61,7 +61,7 @@ #' #' #################### GetCompound #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_compound_id <- "compound_id_example" # character | identifier of the compound (group of ion identities) to access. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -79,7 +79,7 @@ #' #' #################### GetCompoundQuantTableExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) #' @@ -94,7 +94,7 @@ #' #' #################### GetCompoundQuantTableRowExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_compound_id <- "compound_id_example" # character | compound which should be read out #' var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) @@ -110,7 +110,7 @@ #' #' #################### GetCompoundTracesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_compound_id <- "compound_id_example" # character | compound which intensities should be read out #' var_feature_id <- "" # character | (Optional) @@ -126,7 +126,7 @@ #' #' #################### GetCompounds #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -143,7 +143,7 @@ #' #' #################### GetCompoundsByGroupExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_group_name <- "group_name_example" # character | tag group name. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -162,7 +162,7 @@ #' #' #################### GetCompoundsByTagExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project space to get compounds (group of ion identities) from. #' var_filter <- "" # character | tag filter. (Optional) #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -181,7 +181,7 @@ #' #' #################### GetCompoundsPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) #' var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -201,7 +201,7 @@ #' #' #################### GetTagsForCompoundExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to get from. #' var_object_id <- "object_id_example" # character | CompoundId to get tags for. #' @@ -216,7 +216,7 @@ #' #' #################### RemoveTagFromCompoundExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to delete tag from. #' var_tag_name <- "tag_name_example" # character | name of the tag to delete. @@ -402,7 +402,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Compound]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Compound]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -555,7 +555,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -810,7 +810,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Compound", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Compound", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -940,7 +940,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1081,7 +1081,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1219,7 +1219,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1370,7 +1370,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Compound]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Compound]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1537,7 +1537,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1700,7 +1700,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1875,7 +1875,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelCompound", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2008,7 +2008,7 @@ CompoundsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/connection_check.R b/client-api_r/generated/R/connection_check.R index db494827..0926a2c0 100644 --- a/client-api_r/generated/R/connection_check.R +++ b/client-api_r/generated/R/connection_check.R @@ -91,7 +91,7 @@ ConnectionCheck <- R6::R6Class( self$`licenseInfo` <- `licenseinfo_object` } if (!is.null(this_object$`errors`)) { - self$`errors` <- ApiClient$new()$deserializeObj(this_object$`errors`, "array[ConnectionError]", loadNamespace("Rsirius")) + self$`errors` <- ApiClient$new()$deserializeObj(this_object$`errors`, "array[ConnectionError]", loadNamespace("RSirius")) } self }, @@ -115,7 +115,7 @@ ConnectionCheck <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`licenseInfo` <- LicenseInfo$new()$fromJSON(jsonlite::toJSON(this_object$`licenseInfo`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`errors` <- ApiClient$new()$deserializeObj(this_object$`errors`, "array[ConnectionError]", loadNamespace("Rsirius")) + self$`errors` <- ApiClient$new()$deserializeObj(this_object$`errors`, "array[ConnectionError]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/consensus_annotations_csi.R b/client-api_r/generated/R/consensus_annotations_csi.R index c8f8baa2..69d30eae 100644 --- a/client-api_r/generated/R/consensus_annotations_csi.R +++ b/client-api_r/generated/R/consensus_annotations_csi.R @@ -160,7 +160,7 @@ ConsensusAnnotationsCSI <- R6::R6Class( self$`compoundClasses` <- `compoundclasses_object` } if (!is.null(this_object$`supportingFeatureIds`)) { - self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`selectionCriterion`)) { if (!is.null(this_object$`selectionCriterion`) && !(this_object$`selectionCriterion` %in% c("MAJORITY_STRUCTURE", "CONFIDENCE_STRUCTURE", "SINGLETON_STRUCTURE", "MAJORITY_FORMULA", "TOP_FORMULA", "SINGLETON_FORMULA"))) { @@ -202,7 +202,7 @@ ConsensusAnnotationsCSI <- R6::R6Class( this_object <- jsonlite::fromJSON(input_json) self$`molecularFormula` <- this_object$`molecularFormula` self$`compoundClasses` <- CompoundClasses$new()$fromJSON(jsonlite::toJSON(this_object$`compoundClasses`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("RSirius")) if (!is.null(this_object$`selectionCriterion`) && !(this_object$`selectionCriterion` %in% c("MAJORITY_STRUCTURE", "CONFIDENCE_STRUCTURE", "SINGLETON_STRUCTURE", "MAJORITY_FORMULA", "TOP_FORMULA", "SINGLETON_FORMULA"))) { stop(paste("Error! \"", this_object$`selectionCriterion`, "\" cannot be assigned to `selectionCriterion`. Must be \"MAJORITY_STRUCTURE\", \"CONFIDENCE_STRUCTURE\", \"SINGLETON_STRUCTURE\", \"MAJORITY_FORMULA\", \"TOP_FORMULA\", \"SINGLETON_FORMULA\".", sep = "")) } diff --git a/client-api_r/generated/R/consensus_annotations_de_novo.R b/client-api_r/generated/R/consensus_annotations_de_novo.R index 86f8a8cf..76b908fb 100644 --- a/client-api_r/generated/R/consensus_annotations_de_novo.R +++ b/client-api_r/generated/R/consensus_annotations_de_novo.R @@ -123,7 +123,7 @@ ConsensusAnnotationsDeNovo <- R6::R6Class( self$`compoundClasses` <- `compoundclasses_object` } if (!is.null(this_object$`supportingFeatureIds`)) { - self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`selectionCriterion`)) { if (!is.null(this_object$`selectionCriterion`) && !(this_object$`selectionCriterion` %in% c("MAJORITY_FORMULA", "TOP_FORMULA", "SINGLETON_FORMULA"))) { @@ -154,7 +154,7 @@ ConsensusAnnotationsDeNovo <- R6::R6Class( this_object <- jsonlite::fromJSON(input_json) self$`molecularFormula` <- this_object$`molecularFormula` self$`compoundClasses` <- CompoundClasses$new()$fromJSON(jsonlite::toJSON(this_object$`compoundClasses`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`supportingFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`supportingFeatureIds`, "array[character]", loadNamespace("RSirius")) if (!is.null(this_object$`selectionCriterion`) && !(this_object$`selectionCriterion` %in% c("MAJORITY_FORMULA", "TOP_FORMULA", "SINGLETON_FORMULA"))) { stop(paste("Error! \"", this_object$`selectionCriterion`, "\" cannot be assigned to `selectionCriterion`. Must be \"MAJORITY_FORMULA\", \"TOP_FORMULA\", \"SINGLETON_FORMULA\".", sep = "")) } diff --git a/client-api_r/generated/R/data_import_event.R b/client-api_r/generated/R/data_import_event.R index 102161f8..38f2f640 100644 --- a/client-api_r/generated/R/data_import_event.R +++ b/client-api_r/generated/R/data_import_event.R @@ -103,10 +103,10 @@ DataImportEvent <- R6::R6Class( self$`importJobId` <- this_object$`importJobId` } if (!is.null(this_object$`importedCompoundIds`)) { - self$`importedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`importedCompoundIds`, "array[character]", loadNamespace("Rsirius")) + self$`importedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`importedCompoundIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`importedFeatureIds`)) { - self$`importedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`importedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`importedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`importedFeatureIds`, "array[character]", loadNamespace("RSirius")) } self }, @@ -130,8 +130,8 @@ DataImportEvent <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`importJobId` <- this_object$`importJobId` - self$`importedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`importedCompoundIds`, "array[character]", loadNamespace("Rsirius")) - self$`importedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`importedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`importedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`importedCompoundIds`, "array[character]", loadNamespace("RSirius")) + self$`importedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`importedFeatureIds`, "array[character]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/feature_annotations.R b/client-api_r/generated/R/feature_annotations.R index d076594a..3672edbf 100644 --- a/client-api_r/generated/R/feature_annotations.R +++ b/client-api_r/generated/R/feature_annotations.R @@ -189,10 +189,10 @@ FeatureAnnotations <- R6::R6Class( self$`expansiveSearchState` <- this_object$`expansiveSearchState` } if (!is.null(this_object$`specifiedDatabases`)) { - self$`specifiedDatabases` <- ApiClient$new()$deserializeObj(this_object$`specifiedDatabases`, "array[character]", loadNamespace("Rsirius")) + self$`specifiedDatabases` <- ApiClient$new()$deserializeObj(this_object$`specifiedDatabases`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`expandedDatabases`)) { - self$`expandedDatabases` <- ApiClient$new()$deserializeObj(this_object$`expandedDatabases`, "array[character]", loadNamespace("Rsirius")) + self$`expandedDatabases` <- ApiClient$new()$deserializeObj(this_object$`expandedDatabases`, "array[character]", loadNamespace("RSirius")) } self }, @@ -224,8 +224,8 @@ FeatureAnnotations <- R6::R6Class( stop(paste("Error! \"", this_object$`expansiveSearchState`, "\" cannot be assigned to `expansiveSearchState`. Must be \"OFF\", \"EXACT\", \"APPROXIMATE\".", sep = "")) } self$`expansiveSearchState` <- this_object$`expansiveSearchState` - self$`specifiedDatabases` <- ApiClient$new()$deserializeObj(this_object$`specifiedDatabases`, "array[character]", loadNamespace("Rsirius")) - self$`expandedDatabases` <- ApiClient$new()$deserializeObj(this_object$`expandedDatabases`, "array[character]", loadNamespace("Rsirius")) + self$`specifiedDatabases` <- ApiClient$new()$deserializeObj(this_object$`specifiedDatabases`, "array[character]", loadNamespace("RSirius")) + self$`expandedDatabases` <- ApiClient$new()$deserializeObj(this_object$`expandedDatabases`, "array[character]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/feature_import.R b/client-api_r/generated/R/feature_import.R index f9605b50..d6373a0a 100644 --- a/client-api_r/generated/R/feature_import.R +++ b/client-api_r/generated/R/feature_import.R @@ -232,7 +232,7 @@ FeatureImport <- R6::R6Class( self$`charge` <- this_object$`charge` } if (!is.null(this_object$`detectedAdducts`)) { - self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("Rsirius")) + self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("RSirius")) if (!identical(self$`detectedAdducts`, unique(self$`detectedAdducts`))) { stop("Error! Items in `detectedAdducts` are not unique.") } @@ -258,10 +258,10 @@ FeatureImport <- R6::R6Class( self$`mergedMs1` <- `mergedms1_object` } if (!is.null(this_object$`ms1Spectra`)) { - self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) } if (!is.null(this_object$`ms2Spectra`)) { - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) } self }, @@ -288,7 +288,7 @@ FeatureImport <- R6::R6Class( self$`externalFeatureId` <- this_object$`externalFeatureId` self$`ionMass` <- this_object$`ionMass` self$`charge` <- this_object$`charge` - self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("Rsirius")) + self$`detectedAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectedAdducts`, "set[character]", loadNamespace("RSirius")) if (!identical(self$`detectedAdducts`, unique(self$`detectedAdducts`))) { stop("Error! Items in `detectedAdducts` are not unique.") } @@ -300,8 +300,8 @@ FeatureImport <- R6::R6Class( } self$`dataQuality` <- this_object$`dataQuality` self$`mergedMs1` <- BasicSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`mergedMs1`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/feature_statistics_api.R b/client-api_r/generated/R/feature_statistics_api.R index cdd55b6d..075ad1bb 100644 --- a/client-api_r/generated/R/feature_statistics_api.R +++ b/client-api_r/generated/R/feature_statistics_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### ComputeAlignedFeatureFoldChangesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to compute the fold change in. #' var_left_group_name <- "left_group_name_example" # character | name of the left tag group. #' var_right_group_name <- "right_group_name_example" # character | name of the right tag group. @@ -34,7 +34,7 @@ #' #' #################### DeleteAlignedFeatureFoldChangesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_left_group_name <- "left_group_name_example" # character | name of the left group. #' var_right_group_name <- "right_group_name_example" # character | name of the right group. @@ -49,7 +49,7 @@ #' #' #################### GetAlignedFeatureFoldChangeTableExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aggregation <- "AVG" # character | aggregation type. (Optional) #' var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional) @@ -65,7 +65,7 @@ #' #' #################### GetFoldChangesByAlignedFeatureExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to. #' @@ -247,7 +247,7 @@ FeatureStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -501,7 +501,7 @@ FeatureStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "StatisticsTable", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "StatisticsTable", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -634,7 +634,7 @@ FeatureStatisticsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[FoldChange]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[FoldChange]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/features_api.R b/client-api_r/generated/R/features_api.R index 89e76984..6aeea61f 100644 --- a/client-api_r/generated/R/features_api.R +++ b/client-api_r/generated/R/features_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### AddAlignedFeatures #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to import into. #' var_feature_import <- c(FeatureImport$new(123, 123, "name_example", "externalFeatureId_example", c("detectedAdducts_example"), 123, 123, 123, "NOT_APPLICABLE", BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)))) # array[FeatureImport] | the feature data to be imported #' var_profile <- "profile_example" # character | profile describing the instrument used to measure the data. Used to merge spectra. (Optional) @@ -32,7 +32,7 @@ #' #' #################### AddDeNovoStructureCandidate #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_smiles <- "none" # character | smiles (Optional) @@ -48,7 +48,7 @@ #' #' #################### AddTagsToAlignedFeatureExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | run to add tags to. #' var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -64,7 +64,7 @@ #' #' #################### DeleteAlignedFeature #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to delete. #' @@ -76,7 +76,7 @@ #' #' #################### DeleteAlignedFeatures #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_request_body <- c("property_example") # array[character] | #' @@ -88,7 +88,7 @@ #' #' #################### GetAdductNetworkWithMergedTracesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | one feature that is considered the main feature of the adduct network #' @@ -103,7 +103,7 @@ #' #' #################### GetAlignedFeature #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to access. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -120,7 +120,7 @@ #' #' #################### GetAlignedFeatureQualityExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to access. #' @@ -135,7 +135,7 @@ #' #' #################### GetAlignedFeatures #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -151,7 +151,7 @@ #' #' #################### GetAlignedFeaturesByGroupExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_group_name <- "group_name_example" # character | tag group name. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -170,7 +170,7 @@ #' #' #################### GetAlignedFeaturesByTagExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project space to get features (aligned over runs) from. #' var_filter <- "" # character | tag filter. (Optional) #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -189,7 +189,7 @@ #' #' #################### GetAlignedFeaturesPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) #' var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -208,7 +208,7 @@ #' #' #################### GetBestMatchingCompoundClasses #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -224,7 +224,7 @@ #' #' #################### GetCanopusPrediction #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -240,7 +240,7 @@ #' #' #################### GetDeNovoStructureCandidates #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -256,7 +256,7 @@ #' #' #################### GetDeNovoStructureCandidatesByFormula #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -273,7 +273,7 @@ #' #' #################### GetDeNovoStructureCandidatesByFormulaPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -293,7 +293,7 @@ #' #' #################### GetDeNovoStructureCandidatesPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -312,7 +312,7 @@ #' #' #################### GetFeatureQuantTableExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) #' @@ -327,7 +327,7 @@ #' #' #################### GetFingerprintPrediction #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -343,7 +343,7 @@ #' #' #################### GetFormulaAnnotatedMsMsData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -360,7 +360,7 @@ #' #' #################### GetFormulaAnnotatedSpectrum #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -378,7 +378,7 @@ #' #' #################### GetFormulaCandidate #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -396,7 +396,7 @@ #' #' #################### GetFormulaCandidates #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -413,7 +413,7 @@ #' #' #################### GetFormulaCandidatesPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -433,7 +433,7 @@ #' #' #################### GetFragTree #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -449,7 +449,7 @@ #' #' #################### GetIsotopePatternAnnotation #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -465,7 +465,7 @@ #' #' #################### GetLipidAnnotation #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -481,7 +481,7 @@ #' #' #################### GetMsData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the Mass Spec data belongs to. #' var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -497,7 +497,7 @@ #' #' #################### GetQuantTableRowExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which quantity should be read out #' var_type <- "APEX_HEIGHT" # character | quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. (Optional) @@ -513,7 +513,7 @@ #' #' #################### GetSpectralLibraryMatch #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_match_id <- "match_id_example" # character | id of the library match to be returned. @@ -530,7 +530,7 @@ #' #' #################### GetSpectralLibraryMatches #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_min_shared_peaks <- 1 # integer | (Optional) @@ -549,7 +549,7 @@ #' #' #################### GetSpectralLibraryMatchesPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -571,7 +571,7 @@ #' #' #################### GetSpectralLibraryMatchesSummary #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_min_shared_peaks <- 1 # integer | min threshold of shared peaks. (Optional) @@ -589,7 +589,7 @@ #' #' #################### GetStructureAnnotatedMsDataExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -607,7 +607,7 @@ #' #' #################### GetStructureAnnotatedSpectralLibraryMatchExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_match_id <- "match_id_example" # character | id of the library match to be returned. @@ -623,7 +623,7 @@ #' #' #################### GetStructureAnnotatedSpectrumExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -642,7 +642,7 @@ #' #' #################### GetStructureCandidates #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -658,7 +658,7 @@ #' #' #################### GetStructureCandidatesByFormula #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -675,7 +675,7 @@ #' #' #################### GetStructureCandidatesByFormulaPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. #' var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -695,7 +695,7 @@ #' #' #################### GetStructureCandidatesPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -714,7 +714,7 @@ #' #' #################### GetTagsForAlignedFeaturesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to get from. #' var_object_id <- "object_id_example" # character | object to get tags for. #' @@ -729,7 +729,7 @@ #' #' #################### GetTracesExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which intensities should be read out #' var_include_all <- FALSE # character | when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. (Optional) @@ -745,7 +745,7 @@ #' #' #################### RemoveTagFromAlignedFeatureExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) to delete tag from. #' var_tag_name <- "tag_name_example" # character | name of the tag to delete. @@ -919,7 +919,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[AlignedFeature]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[AlignedFeature]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1057,7 +1057,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1210,7 +1210,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1538,7 +1538,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1688,7 +1688,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AlignedFeature", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AlignedFeature", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1821,7 +1821,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AlignedFeatureQualityExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AlignedFeatureQualityExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1960,7 +1960,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[AlignedFeature]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[AlignedFeature]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2127,7 +2127,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2290,7 +2290,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2453,7 +2453,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelAlignedFeature", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2597,7 +2597,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "CompoundClasses", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "CompoundClasses", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2741,7 +2741,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "CanopusPrediction", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "CanopusPrediction", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2886,7 +2886,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3042,7 +3042,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateScored]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateScored]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3222,7 +3222,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateScored", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateScored", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3391,7 +3391,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateFormula", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateFormula", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3521,7 +3521,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3665,7 +3665,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[numeric]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[numeric]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3814,7 +3814,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedMsMsData", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedMsMsData", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -3968,7 +3968,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4129,7 +4129,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "FormulaCandidate", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "FormulaCandidate", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4279,7 +4279,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[FormulaCandidate]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[FormulaCandidate]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4453,7 +4453,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelFormulaCandidate", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelFormulaCandidate", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4597,7 +4597,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "FragmentationTree", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "FragmentationTree", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4741,7 +4741,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "IsotopePatternAnnotation", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "IsotopePatternAnnotation", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -4885,7 +4885,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "LipidAnnotation", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "LipidAnnotation", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5023,7 +5023,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "MsData", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "MsData", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5164,7 +5164,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "QuantTableExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5320,7 +5320,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SpectralLibraryMatch", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SpectralLibraryMatch", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5480,7 +5480,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[SpectralLibraryMatch]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[SpectralLibraryMatch]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5664,7 +5664,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelSpectralLibraryMatch", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelSpectralLibraryMatch", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5812,7 +5812,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SpectralLibraryMatchSummary", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SpectralLibraryMatchSummary", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -5972,7 +5972,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedMsMsData", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedMsMsData", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6116,7 +6116,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6281,7 +6281,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AnnotatedSpectrum", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6426,7 +6426,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateFormula]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6582,7 +6582,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateScored]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StructureCandidateScored]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6762,7 +6762,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateScored", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateScored", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -6931,7 +6931,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateFormula", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelStructureCandidateFormula", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -7064,7 +7064,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -7202,7 +7202,7 @@ FeaturesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TraceSetExperimental", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/formula_candidate.R b/client-api_r/generated/R/formula_candidate.R index fd2168a1..af5c86d4 100644 --- a/client-api_r/generated/R/formula_candidate.R +++ b/client-api_r/generated/R/formula_candidate.R @@ -369,7 +369,7 @@ FormulaCandidate <- R6::R6Class( self$`lipidAnnotation` <- `lipidannotation_object` } if (!is.null(this_object$`predictedFingerprint`)) { - self$`predictedFingerprint` <- ApiClient$new()$deserializeObj(this_object$`predictedFingerprint`, "array[numeric]", loadNamespace("Rsirius")) + self$`predictedFingerprint` <- ApiClient$new()$deserializeObj(this_object$`predictedFingerprint`, "array[numeric]", loadNamespace("RSirius")) } if (!is.null(this_object$`compoundClasses`)) { `compoundclasses_object` <- CompoundClasses$new() @@ -419,7 +419,7 @@ FormulaCandidate <- R6::R6Class( self$`annotatedSpectrum` <- AnnotatedSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`annotatedSpectrum`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`isotopePatternAnnotation` <- IsotopePatternAnnotation$new()$fromJSON(jsonlite::toJSON(this_object$`isotopePatternAnnotation`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`lipidAnnotation` <- LipidAnnotation$new()$fromJSON(jsonlite::toJSON(this_object$`lipidAnnotation`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`predictedFingerprint` <- ApiClient$new()$deserializeObj(this_object$`predictedFingerprint`, "array[numeric]", loadNamespace("Rsirius")) + self$`predictedFingerprint` <- ApiClient$new()$deserializeObj(this_object$`predictedFingerprint`, "array[numeric]", loadNamespace("RSirius")) self$`compoundClasses` <- CompoundClasses$new()$fromJSON(jsonlite::toJSON(this_object$`compoundClasses`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`canopusPrediction` <- CanopusPrediction$new()$fromJSON(jsonlite::toJSON(this_object$`canopusPrediction`, auto_unbox = TRUE, digits = NA, null = 'null')) self diff --git a/client-api_r/generated/R/fragmentation_tree.R b/client-api_r/generated/R/fragmentation_tree.R index 4989fbde..6247a836 100644 --- a/client-api_r/generated/R/fragmentation_tree.R +++ b/client-api_r/generated/R/fragmentation_tree.R @@ -126,10 +126,10 @@ FragmentationTree <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`fragments`)) { - self$`fragments` <- ApiClient$new()$deserializeObj(this_object$`fragments`, "array[FragmentNode]", loadNamespace("Rsirius")) + self$`fragments` <- ApiClient$new()$deserializeObj(this_object$`fragments`, "array[FragmentNode]", loadNamespace("RSirius")) } if (!is.null(this_object$`losses`)) { - self$`losses` <- ApiClient$new()$deserializeObj(this_object$`losses`, "array[LossEdge]", loadNamespace("Rsirius")) + self$`losses` <- ApiClient$new()$deserializeObj(this_object$`losses`, "array[LossEdge]", loadNamespace("RSirius")) } if (!is.null(this_object$`treeScore`)) { self$`treeScore` <- this_object$`treeScore` @@ -161,8 +161,8 @@ FragmentationTree <- R6::R6Class( #' @return the instance of FragmentationTree fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`fragments` <- ApiClient$new()$deserializeObj(this_object$`fragments`, "array[FragmentNode]", loadNamespace("Rsirius")) - self$`losses` <- ApiClient$new()$deserializeObj(this_object$`losses`, "array[LossEdge]", loadNamespace("Rsirius")) + self$`fragments` <- ApiClient$new()$deserializeObj(this_object$`fragments`, "array[FragmentNode]", loadNamespace("RSirius")) + self$`losses` <- ApiClient$new()$deserializeObj(this_object$`losses`, "array[LossEdge]", loadNamespace("RSirius")) self$`treeScore` <- this_object$`treeScore` self$`molecularFormula` <- this_object$`molecularFormula` self$`adduct` <- this_object$`adduct` diff --git a/client-api_r/generated/R/import_result.R b/client-api_r/generated/R/import_result.R index 6b586cd4..757919f8 100644 --- a/client-api_r/generated/R/import_result.R +++ b/client-api_r/generated/R/import_result.R @@ -87,10 +87,10 @@ ImportResult <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`affectedCompoundIds`)) { - self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`affectedAlignedFeatureIds`)) { - self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("RSirius")) } self }, @@ -113,8 +113,8 @@ ImportResult <- R6::R6Class( #' @return the instance of ImportResult fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("Rsirius")) - self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("RSirius")) + self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/info.R b/client-api_r/generated/R/info.R index 2d88e86c..ee988a51 100644 --- a/client-api_r/generated/R/info.R +++ b/client-api_r/generated/R/info.R @@ -247,10 +247,10 @@ Info <- R6::R6Class( self$`fingerprintId` <- this_object$`fingerprintId` } if (!is.null(this_object$`availableILPSolvers`)) { - self$`availableILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`availableILPSolvers`, "array[character]", loadNamespace("Rsirius")) + self$`availableILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`availableILPSolvers`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`supportedILPSolvers`)) { - self$`supportedILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`supportedILPSolvers`, "map(character)", loadNamespace("Rsirius")) + self$`supportedILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`supportedILPSolvers`, "map(character)", loadNamespace("RSirius")) } self }, @@ -283,8 +283,8 @@ Info <- R6::R6Class( self$`chemDbVersion` <- this_object$`chemDbVersion` self$`fingerIdModelVersion` <- this_object$`fingerIdModelVersion` self$`fingerprintId` <- this_object$`fingerprintId` - self$`availableILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`availableILPSolvers`, "array[character]", loadNamespace("Rsirius")) - self$`supportedILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`supportedILPSolvers`, "map(character)", loadNamespace("Rsirius")) + self$`availableILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`availableILPSolvers`, "array[character]", loadNamespace("RSirius")) + self$`supportedILPSolvers` <- ApiClient$new()$deserializeObj(this_object$`supportedILPSolvers`, "map(character)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/info_api.R b/client-api_r/generated/R/info_api.R index cd58a20d..c8f4bfd1 100644 --- a/client-api_r/generated/R/info_api.R +++ b/client-api_r/generated/R/info_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### GetConnectionCheck #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' api_instance <- rsirius_api$new() #' @@ -27,7 +27,7 @@ #' #' #################### GetInfo #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_server_info <- TRUE # character | (Optional) #' var_update_info <- TRUE # character | (Optional) #' @@ -151,7 +151,7 @@ InfoApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ConnectionCheck", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ConnectionCheck", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -272,7 +272,7 @@ InfoApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Info", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Info", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/job.R b/client-api_r/generated/R/job.R index 0417d4d6..5a0f17a8 100644 --- a/client-api_r/generated/R/job.R +++ b/client-api_r/generated/R/job.R @@ -151,10 +151,10 @@ Job <- R6::R6Class( self$`progress` <- `progress_object` } if (!is.null(this_object$`affectedCompoundIds`)) { - self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`affectedAlignedFeatureIds`)) { - self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`jobEffect`)) { if (!is.null(this_object$`jobEffect`) && !(this_object$`jobEffect` %in% c("IMPORT", "COMPUTATION", "DELETION"))) { @@ -186,8 +186,8 @@ Job <- R6::R6Class( self$`id` <- this_object$`id` self$`command` <- this_object$`command` self$`progress` <- JobProgress$new()$fromJSON(jsonlite::toJSON(this_object$`progress`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("Rsirius")) - self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`affectedCompoundIds` <- ApiClient$new()$deserializeObj(this_object$`affectedCompoundIds`, "array[character]", loadNamespace("RSirius")) + self$`affectedAlignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`affectedAlignedFeatureIds`, "array[character]", loadNamespace("RSirius")) if (!is.null(this_object$`jobEffect`) && !(this_object$`jobEffect` %in% c("IMPORT", "COMPUTATION", "DELETION"))) { stop(paste("Error! \"", this_object$`jobEffect`, "\" cannot be assigned to `jobEffect`. Must be \"IMPORT\", \"COMPUTATION\", \"DELETION\".", sep = "")) } diff --git a/client-api_r/generated/R/job_submission.R b/client-api_r/generated/R/job_submission.R index 15054183..348db166 100644 --- a/client-api_r/generated/R/job_submission.R +++ b/client-api_r/generated/R/job_submission.R @@ -225,19 +225,19 @@ JobSubmission <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`compoundIds`)) { - self$`compoundIds` <- ApiClient$new()$deserializeObj(this_object$`compoundIds`, "array[character]", loadNamespace("Rsirius")) + self$`compoundIds` <- ApiClient$new()$deserializeObj(this_object$`compoundIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`alignedFeatureIds`)) { - self$`alignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`alignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) + self$`alignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`alignedFeatureIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`fallbackAdducts`)) { - self$`fallbackAdducts` <- ApiClient$new()$deserializeObj(this_object$`fallbackAdducts`, "array[character]", loadNamespace("Rsirius")) + self$`fallbackAdducts` <- ApiClient$new()$deserializeObj(this_object$`fallbackAdducts`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`enforcedAdducts`)) { - self$`enforcedAdducts` <- ApiClient$new()$deserializeObj(this_object$`enforcedAdducts`, "array[character]", loadNamespace("Rsirius")) + self$`enforcedAdducts` <- ApiClient$new()$deserializeObj(this_object$`enforcedAdducts`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`detectableAdducts`)) { - self$`detectableAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectableAdducts`, "array[character]", loadNamespace("Rsirius")) + self$`detectableAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectableAdducts`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`recompute`)) { self$`recompute` <- this_object$`recompute` @@ -278,7 +278,7 @@ JobSubmission <- R6::R6Class( self$`msNovelistParams` <- `msnovelistparams_object` } if (!is.null(this_object$`configMap`)) { - self$`configMap` <- ApiClient$new()$deserializeObj(this_object$`configMap`, "map(character)", loadNamespace("Rsirius")) + self$`configMap` <- ApiClient$new()$deserializeObj(this_object$`configMap`, "map(character)", loadNamespace("RSirius")) } self }, @@ -301,11 +301,11 @@ JobSubmission <- R6::R6Class( #' @return the instance of JobSubmission fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`compoundIds` <- ApiClient$new()$deserializeObj(this_object$`compoundIds`, "array[character]", loadNamespace("Rsirius")) - self$`alignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`alignedFeatureIds`, "array[character]", loadNamespace("Rsirius")) - self$`fallbackAdducts` <- ApiClient$new()$deserializeObj(this_object$`fallbackAdducts`, "array[character]", loadNamespace("Rsirius")) - self$`enforcedAdducts` <- ApiClient$new()$deserializeObj(this_object$`enforcedAdducts`, "array[character]", loadNamespace("Rsirius")) - self$`detectableAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectableAdducts`, "array[character]", loadNamespace("Rsirius")) + self$`compoundIds` <- ApiClient$new()$deserializeObj(this_object$`compoundIds`, "array[character]", loadNamespace("RSirius")) + self$`alignedFeatureIds` <- ApiClient$new()$deserializeObj(this_object$`alignedFeatureIds`, "array[character]", loadNamespace("RSirius")) + self$`fallbackAdducts` <- ApiClient$new()$deserializeObj(this_object$`fallbackAdducts`, "array[character]", loadNamespace("RSirius")) + self$`enforcedAdducts` <- ApiClient$new()$deserializeObj(this_object$`enforcedAdducts`, "array[character]", loadNamespace("RSirius")) + self$`detectableAdducts` <- ApiClient$new()$deserializeObj(this_object$`detectableAdducts`, "array[character]", loadNamespace("RSirius")) self$`recompute` <- this_object$`recompute` self$`spectraSearchParams` <- SpectralLibrarySearch$new()$fromJSON(jsonlite::toJSON(this_object$`spectraSearchParams`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`formulaIdParams` <- Sirius$new()$fromJSON(jsonlite::toJSON(this_object$`formulaIdParams`, auto_unbox = TRUE, digits = NA, null = 'null')) @@ -314,7 +314,7 @@ JobSubmission <- R6::R6Class( self$`canopusParams` <- Canopus$new()$fromJSON(jsonlite::toJSON(this_object$`canopusParams`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`structureDbSearchParams` <- StructureDbSearch$new()$fromJSON(jsonlite::toJSON(this_object$`structureDbSearchParams`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`msNovelistParams` <- MsNovelist$new()$fromJSON(jsonlite::toJSON(this_object$`msNovelistParams`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`configMap` <- ApiClient$new()$deserializeObj(this_object$`configMap`, "map(character)", loadNamespace("Rsirius")) + self$`configMap` <- ApiClient$new()$deserializeObj(this_object$`configMap`, "map(character)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/jobs_api.R b/client-api_r/generated/R/jobs_api.R index 8e3c3dcf..73812c5e 100644 --- a/client-api_r/generated/R/jobs_api.R +++ b/client-api_r/generated/R/jobs_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### DeleteJob #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete job from #' var_job_id <- "job_id_example" # character | of the job to be deleted #' var_cancel_if_running <- TRUE # character | If true, job will be canceled if it is not finished. Otherwise, deletion will fail for running jobs or request will block until job has finished. (Optional) @@ -29,7 +29,7 @@ #' #' #################### DeleteJobConfig #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_name <- "name_example" # character | name of the job-config to delete #' #' #Delete job configuration with given name. @@ -40,7 +40,7 @@ #' #' #################### DeleteJobs #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete jobs from #' var_cancel_if_running <- TRUE # character | If true, job will be canceled if it is not finished. Otherwise, deletion will fail for running jobs or request will block until job has finished. (Optional) #' var_await_deletion <- TRUE # character | If true, request will block until deletion succeeded or failed. If the job is still running the request will wait until the job has finished. (Optional) @@ -53,7 +53,7 @@ #' #' #################### GetCommand #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | #' #' #Get a CLI command for the given job configuration. @@ -67,7 +67,7 @@ #' #' #################### GetDefaultJobConfig #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_include_config_map <- FALSE # character | if true, generic configmap with-defaults will be included (Optional) #' var_move_parameters_to_config_map <- FALSE # character | if true, object-based parameters will be converted to and added to the generic configMap parameters (Optional) #' var_include_custom_dbs_for_structure_search <- FALSE # character | if true, default database selection of structure db search spectral library search contains also all available custom DB. If No custom dbs are selected, spectral library search is disabled by default. (Optional) @@ -83,7 +83,7 @@ #' #' #################### GetJob #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to run jobs on #' var_job_id <- "job_id_example" # character | of the job to be returned #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -99,7 +99,7 @@ #' #' #################### GetJobConfig #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_name <- "name_example" # character | name of the job-config to return #' var_move_parameters_to_config_map <- FALSE # character | if true, object-based parameters will be converted to and added to the generic configMap parameters (Optional) #' @@ -114,7 +114,7 @@ #' #' #################### GetJobConfigNames #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #[DEPRECATED] Get all (non-default) job configuration names #' api_instance <- rsirius_api$new() @@ -127,7 +127,7 @@ #' #' #################### GetJobConfigs #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Request all available job configurations #' api_instance <- rsirius_api$new() @@ -140,7 +140,7 @@ #' #' #################### GetJobs #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to run jobs on #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) #' @@ -155,7 +155,7 @@ #' #' #################### GetJobsPaged #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to run jobs on #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) #' var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -173,7 +173,7 @@ #' #' #################### HasJobs #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | #' var_include_finished <- FALSE # character | (Optional) #' @@ -187,7 +187,7 @@ #' #' #################### SaveJobConfig #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_name <- "name_example" # character | name of the job-config to add #' var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | to add #' var_override_existing <- FALSE # character | (Optional) @@ -204,7 +204,7 @@ #' #' #################### StartJob #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to run jobs on #' var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | configuration of the job that will be submitted of the job to be returned #' var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -220,7 +220,7 @@ #' #' #################### StartJobFromConfig #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to run jobs on #' var_job_config_name <- "job_config_name_example" # character | name if the config to be used #' var_request_body <- c("property_example") # array[character] | List of alignedFeatureIds to be computed @@ -638,7 +638,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[character]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[character]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -764,7 +764,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "JobSubmission", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "JobSubmission", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -909,7 +909,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1036,7 +1036,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "StoredJobSubmission", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "StoredJobSubmission", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1147,7 +1147,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[character]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[character]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1258,7 +1258,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[StoredJobSubmission]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[StoredJobSubmission]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1392,7 +1392,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Job]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Job]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1550,7 +1550,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelJob", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelJob", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1677,7 +1677,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1822,7 +1822,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "StoredJobSubmission", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "StoredJobSubmission", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1969,7 +1969,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -2137,7 +2137,7 @@ JobsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/license_info.R b/client-api_r/generated/R/license_info.R index 3f7c2a28..29bb15e5 100644 --- a/client-api_r/generated/R/license_info.R +++ b/client-api_r/generated/R/license_info.R @@ -139,7 +139,7 @@ LicenseInfo <- R6::R6Class( self$`consumables` <- `consumables_object` } if (!is.null(this_object$`terms`)) { - self$`terms` <- ApiClient$new()$deserializeObj(this_object$`terms`, "array[Term]", loadNamespace("Rsirius")) + self$`terms` <- ApiClient$new()$deserializeObj(this_object$`terms`, "array[Term]", loadNamespace("RSirius")) } self }, @@ -166,7 +166,7 @@ LicenseInfo <- R6::R6Class( self$`userId` <- this_object$`userId` self$`subscription` <- Subscription$new()$fromJSON(jsonlite::toJSON(this_object$`subscription`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`consumables` <- SubscriptionConsumables$new()$fromJSON(jsonlite::toJSON(this_object$`consumables`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`terms` <- ApiClient$new()$deserializeObj(this_object$`terms`, "array[Term]", loadNamespace("Rsirius")) + self$`terms` <- ApiClient$new()$deserializeObj(this_object$`terms`, "array[Term]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/login_and_account_api.R b/client-api_r/generated/R/login_and_account_api.R index d0d13d85..4e6ee059 100644 --- a/client-api_r/generated/R/login_and_account_api.R +++ b/client-api_r/generated/R/login_and_account_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### GetAccountInfo #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_include_subs <- FALSE # character | include available and active subscriptions in {@link AccountInfo AccountInfo}. (Optional) #' #' #Get information about the account currently logged in. @@ -29,7 +29,7 @@ #' #' #################### GetSignUpURL #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Get SignUp URL (For signUp via web browser) #' api_instance <- rsirius_api$new() @@ -42,7 +42,7 @@ #' #' #################### GetSubscriptions #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Get available subscriptions of the account currently logged in. #' api_instance <- rsirius_api$new() @@ -55,7 +55,7 @@ #' #' #################### IsLoggedIn #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Check if a user is logged in. #' api_instance <- rsirius_api$new() @@ -68,7 +68,7 @@ #' #' #################### Login #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_accept_terms <- "accept_terms_example" # character | #' var_account_credentials <- AccountCredentials$new("username_example", "password_example", "refreshToken_example") # AccountCredentials | used to log in. #' var_fail_when_logged_in <- FALSE # character | if true request fails if an active login already exists. (Optional) @@ -85,7 +85,7 @@ #' #' #################### Logout #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Logout from SIRIUS web services. #' api_instance <- rsirius_api$new() @@ -95,7 +95,7 @@ #' #' #################### OpenPortal #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Open User portal in browser. #' api_instance <- rsirius_api$new() @@ -105,7 +105,7 @@ #' #' #################### SelectSubscription #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_sid <- "sid_example" # character | #' #' #Select a subscription as active subscription to be used for computations. @@ -119,7 +119,7 @@ #' #' #################### SignUp #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #Open SignUp window in system browser and return signUp link. #' api_instance <- rsirius_api$new() @@ -247,7 +247,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -358,7 +358,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -469,7 +469,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Subscription]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Subscription]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -580,7 +580,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -723,7 +723,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -985,7 +985,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "AccountInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1096,7 +1096,7 @@ LoginAndAccountApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/ms_data.R b/client-api_r/generated/R/ms_data.R index d546b217..82713fba 100644 --- a/client-api_r/generated/R/ms_data.R +++ b/client-api_r/generated/R/ms_data.R @@ -135,10 +135,10 @@ MsData <- R6::R6Class( self$`mergedMs2` <- `mergedms2_object` } if (!is.null(this_object$`ms1Spectra`)) { - self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) } if (!is.null(this_object$`ms2Spectra`)) { - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) } self }, @@ -164,8 +164,8 @@ MsData <- R6::R6Class( self$`isotopePattern` <- BasicSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`isotopePattern`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`mergedMs1` <- BasicSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`mergedMs1`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`mergedMs2` <- BasicSpectrum$new()$fromJSON(jsonlite::toJSON(this_object$`mergedMs2`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) - self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("Rsirius")) + self$`ms1Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms1Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) + self$`ms2Spectra` <- ApiClient$new()$deserializeObj(this_object$`ms2Spectra`, "array[BasicSpectrum]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/paged_model_aligned_feature.R b/client-api_r/generated/R/paged_model_aligned_feature.R index 3a7eb43a..14d125d9 100644 --- a/client-api_r/generated/R/paged_model_aligned_feature.R +++ b/client-api_r/generated/R/paged_model_aligned_feature.R @@ -86,7 +86,7 @@ PagedModelAlignedFeature <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[AlignedFeature]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[AlignedFeature]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelAlignedFeature <- R6::R6Class( #' @return the instance of PagedModelAlignedFeature fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[AlignedFeature]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[AlignedFeature]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_compound.R b/client-api_r/generated/R/paged_model_compound.R index 35534b55..ab411301 100644 --- a/client-api_r/generated/R/paged_model_compound.R +++ b/client-api_r/generated/R/paged_model_compound.R @@ -86,7 +86,7 @@ PagedModelCompound <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Compound]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Compound]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelCompound <- R6::R6Class( #' @return the instance of PagedModelCompound fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Compound]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Compound]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_formula_candidate.R b/client-api_r/generated/R/paged_model_formula_candidate.R index 4411ee37..9126899b 100644 --- a/client-api_r/generated/R/paged_model_formula_candidate.R +++ b/client-api_r/generated/R/paged_model_formula_candidate.R @@ -86,7 +86,7 @@ PagedModelFormulaCandidate <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[FormulaCandidate]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[FormulaCandidate]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelFormulaCandidate <- R6::R6Class( #' @return the instance of PagedModelFormulaCandidate fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[FormulaCandidate]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[FormulaCandidate]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_job.R b/client-api_r/generated/R/paged_model_job.R index cad8d492..525f3948 100644 --- a/client-api_r/generated/R/paged_model_job.R +++ b/client-api_r/generated/R/paged_model_job.R @@ -86,7 +86,7 @@ PagedModelJob <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Job]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Job]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelJob <- R6::R6Class( #' @return the instance of PagedModelJob fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Job]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Job]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_run.R b/client-api_r/generated/R/paged_model_run.R index 11b15c7d..1c0ae1f2 100644 --- a/client-api_r/generated/R/paged_model_run.R +++ b/client-api_r/generated/R/paged_model_run.R @@ -86,7 +86,7 @@ PagedModelRun <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Run]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Run]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelRun <- R6::R6Class( #' @return the instance of PagedModelRun fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Run]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[Run]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_spectral_library_match.R b/client-api_r/generated/R/paged_model_spectral_library_match.R index b51b4f5a..b2d4be23 100644 --- a/client-api_r/generated/R/paged_model_spectral_library_match.R +++ b/client-api_r/generated/R/paged_model_spectral_library_match.R @@ -86,7 +86,7 @@ PagedModelSpectralLibraryMatch <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelSpectralLibraryMatch <- R6::R6Class( #' @return the instance of PagedModelSpectralLibraryMatch fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_structure_candidate_formula.R b/client-api_r/generated/R/paged_model_structure_candidate_formula.R index 3e4f1474..41d60569 100644 --- a/client-api_r/generated/R/paged_model_structure_candidate_formula.R +++ b/client-api_r/generated/R/paged_model_structure_candidate_formula.R @@ -86,7 +86,7 @@ PagedModelStructureCandidateFormula <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateFormula]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateFormula]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelStructureCandidateFormula <- R6::R6Class( #' @return the instance of PagedModelStructureCandidateFormula fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateFormula]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateFormula]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/paged_model_structure_candidate_scored.R b/client-api_r/generated/R/paged_model_structure_candidate_scored.R index df7321a3..1e4aa531 100644 --- a/client-api_r/generated/R/paged_model_structure_candidate_scored.R +++ b/client-api_r/generated/R/paged_model_structure_candidate_scored.R @@ -86,7 +86,7 @@ PagedModelStructureCandidateScored <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`content`)) { - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateScored]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateScored]", loadNamespace("RSirius")) } if (!is.null(this_object$`page`)) { `page_object` <- PageMetadata$new() @@ -114,7 +114,7 @@ PagedModelStructureCandidateScored <- R6::R6Class( #' @return the instance of PagedModelStructureCandidateScored fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateScored]", loadNamespace("Rsirius")) + self$`content` <- ApiClient$new()$deserializeObj(this_object$`content`, "array[StructureCandidateScored]", loadNamespace("RSirius")) self$`page` <- PageMetadata$new()$fromJSON(jsonlite::toJSON(this_object$`page`, auto_unbox = TRUE, digits = NA, null = 'null')) self }, diff --git a/client-api_r/generated/R/peak_annotation.R b/client-api_r/generated/R/peak_annotation.R index d7ee56cd..6bb9b1b7 100644 --- a/client-api_r/generated/R/peak_annotation.R +++ b/client-api_r/generated/R/peak_annotation.R @@ -269,13 +269,13 @@ PeakAnnotation <- R6::R6Class( self$`parentPeak` <- `parentpeak_object` } if (!is.null(this_object$`substructureAtoms`)) { - self$`substructureAtoms` <- ApiClient$new()$deserializeObj(this_object$`substructureAtoms`, "array[integer]", loadNamespace("Rsirius")) + self$`substructureAtoms` <- ApiClient$new()$deserializeObj(this_object$`substructureAtoms`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`substructureBonds`)) { - self$`substructureBonds` <- ApiClient$new()$deserializeObj(this_object$`substructureBonds`, "array[integer]", loadNamespace("Rsirius")) + self$`substructureBonds` <- ApiClient$new()$deserializeObj(this_object$`substructureBonds`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`substructureBondsCut`)) { - self$`substructureBondsCut` <- ApiClient$new()$deserializeObj(this_object$`substructureBondsCut`, "array[integer]", loadNamespace("Rsirius")) + self$`substructureBondsCut` <- ApiClient$new()$deserializeObj(this_object$`substructureBondsCut`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`substructureScore`)) { self$`substructureScore` <- this_object$`substructureScore` @@ -313,9 +313,9 @@ PeakAnnotation <- R6::R6Class( self$`recalibratedMassDeviationMz` <- this_object$`recalibratedMassDeviationMz` self$`recalibratedMassDeviationPpm` <- this_object$`recalibratedMassDeviationPpm` self$`parentPeak` <- ParentPeak$new()$fromJSON(jsonlite::toJSON(this_object$`parentPeak`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`substructureAtoms` <- ApiClient$new()$deserializeObj(this_object$`substructureAtoms`, "array[integer]", loadNamespace("Rsirius")) - self$`substructureBonds` <- ApiClient$new()$deserializeObj(this_object$`substructureBonds`, "array[integer]", loadNamespace("Rsirius")) - self$`substructureBondsCut` <- ApiClient$new()$deserializeObj(this_object$`substructureBondsCut`, "array[integer]", loadNamespace("Rsirius")) + self$`substructureAtoms` <- ApiClient$new()$deserializeObj(this_object$`substructureAtoms`, "array[integer]", loadNamespace("RSirius")) + self$`substructureBonds` <- ApiClient$new()$deserializeObj(this_object$`substructureBonds`, "array[integer]", loadNamespace("RSirius")) + self$`substructureBondsCut` <- ApiClient$new()$deserializeObj(this_object$`substructureBondsCut`, "array[integer]", loadNamespace("RSirius")) self$`substructureScore` <- this_object$`substructureScore` self$`hydrogenRearrangements` <- this_object$`hydrogenRearrangements` self diff --git a/client-api_r/generated/R/projects_api.R b/client-api_r/generated/R/projects_api.R index 581e433d..8a7aac4c 100644 --- a/client-api_r/generated/R/projects_api.R +++ b/client-api_r/generated/R/projects_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### CloseProject #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | unique name/identifier of the project-space to be closed. #' var_compact <- FALSE # character | if true, compact project storage after closing. DEPRECATED: Compacting acts on the local filesystem and will likely be removed in a later version. (Optional) #' @@ -27,7 +27,7 @@ #' #' #################### CreateProject #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | unique name/identifier that shall be used to access the newly created project-space. Must consist only of [a-zA-Z0-9_-]. #' var_path_to_project <- "path_to_project_example" # character | local file path where the project will be created. If NULL, project will be stored by its projectId in default project location. DEPRECATED: This parameter relies on the local filesystem and will likely be removed in later versions of this API to allow for more flexible use cases. (Optional) #' var_opt_fields <- c("none") # array[character] | (Optional) @@ -43,7 +43,7 @@ #' #' #################### GetCanopusClassyFireData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | #' var_charge <- 56 # integer | #' @@ -58,7 +58,7 @@ #' #' #################### GetCanopusNpcData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | #' var_charge <- 56 # integer | #' @@ -73,7 +73,7 @@ #' #' #################### GetFingerIdData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | #' var_charge <- 56 # integer | #' @@ -88,7 +88,7 @@ #' #' #################### GetProject #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | unique name/identifier tof the project-space to be accessed. #' var_opt_fields <- c("none") # array[character] | (Optional) #' @@ -103,7 +103,7 @@ #' #' #################### GetProjects #################### #' -#' library(Rsirius) +#' library(RSirius) #' #' #List opened project spaces. #' api_instance <- rsirius_api$new() @@ -116,7 +116,7 @@ #' #' #################### ImportMsRunData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | Project-space to import into. #' var_input_files <- c(123) # array[data.frame] | Files to import into project. #' var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters | @@ -132,7 +132,7 @@ #' #' #################### ImportMsRunDataAsJob #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | Project-space to import into. #' var_input_files <- c(123) # array[data.frame] | Files to import into project. #' var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters | @@ -149,7 +149,7 @@ #' #' #################### ImportPreprocessedData #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to import into. #' var_input_files <- c(123) # array[data.frame] | files to import into project #' var_ignore_formulas <- FALSE # character | (Optional) @@ -166,7 +166,7 @@ #' #' #################### ImportPreprocessedDataAsJob #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to import into. #' var_input_files <- c(123) # array[data.frame] | #' var_ignore_formulas <- FALSE # character | (Optional) @@ -184,7 +184,7 @@ #' #' #################### OpenProject #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | unique name/identifier that shall be used to access the opened project-space. Must consist only of [a-zA-Z0-9_-]. #' var_path_to_project <- "path_to_project_example" # character | local file path to open the project from. If NULL, project will be loaded by it projectId from default project location. DEPRECATED: This parameter relies on the local filesystem and will likely be removed in later versions of this API to allow for more flexible use cases. (Optional) #' var_opt_fields <- c("none") # array[character] | (Optional) @@ -425,7 +425,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -556,7 +556,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -687,7 +687,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -818,7 +818,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "character", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -952,7 +952,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1063,7 +1063,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[ProjectInfo]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[ProjectInfo]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1209,7 +1209,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ImportResult", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ImportResult", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1367,7 +1367,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1509,7 +1509,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ImportResult", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ImportResult", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1663,7 +1663,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1802,7 +1802,7 @@ ProjectsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "ProjectInfo", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/quant_table_experimental.R b/client-api_r/generated/R/quant_table_experimental.R index 7c0f18eb..56a76d70 100644 --- a/client-api_r/generated/R/quant_table_experimental.R +++ b/client-api_r/generated/R/quant_table_experimental.R @@ -167,19 +167,19 @@ QuantTableExperimental <- R6::R6Class( self$`rowType` <- this_object$`rowType` } if (!is.null(this_object$`rowIds`)) { - self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[integer]", loadNamespace("Rsirius")) + self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`columnIds`)) { - self$`columnIds` <- ApiClient$new()$deserializeObj(this_object$`columnIds`, "array[integer]", loadNamespace("Rsirius")) + self$`columnIds` <- ApiClient$new()$deserializeObj(this_object$`columnIds`, "array[integer]", loadNamespace("RSirius")) } if (!is.null(this_object$`rowNames`)) { - self$`rowNames` <- ApiClient$new()$deserializeObj(this_object$`rowNames`, "array[character]", loadNamespace("Rsirius")) + self$`rowNames` <- ApiClient$new()$deserializeObj(this_object$`rowNames`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`columnNames`)) { - self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("Rsirius")) + self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`values`)) { - self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("Rsirius")) + self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("RSirius")) } self }, @@ -210,11 +210,11 @@ QuantTableExperimental <- R6::R6Class( stop(paste("Error! \"", this_object$`rowType`, "\" cannot be assigned to `rowType`. Must be \"FEATURES\", \"COMPOUNDS\".", sep = "")) } self$`rowType` <- this_object$`rowType` - self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[integer]", loadNamespace("Rsirius")) - self$`columnIds` <- ApiClient$new()$deserializeObj(this_object$`columnIds`, "array[integer]", loadNamespace("Rsirius")) - self$`rowNames` <- ApiClient$new()$deserializeObj(this_object$`rowNames`, "array[character]", loadNamespace("Rsirius")) - self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("Rsirius")) - self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("Rsirius")) + self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[integer]", loadNamespace("RSirius")) + self$`columnIds` <- ApiClient$new()$deserializeObj(this_object$`columnIds`, "array[integer]", loadNamespace("RSirius")) + self$`rowNames` <- ApiClient$new()$deserializeObj(this_object$`rowNames`, "array[character]", loadNamespace("RSirius")) + self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("RSirius")) + self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/rsirius_api.R b/client-api_r/generated/R/rsirius_api.R index ed214441..93ae5024 100644 --- a/client-api_r/generated/R/rsirius_api.R +++ b/client-api_r/generated/R/rsirius_api.R @@ -5,9 +5,9 @@ #' The version of the OpenAPI document: 3.1 #' Generated by: https://openapi-generator.tech #' -#' Rsirius API Class +#' RSirius API Class #' -#' A single point of access to the Rsirius API. +#' A single point of access to the RSirius API. #' #' NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). #' Ref: https://openapi-generator.tech @@ -47,10 +47,10 @@ rsirius_api <- R6::R6Class( runs_api = NULL, searchable_databases_api = NULL, tags_api = NULL, - #' Initialize a new Rsirius API Class. + #' Initialize a new RSirius API Class. #' #' @description - #' Initialize a new Rsirius API Class. + #' Initialize a new RSirius API Class. #' #' @param api_client An instance of API client (optional). #' @export diff --git a/client-api_r/generated/R/run.R b/client-api_r/generated/R/run.R index ef77c7a7..4d7fa227 100644 --- a/client-api_r/generated/R/run.R +++ b/client-api_r/generated/R/run.R @@ -183,10 +183,10 @@ Run <- R6::R6Class( self$`fragmentation` <- this_object$`fragmentation` } if (!is.null(this_object$`massAnalyzers`)) { - self$`massAnalyzers` <- ApiClient$new()$deserializeObj(this_object$`massAnalyzers`, "array[character]", loadNamespace("Rsirius")) + self$`massAnalyzers` <- ApiClient$new()$deserializeObj(this_object$`massAnalyzers`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`tags`)) { - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) } self }, @@ -215,8 +215,8 @@ Run <- R6::R6Class( self$`chromatography` <- this_object$`chromatography` self$`ionization` <- this_object$`ionization` self$`fragmentation` <- this_object$`fragmentation` - self$`massAnalyzers` <- ApiClient$new()$deserializeObj(this_object$`massAnalyzers`, "array[character]", loadNamespace("Rsirius")) - self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("Rsirius")) + self$`massAnalyzers` <- ApiClient$new()$deserializeObj(this_object$`massAnalyzers`, "array[character]", loadNamespace("RSirius")) + self$`tags` <- ApiClient$new()$deserializeObj(this_object$`tags`, "map(Tag)", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/runs_api.R b/client-api_r/generated/R/runs_api.R index f39e865e..b9dca755 100644 --- a/client-api_r/generated/R/runs_api.R +++ b/client-api_r/generated/R/runs_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### AddTagsToRunExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_run_id <- "run_id_example" # character | run to add tags to. #' var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -31,7 +31,7 @@ #' #' #################### ComputeFoldChangeForBlankSubtraction #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to compute the fold change in. #' var_sample_type_fold_change_request <- SampleTypeFoldChangeRequest$new(c("sampleRunIds_example"), c("blankRunIds_example"), c("controlRunIds_example")) # SampleTypeFoldChangeRequest | request with lists of run IDs that are sample, blank, and control runs #' var_opt_fields <- c("none") # array[character] | job opt fields. (Optional) @@ -47,7 +47,7 @@ #' #' #################### GetRunExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_run_id <- "run_id_example" # character | identifier of run to access. #' var_opt_fields <- c(RunOptField$new()) # array[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -63,7 +63,7 @@ #' #' #################### GetRunPageExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) #' var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -81,7 +81,7 @@ #' #' #################### GetRunsByGroupExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_group_name <- "group_name_example" # character | tag group name. #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -100,7 +100,7 @@ #' #' #################### GetRunsByTagExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project space to get runs from. #' var_filter <- "" # character | tag filter. (Optional) #' var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -119,7 +119,7 @@ #' #' #################### GetTagsForRunExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to get from. #' var_object_id <- "object_id_example" # character | RunId to get tags for. #' @@ -134,7 +134,7 @@ #' #' #################### RemoveTagFromRunExperimental #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_run_id <- "run_id_example" # character | run to delete tag from. #' var_tag_name <- "tag_name_example" # character | name of the tag to delete. @@ -299,7 +299,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -446,7 +446,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Job", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -587,7 +587,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "Run", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "Run", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -741,7 +741,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -904,7 +904,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1063,7 +1063,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "PagedModelRun", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1196,7 +1196,7 @@ RunsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[Tag]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/sample_type_fold_change_request.R b/client-api_r/generated/R/sample_type_fold_change_request.R index 49878fb6..74227c24 100644 --- a/client-api_r/generated/R/sample_type_fold_change_request.R +++ b/client-api_r/generated/R/sample_type_fold_change_request.R @@ -99,13 +99,13 @@ SampleTypeFoldChangeRequest <- R6::R6Class( fromJSON = function(input_json) { this_object <- jsonlite::fromJSON(input_json) if (!is.null(this_object$`sampleRunIds`)) { - self$`sampleRunIds` <- ApiClient$new()$deserializeObj(this_object$`sampleRunIds`, "array[character]", loadNamespace("Rsirius")) + self$`sampleRunIds` <- ApiClient$new()$deserializeObj(this_object$`sampleRunIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`blankRunIds`)) { - self$`blankRunIds` <- ApiClient$new()$deserializeObj(this_object$`blankRunIds`, "array[character]", loadNamespace("Rsirius")) + self$`blankRunIds` <- ApiClient$new()$deserializeObj(this_object$`blankRunIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`controlRunIds`)) { - self$`controlRunIds` <- ApiClient$new()$deserializeObj(this_object$`controlRunIds`, "array[character]", loadNamespace("Rsirius")) + self$`controlRunIds` <- ApiClient$new()$deserializeObj(this_object$`controlRunIds`, "array[character]", loadNamespace("RSirius")) } self }, @@ -128,9 +128,9 @@ SampleTypeFoldChangeRequest <- R6::R6Class( #' @return the instance of SampleTypeFoldChangeRequest fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) - self$`sampleRunIds` <- ApiClient$new()$deserializeObj(this_object$`sampleRunIds`, "array[character]", loadNamespace("Rsirius")) - self$`blankRunIds` <- ApiClient$new()$deserializeObj(this_object$`blankRunIds`, "array[character]", loadNamespace("Rsirius")) - self$`controlRunIds` <- ApiClient$new()$deserializeObj(this_object$`controlRunIds`, "array[character]", loadNamespace("Rsirius")) + self$`sampleRunIds` <- ApiClient$new()$deserializeObj(this_object$`sampleRunIds`, "array[character]", loadNamespace("RSirius")) + self$`blankRunIds` <- ApiClient$new()$deserializeObj(this_object$`blankRunIds`, "array[character]", loadNamespace("RSirius")) + self$`controlRunIds` <- ApiClient$new()$deserializeObj(this_object$`controlRunIds`, "array[character]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/searchable_databases_api.R b/client-api_r/generated/R/searchable_databases_api.R index 6e1176be..fe9b4cc5 100644 --- a/client-api_r/generated/R/searchable_databases_api.R +++ b/client-api_r/generated/R/searchable_databases_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### AddDatabases #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_request_body <- c("property_example") # array[character] | #' #' #DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. @@ -29,7 +29,7 @@ #' #' #################### CreateDatabase #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_database_id <- "database_id_example" # character | #' var_searchable_database_parameters <- SearchableDatabaseParameters$new("displayName_example", "location_example", "matchRtOfReferenceSpectra_example") # SearchableDatabaseParameters | (Optional) #' @@ -43,7 +43,7 @@ #' #' #################### GetCustomDatabases #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_include_stats <- FALSE # character | (Optional) #' var_include_with_errors <- FALSE # character | (Optional) #' @@ -57,7 +57,7 @@ #' #' #################### GetDatabase #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_database_id <- "database_id_example" # character | #' var_include_stats <- TRUE # character | (Optional) #' @@ -71,7 +71,7 @@ #' #' #################### GetDatabases #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_include_stats <- FALSE # character | (Optional) #' var_include_with_errors <- FALSE # character | (Optional) #' @@ -85,7 +85,7 @@ #' #' #################### GetIncludedDatabases #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_include_stats <- FALSE # character | (Optional) #' #' api_instance <- rsirius_api$new() @@ -98,7 +98,7 @@ #' #' #################### ImportIntoDatabase #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_database_id <- "database_id_example" # character | database to import into #' var_input_files <- c(123) # array[data.frame] | files to be imported #' var_buffer_size <- 1000 # integer | (Optional) @@ -115,7 +115,7 @@ #' #' #################### RemoveDatabase #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_database_id <- "database_id_example" # character | #' var_delete <- FALSE # character | (Optional) #' @@ -126,7 +126,7 @@ #' #' #################### UpdateDatabase #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_database_id <- "database_id_example" # character | #' var_searchable_database_parameters <- SearchableDatabaseParameters$new("displayName_example", "location_example", "matchRtOfReferenceSpectra_example") # SearchableDatabaseParameters | (Optional) #' @@ -270,7 +270,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -404,7 +404,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -525,7 +525,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -652,7 +652,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -773,7 +773,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -889,7 +889,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[SearchableDatabase]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1036,7 +1036,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1254,7 +1254,7 @@ SearchableDatabasesApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "SearchableDatabase", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/sirius.R b/client-api_r/generated/R/sirius.R index 5f3fb9ed..2e7d5606 100644 --- a/client-api_r/generated/R/sirius.R +++ b/client-api_r/generated/R/sirius.R @@ -359,7 +359,7 @@ Sirius <- R6::R6Class( self$`performDenovoBelowMz` <- this_object$`performDenovoBelowMz` } if (!is.null(this_object$`formulaSearchDBs`)) { - self$`formulaSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`formulaSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`formulaSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`formulaSearchDBs`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`applyFormulaConstraintsToDBAndBottomUpSearch`)) { self$`applyFormulaConstraintsToDBAndBottomUpSearch` <- this_object$`applyFormulaConstraintsToDBAndBottomUpSearch` @@ -371,7 +371,7 @@ Sirius <- R6::R6Class( self$`fallbackFormulaConstraints` <- this_object$`fallbackFormulaConstraints` } if (!is.null(this_object$`detectableElements`)) { - self$`detectableElements` <- ApiClient$new()$deserializeObj(this_object$`detectableElements`, "array[character]", loadNamespace("Rsirius")) + self$`detectableElements` <- ApiClient$new()$deserializeObj(this_object$`detectableElements`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`ilpTimeout`)) { `ilptimeout_object` <- Timeout$new() @@ -429,11 +429,11 @@ Sirius <- R6::R6Class( self$`enforceElGordoFormula` <- this_object$`enforceElGordoFormula` self$`performBottomUpSearch` <- this_object$`performBottomUpSearch` self$`performDenovoBelowMz` <- this_object$`performDenovoBelowMz` - self$`formulaSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`formulaSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`formulaSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`formulaSearchDBs`, "array[character]", loadNamespace("RSirius")) self$`applyFormulaConstraintsToDBAndBottomUpSearch` <- this_object$`applyFormulaConstraintsToDBAndBottomUpSearch` self$`enforcedFormulaConstraints` <- this_object$`enforcedFormulaConstraints` self$`fallbackFormulaConstraints` <- this_object$`fallbackFormulaConstraints` - self$`detectableElements` <- ApiClient$new()$deserializeObj(this_object$`detectableElements`, "array[character]", loadNamespace("Rsirius")) + self$`detectableElements` <- ApiClient$new()$deserializeObj(this_object$`detectableElements`, "array[character]", loadNamespace("RSirius")) self$`ilpTimeout` <- Timeout$new()$fromJSON(jsonlite::toJSON(this_object$`ilpTimeout`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`useHeuristic` <- UseHeuristic$new()$fromJSON(jsonlite::toJSON(this_object$`useHeuristic`, auto_unbox = TRUE, digits = NA, null = 'null')) self$`injectSpecLibMatchFormulas` <- this_object$`injectSpecLibMatchFormulas` diff --git a/client-api_r/generated/R/spectral_library_match.R b/client-api_r/generated/R/spectral_library_match.R index 2797eb9b..18ab98f4 100644 --- a/client-api_r/generated/R/spectral_library_match.R +++ b/client-api_r/generated/R/spectral_library_match.R @@ -328,7 +328,7 @@ SpectralLibraryMatch <- R6::R6Class( self$`sharedPeaks` <- this_object$`sharedPeaks` } if (!is.null(this_object$`sharedPeakMapping`)) { - self$`sharedPeakMapping` <- ApiClient$new()$deserializeObj(this_object$`sharedPeakMapping`, "array[PeakPair]", loadNamespace("Rsirius")) + self$`sharedPeakMapping` <- ApiClient$new()$deserializeObj(this_object$`sharedPeakMapping`, "array[PeakPair]", loadNamespace("RSirius")) } if (!is.null(this_object$`querySpectrumIndex`)) { self$`querySpectrumIndex` <- this_object$`querySpectrumIndex` @@ -408,7 +408,7 @@ SpectralLibraryMatch <- R6::R6Class( self$`rank` <- this_object$`rank` self$`similarity` <- this_object$`similarity` self$`sharedPeaks` <- this_object$`sharedPeaks` - self$`sharedPeakMapping` <- ApiClient$new()$deserializeObj(this_object$`sharedPeakMapping`, "array[PeakPair]", loadNamespace("Rsirius")) + self$`sharedPeakMapping` <- ApiClient$new()$deserializeObj(this_object$`sharedPeakMapping`, "array[PeakPair]", loadNamespace("RSirius")) self$`querySpectrumIndex` <- this_object$`querySpectrumIndex` self$`dbName` <- this_object$`dbName` self$`dbId` <- this_object$`dbId` diff --git a/client-api_r/generated/R/spectral_library_search.R b/client-api_r/generated/R/spectral_library_search.R index a37a159e..2e87f360 100644 --- a/client-api_r/generated/R/spectral_library_search.R +++ b/client-api_r/generated/R/spectral_library_search.R @@ -198,7 +198,7 @@ SpectralLibrarySearch <- R6::R6Class( self$`enabled` <- this_object$`enabled` } if (!is.null(this_object$`spectraSearchDBs`)) { - self$`spectraSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`spectraSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`spectraSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`spectraSearchDBs`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`precursorDeviationPpm`)) { self$`precursorDeviationPpm` <- this_object$`precursorDeviationPpm` @@ -249,7 +249,7 @@ SpectralLibrarySearch <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`enabled` <- this_object$`enabled` - self$`spectraSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`spectraSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`spectraSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`spectraSearchDBs`, "array[character]", loadNamespace("RSirius")) self$`precursorDeviationPpm` <- this_object$`precursorDeviationPpm` self$`minSimilarity` <- this_object$`minSimilarity` self$`minNumOfPeaks` <- this_object$`minNumOfPeaks` diff --git a/client-api_r/generated/R/statistics_table.R b/client-api_r/generated/R/statistics_table.R index 3009636f..f712b56b 100644 --- a/client-api_r/generated/R/statistics_table.R +++ b/client-api_r/generated/R/statistics_table.R @@ -211,19 +211,19 @@ StatisticsTable <- R6::R6Class( self$`rowType` <- this_object$`rowType` } if (!is.null(this_object$`rowIds`)) { - self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[character]", loadNamespace("Rsirius")) + self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`columnNames`)) { - self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("Rsirius")) + self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`columnLeftGroups`)) { - self$`columnLeftGroups` <- ApiClient$new()$deserializeObj(this_object$`columnLeftGroups`, "array[character]", loadNamespace("Rsirius")) + self$`columnLeftGroups` <- ApiClient$new()$deserializeObj(this_object$`columnLeftGroups`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`columnRightGroups`)) { - self$`columnRightGroups` <- ApiClient$new()$deserializeObj(this_object$`columnRightGroups`, "array[character]", loadNamespace("Rsirius")) + self$`columnRightGroups` <- ApiClient$new()$deserializeObj(this_object$`columnRightGroups`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`values`)) { - self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("Rsirius")) + self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("RSirius")) } self }, @@ -262,11 +262,11 @@ StatisticsTable <- R6::R6Class( stop(paste("Error! \"", this_object$`rowType`, "\" cannot be assigned to `rowType`. Must be \"FEATURES\", \"COMPOUNDS\".", sep = "")) } self$`rowType` <- this_object$`rowType` - self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[character]", loadNamespace("Rsirius")) - self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("Rsirius")) - self$`columnLeftGroups` <- ApiClient$new()$deserializeObj(this_object$`columnLeftGroups`, "array[character]", loadNamespace("Rsirius")) - self$`columnRightGroups` <- ApiClient$new()$deserializeObj(this_object$`columnRightGroups`, "array[character]", loadNamespace("Rsirius")) - self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("Rsirius")) + self$`rowIds` <- ApiClient$new()$deserializeObj(this_object$`rowIds`, "array[character]", loadNamespace("RSirius")) + self$`columnNames` <- ApiClient$new()$deserializeObj(this_object$`columnNames`, "array[character]", loadNamespace("RSirius")) + self$`columnLeftGroups` <- ApiClient$new()$deserializeObj(this_object$`columnLeftGroups`, "array[character]", loadNamespace("RSirius")) + self$`columnRightGroups` <- ApiClient$new()$deserializeObj(this_object$`columnRightGroups`, "array[character]", loadNamespace("RSirius")) + self$`values` <- ApiClient$new()$deserializeObj(this_object$`values`, "array[array[numeric]]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/R/structure_candidate.R b/client-api_r/generated/R/structure_candidate.R index 7cee81da..e21e9577 100644 --- a/client-api_r/generated/R/structure_candidate.R +++ b/client-api_r/generated/R/structure_candidate.R @@ -164,10 +164,10 @@ StructureCandidate <- R6::R6Class( self$`structureSvg` <- this_object$`structureSvg` } if (!is.null(this_object$`dbLinks`)) { - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) } if (!is.null(this_object$`spectralLibraryMatches`)) { - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) } if (!is.null(this_object$`xlogP`)) { self$`xlogP` <- this_object$`xlogP` @@ -197,8 +197,8 @@ StructureCandidate <- R6::R6Class( self$`smiles` <- this_object$`smiles` self$`structureName` <- this_object$`structureName` self$`structureSvg` <- this_object$`structureSvg` - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) self$`xlogP` <- this_object$`xlogP` self }, diff --git a/client-api_r/generated/R/structure_candidate_formula.R b/client-api_r/generated/R/structure_candidate_formula.R index 7fc1ffe4..1d02ded7 100644 --- a/client-api_r/generated/R/structure_candidate_formula.R +++ b/client-api_r/generated/R/structure_candidate_formula.R @@ -266,10 +266,10 @@ StructureCandidateFormula <- R6::R6Class( self$`structureSvg` <- this_object$`structureSvg` } if (!is.null(this_object$`dbLinks`)) { - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) } if (!is.null(this_object$`spectralLibraryMatches`)) { - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) } if (!is.null(this_object$`xlogP`)) { self$`xlogP` <- this_object$`xlogP` @@ -325,8 +325,8 @@ StructureCandidateFormula <- R6::R6Class( self$`smiles` <- this_object$`smiles` self$`structureName` <- this_object$`structureName` self$`structureSvg` <- this_object$`structureSvg` - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) self$`xlogP` <- this_object$`xlogP` self$`rank` <- this_object$`rank` self$`csiScore` <- this_object$`csiScore` diff --git a/client-api_r/generated/R/structure_candidate_scored.R b/client-api_r/generated/R/structure_candidate_scored.R index 20208b10..62578259 100644 --- a/client-api_r/generated/R/structure_candidate_scored.R +++ b/client-api_r/generated/R/structure_candidate_scored.R @@ -227,10 +227,10 @@ StructureCandidateScored <- R6::R6Class( self$`structureSvg` <- this_object$`structureSvg` } if (!is.null(this_object$`dbLinks`)) { - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) } if (!is.null(this_object$`spectralLibraryMatches`)) { - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) } if (!is.null(this_object$`xlogP`)) { self$`xlogP` <- this_object$`xlogP` @@ -277,8 +277,8 @@ StructureCandidateScored <- R6::R6Class( self$`smiles` <- this_object$`smiles` self$`structureName` <- this_object$`structureName` self$`structureSvg` <- this_object$`structureSvg` - self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("Rsirius")) - self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("Rsirius")) + self$`dbLinks` <- ApiClient$new()$deserializeObj(this_object$`dbLinks`, "array[DBLink]", loadNamespace("RSirius")) + self$`spectralLibraryMatches` <- ApiClient$new()$deserializeObj(this_object$`spectralLibraryMatches`, "array[SpectralLibraryMatch]", loadNamespace("RSirius")) self$`xlogP` <- this_object$`xlogP` self$`rank` <- this_object$`rank` self$`csiScore` <- this_object$`csiScore` diff --git a/client-api_r/generated/R/structure_db_search.R b/client-api_r/generated/R/structure_db_search.R index 4740309d..0fc81c42 100644 --- a/client-api_r/generated/R/structure_db_search.R +++ b/client-api_r/generated/R/structure_db_search.R @@ -120,7 +120,7 @@ StructureDbSearch <- R6::R6Class( self$`enabled` <- this_object$`enabled` } if (!is.null(this_object$`structureSearchDBs`)) { - self$`structureSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`structureSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`structureSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`structureSearchDBs`, "array[character]", loadNamespace("RSirius")) } if (!is.null(this_object$`tagStructuresWithLipidClass`)) { self$`tagStructuresWithLipidClass` <- this_object$`tagStructuresWithLipidClass` @@ -153,7 +153,7 @@ StructureDbSearch <- R6::R6Class( fromJSONString = function(input_json) { this_object <- jsonlite::fromJSON(input_json) self$`enabled` <- this_object$`enabled` - self$`structureSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`structureSearchDBs`, "array[character]", loadNamespace("Rsirius")) + self$`structureSearchDBs` <- ApiClient$new()$deserializeObj(this_object$`structureSearchDBs`, "array[character]", loadNamespace("RSirius")) self$`tagStructuresWithLipidClass` <- this_object$`tagStructuresWithLipidClass` if (!is.null(this_object$`expansiveSearchConfidenceMode`) && !(this_object$`expansiveSearchConfidenceMode` %in% c("OFF", "EXACT", "APPROXIMATE"))) { stop(paste("Error! \"", this_object$`expansiveSearchConfidenceMode`, "\" cannot be assigned to `expansiveSearchConfidenceMode`. Must be \"OFF\", \"EXACT\", \"APPROXIMATE\".", sep = "")) diff --git a/client-api_r/generated/R/tag_definition.R b/client-api_r/generated/R/tag_definition.R index 1c987ae2..37578f74 100644 --- a/client-api_r/generated/R/tag_definition.R +++ b/client-api_r/generated/R/tag_definition.R @@ -178,7 +178,7 @@ TagDefinition <- R6::R6Class( self$`valueType` <- this_object$`valueType` } if (!is.null(this_object$`possibleValues`)) { - self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("Rsirius")) + self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("RSirius")) } if (!is.null(this_object$`minValue`)) { self$`minValue` <- this_object$`minValue` @@ -217,7 +217,7 @@ TagDefinition <- R6::R6Class( stop(paste("Error! \"", this_object$`valueType`, "\" cannot be assigned to `valueType`. Must be \"NONE\", \"BOOLEAN\", \"INTEGER\", \"REAL\", \"TEXT\", \"DATE\", \"TIME\".", sep = "")) } self$`valueType` <- this_object$`valueType` - self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("Rsirius")) + self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("RSirius")) self$`minValue` <- this_object$`minValue` self$`maxValue` <- this_object$`maxValue` self$`editable` <- this_object$`editable` diff --git a/client-api_r/generated/R/tag_definition_import.R b/client-api_r/generated/R/tag_definition_import.R index 8382e7bb..f8fbd078 100644 --- a/client-api_r/generated/R/tag_definition_import.R +++ b/client-api_r/generated/R/tag_definition_import.R @@ -165,7 +165,7 @@ TagDefinitionImport <- R6::R6Class( self$`valueType` <- this_object$`valueType` } if (!is.null(this_object$`possibleValues`)) { - self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("Rsirius")) + self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("RSirius")) } if (!is.null(this_object$`minValue`)) { self$`minValue` <- this_object$`minValue` @@ -201,7 +201,7 @@ TagDefinitionImport <- R6::R6Class( stop(paste("Error! \"", this_object$`valueType`, "\" cannot be assigned to `valueType`. Must be \"NONE\", \"BOOLEAN\", \"INTEGER\", \"REAL\", \"TEXT\", \"DATE\", \"TIME\".", sep = "")) } self$`valueType` <- this_object$`valueType` - self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("Rsirius")) + self$`possibleValues` <- ApiClient$new()$deserializeObj(this_object$`possibleValues`, "array[object]", loadNamespace("RSirius")) self$`minValue` <- this_object$`minValue` self$`maxValue` <- this_object$`maxValue` self diff --git a/client-api_r/generated/R/tags_api.R b/client-api_r/generated/R/tags_api.R index aa3c292d..5cce7801 100644 --- a/client-api_r/generated/R/tags_api.R +++ b/client-api_r/generated/R/tags_api.R @@ -15,7 +15,7 @@ #' \dontrun{ #' #################### AddGroup #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_group_name <- "group_name_example" # character | name of the new group #' var_filter <- "filter_example" # character | filter query to create the group @@ -32,7 +32,7 @@ #' #' #################### AddPossibleValuesToTagDefinition #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_tag_name <- "tag_name_example" # character | the tag definition to add the values to #' var_request_body <- c(123) # array[object] | @@ -48,7 +48,7 @@ #' #' #################### CreateTags #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to add to. #' var_tag_definition_import <- c(TagDefinitionImport$new("tagName_example", "NONE", "description_example", "tagType_example", c(123), 123, 123)) # array[TagDefinitionImport] | the tag definitions to be created #' @@ -63,7 +63,7 @@ #' #' #################### DeleteGroup #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_group_name <- "group_name_example" # character | name of group to delete. #' @@ -75,7 +75,7 @@ #' #' #################### DeleteTag #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to delete from. #' var_tag_name <- "tag_name_example" # character | name of the tag definition to delete. #' @@ -87,7 +87,7 @@ #' #' #################### GetGroupByName #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_group_name <- "group_name_example" # character | name of the group #' @@ -102,7 +102,7 @@ #' #' #################### GetGroups #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_group_type <- "group_type_example" # character | type of the group (Optional) #' @@ -117,7 +117,7 @@ #' #' #################### GetTag #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_tag_name <- "tag_name_example" # character | name of the tag #' @@ -132,7 +132,7 @@ #' #' #################### GetTags #################### #' -#' library(Rsirius) +#' library(RSirius) #' var_project_id <- "project_id_example" # character | project-space to read from. #' var_tag_type <- "tag_type_example" # character | scope of the tag (optional) (Optional) #' @@ -297,7 +297,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TagGroup", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TagGroup", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -450,7 +450,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TagDefinition", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TagDefinition", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -592,7 +592,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagDefinition]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagDefinition]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -911,7 +911,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TagGroup", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TagGroup", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1038,7 +1038,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagGroup]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagGroup]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1171,7 +1171,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "TagDefinition", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "TagDefinition", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } @@ -1298,7 +1298,7 @@ TagsApi <- R6::R6Class( } else { # For JSON responses, deserialize normally deserialized_resp_obj <- tryCatch( - self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagDefinition]", loadNamespace("Rsirius")), + self$api_client$deserialize(local_var_resp$response_as_text(), "array[TagDefinition]", loadNamespace("RSirius")), error = function(e) { stop("Failed to deserialize response") } diff --git a/client-api_r/generated/R/trace_experimental.R b/client-api_r/generated/R/trace_experimental.R index b42c0be4..d3c7eebb 100644 --- a/client-api_r/generated/R/trace_experimental.R +++ b/client-api_r/generated/R/trace_experimental.R @@ -219,10 +219,10 @@ TraceExperimental <- R6::R6Class( self$`color` <- this_object$`color` } if (!is.null(this_object$`intensities`)) { - self$`intensities` <- ApiClient$new()$deserializeObj(this_object$`intensities`, "array[numeric]", loadNamespace("Rsirius")) + self$`intensities` <- ApiClient$new()$deserializeObj(this_object$`intensities`, "array[numeric]", loadNamespace("RSirius")) } if (!is.null(this_object$`annotations`)) { - self$`annotations` <- ApiClient$new()$deserializeObj(this_object$`annotations`, "array[TraceAnnotationExperimental]", loadNamespace("Rsirius")) + self$`annotations` <- ApiClient$new()$deserializeObj(this_object$`annotations`, "array[TraceAnnotationExperimental]", loadNamespace("RSirius")) } if (!is.null(this_object$`mz`)) { self$`mz` <- this_object$`mz` @@ -262,8 +262,8 @@ TraceExperimental <- R6::R6Class( self$`sampleName` <- this_object$`sampleName` self$`label` <- this_object$`label` self$`color` <- this_object$`color` - self$`intensities` <- ApiClient$new()$deserializeObj(this_object$`intensities`, "array[numeric]", loadNamespace("Rsirius")) - self$`annotations` <- ApiClient$new()$deserializeObj(this_object$`annotations`, "array[TraceAnnotationExperimental]", loadNamespace("Rsirius")) + self$`intensities` <- ApiClient$new()$deserializeObj(this_object$`intensities`, "array[numeric]", loadNamespace("RSirius")) + self$`annotations` <- ApiClient$new()$deserializeObj(this_object$`annotations`, "array[TraceAnnotationExperimental]", loadNamespace("RSirius")) self$`mz` <- this_object$`mz` self$`merged` <- this_object$`merged` self$`normalizationFactor` <- this_object$`normalizationFactor` diff --git a/client-api_r/generated/R/trace_set_experimental.R b/client-api_r/generated/R/trace_set_experimental.R index b7d0cd87..40f31f5e 100644 --- a/client-api_r/generated/R/trace_set_experimental.R +++ b/client-api_r/generated/R/trace_set_experimental.R @@ -139,7 +139,7 @@ TraceSetExperimental <- R6::R6Class( self$`axes` <- `axes_object` } if (!is.null(this_object$`traces`)) { - self$`traces` <- ApiClient$new()$deserializeObj(this_object$`traces`, "array[TraceExperimental]", loadNamespace("Rsirius")) + self$`traces` <- ApiClient$new()$deserializeObj(this_object$`traces`, "array[TraceExperimental]", loadNamespace("RSirius")) } self }, @@ -166,7 +166,7 @@ TraceSetExperimental <- R6::R6Class( self$`sampleId` <- this_object$`sampleId` self$`sampleName` <- this_object$`sampleName` self$`axes` <- Axes$new()$fromJSON(jsonlite::toJSON(this_object$`axes`, auto_unbox = TRUE, digits = NA, null = 'null')) - self$`traces` <- ApiClient$new()$deserializeObj(this_object$`traces`, "array[TraceExperimental]", loadNamespace("Rsirius")) + self$`traces` <- ApiClient$new()$deserializeObj(this_object$`traces`, "array[TraceExperimental]", loadNamespace("RSirius")) self }, diff --git a/client-api_r/generated/README.md b/client-api_r/generated/README.md index 06d49162..58b34edb 100644 --- a/client-api_r/generated/README.md +++ b/client-api_r/generated/README.md @@ -1,4 +1,4 @@ -# R API client for Rsirius +# R API client for RSirius REST API that provides the full functionality of SIRIUS and its web services as background service. It is intended as entry-point for scripting languages and software integration SDKs.This API is exposed by SIRIUS 6 @@ -28,14 +28,14 @@ install.packages("base64enc") git clone https://github.com/GIT_USER_ID/GIT_REPO_ID cd GIT_REPO_ID R CMD build . -R CMD check Rsirius_6.3.3.tar.gz --no-manual -R CMD INSTALL --preclean Rsirius_6.3.3.tar.gz +R CMD check RSirius_6.3.3.tar.gz --no-manual +R CMD INSTALL --preclean RSirius_6.3.3.tar.gz ``` ### Install the package ```R -install.packages("Rsirius") +install.packages("RSirius") ``` To install directly from Github, use `devtools`: @@ -47,13 +47,13 @@ install_github("GIT_USER_ID/GIT_REPO_ID") To install the package from a local file: ```R -install.packages("Rsirius_6.3.3.tar.gz", repos = NULL, type = "source") +install.packages("RSirius_6.3.3.tar.gz", repos = NULL, type = "source") ``` ### Usage ```R -library(Rsirius) +library(RSirius) ``` ### Reformat code diff --git a/client-api_r/generated/docs/AccountCredentials.md b/client-api_r/generated/docs/AccountCredentials.md index 342a50d9..71450047 100644 --- a/client-api_r/generated/docs/AccountCredentials.md +++ b/client-api_r/generated/docs/AccountCredentials.md @@ -1,4 +1,4 @@ -# Rsirius::AccountCredentials +# RSirius::AccountCredentials Simple object to hold account credentials, e.g. to perform login operations. If refreshToken is given, it is usually preferred over password based authentication. But in the end this is up to the respective web service. diff --git a/client-api_r/generated/docs/AccountInfo.md b/client-api_r/generated/docs/AccountInfo.md index a04c712c..e5f0da2a 100644 --- a/client-api_r/generated/docs/AccountInfo.md +++ b/client-api_r/generated/docs/AccountInfo.md @@ -1,4 +1,4 @@ -# Rsirius::AccountInfo +# RSirius::AccountInfo ## Properties diff --git a/client-api_r/generated/docs/ActuatorApi.md b/client-api_r/generated/docs/ActuatorApi.md index db4b6963..3160b455 100644 --- a/client-api_r/generated/docs/ActuatorApi.md +++ b/client-api_r/generated/docs/ActuatorApi.md @@ -15,7 +15,7 @@ Actuator web endpoint 'health' ### Example ```R -library(Rsirius) +library(RSirius) # Actuator web endpoint 'health' # @@ -55,7 +55,7 @@ Actuator web endpoint 'shutdown' ### Example ```R -library(Rsirius) +library(RSirius) # Actuator web endpoint 'shutdown' # diff --git a/client-api_r/generated/docs/AdductEdgeExperimental.md b/client-api_r/generated/docs/AdductEdgeExperimental.md index 916daec2..ee7bd754 100644 --- a/client-api_r/generated/docs/AdductEdgeExperimental.md +++ b/client-api_r/generated/docs/AdductEdgeExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::AdductEdgeExperimental +# RSirius::AdductEdgeExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/AdductNetworkExperimental.md b/client-api_r/generated/docs/AdductNetworkExperimental.md index 65853c50..2809fc7c 100644 --- a/client-api_r/generated/docs/AdductNetworkExperimental.md +++ b/client-api_r/generated/docs/AdductNetworkExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::AdductNetworkExperimental +# RSirius::AdductNetworkExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/AdductNodeExperimental.md b/client-api_r/generated/docs/AdductNodeExperimental.md index 9864fb91..9f2f6fe3 100644 --- a/client-api_r/generated/docs/AdductNodeExperimental.md +++ b/client-api_r/generated/docs/AdductNodeExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::AdductNodeExperimental +# RSirius::AdductNodeExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/AlignedFeature.md b/client-api_r/generated/docs/AlignedFeature.md index 2c94ead3..72fd8ac7 100644 --- a/client-api_r/generated/docs/AlignedFeature.md +++ b/client-api_r/generated/docs/AlignedFeature.md @@ -1,4 +1,4 @@ -# Rsirius::AlignedFeature +# RSirius::AlignedFeature The AlignedFeature contains the ID of a feature (aligned over runs) together with some read-only information that might be displayed in some summary view. diff --git a/client-api_r/generated/docs/AlignedFeatureQualityExperimental.md b/client-api_r/generated/docs/AlignedFeatureQualityExperimental.md index 697b647a..d493f3b5 100644 --- a/client-api_r/generated/docs/AlignedFeatureQualityExperimental.md +++ b/client-api_r/generated/docs/AlignedFeatureQualityExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::AlignedFeatureQualityExperimental +# RSirius::AlignedFeatureQualityExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/AllowedFeatures.md b/client-api_r/generated/docs/AllowedFeatures.md index 7a2db00e..d6bf7438 100644 --- a/client-api_r/generated/docs/AllowedFeatures.md +++ b/client-api_r/generated/docs/AllowedFeatures.md @@ -1,4 +1,4 @@ -# Rsirius::AllowedFeatures +# RSirius::AllowedFeatures ## Properties diff --git a/client-api_r/generated/docs/AnnotatedMsMsData.md b/client-api_r/generated/docs/AnnotatedMsMsData.md index 5a47d6ef..d950e9af 100644 --- a/client-api_r/generated/docs/AnnotatedMsMsData.md +++ b/client-api_r/generated/docs/AnnotatedMsMsData.md @@ -1,4 +1,4 @@ -# Rsirius::AnnotatedMsMsData +# RSirius::AnnotatedMsMsData ## Properties diff --git a/client-api_r/generated/docs/AnnotatedPeak.md b/client-api_r/generated/docs/AnnotatedPeak.md index f6ec8765..da03726c 100644 --- a/client-api_r/generated/docs/AnnotatedPeak.md +++ b/client-api_r/generated/docs/AnnotatedPeak.md @@ -1,4 +1,4 @@ -# Rsirius::AnnotatedPeak +# RSirius::AnnotatedPeak ## Properties diff --git a/client-api_r/generated/docs/AnnotatedSpectrum.md b/client-api_r/generated/docs/AnnotatedSpectrum.md index 3e65ae3b..77a7205e 100644 --- a/client-api_r/generated/docs/AnnotatedSpectrum.md +++ b/client-api_r/generated/docs/AnnotatedSpectrum.md @@ -1,4 +1,4 @@ -# Rsirius::AnnotatedSpectrum +# RSirius::AnnotatedSpectrum Spectrum model with peak annotations based on the fragmentation tree and Epimetheus substructure annotations. Molecular formula and adduct of the spectrum are identical to the ones of the corresponding molecular formula candidate and FragmentationTree. Fragment molecular formulas and adducts correspond to the FragmentationTree's FragmentNodes diff --git a/client-api_r/generated/docs/Axes.md b/client-api_r/generated/docs/Axes.md index d7251834..a5d7b36e 100644 --- a/client-api_r/generated/docs/Axes.md +++ b/client-api_r/generated/docs/Axes.md @@ -1,4 +1,4 @@ -# Rsirius::Axes +# RSirius::Axes ## Properties diff --git a/client-api_r/generated/docs/BackgroundComputationsStateEvent.md b/client-api_r/generated/docs/BackgroundComputationsStateEvent.md index e160f459..b9877eaa 100644 --- a/client-api_r/generated/docs/BackgroundComputationsStateEvent.md +++ b/client-api_r/generated/docs/BackgroundComputationsStateEvent.md @@ -1,4 +1,4 @@ -# Rsirius::BackgroundComputationsStateEvent +# RSirius::BackgroundComputationsStateEvent ## Properties diff --git a/client-api_r/generated/docs/BasicSpectrum.md b/client-api_r/generated/docs/BasicSpectrum.md index 0100ed07..138c7370 100644 --- a/client-api_r/generated/docs/BasicSpectrum.md +++ b/client-api_r/generated/docs/BasicSpectrum.md @@ -1,4 +1,4 @@ -# Rsirius::BasicSpectrum +# RSirius::BasicSpectrum ## Properties diff --git a/client-api_r/generated/docs/BinaryFingerprint.md b/client-api_r/generated/docs/BinaryFingerprint.md index 30273262..2576984b 100644 --- a/client-api_r/generated/docs/BinaryFingerprint.md +++ b/client-api_r/generated/docs/BinaryFingerprint.md @@ -1,4 +1,4 @@ -# Rsirius::BinaryFingerprint +# RSirius::BinaryFingerprint ## Properties diff --git a/client-api_r/generated/docs/BioTransformerParameters.md b/client-api_r/generated/docs/BioTransformerParameters.md index 40e953e0..cf164dea 100644 --- a/client-api_r/generated/docs/BioTransformerParameters.md +++ b/client-api_r/generated/docs/BioTransformerParameters.md @@ -1,4 +1,4 @@ -# Rsirius::BioTransformerParameters +# RSirius::BioTransformerParameters ## Properties diff --git a/client-api_r/generated/docs/BioTransformerSequenceStep.md b/client-api_r/generated/docs/BioTransformerSequenceStep.md index ac06c883..79db6fec 100644 --- a/client-api_r/generated/docs/BioTransformerSequenceStep.md +++ b/client-api_r/generated/docs/BioTransformerSequenceStep.md @@ -1,4 +1,4 @@ -# Rsirius::BioTransformerSequenceStep +# RSirius::BioTransformerSequenceStep ## Properties diff --git a/client-api_r/generated/docs/Canopus.md b/client-api_r/generated/docs/Canopus.md index ee52da60..1e045c18 100644 --- a/client-api_r/generated/docs/Canopus.md +++ b/client-api_r/generated/docs/Canopus.md @@ -1,4 +1,4 @@ -# Rsirius::Canopus +# RSirius::Canopus User/developer friendly parameter subset for the CANOPUS tool CANOPUS is parameter free, so this Object is just a flag that canopus should be executed. Needs results from FingerprintPrediction Tool diff --git a/client-api_r/generated/docs/CanopusPrediction.md b/client-api_r/generated/docs/CanopusPrediction.md index 71423036..47101bed 100644 --- a/client-api_r/generated/docs/CanopusPrediction.md +++ b/client-api_r/generated/docs/CanopusPrediction.md @@ -1,4 +1,4 @@ -# Rsirius::CanopusPrediction +# RSirius::CanopusPrediction Container class that holds the CANOPUS compound class predictions for alle predictable compound classes. This is the full CANOPUS result. diff --git a/client-api_r/generated/docs/Category.md b/client-api_r/generated/docs/Category.md index 051d9166..75000b9b 100644 --- a/client-api_r/generated/docs/Category.md +++ b/client-api_r/generated/docs/Category.md @@ -1,4 +1,4 @@ -# Rsirius::Category +# RSirius::Category ## Properties diff --git a/client-api_r/generated/docs/Compound.md b/client-api_r/generated/docs/Compound.md index c64c5541..4c97a8b6 100644 --- a/client-api_r/generated/docs/Compound.md +++ b/client-api_r/generated/docs/Compound.md @@ -1,4 +1,4 @@ -# Rsirius::Compound +# RSirius::Compound ## Properties diff --git a/client-api_r/generated/docs/CompoundClass.md b/client-api_r/generated/docs/CompoundClass.md index 7777d4ca..a39238a8 100644 --- a/client-api_r/generated/docs/CompoundClass.md +++ b/client-api_r/generated/docs/CompoundClass.md @@ -1,4 +1,4 @@ -# Rsirius::CompoundClass +# RSirius::CompoundClass Predicted compound class with name, probability and id if available. (ClassyFire and NPC). This can be seen as the set of classes a feature most likely belongs to diff --git a/client-api_r/generated/docs/CompoundClasses.md b/client-api_r/generated/docs/CompoundClasses.md index 8d1a4877..b403a1ee 100644 --- a/client-api_r/generated/docs/CompoundClasses.md +++ b/client-api_r/generated/docs/CompoundClasses.md @@ -1,4 +1,4 @@ -# Rsirius::CompoundClasses +# RSirius::CompoundClasses Container class that holds the most likely compound class for different levels of each ontology for a certain Compound/Feature/FormulaCandidate/PredictedFingerprint. diff --git a/client-api_r/generated/docs/CompoundImport.md b/client-api_r/generated/docs/CompoundImport.md index 077f27cf..f00bc59b 100644 --- a/client-api_r/generated/docs/CompoundImport.md +++ b/client-api_r/generated/docs/CompoundImport.md @@ -1,4 +1,4 @@ -# Rsirius::CompoundImport +# RSirius::CompoundImport ## Properties diff --git a/client-api_r/generated/docs/CompoundStatisticsApi.md b/client-api_r/generated/docs/CompoundStatisticsApi.md index b8f7e6d5..bffddbce 100644 --- a/client-api_r/generated/docs/CompoundStatisticsApi.md +++ b/client-api_r/generated/docs/CompoundStatisticsApi.md @@ -19,7 +19,7 @@ Method | HTTP request | Description ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Compute the fold change between two groups of runs # @@ -76,7 +76,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete fold changes # @@ -128,7 +128,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get table of all fold changes in the project space # @@ -179,7 +179,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] List all fold changes that are associated with an object # diff --git a/client-api_r/generated/docs/CompoundsApi.md b/client-api_r/generated/docs/CompoundsApi.md index 6c103fee..e1703d0c 100644 --- a/client-api_r/generated/docs/CompoundsApi.md +++ b/client-api_r/generated/docs/CompoundsApi.md @@ -28,7 +28,7 @@ Import Compounds and its contained features. Compounds and Features must not exi ### Example ```R -library(Rsirius) +library(RSirius) # Import Compounds and its contained features. # @@ -83,7 +83,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Tags with the same name will be overwritten # @@ -134,7 +134,7 @@ Delete compound (group of ion identities) with the given identifier (and the inc ### Example ```R -library(Rsirius) +library(RSirius) # Delete compound (group of ion identities) with the given identifier (and the included features) from the specified project-space. # @@ -180,7 +180,7 @@ Get compound (group of ion identities) with the given identifier from the specif ### Example ```R -library(Rsirius) +library(RSirius) # Get compound (group of ion identities) with the given identifier from the specified project-space. # @@ -235,7 +235,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns the full quantification table of compounds # @@ -284,7 +284,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns a single quantification table row for the given compound # @@ -335,7 +335,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns the traces of the given compound # @@ -386,7 +386,7 @@ List of all available compounds (group of ion identities) in the given project-s ### Example ```R -library(Rsirius) +library(RSirius) # List of all available compounds (group of ion identities) in the given project-space. # @@ -439,7 +439,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get compounds (group of ion identities) by tag group # @@ -496,7 +496,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get compounds (group of ion identities) by tag # @@ -553,7 +553,7 @@ Page of available compounds (group of ion identities) in the given project-space ### Example ```R -library(Rsirius) +library(RSirius) # Page of available compounds (group of ion identities) in the given project-space. # @@ -612,7 +612,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all tags associated with this Compound # @@ -661,7 +661,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete tag with the given name from the compound (group of ion identities) with the specified ID in the specified project-space # diff --git a/client-api_r/generated/docs/ComputedSubtools.md b/client-api_r/generated/docs/ComputedSubtools.md index 2819b4a8..97782f40 100644 --- a/client-api_r/generated/docs/ComputedSubtools.md +++ b/client-api_r/generated/docs/ComputedSubtools.md @@ -1,4 +1,4 @@ -# Rsirius::ComputedSubtools +# RSirius::ComputedSubtools Specifies which tools have been executed for this feature. Can be used to estimate which results can be expected. Null if it was not requested und non-null otherwise. diff --git a/client-api_r/generated/docs/ConnectionCheck.md b/client-api_r/generated/docs/ConnectionCheck.md index a23a62f0..f7a37544 100644 --- a/client-api_r/generated/docs/ConnectionCheck.md +++ b/client-api_r/generated/docs/ConnectionCheck.md @@ -1,4 +1,4 @@ -# Rsirius::ConnectionCheck +# RSirius::ConnectionCheck ## Properties diff --git a/client-api_r/generated/docs/ConnectionError.md b/client-api_r/generated/docs/ConnectionError.md index 39aef106..63a81304 100644 --- a/client-api_r/generated/docs/ConnectionError.md +++ b/client-api_r/generated/docs/ConnectionError.md @@ -1,4 +1,4 @@ -# Rsirius::ConnectionError +# RSirius::ConnectionError ## Properties diff --git a/client-api_r/generated/docs/ConsensusAnnotationsCSI.md b/client-api_r/generated/docs/ConsensusAnnotationsCSI.md index a2a8300b..733de37f 100644 --- a/client-api_r/generated/docs/ConsensusAnnotationsCSI.md +++ b/client-api_r/generated/docs/ConsensusAnnotationsCSI.md @@ -1,4 +1,4 @@ -# Rsirius::ConsensusAnnotationsCSI +# RSirius::ConsensusAnnotationsCSI ## Properties diff --git a/client-api_r/generated/docs/ConsensusAnnotationsDeNovo.md b/client-api_r/generated/docs/ConsensusAnnotationsDeNovo.md index 2114f54f..7c6d0f0c 100644 --- a/client-api_r/generated/docs/ConsensusAnnotationsDeNovo.md +++ b/client-api_r/generated/docs/ConsensusAnnotationsDeNovo.md @@ -1,4 +1,4 @@ -# Rsirius::ConsensusAnnotationsDeNovo +# RSirius::ConsensusAnnotationsDeNovo ## Properties diff --git a/client-api_r/generated/docs/DBLink.md b/client-api_r/generated/docs/DBLink.md index 3c3bfc1a..af344709 100644 --- a/client-api_r/generated/docs/DBLink.md +++ b/client-api_r/generated/docs/DBLink.md @@ -1,4 +1,4 @@ -# Rsirius::DBLink +# RSirius::DBLink ## Properties diff --git a/client-api_r/generated/docs/DataImportEvent.md b/client-api_r/generated/docs/DataImportEvent.md index 5b77f815..e990d2c9 100644 --- a/client-api_r/generated/docs/DataImportEvent.md +++ b/client-api_r/generated/docs/DataImportEvent.md @@ -1,4 +1,4 @@ -# Rsirius::DataImportEvent +# RSirius::DataImportEvent ## Properties diff --git a/client-api_r/generated/docs/Deviation.md b/client-api_r/generated/docs/Deviation.md index 700ed796..5495b767 100644 --- a/client-api_r/generated/docs/Deviation.md +++ b/client-api_r/generated/docs/Deviation.md @@ -1,4 +1,4 @@ -# Rsirius::Deviation +# RSirius::Deviation ## Properties diff --git a/client-api_r/generated/docs/FeatureAnnotations.md b/client-api_r/generated/docs/FeatureAnnotations.md index b6cf1354..3f3c34b8 100644 --- a/client-api_r/generated/docs/FeatureAnnotations.md +++ b/client-api_r/generated/docs/FeatureAnnotations.md @@ -1,4 +1,4 @@ -# Rsirius::FeatureAnnotations +# RSirius::FeatureAnnotations Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature. The different annotation fields within this summary object are null if the corresponding feature does not contain the represented results. If fields are non-null the corresponding result has been computed but might still be empty. diff --git a/client-api_r/generated/docs/FeatureImport.md b/client-api_r/generated/docs/FeatureImport.md index cc9339e2..48fae213 100644 --- a/client-api_r/generated/docs/FeatureImport.md +++ b/client-api_r/generated/docs/FeatureImport.md @@ -1,4 +1,4 @@ -# Rsirius::FeatureImport +# RSirius::FeatureImport Represents an (aligned) feature to be imported into a SIRIUS project. At least one of the Mass Spec data sources (e.g. mergedMs1, ms1Spectra, ms2Spectra) needs to be given. Otherwise, the import will fail. diff --git a/client-api_r/generated/docs/FeatureStatisticsApi.md b/client-api_r/generated/docs/FeatureStatisticsApi.md index 0f6c00d3..e057f74b 100644 --- a/client-api_r/generated/docs/FeatureStatisticsApi.md +++ b/client-api_r/generated/docs/FeatureStatisticsApi.md @@ -19,7 +19,7 @@ Method | HTTP request | Description ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Compute the fold change between two groups of runs # @@ -76,7 +76,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete fold changes # @@ -128,7 +128,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get table of all fold changes in the project space # @@ -179,7 +179,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] List all fold changes that are associated with an object # diff --git a/client-api_r/generated/docs/FeaturesApi.md b/client-api_r/generated/docs/FeaturesApi.md index 260b400e..0e0c184c 100644 --- a/client-api_r/generated/docs/FeaturesApi.md +++ b/client-api_r/generated/docs/FeaturesApi.md @@ -59,7 +59,7 @@ Import (aligned) features into the project. Features must not exist in the proje ### Example ```R -library(Rsirius) +library(RSirius) # Import (aligned) features into the project. # @@ -112,7 +112,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Add molecular structures (as SMILES) to the list of de novo structures. # @@ -163,7 +163,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Add tags to a feature (aligned over runs) in the project # @@ -214,7 +214,7 @@ Delete feature (aligned over runs) with the given identifier from the specified ### Example ```R -library(Rsirius) +library(RSirius) # Delete feature (aligned over runs) with the given identifier from the specified project-space. # @@ -260,7 +260,7 @@ Delete feature (aligned over runs) with the given identifier from the specified ### Example ```R -library(Rsirius) +library(RSirius) # Delete feature (aligned over runs) with the given identifier from the specified project-space. # @@ -306,7 +306,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns the adduct network for a given alignedFeatureId together with all merged traces contained in the network # @@ -355,7 +355,7 @@ Get feature (aligned over runs) with the given identifier from the specified pro ### Example ```R -library(Rsirius) +library(RSirius) # Get feature (aligned over runs) with the given identifier from the specified project-space. # @@ -408,7 +408,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns data quality information for given feature (alignedFeatureId) # @@ -457,7 +457,7 @@ Get all available features (aligned over runs) in the given project-space. ### Example ```R -library(Rsirius) +library(RSirius) # Get all available features (aligned over runs) in the given project-space. # @@ -508,7 +508,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get features (aligned over runs) by tag group # @@ -565,7 +565,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get features (aligned over runs) by tag # @@ -622,7 +622,7 @@ Get all available features (aligned over runs) in the given project-space. ### Example ```R -library(Rsirius) +library(RSirius) # Get all available features (aligned over runs) in the given project-space. # @@ -679,7 +679,7 @@ Return Best matching compound classes for given formulaId.

Set of the high ### Example ```R -library(Rsirius) +library(RSirius) # Return Best matching compound classes for given formulaId # @@ -730,7 +730,7 @@ All predicted compound classes (CANOPUS) from ClassyFire and NPC and their proba ### Example ```R -library(Rsirius) +library(RSirius) # All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, # @@ -781,7 +781,7 @@ List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CS ### Example ```R -library(Rsirius) +library(RSirius) # List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. # @@ -832,7 +832,7 @@ List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CS ### Example ```R -library(Rsirius) +library(RSirius) # List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. # @@ -885,7 +885,7 @@ Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CS ### Example ```R -library(Rsirius) +library(RSirius) # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. # @@ -944,7 +944,7 @@ Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CS ### Example ```R -library(Rsirius) +library(RSirius) # Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. # @@ -1001,7 +1001,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns the full quantification table for the given feature (alignedFeatureId) # @@ -1050,7 +1050,7 @@ Returns predicted fingerprint (CSI:FingerID) for the given formula result identi ### Example ```R -library(Rsirius) +library(RSirius) # Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) # @@ -1101,7 +1101,7 @@ Returns MS/MS Spectrum annotated with fragments and losses for provided formulaI ### Example ```R -library(Rsirius) +library(RSirius) # Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId # @@ -1154,7 +1154,7 @@ Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fra ### Example ```R -library(Rsirius) +library(RSirius) # Returns a fragmentation spectrum (e # @@ -1209,7 +1209,7 @@ FormulaResultContainers for the given 'formulaId' with minimal information. Can ### Example ```R -library(Rsirius) +library(RSirius) # FormulaResultContainers for the given 'formulaId' with minimal information. # @@ -1264,7 +1264,7 @@ List of FormulaResultContainers available for this feature with minimal informat ### Example ```R -library(Rsirius) +library(RSirius) # List of FormulaResultContainers available for this feature with minimal information. # @@ -1317,7 +1317,7 @@ Page of FormulaResultContainers available for this feature with minimal informat ### Example ```R -library(Rsirius) +library(RSirius) # Page of FormulaResultContainers available for this feature with minimal information. # @@ -1376,7 +1376,7 @@ Returns fragmentation tree (SIRIUS) for the given formula result identifier

### Example ```R -library(Rsirius) +library(RSirius) # Returns fragmentation tree (SIRIUS) for the given formula result identifier # @@ -1427,7 +1427,7 @@ Returns Isotope pattern information for given formulaId

Returns Isotope pa ### Example ```R -library(Rsirius) +library(RSirius) # Returns Isotope pattern information for given formulaId # @@ -1478,7 +1478,7 @@ Returns Lipid annotation (ElGordo) for the given formulaId.

ElGordo lipid ### Example ```R -library(Rsirius) +library(RSirius) # Returns Lipid annotation (ElGordo) for the given formulaId # @@ -1529,7 +1529,7 @@ Mass Spec data (input data) for the given 'alignedFeatureId' . ### Example ```R -library(Rsirius) +library(RSirius) # Mass Spec data (input data) for the given 'alignedFeatureId' . # @@ -1580,7 +1580,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns a single quantification table row for the given feature (alignedFeatureId) # @@ -1631,7 +1631,7 @@ Spectral library match for the given 'alignedFeatureId'. ### Example ```R -library(Rsirius) +library(RSirius) # Spectral library match for the given 'alignedFeatureId'. # @@ -1684,7 +1684,7 @@ List of spectral library matches for the given 'alignedFeatureId'. ### Example ```R -library(Rsirius) +library(RSirius) # List of spectral library matches for the given 'alignedFeatureId'. # @@ -1741,7 +1741,7 @@ Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiK ### Example ```R -library(Rsirius) +library(RSirius) # Page of spectral library matches for the given 'alignedFeatureId'. # @@ -1804,7 +1804,7 @@ Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inc ### Example ```R -library(Rsirius) +library(RSirius) # Summarize matched reference spectra for the given 'alignedFeatureId'. # @@ -1859,7 +1859,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns MS/MS Data annotated with fragments and losses for given formulaId and inChIKey # @@ -1914,7 +1914,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Spectral library match for the given 'alignedFeatureId' with additional molecular formula and substructure annotations # @@ -1965,7 +1965,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns a fragmentation spectrum annotated with fragments and losses for the given formulaId and inChIKey # @@ -2022,7 +2022,7 @@ List of structure database search candidates ranked by CSI:FingerID score for th ### Example ```R -library(Rsirius) +library(RSirius) # List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. # @@ -2073,7 +2073,7 @@ List of CSI:FingerID structure database search candidates for the given 'formula ### Example ```R -library(Rsirius) +library(RSirius) # List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. # @@ -2126,7 +2126,7 @@ Page of CSI:FingerID structure database search candidates for the given 'formula ### Example ```R -library(Rsirius) +library(RSirius) # Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. # @@ -2185,7 +2185,7 @@ Page of structure database search candidates ranked by CSI:FingerID score for th ### Example ```R -library(Rsirius) +library(RSirius) # Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. # @@ -2242,7 +2242,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all tags associated with this Object # @@ -2291,7 +2291,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Returns the traces of the given feature (alignedFeatureId) # @@ -2342,7 +2342,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete tag with the given name from the feature (aligned over runs) with the specified ID in the specified project-space # diff --git a/client-api_r/generated/docs/FingerprintPrediction.md b/client-api_r/generated/docs/FingerprintPrediction.md index 3167009c..c6973a37 100644 --- a/client-api_r/generated/docs/FingerprintPrediction.md +++ b/client-api_r/generated/docs/FingerprintPrediction.md @@ -1,4 +1,4 @@ -# Rsirius::FingerprintPrediction +# RSirius::FingerprintPrediction User/developer friendly parameter subset for the CSI:FingerID Fingerprint tool Needs results from Formula/SIRIUS Tool diff --git a/client-api_r/generated/docs/FoldChange.md b/client-api_r/generated/docs/FoldChange.md index 4711f1d9..02ef1381 100644 --- a/client-api_r/generated/docs/FoldChange.md +++ b/client-api_r/generated/docs/FoldChange.md @@ -1,4 +1,4 @@ -# Rsirius::FoldChange +# RSirius::FoldChange ## Properties diff --git a/client-api_r/generated/docs/FormulaCandidate.md b/client-api_r/generated/docs/FormulaCandidate.md index 144b0bc5..3eed1c8c 100644 --- a/client-api_r/generated/docs/FormulaCandidate.md +++ b/client-api_r/generated/docs/FormulaCandidate.md @@ -1,4 +1,4 @@ -# Rsirius::FormulaCandidate +# RSirius::FormulaCandidate Molecular formula candidate that holds a unique identifier (molecular formula + adduct). It can be extended with optional scoring metrics and the raw results such as fragmentation trees and simulated isotope pattern. diff --git a/client-api_r/generated/docs/FragmentNode.md b/client-api_r/generated/docs/FragmentNode.md index 692e983f..7b554063 100644 --- a/client-api_r/generated/docs/FragmentNode.md +++ b/client-api_r/generated/docs/FragmentNode.md @@ -1,4 +1,4 @@ -# Rsirius::FragmentNode +# RSirius::FragmentNode ## Properties diff --git a/client-api_r/generated/docs/FragmentationTree.md b/client-api_r/generated/docs/FragmentationTree.md index f57a9396..e31b5a96 100644 --- a/client-api_r/generated/docs/FragmentationTree.md +++ b/client-api_r/generated/docs/FragmentationTree.md @@ -1,4 +1,4 @@ -# Rsirius::FragmentationTree +# RSirius::FragmentationTree Simple and easy serializable fragmentation tree model with annotated fragments/nodes abd losses/edges Root fragment has index 0; Molecular formula and adduct are identical to the ones of the corresponding molecular formula candidate and SpectrumAnnotation diff --git a/client-api_r/generated/docs/ImportResult.md b/client-api_r/generated/docs/ImportResult.md index 6a70fb9e..819475ab 100644 --- a/client-api_r/generated/docs/ImportResult.md +++ b/client-api_r/generated/docs/ImportResult.md @@ -1,4 +1,4 @@ -# Rsirius::ImportResult +# RSirius::ImportResult ## Properties diff --git a/client-api_r/generated/docs/Info.md b/client-api_r/generated/docs/Info.md index fa67e193..5407e74c 100644 --- a/client-api_r/generated/docs/Info.md +++ b/client-api_r/generated/docs/Info.md @@ -1,4 +1,4 @@ -# Rsirius::Info +# RSirius::Info ## Properties diff --git a/client-api_r/generated/docs/InfoApi.md b/client-api_r/generated/docs/InfoApi.md index f7b693e0..e51acc0e 100644 --- a/client-api_r/generated/docs/InfoApi.md +++ b/client-api_r/generated/docs/InfoApi.md @@ -15,7 +15,7 @@ Method | HTTP request | Description ### Example ```R -library(Rsirius) +library(RSirius) api_instance <- rsirius_api$new() @@ -53,7 +53,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_server_info <- TRUE # character | (Optional) diff --git a/client-api_r/generated/docs/IsotopePatternAnnotation.md b/client-api_r/generated/docs/IsotopePatternAnnotation.md index eaac0636..3335d768 100644 --- a/client-api_r/generated/docs/IsotopePatternAnnotation.md +++ b/client-api_r/generated/docs/IsotopePatternAnnotation.md @@ -1,4 +1,4 @@ -# Rsirius::IsotopePatternAnnotation +# RSirius::IsotopePatternAnnotation ## Properties diff --git a/client-api_r/generated/docs/Job.md b/client-api_r/generated/docs/Job.md index bbd830d4..280a56c0 100644 --- a/client-api_r/generated/docs/Job.md +++ b/client-api_r/generated/docs/Job.md @@ -1,4 +1,4 @@ -# Rsirius::Job +# RSirius::Job Identifier created by the SIRIUS Nightsky API for a newly created Job. Object can be enriched with Job status/progress information ({@link JobProgress JobProgress}) and/or Job command information. This is a return value of the API. So nullable values can also be NOT_REQUIRED to allow for easy removal. diff --git a/client-api_r/generated/docs/JobProgress.md b/client-api_r/generated/docs/JobProgress.md index 2f5805cc..3699e1f3 100644 --- a/client-api_r/generated/docs/JobProgress.md +++ b/client-api_r/generated/docs/JobProgress.md @@ -1,4 +1,4 @@ -# Rsirius::JobProgress +# RSirius::JobProgress Progress information of a computation job that has already been submitted to SIRIUS. if currentProgress == maxProgress job is finished and should change to state done soon. if a job is DONE all results can be accessed via the Project-Spaces api. diff --git a/client-api_r/generated/docs/JobSubmission.md b/client-api_r/generated/docs/JobSubmission.md index 08c0a027..d4895b4b 100644 --- a/client-api_r/generated/docs/JobSubmission.md +++ b/client-api_r/generated/docs/JobSubmission.md @@ -1,4 +1,4 @@ -# Rsirius::JobSubmission +# RSirius::JobSubmission Object to submit a job to be executed by SIRIUS diff --git a/client-api_r/generated/docs/JobsApi.md b/client-api_r/generated/docs/JobsApi.md index 03e3cc0c..a21aedfb 100644 --- a/client-api_r/generated/docs/JobsApi.md +++ b/client-api_r/generated/docs/JobsApi.md @@ -30,7 +30,7 @@ Delete job. Specify how to behave for running jobs. ### Example ```R -library(Rsirius) +library(RSirius) # Delete job. # @@ -80,7 +80,7 @@ Delete job configuration with given name. ### Example ```R -library(Rsirius) +library(RSirius) # Delete job configuration with given name. # @@ -124,7 +124,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # * Delete ALL jobs. # @@ -172,7 +172,7 @@ Get a CLI command for the given job configuration. ### Example ```R -library(Rsirius) +library(RSirius) # Get a CLI command for the given job configuration. # @@ -219,7 +219,7 @@ Request default job configuration ### Example ```R -library(Rsirius) +library(RSirius) # Request default job configuration # @@ -270,7 +270,7 @@ Get job information and its current state and progress (if available). ### Example ```R -library(Rsirius) +library(RSirius) # Get job information and its current state and progress (if available). # @@ -321,7 +321,7 @@ Request job configuration with given name. ### Example ```R -library(Rsirius) +library(RSirius) # Request job configuration with given name. # @@ -370,7 +370,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [DEPRECATED] Get all (non-default) job configuration names # @@ -412,7 +412,7 @@ Request all available job configurations ### Example ```R -library(Rsirius) +library(RSirius) # Request all available job configurations # @@ -454,7 +454,7 @@ Get List of all available jobs with information such as current state and progre ### Example ```R -library(Rsirius) +library(RSirius) # Get List of all available jobs with information such as current state and progress (if available). # @@ -503,7 +503,7 @@ Get Page of jobs with information such as current state and progress (if availab ### Example ```R -library(Rsirius) +library(RSirius) # Get Page of jobs with information such as current state and progress (if available). # @@ -556,7 +556,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_project_id <- "project_id_example" # character | @@ -603,7 +603,7 @@ Add new job configuration with given name. ### Example ```R -library(Rsirius) +library(RSirius) # Add new job configuration with given name. # @@ -656,7 +656,7 @@ Start computation for given compounds and with given parameters. ### Example ```R -library(Rsirius) +library(RSirius) # Start computation for given compounds and with given parameters. # @@ -707,7 +707,7 @@ Start computation for given compounds and with parameters from a stored job-conf ### Example ```R -library(Rsirius) +library(RSirius) # Start computation for given compounds and with parameters from a stored job-config. # diff --git a/client-api_r/generated/docs/LcmsSubmissionParameters.md b/client-api_r/generated/docs/LcmsSubmissionParameters.md index a1ed70a9..0636f8db 100644 --- a/client-api_r/generated/docs/LcmsSubmissionParameters.md +++ b/client-api_r/generated/docs/LcmsSubmissionParameters.md @@ -1,4 +1,4 @@ -# Rsirius::LcmsSubmissionParameters +# RSirius::LcmsSubmissionParameters ## Properties diff --git a/client-api_r/generated/docs/LicenseInfo.md b/client-api_r/generated/docs/LicenseInfo.md index d77dfb4f..ffe83e45 100644 --- a/client-api_r/generated/docs/LicenseInfo.md +++ b/client-api_r/generated/docs/LicenseInfo.md @@ -1,4 +1,4 @@ -# Rsirius::LicenseInfo +# RSirius::LicenseInfo ## Properties diff --git a/client-api_r/generated/docs/LipidAnnotation.md b/client-api_r/generated/docs/LipidAnnotation.md index dbfd2720..45919d97 100644 --- a/client-api_r/generated/docs/LipidAnnotation.md +++ b/client-api_r/generated/docs/LipidAnnotation.md @@ -1,4 +1,4 @@ -# Rsirius::LipidAnnotation +# RSirius::LipidAnnotation ## Properties diff --git a/client-api_r/generated/docs/LoginAndAccountApi.md b/client-api_r/generated/docs/LoginAndAccountApi.md index d208aea8..1af1e463 100644 --- a/client-api_r/generated/docs/LoginAndAccountApi.md +++ b/client-api_r/generated/docs/LoginAndAccountApi.md @@ -24,7 +24,7 @@ Get information about the account currently logged in. Fails if not logged in. ### Example ```R -library(Rsirius) +library(RSirius) # Get information about the account currently logged in. # @@ -71,7 +71,7 @@ Get SignUp URL (For signUp via web browser) ### Example ```R -library(Rsirius) +library(RSirius) # Get SignUp URL (For signUp via web browser) # @@ -113,7 +113,7 @@ Get available subscriptions of the account currently logged in. Fails if not log ### Example ```R -library(Rsirius) +library(RSirius) # Get available subscriptions of the account currently logged in. # @@ -155,7 +155,7 @@ Check if a user is logged in. ### Example ```R -library(Rsirius) +library(RSirius) # Check if a user is logged in. # @@ -197,7 +197,7 @@ Login into SIRIUS web services and activate default subscription if available. ### Example ```R -library(Rsirius) +library(RSirius) # Login into SIRIUS web services and activate default subscription if available. # @@ -250,7 +250,7 @@ Logout from SIRIUS web services. ### Example ```R -library(Rsirius) +library(RSirius) # Logout from SIRIUS web services. # @@ -289,7 +289,7 @@ Open User portal in browser. If user is logged in SIRIUS tries to transfer the l ### Example ```R -library(Rsirius) +library(RSirius) # Open User portal in browser. # @@ -328,7 +328,7 @@ Select a subscription as active subscription to be used for computations. ### Example ```R -library(Rsirius) +library(RSirius) # Select a subscription as active subscription to be used for computations. # @@ -375,7 +375,7 @@ Open SignUp window in system browser and return signUp link. ### Example ```R -library(Rsirius) +library(RSirius) # Open SignUp window in system browser and return signUp link. # diff --git a/client-api_r/generated/docs/LossEdge.md b/client-api_r/generated/docs/LossEdge.md index 639efd14..41e26575 100644 --- a/client-api_r/generated/docs/LossEdge.md +++ b/client-api_r/generated/docs/LossEdge.md @@ -1,4 +1,4 @@ -# Rsirius::LossEdge +# RSirius::LossEdge ## Properties diff --git a/client-api_r/generated/docs/MsData.md b/client-api_r/generated/docs/MsData.md index 545ca3fe..553272d3 100644 --- a/client-api_r/generated/docs/MsData.md +++ b/client-api_r/generated/docs/MsData.md @@ -1,4 +1,4 @@ -# Rsirius::MsData +# RSirius::MsData The MsData wraps all spectral input data belonging to a (aligned) feature. All spectra fields are optional. However, at least one Spectrum field needs to be set to create a valid MsData Object. The different types of spectra fields can be extended to adapt to other MassSpec measurement techniques not covered yet.

Each Feature can have: - One extracted isotope pattern (optional) - One merged MS/MS spectrum (optional) - One merged MS spectrum (optional) - many MS/MS spectra (optional) - many MS spectra (optional)

Each non-merged spectrum has an index which can be used to access the spectrum.

In the future we might add some additional information like chromatographic peak or something similar diff --git a/client-api_r/generated/docs/MsNovelist.md b/client-api_r/generated/docs/MsNovelist.md index ebf6a108..f1d8dd98 100644 --- a/client-api_r/generated/docs/MsNovelist.md +++ b/client-api_r/generated/docs/MsNovelist.md @@ -1,4 +1,4 @@ -# Rsirius::MsNovelist +# RSirius::MsNovelist ## Properties diff --git a/client-api_r/generated/docs/PageMetadata.md b/client-api_r/generated/docs/PageMetadata.md index 06d67b93..d3712b06 100644 --- a/client-api_r/generated/docs/PageMetadata.md +++ b/client-api_r/generated/docs/PageMetadata.md @@ -1,4 +1,4 @@ -# Rsirius::PageMetadata +# RSirius::PageMetadata ## Properties diff --git a/client-api_r/generated/docs/PagedModelAlignedFeature.md b/client-api_r/generated/docs/PagedModelAlignedFeature.md index fbb13038..71abfe09 100644 --- a/client-api_r/generated/docs/PagedModelAlignedFeature.md +++ b/client-api_r/generated/docs/PagedModelAlignedFeature.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelAlignedFeature +# RSirius::PagedModelAlignedFeature ## Properties diff --git a/client-api_r/generated/docs/PagedModelCompound.md b/client-api_r/generated/docs/PagedModelCompound.md index 45b01221..4a9beed9 100644 --- a/client-api_r/generated/docs/PagedModelCompound.md +++ b/client-api_r/generated/docs/PagedModelCompound.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelCompound +# RSirius::PagedModelCompound ## Properties diff --git a/client-api_r/generated/docs/PagedModelFormulaCandidate.md b/client-api_r/generated/docs/PagedModelFormulaCandidate.md index e0661457..eba3d53e 100644 --- a/client-api_r/generated/docs/PagedModelFormulaCandidate.md +++ b/client-api_r/generated/docs/PagedModelFormulaCandidate.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelFormulaCandidate +# RSirius::PagedModelFormulaCandidate ## Properties diff --git a/client-api_r/generated/docs/PagedModelJob.md b/client-api_r/generated/docs/PagedModelJob.md index 8aea2b05..c9e820b2 100644 --- a/client-api_r/generated/docs/PagedModelJob.md +++ b/client-api_r/generated/docs/PagedModelJob.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelJob +# RSirius::PagedModelJob ## Properties diff --git a/client-api_r/generated/docs/PagedModelRun.md b/client-api_r/generated/docs/PagedModelRun.md index 3b9b8a09..a467c744 100644 --- a/client-api_r/generated/docs/PagedModelRun.md +++ b/client-api_r/generated/docs/PagedModelRun.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelRun +# RSirius::PagedModelRun ## Properties diff --git a/client-api_r/generated/docs/PagedModelSpectralLibraryMatch.md b/client-api_r/generated/docs/PagedModelSpectralLibraryMatch.md index e532ad0d..26166090 100644 --- a/client-api_r/generated/docs/PagedModelSpectralLibraryMatch.md +++ b/client-api_r/generated/docs/PagedModelSpectralLibraryMatch.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelSpectralLibraryMatch +# RSirius::PagedModelSpectralLibraryMatch ## Properties diff --git a/client-api_r/generated/docs/PagedModelStructureCandidateFormula.md b/client-api_r/generated/docs/PagedModelStructureCandidateFormula.md index d8c3cef6..7612e6de 100644 --- a/client-api_r/generated/docs/PagedModelStructureCandidateFormula.md +++ b/client-api_r/generated/docs/PagedModelStructureCandidateFormula.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelStructureCandidateFormula +# RSirius::PagedModelStructureCandidateFormula ## Properties diff --git a/client-api_r/generated/docs/PagedModelStructureCandidateScored.md b/client-api_r/generated/docs/PagedModelStructureCandidateScored.md index fddc8ad3..5ff58056 100644 --- a/client-api_r/generated/docs/PagedModelStructureCandidateScored.md +++ b/client-api_r/generated/docs/PagedModelStructureCandidateScored.md @@ -1,4 +1,4 @@ -# Rsirius::PagedModelStructureCandidateScored +# RSirius::PagedModelStructureCandidateScored ## Properties diff --git a/client-api_r/generated/docs/ParentPeak.md b/client-api_r/generated/docs/ParentPeak.md index 77f39487..d0cb190f 100644 --- a/client-api_r/generated/docs/ParentPeak.md +++ b/client-api_r/generated/docs/ParentPeak.md @@ -1,4 +1,4 @@ -# Rsirius::ParentPeak +# RSirius::ParentPeak Link from annotated fragment peak to its parent fragment peak connected by their neutral loss. diff --git a/client-api_r/generated/docs/PeakAnnotation.md b/client-api_r/generated/docs/PeakAnnotation.md index d9fff0b6..1956f330 100644 --- a/client-api_r/generated/docs/PeakAnnotation.md +++ b/client-api_r/generated/docs/PeakAnnotation.md @@ -1,4 +1,4 @@ -# Rsirius::PeakAnnotation +# RSirius::PeakAnnotation ## Properties diff --git a/client-api_r/generated/docs/PeakPair.md b/client-api_r/generated/docs/PeakPair.md index d3d6a5ce..30737eea 100644 --- a/client-api_r/generated/docs/PeakPair.md +++ b/client-api_r/generated/docs/PeakPair.md @@ -1,4 +1,4 @@ -# Rsirius::PeakPair +# RSirius::PeakPair ## Properties diff --git a/client-api_r/generated/docs/ProjectChangeEvent.md b/client-api_r/generated/docs/ProjectChangeEvent.md index 3a5d1bbb..0070b7ec 100644 --- a/client-api_r/generated/docs/ProjectChangeEvent.md +++ b/client-api_r/generated/docs/ProjectChangeEvent.md @@ -1,4 +1,4 @@ -# Rsirius::ProjectChangeEvent +# RSirius::ProjectChangeEvent ## Properties diff --git a/client-api_r/generated/docs/ProjectInfo.md b/client-api_r/generated/docs/ProjectInfo.md index b2c0a208..a9a12105 100644 --- a/client-api_r/generated/docs/ProjectInfo.md +++ b/client-api_r/generated/docs/ProjectInfo.md @@ -1,4 +1,4 @@ -# Rsirius::ProjectInfo +# RSirius::ProjectInfo ## Properties diff --git a/client-api_r/generated/docs/ProjectsApi.md b/client-api_r/generated/docs/ProjectsApi.md index 693147c9..75b0baa5 100644 --- a/client-api_r/generated/docs/ProjectsApi.md +++ b/client-api_r/generated/docs/ProjectsApi.md @@ -27,7 +27,7 @@ Close project-space and remove it from the application. The Project will NOT be ### Example ```R -library(Rsirius) +library(RSirius) # Close project-space and remove it from the application # @@ -73,7 +73,7 @@ Create and open a new project-space at given location and make it accessible via ### Example ```R -library(Rsirius) +library(RSirius) # Create and open a new project-space at given location and make it accessible via the given projectId. # @@ -122,7 +122,7 @@ Get CANOPUS prediction vector definition for ClassyFire classes ### Example ```R -library(Rsirius) +library(RSirius) # Get CANOPUS prediction vector definition for ClassyFire classes # @@ -169,7 +169,7 @@ Get CANOPUS prediction vector definition for NPC classes ### Example ```R -library(Rsirius) +library(RSirius) # Get CANOPUS prediction vector definition for NPC classes # @@ -216,7 +216,7 @@ Get CSI:FingerID fingerprint (prediction vector) definition ### Example ```R -library(Rsirius) +library(RSirius) # Get CSI:FingerID fingerprint (prediction vector) definition # @@ -265,7 +265,7 @@ Get project space info by its projectId. ### Example ```R -library(Rsirius) +library(RSirius) # Get project space info by its projectId. # @@ -314,7 +314,7 @@ List opened project spaces. ### Example ```R -library(Rsirius) +library(RSirius) # List opened project spaces. # @@ -356,7 +356,7 @@ Import and Align full MS-Runs from various formats into the specified project P ### Example ```R -library(Rsirius) +library(RSirius) # Import and Align full MS-Runs from various formats into the specified project Possible formats (mzML, mzXML) # @@ -407,7 +407,7 @@ Import and Align full MS-Runs from various formats into the specified project as ### Example ```R -library(Rsirius) +library(RSirius) # Import and Align full MS-Runs from various formats into the specified project as background job. # @@ -460,7 +460,7 @@ Import already preprocessed ms/ms data from various formats into the specified p ### Example ```R -library(Rsirius) +library(RSirius) # Import already preprocessed ms/ms data from various formats into the specified project Possible formats (ms, mgf, cef, msp) # @@ -513,7 +513,7 @@ Import ms/ms data from the given format into the specified project-space as back ### Example ```R -library(Rsirius) +library(RSirius) # Import ms/ms data from the given format into the specified project-space as background job. # @@ -568,7 +568,7 @@ Open an existing project-space and make it accessible via the given projectId. ### Example ```R -library(Rsirius) +library(RSirius) # Open an existing project-space and make it accessible via the given projectId. # diff --git a/client-api_r/generated/docs/QualityItem.md b/client-api_r/generated/docs/QualityItem.md index 0fcddfb9..15784b99 100644 --- a/client-api_r/generated/docs/QualityItem.md +++ b/client-api_r/generated/docs/QualityItem.md @@ -1,4 +1,4 @@ -# Rsirius::QualityItem +# RSirius::QualityItem ## Properties diff --git a/client-api_r/generated/docs/QuantTableExperimental.md b/client-api_r/generated/docs/QuantTableExperimental.md index bc4d99fd..3dc57383 100644 --- a/client-api_r/generated/docs/QuantTableExperimental.md +++ b/client-api_r/generated/docs/QuantTableExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::QuantTableExperimental +# RSirius::QuantTableExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/Run.md b/client-api_r/generated/docs/Run.md index 956854b9..a645dab4 100644 --- a/client-api_r/generated/docs/Run.md +++ b/client-api_r/generated/docs/Run.md @@ -1,4 +1,4 @@ -# Rsirius::Run +# RSirius::Run ## Properties diff --git a/client-api_r/generated/docs/RunOptField.md b/client-api_r/generated/docs/RunOptField.md index 18388545..46fc9215 100644 --- a/client-api_r/generated/docs/RunOptField.md +++ b/client-api_r/generated/docs/RunOptField.md @@ -1,4 +1,4 @@ -# Rsirius::RunOptField +# RSirius::RunOptField ## Properties diff --git a/client-api_r/generated/docs/RunsApi.md b/client-api_r/generated/docs/RunsApi.md index 81f41679..2cfbbcf2 100644 --- a/client-api_r/generated/docs/RunsApi.md +++ b/client-api_r/generated/docs/RunsApi.md @@ -23,7 +23,7 @@ Method | HTTP request | Description ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Add tags to a run in the project # @@ -74,7 +74,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # **EXPERIMENTAL** Compute the fold changes that are required for the fold change filter # @@ -125,7 +125,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get run with the given identifier from the specified project-space # @@ -176,7 +176,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all available runs in the given project-space # @@ -231,7 +231,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get runs by tag group # @@ -288,7 +288,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get runs by tag # @@ -345,7 +345,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all tags associated with this Run # @@ -394,7 +394,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete tag with the given name from the run with the specified ID in the specified project-space # diff --git a/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md b/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md index ec716182..b970f32c 100644 --- a/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md +++ b/client-api_r/generated/docs/SampleTypeFoldChangeRequest.md @@ -1,4 +1,4 @@ -# Rsirius::SampleTypeFoldChangeRequest +# RSirius::SampleTypeFoldChangeRequest ## Properties diff --git a/client-api_r/generated/docs/SearchableDatabase.md b/client-api_r/generated/docs/SearchableDatabase.md index 25739422..1a1f1829 100644 --- a/client-api_r/generated/docs/SearchableDatabase.md +++ b/client-api_r/generated/docs/SearchableDatabase.md @@ -1,4 +1,4 @@ -# Rsirius::SearchableDatabase +# RSirius::SearchableDatabase ## Properties diff --git a/client-api_r/generated/docs/SearchableDatabaseParameters.md b/client-api_r/generated/docs/SearchableDatabaseParameters.md index f1b88703..b3a15b63 100644 --- a/client-api_r/generated/docs/SearchableDatabaseParameters.md +++ b/client-api_r/generated/docs/SearchableDatabaseParameters.md @@ -1,4 +1,4 @@ -# Rsirius::SearchableDatabaseParameters +# RSirius::SearchableDatabaseParameters ## Properties diff --git a/client-api_r/generated/docs/SearchableDatabasesApi.md b/client-api_r/generated/docs/SearchableDatabasesApi.md index eb719261..5fc68684 100644 --- a/client-api_r/generated/docs/SearchableDatabasesApi.md +++ b/client-api_r/generated/docs/SearchableDatabasesApi.md @@ -22,7 +22,7 @@ DEPRECATED: this endpoint is based on local file paths and will likely be replac ### Example ```R -library(Rsirius) +library(RSirius) # DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. # @@ -67,7 +67,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_database_id <- "database_id_example" # character | @@ -112,7 +112,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_include_stats <- FALSE # character | (Optional) @@ -157,7 +157,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_database_id <- "database_id_example" # character | @@ -202,7 +202,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_include_stats <- FALSE # character | (Optional) @@ -247,7 +247,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_include_stats <- FALSE # character | (Optional) @@ -292,7 +292,7 @@ Start import of structure and spectra files into the specified database. ### Example ```R -library(Rsirius) +library(RSirius) # Start import of structure and spectra files into the specified database. # @@ -343,7 +343,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_database_id <- "database_id_example" # character | @@ -385,7 +385,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # prepare function argument(s) var_database_id <- "database_id_example" # character | diff --git a/client-api_r/generated/docs/SecurityContext.md b/client-api_r/generated/docs/SecurityContext.md index d97a00d1..2cd98508 100644 --- a/client-api_r/generated/docs/SecurityContext.md +++ b/client-api_r/generated/docs/SecurityContext.md @@ -1,4 +1,4 @@ -# Rsirius::SecurityContext +# RSirius::SecurityContext ## Properties diff --git a/client-api_r/generated/docs/SecurityContextPrincipal.md b/client-api_r/generated/docs/SecurityContextPrincipal.md index 8974aee3..062d87e5 100644 --- a/client-api_r/generated/docs/SecurityContextPrincipal.md +++ b/client-api_r/generated/docs/SecurityContextPrincipal.md @@ -1,4 +1,4 @@ -# Rsirius::SecurityContextPrincipal +# RSirius::SecurityContextPrincipal ## Properties diff --git a/client-api_r/generated/docs/SimplePeak.md b/client-api_r/generated/docs/SimplePeak.md index cb1a751c..48410243 100644 --- a/client-api_r/generated/docs/SimplePeak.md +++ b/client-api_r/generated/docs/SimplePeak.md @@ -1,4 +1,4 @@ -# Rsirius::SimplePeak +# RSirius::SimplePeak ## Properties diff --git a/client-api_r/generated/docs/Sirius.md b/client-api_r/generated/docs/Sirius.md index 4e0efc9b..40b55113 100644 --- a/client-api_r/generated/docs/Sirius.md +++ b/client-api_r/generated/docs/Sirius.md @@ -1,4 +1,4 @@ -# Rsirius::Sirius +# RSirius::Sirius User/developer friendly parameter subset for the Formula/SIRIUS tool Can use results from Spectral library search tool. diff --git a/client-api_r/generated/docs/SpectralLibraryMatch.md b/client-api_r/generated/docs/SpectralLibraryMatch.md index 4a4a6d47..0a347956 100644 --- a/client-api_r/generated/docs/SpectralLibraryMatch.md +++ b/client-api_r/generated/docs/SpectralLibraryMatch.md @@ -1,4 +1,4 @@ -# Rsirius::SpectralLibraryMatch +# RSirius::SpectralLibraryMatch ## Properties diff --git a/client-api_r/generated/docs/SpectralLibraryMatchSummary.md b/client-api_r/generated/docs/SpectralLibraryMatchSummary.md index 6a01e5e4..95019d26 100644 --- a/client-api_r/generated/docs/SpectralLibraryMatchSummary.md +++ b/client-api_r/generated/docs/SpectralLibraryMatchSummary.md @@ -1,4 +1,4 @@ -# Rsirius::SpectralLibraryMatchSummary +# RSirius::SpectralLibraryMatchSummary ## Properties diff --git a/client-api_r/generated/docs/SpectralLibrarySearch.md b/client-api_r/generated/docs/SpectralLibrarySearch.md index a96c07da..8c5b5366 100644 --- a/client-api_r/generated/docs/SpectralLibrarySearch.md +++ b/client-api_r/generated/docs/SpectralLibrarySearch.md @@ -1,4 +1,4 @@ -# Rsirius::SpectralLibrarySearch +# RSirius::SpectralLibrarySearch User/developer friendly parameter subset for the Spectral library search tool. diff --git a/client-api_r/generated/docs/SpectrumAnnotation.md b/client-api_r/generated/docs/SpectrumAnnotation.md index 824bcd18..d9204f15 100644 --- a/client-api_r/generated/docs/SpectrumAnnotation.md +++ b/client-api_r/generated/docs/SpectrumAnnotation.md @@ -1,4 +1,4 @@ -# Rsirius::SpectrumAnnotation +# RSirius::SpectrumAnnotation ## Properties diff --git a/client-api_r/generated/docs/StatisticsTable.md b/client-api_r/generated/docs/StatisticsTable.md index d7f79e37..eba0c44a 100644 --- a/client-api_r/generated/docs/StatisticsTable.md +++ b/client-api_r/generated/docs/StatisticsTable.md @@ -1,4 +1,4 @@ -# Rsirius::StatisticsTable +# RSirius::StatisticsTable ## Properties diff --git a/client-api_r/generated/docs/StoredJobSubmission.md b/client-api_r/generated/docs/StoredJobSubmission.md index ba384520..7dbd76c2 100644 --- a/client-api_r/generated/docs/StoredJobSubmission.md +++ b/client-api_r/generated/docs/StoredJobSubmission.md @@ -1,4 +1,4 @@ -# Rsirius::StoredJobSubmission +# RSirius::StoredJobSubmission ## Properties diff --git a/client-api_r/generated/docs/StructureCandidate.md b/client-api_r/generated/docs/StructureCandidate.md index f6b9a89c..73d98164 100644 --- a/client-api_r/generated/docs/StructureCandidate.md +++ b/client-api_r/generated/docs/StructureCandidate.md @@ -1,4 +1,4 @@ -# Rsirius::StructureCandidate +# RSirius::StructureCandidate ## Properties diff --git a/client-api_r/generated/docs/StructureCandidateFormula.md b/client-api_r/generated/docs/StructureCandidateFormula.md index 8e7cb79d..9e7479ce 100644 --- a/client-api_r/generated/docs/StructureCandidateFormula.md +++ b/client-api_r/generated/docs/StructureCandidateFormula.md @@ -1,4 +1,4 @@ -# Rsirius::StructureCandidateFormula +# RSirius::StructureCandidateFormula ## Properties diff --git a/client-api_r/generated/docs/StructureCandidateScored.md b/client-api_r/generated/docs/StructureCandidateScored.md index 2b89c15f..cc326263 100644 --- a/client-api_r/generated/docs/StructureCandidateScored.md +++ b/client-api_r/generated/docs/StructureCandidateScored.md @@ -1,4 +1,4 @@ -# Rsirius::StructureCandidateScored +# RSirius::StructureCandidateScored ## Properties diff --git a/client-api_r/generated/docs/StructureDbSearch.md b/client-api_r/generated/docs/StructureDbSearch.md index bbc7c1d0..2079f80a 100644 --- a/client-api_r/generated/docs/StructureDbSearch.md +++ b/client-api_r/generated/docs/StructureDbSearch.md @@ -1,4 +1,4 @@ -# Rsirius::StructureDbSearch +# RSirius::StructureDbSearch User/developer friendly parameter subset for the CSI:FingerID structure db search tool. Needs results from FingerprintPrediction and Canopus Tool. Non-Null parameters in this Object well override their equivalent value in the config map. diff --git a/client-api_r/generated/docs/Subscription.md b/client-api_r/generated/docs/Subscription.md index 3fd709f8..08fd3a43 100644 --- a/client-api_r/generated/docs/Subscription.md +++ b/client-api_r/generated/docs/Subscription.md @@ -1,4 +1,4 @@ -# Rsirius::Subscription +# RSirius::Subscription ## Properties diff --git a/client-api_r/generated/docs/SubscriptionConsumables.md b/client-api_r/generated/docs/SubscriptionConsumables.md index b1f901f3..3ed86a90 100644 --- a/client-api_r/generated/docs/SubscriptionConsumables.md +++ b/client-api_r/generated/docs/SubscriptionConsumables.md @@ -1,4 +1,4 @@ -# Rsirius::SubscriptionConsumables +# RSirius::SubscriptionConsumables ## Properties diff --git a/client-api_r/generated/docs/Tag.md b/client-api_r/generated/docs/Tag.md index 04a4d77c..3f5b2698 100644 --- a/client-api_r/generated/docs/Tag.md +++ b/client-api_r/generated/docs/Tag.md @@ -1,4 +1,4 @@ -# Rsirius::Tag +# RSirius::Tag ## Properties diff --git a/client-api_r/generated/docs/TagDefinition.md b/client-api_r/generated/docs/TagDefinition.md index 90ee4d77..53ab3538 100644 --- a/client-api_r/generated/docs/TagDefinition.md +++ b/client-api_r/generated/docs/TagDefinition.md @@ -1,4 +1,4 @@ -# Rsirius::TagDefinition +# RSirius::TagDefinition ## Properties diff --git a/client-api_r/generated/docs/TagDefinitionImport.md b/client-api_r/generated/docs/TagDefinitionImport.md index 3ad7f31f..f7541234 100644 --- a/client-api_r/generated/docs/TagDefinitionImport.md +++ b/client-api_r/generated/docs/TagDefinitionImport.md @@ -1,4 +1,4 @@ -# Rsirius::TagDefinitionImport +# RSirius::TagDefinitionImport ## Properties diff --git a/client-api_r/generated/docs/TagGroup.md b/client-api_r/generated/docs/TagGroup.md index db797d6f..1554e828 100644 --- a/client-api_r/generated/docs/TagGroup.md +++ b/client-api_r/generated/docs/TagGroup.md @@ -1,4 +1,4 @@ -# Rsirius::TagGroup +# RSirius::TagGroup ## Properties diff --git a/client-api_r/generated/docs/TagsApi.md b/client-api_r/generated/docs/TagsApi.md index 909faa9e..1b86b8e3 100644 --- a/client-api_r/generated/docs/TagsApi.md +++ b/client-api_r/generated/docs/TagsApi.md @@ -24,7 +24,7 @@ Method | HTTP request | Description ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Group tags in the project # @@ -77,7 +77,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Add a possible value to the tag definition in the project # @@ -128,7 +128,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Add tags to the project # @@ -177,7 +177,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete tag groups with the given name from the specified project-space # @@ -223,7 +223,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Delete tag definition with the given name from the specified project-space # @@ -269,7 +269,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get tag group by name in the given project-space # @@ -318,7 +318,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all tag based groups in the given project-space # @@ -367,7 +367,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get tag definition by its name in the given project-space # @@ -416,7 +416,7 @@ No authorization required ### Example ```R -library(Rsirius) +library(RSirius) # [EXPERIMENTAL] Get all tag definitions in the given project-space # diff --git a/client-api_r/generated/docs/Term.md b/client-api_r/generated/docs/Term.md index 9f6622f6..06f3afa1 100644 --- a/client-api_r/generated/docs/Term.md +++ b/client-api_r/generated/docs/Term.md @@ -1,4 +1,4 @@ -# Rsirius::Term +# RSirius::Term ## Properties diff --git a/client-api_r/generated/docs/Timeout.md b/client-api_r/generated/docs/Timeout.md index fb197668..4b2cb499 100644 --- a/client-api_r/generated/docs/Timeout.md +++ b/client-api_r/generated/docs/Timeout.md @@ -1,4 +1,4 @@ -# Rsirius::Timeout +# RSirius::Timeout ## Properties diff --git a/client-api_r/generated/docs/TraceAnnotationExperimental.md b/client-api_r/generated/docs/TraceAnnotationExperimental.md index 55e04cf2..128cdca0 100644 --- a/client-api_r/generated/docs/TraceAnnotationExperimental.md +++ b/client-api_r/generated/docs/TraceAnnotationExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::TraceAnnotationExperimental +# RSirius::TraceAnnotationExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/TraceExperimental.md b/client-api_r/generated/docs/TraceExperimental.md index 707df5f1..e684d77a 100644 --- a/client-api_r/generated/docs/TraceExperimental.md +++ b/client-api_r/generated/docs/TraceExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::TraceExperimental +# RSirius::TraceExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/TraceSetExperimental.md b/client-api_r/generated/docs/TraceSetExperimental.md index e3dff252..19cc3cbf 100644 --- a/client-api_r/generated/docs/TraceSetExperimental.md +++ b/client-api_r/generated/docs/TraceSetExperimental.md @@ -1,4 +1,4 @@ -# Rsirius::TraceSetExperimental +# RSirius::TraceSetExperimental EXPERIMENTAL: This schema is experimental and may be changed (or even removed) without notice until it is declared stable. diff --git a/client-api_r/generated/docs/UseHeuristic.md b/client-api_r/generated/docs/UseHeuristic.md index dd9849d8..8d6a8100 100644 --- a/client-api_r/generated/docs/UseHeuristic.md +++ b/client-api_r/generated/docs/UseHeuristic.md @@ -1,4 +1,4 @@ -# Rsirius::UseHeuristic +# RSirius::UseHeuristic ## Properties diff --git a/client-api_r/generated/docs/WebServerNamespace.md b/client-api_r/generated/docs/WebServerNamespace.md index 003ec706..f9ed0afb 100644 --- a/client-api_r/generated/docs/WebServerNamespace.md +++ b/client-api_r/generated/docs/WebServerNamespace.md @@ -1,4 +1,4 @@ -# Rsirius::WebServerNamespace +# RSirius::WebServerNamespace ## Properties diff --git a/client-api_r/generated/docs/Zodiac.md b/client-api_r/generated/docs/Zodiac.md index 5b274c47..fba53929 100644 --- a/client-api_r/generated/docs/Zodiac.md +++ b/client-api_r/generated/docs/Zodiac.md @@ -1,4 +1,4 @@ -# Rsirius::Zodiac +# RSirius::Zodiac User/developer friendly parameter subset for the ZODIAC tool (Network base molecular formula re-ranking). Needs results from Formula/SIRIUS Tool diff --git a/client-api_r/generated/docs/ZodiacAnalogueNodes.md b/client-api_r/generated/docs/ZodiacAnalogueNodes.md index 5449a99f..5054bc2b 100644 --- a/client-api_r/generated/docs/ZodiacAnalogueNodes.md +++ b/client-api_r/generated/docs/ZodiacAnalogueNodes.md @@ -1,4 +1,4 @@ -# Rsirius::ZodiacAnalogueNodes +# RSirius::ZodiacAnalogueNodes ## Properties diff --git a/client-api_r/generated/docs/ZodiacEdgeFilterThresholds.md b/client-api_r/generated/docs/ZodiacEdgeFilterThresholds.md index ad0a7e55..006875e4 100644 --- a/client-api_r/generated/docs/ZodiacEdgeFilterThresholds.md +++ b/client-api_r/generated/docs/ZodiacEdgeFilterThresholds.md @@ -1,4 +1,4 @@ -# Rsirius::ZodiacEdgeFilterThresholds +# RSirius::ZodiacEdgeFilterThresholds ## Properties diff --git a/client-api_r/generated/docs/ZodiacEpochs.md b/client-api_r/generated/docs/ZodiacEpochs.md index 3d9ae04f..a0f46713 100644 --- a/client-api_r/generated/docs/ZodiacEpochs.md +++ b/client-api_r/generated/docs/ZodiacEpochs.md @@ -1,4 +1,4 @@ -# Rsirius::ZodiacEpochs +# RSirius::ZodiacEpochs ## Properties diff --git a/client-api_r/generated/docs/ZodiacLibraryScoring.md b/client-api_r/generated/docs/ZodiacLibraryScoring.md index 840c4b7c..f2ec41c3 100644 --- a/client-api_r/generated/docs/ZodiacLibraryScoring.md +++ b/client-api_r/generated/docs/ZodiacLibraryScoring.md @@ -1,4 +1,4 @@ -# Rsirius::ZodiacLibraryScoring +# RSirius::ZodiacLibraryScoring ## Properties diff --git a/client-api_r/generated/man/ActuatorApi.Rd b/client-api_r/generated/man/ActuatorApi.Rd index 0df45e5f..74c92417 100644 --- a/client-api_r/generated/man/ActuatorApi.Rd +++ b/client-api_r/generated/man/ActuatorApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### Health #################### -library(Rsirius) +library(RSirius) #Actuator web endpoint 'health' api_instance <- rsirius_api$new() @@ -35,7 +35,7 @@ dput(result) #################### Shutdown #################### -library(Rsirius) +library(RSirius) #Actuator web endpoint 'shutdown' api_instance <- rsirius_api$new() diff --git a/client-api_r/generated/man/CompoundStatisticsApi.Rd b/client-api_r/generated/man/CompoundStatisticsApi.Rd index 0309e8a2..b8ba6757 100644 --- a/client-api_r/generated/man/CompoundStatisticsApi.Rd +++ b/client-api_r/generated/man/CompoundStatisticsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### ComputeCompoundFoldChangesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to compute the fold change in. var_left_group_name <- "left_group_name_example" # character | name of the left tag group. var_right_group_name <- "right_group_name_example" # character | name of the right tag group. @@ -41,7 +41,7 @@ dput(result) #################### DeleteCompoundFoldChangesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_left_group_name <- "left_group_name_example" # character | name of the left group. var_right_group_name <- "right_group_name_example" # character | name of the right group. @@ -56,7 +56,7 @@ api_instance$compound_statistics_api$DeleteCompoundFoldChangesExperimental(var_p #################### GetCompoundFoldChangeTableExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aggregation <- "AVG" # character | aggregation type. (Optional) var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional) @@ -72,7 +72,7 @@ dput(result) #################### GetFoldChangesByCompoundExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to. diff --git a/client-api_r/generated/man/CompoundsApi.Rd b/client-api_r/generated/man/CompoundsApi.Rd index 95ae083d..257aa892 100644 --- a/client-api_r/generated/man/CompoundsApi.Rd +++ b/client-api_r/generated/man/CompoundsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### AddCompounds #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to import into. var_compound_import <- c(CompoundImport$new(c(FeatureImport$new(123, 123, "name_example", "externalFeatureId_example", c("detectedAdducts_example"), 123, 123, 123, "NOT_APPLICABLE", BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(..., ...)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)))), "name_example")) # array[CompoundImport] | the compound data to be imported var_profile <- "profile_example" # character | profile describing the instrument used to measure the data. Used to merge spectra. (Optional) @@ -40,7 +40,7 @@ dput(result) #################### AddTagsToCompoundExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to add tags to. var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -56,7 +56,7 @@ dput(result) #################### DeleteCompound #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_compound_id <- "compound_id_example" # character | identifier of the compound to delete. @@ -68,7 +68,7 @@ api_instance$compounds_api$DeleteCompound(var_project_id, var_compound_id) #################### GetCompound #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_compound_id <- "compound_id_example" # character | identifier of the compound (group of ion identities) to access. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -86,7 +86,7 @@ dput(result) #################### GetCompoundQuantTableExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) @@ -101,7 +101,7 @@ dput(result) #################### GetCompoundQuantTableRowExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_compound_id <- "compound_id_example" # character | compound which should be read out var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) @@ -117,7 +117,7 @@ dput(result) #################### GetCompoundTracesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_compound_id <- "compound_id_example" # character | compound which intensities should be read out var_feature_id <- "" # character | (Optional) @@ -133,7 +133,7 @@ dput(result) #################### GetCompounds #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -150,7 +150,7 @@ dput(result) #################### GetCompoundsByGroupExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_group_name <- "group_name_example" # character | tag group name. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -169,7 +169,7 @@ dput(result) #################### GetCompoundsByTagExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project space to get compounds (group of ion identities) from. var_filter <- "" # character | tag filter. (Optional) var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -188,7 +188,7 @@ dput(result) #################### GetCompoundsPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -208,7 +208,7 @@ dput(result) #################### GetTagsForCompoundExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to get from. var_object_id <- "object_id_example" # character | CompoundId to get tags for. @@ -223,7 +223,7 @@ dput(result) #################### RemoveTagFromCompoundExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_compound_id <- "compound_id_example" # character | compound (group of ion identities) to delete tag from. var_tag_name <- "tag_name_example" # character | name of the tag to delete. diff --git a/client-api_r/generated/man/FeatureStatisticsApi.Rd b/client-api_r/generated/man/FeatureStatisticsApi.Rd index 332af028..dfac66ae 100644 --- a/client-api_r/generated/man/FeatureStatisticsApi.Rd +++ b/client-api_r/generated/man/FeatureStatisticsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### ComputeAlignedFeatureFoldChangesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to compute the fold change in. var_left_group_name <- "left_group_name_example" # character | name of the left tag group. var_right_group_name <- "right_group_name_example" # character | name of the right tag group. @@ -41,7 +41,7 @@ dput(result) #################### DeleteAlignedFeatureFoldChangesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_left_group_name <- "left_group_name_example" # character | name of the left group. var_right_group_name <- "right_group_name_example" # character | name of the right group. @@ -56,7 +56,7 @@ api_instance$feature_statistics_api$DeleteAlignedFeatureFoldChangesExperimental( #################### GetAlignedFeatureFoldChangeTableExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aggregation <- "AVG" # character | aggregation type. (Optional) var_quantification <- "APEX_INTENSITY" # character | quantification type. (Optional) @@ -72,7 +72,7 @@ dput(result) #################### GetFoldChangesByAlignedFeatureExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_object_id <- "object_id_example" # character | id of the object the fold changes are assigned to. diff --git a/client-api_r/generated/man/FeaturesApi.Rd b/client-api_r/generated/man/FeaturesApi.Rd index 49494e6e..ac456ace 100644 --- a/client-api_r/generated/man/FeaturesApi.Rd +++ b/client-api_r/generated/man/FeaturesApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### AddAlignedFeatures #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to import into. var_feature_import <- c(FeatureImport$new(123, 123, "name_example", "externalFeatureId_example", c("detectedAdducts_example"), 123, 123, 123, "NOT_APPLICABLE", BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)), c(BasicSpectrum$new("cosineQuery_example", c(SimplePeak$new(123, 123)), "name_example", 123, "collisionEnergy_example", "instrument_example", 123, 123, SimplePeak$new(123, 123), 123, 123, 123, 123, 123)))) # array[FeatureImport] | the feature data to be imported var_profile <- "profile_example" # character | profile describing the instrument used to measure the data. Used to merge spectra. (Optional) @@ -39,7 +39,7 @@ dput(result) #################### AddDeNovoStructureCandidate #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_smiles <- "none" # character | smiles (Optional) @@ -55,7 +55,7 @@ dput(result) #################### AddTagsToAlignedFeatureExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_aligned_feature_id <- "aligned_feature_id_example" # character | run to add tags to. var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -71,7 +71,7 @@ dput(result) #################### DeleteAlignedFeature #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to delete. @@ -83,7 +83,7 @@ api_instance$features_api$DeleteAlignedFeature(var_project_id, var_aligned_featu #################### DeleteAlignedFeatures #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_request_body <- c("property_example") # array[character] | @@ -95,7 +95,7 @@ api_instance$features_api$DeleteAlignedFeatures(var_project_id, var_request_body #################### GetAdductNetworkWithMergedTracesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | one feature that is considered the main feature of the adduct network @@ -110,7 +110,7 @@ dput(result) #################### GetAlignedFeature #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to access. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -127,7 +127,7 @@ dput(result) #################### GetAlignedFeatureQualityExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | identifier of feature (aligned over runs) to access. @@ -142,7 +142,7 @@ dput(result) #################### GetAlignedFeatures #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -158,7 +158,7 @@ dput(result) #################### GetAlignedFeaturesByGroupExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_group_name <- "group_name_example" # character | tag group name. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -177,7 +177,7 @@ dput(result) #################### GetAlignedFeaturesByTagExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project space to get features (aligned over runs) from. var_filter <- "" # character | tag filter. (Optional) var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -196,7 +196,7 @@ dput(result) #################### GetAlignedFeaturesPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -215,7 +215,7 @@ dput(result) #################### GetBestMatchingCompoundClasses #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -231,7 +231,7 @@ dput(result) #################### GetCanopusPrediction #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -247,7 +247,7 @@ dput(result) #################### GetDeNovoStructureCandidates #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -263,7 +263,7 @@ dput(result) #################### GetDeNovoStructureCandidatesByFormula #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -280,7 +280,7 @@ dput(result) #################### GetDeNovoStructureCandidatesByFormulaPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -300,7 +300,7 @@ dput(result) #################### GetDeNovoStructureCandidatesPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -319,7 +319,7 @@ dput(result) #################### GetFeatureQuantTableExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_type <- "APEX_HEIGHT" # character | quantification type. (Optional) @@ -334,7 +334,7 @@ dput(result) #################### GetFingerprintPrediction #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -350,7 +350,7 @@ dput(result) #################### GetFormulaAnnotatedMsMsData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -367,7 +367,7 @@ dput(result) #################### GetFormulaAnnotatedSpectrum #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -385,7 +385,7 @@ dput(result) #################### GetFormulaCandidate #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -403,7 +403,7 @@ dput(result) #################### GetFormulaCandidates #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -420,7 +420,7 @@ dput(result) #################### GetFormulaCandidatesPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -440,7 +440,7 @@ dput(result) #################### GetFragTree #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -456,7 +456,7 @@ dput(result) #################### GetIsotopePatternAnnotation #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -472,7 +472,7 @@ dput(result) #################### GetLipidAnnotation #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -488,7 +488,7 @@ dput(result) #################### GetMsData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the Mass Spec data belongs to. var_ms_data_search_prepared <- FALSE # character | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (Optional) @@ -504,7 +504,7 @@ dput(result) #################### GetQuantTableRowExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which quantity should be read out var_type <- "APEX_HEIGHT" # character | quantification type. Currently, only APEX_HEIGHT is supported, which is the intensity of the feature at its apex. (Optional) @@ -520,7 +520,7 @@ dput(result) #################### GetSpectralLibraryMatch #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_match_id <- "match_id_example" # character | id of the library match to be returned. @@ -537,7 +537,7 @@ dput(result) #################### GetSpectralLibraryMatches #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_min_shared_peaks <- 1 # integer | (Optional) @@ -556,7 +556,7 @@ dput(result) #################### GetSpectralLibraryMatchesPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -578,7 +578,7 @@ dput(result) #################### GetSpectralLibraryMatchesSummary #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_min_shared_peaks <- 1 # integer | min threshold of shared peaks. (Optional) @@ -596,7 +596,7 @@ dput(result) #################### GetStructureAnnotatedMsDataExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -614,7 +614,7 @@ dput(result) #################### GetStructureAnnotatedSpectralLibraryMatchExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_match_id <- "match_id_example" # character | id of the library match to be returned. @@ -630,7 +630,7 @@ dput(result) #################### GetStructureAnnotatedSpectrumExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -649,7 +649,7 @@ dput(result) #################### GetStructureCandidates #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -665,7 +665,7 @@ dput(result) #################### GetStructureCandidatesByFormula #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -682,7 +682,7 @@ dput(result) #################### GetStructureCandidatesByFormulaPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the formula result belongs to. var_formula_id <- "formula_id_example" # character | identifier of the requested formula result @@ -702,7 +702,7 @@ dput(result) #################### GetStructureCandidatesPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) the structure candidates belong to. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -721,7 +721,7 @@ dput(result) #################### GetTagsForAlignedFeaturesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to get from. var_object_id <- "object_id_example" # character | object to get tags for. @@ -736,7 +736,7 @@ dput(result) #################### GetTracesExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature which intensities should be read out var_include_all <- FALSE # character | when true, return all samples that belong to the same merged trace. when false, only return samples which contain the aligned feature. (Optional) @@ -752,7 +752,7 @@ dput(result) #################### RemoveTagFromAlignedFeatureExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_aligned_feature_id <- "aligned_feature_id_example" # character | feature (aligned over runs) to delete tag from. var_tag_name <- "tag_name_example" # character | name of the tag to delete. diff --git a/client-api_r/generated/man/InfoApi.Rd b/client-api_r/generated/man/InfoApi.Rd index cf5d903a..b8077256 100644 --- a/client-api_r/generated/man/InfoApi.Rd +++ b/client-api_r/generated/man/InfoApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### GetConnectionCheck #################### -library(Rsirius) +library(RSirius) api_instance <- rsirius_api$new() @@ -34,7 +34,7 @@ dput(result) #################### GetInfo #################### -library(Rsirius) +library(RSirius) var_server_info <- TRUE # character | (Optional) var_update_info <- TRUE # character | (Optional) diff --git a/client-api_r/generated/man/JobsApi.Rd b/client-api_r/generated/man/JobsApi.Rd index 26854f57..b49e2386 100644 --- a/client-api_r/generated/man/JobsApi.Rd +++ b/client-api_r/generated/man/JobsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### DeleteJob #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete job from var_job_id <- "job_id_example" # character | of the job to be deleted var_cancel_if_running <- TRUE # character | If true, job will be canceled if it is not finished. Otherwise, deletion will fail for running jobs or request will block until job has finished. (Optional) @@ -36,7 +36,7 @@ api_instance$jobs_api$DeleteJob(var_project_id, var_job_id, cancel_if_running = #################### DeleteJobConfig #################### -library(Rsirius) +library(RSirius) var_name <- "name_example" # character | name of the job-config to delete #Delete job configuration with given name. @@ -47,7 +47,7 @@ api_instance$jobs_api$DeleteJobConfig(var_name) #################### DeleteJobs #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete jobs from var_cancel_if_running <- TRUE # character | If true, job will be canceled if it is not finished. Otherwise, deletion will fail for running jobs or request will block until job has finished. (Optional) var_await_deletion <- TRUE # character | If true, request will block until deletion succeeded or failed. If the job is still running the request will wait until the job has finished. (Optional) @@ -60,7 +60,7 @@ api_instance$jobs_api$DeleteJobs(var_project_id, cancel_if_running = var_cancel_ #################### GetCommand #################### -library(Rsirius) +library(RSirius) var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | #Get a CLI command for the given job configuration. @@ -74,7 +74,7 @@ dput(result) #################### GetDefaultJobConfig #################### -library(Rsirius) +library(RSirius) var_include_config_map <- FALSE # character | if true, generic configmap with-defaults will be included (Optional) var_move_parameters_to_config_map <- FALSE # character | if true, object-based parameters will be converted to and added to the generic configMap parameters (Optional) var_include_custom_dbs_for_structure_search <- FALSE # character | if true, default database selection of structure db search spectral library search contains also all available custom DB. If No custom dbs are selected, spectral library search is disabled by default. (Optional) @@ -90,7 +90,7 @@ dput(result) #################### GetJob #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to run jobs on var_job_id <- "job_id_example" # character | of the job to be returned var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -106,7 +106,7 @@ dput(result) #################### GetJobConfig #################### -library(Rsirius) +library(RSirius) var_name <- "name_example" # character | name of the job-config to return var_move_parameters_to_config_map <- FALSE # character | if true, object-based parameters will be converted to and added to the generic configMap parameters (Optional) @@ -121,7 +121,7 @@ dput(result) #################### GetJobConfigNames #################### -library(Rsirius) +library(RSirius) #[DEPRECATED] Get all (non-default) job configuration names api_instance <- rsirius_api$new() @@ -134,7 +134,7 @@ dput(result) #################### GetJobConfigs #################### -library(Rsirius) +library(RSirius) #Request all available job configurations api_instance <- rsirius_api$new() @@ -147,7 +147,7 @@ dput(result) #################### GetJobs #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to run jobs on var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -162,7 +162,7 @@ dput(result) #################### GetJobsPaged #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to run jobs on var_page <- 0 # integer | Zero-based page index (0..N) (Optional) var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -180,7 +180,7 @@ dput(result) #################### HasJobs #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | var_include_finished <- FALSE # character | (Optional) @@ -194,7 +194,7 @@ dput(result) #################### SaveJobConfig #################### -library(Rsirius) +library(RSirius) var_name <- "name_example" # character | name of the job-config to add var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | to add var_override_existing <- FALSE # character | (Optional) @@ -211,7 +211,7 @@ dput(result) #################### StartJob #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to run jobs on var_job_submission <- JobSubmission$new(c("compoundIds_example"), c("alignedFeatureIds_example"), c("fallbackAdducts_example"), c("enforcedAdducts_example"), c("detectableAdducts_example"), "recompute_example", SpectralLibrarySearch$new("enabled_example", c("spectraSearchDBs_example"), 123, 123, 123, "enableAnalogueSearch_example", 123, 123, "INTENSITY", 123), Sirius$new("enabled_example", "QTOF", 123, 123, 123, "IGNORE", "filterByIsotopePattern_example", "enforceElGordoFormula_example", "performBottomUpSearch_example", 123, c("formulaSearchDBs_example"), "applyFormulaConstraintsToDBAndBottomUpSearch_example", "enforcedFormulaConstraints_example", "fallbackFormulaConstraints_example", c("detectableElements_example"), Timeout$new(123, 123), UseHeuristic$new(123, 123), "injectSpecLibMatchFormulas_example", 123, 123), Zodiac$new("enabled_example", 123, 123, "runInTwoSteps_example", ZodiacEdgeFilterThresholds$new(123, 123, 123), ZodiacEpochs$new(123, 123, 123), ZodiacLibraryScoring$new("enabled_example", 123), ZodiacAnalogueNodes$new("enabled_example", 123, 123)), FingerprintPrediction$new("enabled_example", "useScoreThreshold_example", "alwaysPredictHighRefMatches_example"), Canopus$new("enabled_example"), StructureDbSearch$new("enabled_example", c("structureSearchDBs_example"), "tagStructuresWithLipidClass_example", "OFF"), MsNovelist$new("enabled_example", 123), c(key = "inner_example")) # JobSubmission | configuration of the job that will be submitted of the job to be returned var_opt_fields <- c("none") # array[character] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -227,7 +227,7 @@ dput(result) #################### StartJobFromConfig #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to run jobs on var_job_config_name <- "job_config_name_example" # character | name if the config to be used var_request_body <- c("property_example") # array[character] | List of alignedFeatureIds to be computed diff --git a/client-api_r/generated/man/LoginAndAccountApi.Rd b/client-api_r/generated/man/LoginAndAccountApi.Rd index 4b9754ca..42de63a8 100644 --- a/client-api_r/generated/man/LoginAndAccountApi.Rd +++ b/client-api_r/generated/man/LoginAndAccountApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### GetAccountInfo #################### -library(Rsirius) +library(RSirius) var_include_subs <- FALSE # character | include available and active subscriptions in {@link AccountInfo AccountInfo}. (Optional) #Get information about the account currently logged in. @@ -36,7 +36,7 @@ dput(result) #################### GetSignUpURL #################### -library(Rsirius) +library(RSirius) #Get SignUp URL (For signUp via web browser) api_instance <- rsirius_api$new() @@ -49,7 +49,7 @@ dput(result) #################### GetSubscriptions #################### -library(Rsirius) +library(RSirius) #Get available subscriptions of the account currently logged in. api_instance <- rsirius_api$new() @@ -62,7 +62,7 @@ dput(result) #################### IsLoggedIn #################### -library(Rsirius) +library(RSirius) #Check if a user is logged in. api_instance <- rsirius_api$new() @@ -75,7 +75,7 @@ dput(result) #################### Login #################### -library(Rsirius) +library(RSirius) var_accept_terms <- "accept_terms_example" # character | var_account_credentials <- AccountCredentials$new("username_example", "password_example", "refreshToken_example") # AccountCredentials | used to log in. var_fail_when_logged_in <- FALSE # character | if true request fails if an active login already exists. (Optional) @@ -92,7 +92,7 @@ dput(result) #################### Logout #################### -library(Rsirius) +library(RSirius) #Logout from SIRIUS web services. api_instance <- rsirius_api$new() @@ -102,7 +102,7 @@ api_instance$login_and_account_api$Logout() #################### OpenPortal #################### -library(Rsirius) +library(RSirius) #Open User portal in browser. api_instance <- rsirius_api$new() @@ -112,7 +112,7 @@ api_instance$login_and_account_api$OpenPortal() #################### SelectSubscription #################### -library(Rsirius) +library(RSirius) var_sid <- "sid_example" # character | #Select a subscription as active subscription to be used for computations. @@ -126,7 +126,7 @@ dput(result) #################### SignUp #################### -library(Rsirius) +library(RSirius) #Open SignUp window in system browser and return signUp link. api_instance <- rsirius_api$new() diff --git a/client-api_r/generated/man/ProjectsApi.Rd b/client-api_r/generated/man/ProjectsApi.Rd index 54ea31de..e18d8977 100644 --- a/client-api_r/generated/man/ProjectsApi.Rd +++ b/client-api_r/generated/man/ProjectsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### CloseProject #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | unique name/identifier of the project-space to be closed. var_compact <- FALSE # character | if true, compact project storage after closing. DEPRECATED: Compacting acts on the local filesystem and will likely be removed in a later version. (Optional) @@ -34,7 +34,7 @@ api_instance$projects_api$CloseProject(var_project_id, compact = var_compact) #################### CreateProject #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | unique name/identifier that shall be used to access the newly created project-space. Must consist only of [a-zA-Z0-9_-]. var_path_to_project <- "path_to_project_example" # character | local file path where the project will be created. If NULL, project will be stored by its projectId in default project location. DEPRECATED: This parameter relies on the local filesystem and will likely be removed in later versions of this API to allow for more flexible use cases. (Optional) var_opt_fields <- c("none") # array[character] | (Optional) @@ -50,7 +50,7 @@ dput(result) #################### GetCanopusClassyFireData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | var_charge <- 56 # integer | @@ -65,7 +65,7 @@ dput(result) #################### GetCanopusNpcData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | var_charge <- 56 # integer | @@ -80,7 +80,7 @@ dput(result) #################### GetFingerIdData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | var_charge <- 56 # integer | @@ -95,7 +95,7 @@ dput(result) #################### GetProject #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | unique name/identifier tof the project-space to be accessed. var_opt_fields <- c("none") # array[character] | (Optional) @@ -110,7 +110,7 @@ dput(result) #################### GetProjects #################### -library(Rsirius) +library(RSirius) #List opened project spaces. api_instance <- rsirius_api$new() @@ -123,7 +123,7 @@ dput(result) #################### ImportMsRunData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | Project-space to import into. var_input_files <- c(123) # array[data.frame] | Files to import into project. var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters | @@ -139,7 +139,7 @@ dput(result) #################### ImportMsRunDataAsJob #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | Project-space to import into. var_input_files <- c(123) # array[data.frame] | Files to import into project. var_parameters <- LcmsSubmissionParameters$new("alignLCMSRuns_example", 123, Deviation$new(123, 123), Deviation$new(123, 123), 123, 123) # LcmsSubmissionParameters | @@ -156,7 +156,7 @@ dput(result) #################### ImportPreprocessedData #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to import into. var_input_files <- c(123) # array[data.frame] | files to import into project var_ignore_formulas <- FALSE # character | (Optional) @@ -173,7 +173,7 @@ dput(result) #################### ImportPreprocessedDataAsJob #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to import into. var_input_files <- c(123) # array[data.frame] | var_ignore_formulas <- FALSE # character | (Optional) @@ -191,7 +191,7 @@ dput(result) #################### OpenProject #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | unique name/identifier that shall be used to access the opened project-space. Must consist only of [a-zA-Z0-9_-]. var_path_to_project <- "path_to_project_example" # character | local file path to open the project from. If NULL, project will be loaded by it projectId from default project location. DEPRECATED: This parameter relies on the local filesystem and will likely be removed in later versions of this API to allow for more flexible use cases. (Optional) var_opt_fields <- c("none") # array[character] | (Optional) diff --git a/client-api_r/generated/man/RunsApi.Rd b/client-api_r/generated/man/RunsApi.Rd index fc33d241..8dc4e3cc 100644 --- a/client-api_r/generated/man/RunsApi.Rd +++ b/client-api_r/generated/man/RunsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### AddTagsToRunExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_run_id <- "run_id_example" # character | run to add tags to. var_tag <- c(Tag$new("tagName_example", 123)) # array[Tag] | tags to add. @@ -38,7 +38,7 @@ dput(result) #################### ComputeFoldChangeForBlankSubtraction #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to compute the fold change in. var_sample_type_fold_change_request <- SampleTypeFoldChangeRequest$new(c("sampleRunIds_example"), c("blankRunIds_example"), c("controlRunIds_example")) # SampleTypeFoldChangeRequest | request with lists of run IDs that are sample, blank, and control runs var_opt_fields <- c("none") # array[character] | job opt fields. (Optional) @@ -54,7 +54,7 @@ dput(result) #################### GetRunExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_run_id <- "run_id_example" # character | identifier of run to access. var_opt_fields <- c(RunOptField$new()) # array[RunOptField] | set of optional fields to be included. Use 'none' only to override defaults. (Optional) @@ -70,7 +70,7 @@ dput(result) #################### GetRunPageExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) var_size <- 20 # integer | The size of the page to be returned (Optional) @@ -88,7 +88,7 @@ dput(result) #################### GetRunsByGroupExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_group_name <- "group_name_example" # character | tag group name. var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -107,7 +107,7 @@ dput(result) #################### GetRunsByTagExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project space to get runs from. var_filter <- "" # character | tag filter. (Optional) var_page <- 0 # integer | Zero-based page index (0..N) (Optional) @@ -126,7 +126,7 @@ dput(result) #################### GetTagsForRunExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to get from. var_object_id <- "object_id_example" # character | RunId to get tags for. @@ -141,7 +141,7 @@ dput(result) #################### RemoveTagFromRunExperimental #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_run_id <- "run_id_example" # character | run to delete tag from. var_tag_name <- "tag_name_example" # character | name of the tag to delete. diff --git a/client-api_r/generated/man/SearchableDatabasesApi.Rd b/client-api_r/generated/man/SearchableDatabasesApi.Rd index 100cf110..904c3979 100644 --- a/client-api_r/generated/man/SearchableDatabasesApi.Rd +++ b/client-api_r/generated/man/SearchableDatabasesApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### AddDatabases #################### -library(Rsirius) +library(RSirius) var_request_body <- c("property_example") # array[character] | #DEPRECATED: this endpoint is based on local file paths and will likely be replaced in future versions of this API. @@ -36,7 +36,7 @@ dput(result) #################### CreateDatabase #################### -library(Rsirius) +library(RSirius) var_database_id <- "database_id_example" # character | var_searchable_database_parameters <- SearchableDatabaseParameters$new("displayName_example", "location_example", "matchRtOfReferenceSpectra_example") # SearchableDatabaseParameters | (Optional) @@ -50,7 +50,7 @@ dput(result) #################### GetCustomDatabases #################### -library(Rsirius) +library(RSirius) var_include_stats <- FALSE # character | (Optional) var_include_with_errors <- FALSE # character | (Optional) @@ -64,7 +64,7 @@ dput(result) #################### GetDatabase #################### -library(Rsirius) +library(RSirius) var_database_id <- "database_id_example" # character | var_include_stats <- TRUE # character | (Optional) @@ -78,7 +78,7 @@ dput(result) #################### GetDatabases #################### -library(Rsirius) +library(RSirius) var_include_stats <- FALSE # character | (Optional) var_include_with_errors <- FALSE # character | (Optional) @@ -92,7 +92,7 @@ dput(result) #################### GetIncludedDatabases #################### -library(Rsirius) +library(RSirius) var_include_stats <- FALSE # character | (Optional) api_instance <- rsirius_api$new() @@ -105,7 +105,7 @@ dput(result) #################### ImportIntoDatabase #################### -library(Rsirius) +library(RSirius) var_database_id <- "database_id_example" # character | database to import into var_input_files <- c(123) # array[data.frame] | files to be imported var_buffer_size <- 1000 # integer | (Optional) @@ -122,7 +122,7 @@ dput(result) #################### RemoveDatabase #################### -library(Rsirius) +library(RSirius) var_database_id <- "database_id_example" # character | var_delete <- FALSE # character | (Optional) @@ -133,7 +133,7 @@ api_instance$searchable_databases_api$RemoveDatabase(var_database_id, delete = v #################### UpdateDatabase #################### -library(Rsirius) +library(RSirius) var_database_id <- "database_id_example" # character | var_searchable_database_parameters <- SearchableDatabaseParameters$new("displayName_example", "location_example", "matchRtOfReferenceSpectra_example") # SearchableDatabaseParameters | (Optional) diff --git a/client-api_r/generated/man/TagsApi.Rd b/client-api_r/generated/man/TagsApi.Rd index 9d00cea2..b7914703 100644 --- a/client-api_r/generated/man/TagsApi.Rd +++ b/client-api_r/generated/man/TagsApi.Rd @@ -22,7 +22,7 @@ Generated by: https://openapi-generator.tech \dontrun{ #################### AddGroup #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_group_name <- "group_name_example" # character | name of the new group var_filter <- "filter_example" # character | filter query to create the group @@ -39,7 +39,7 @@ dput(result) #################### AddPossibleValuesToTagDefinition #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_tag_name <- "tag_name_example" # character | the tag definition to add the values to var_request_body <- c(123) # array[object] | @@ -55,7 +55,7 @@ dput(result) #################### CreateTags #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to add to. var_tag_definition_import <- c(TagDefinitionImport$new("tagName_example", "NONE", "description_example", "tagType_example", c(123), 123, 123)) # array[TagDefinitionImport] | the tag definitions to be created @@ -70,7 +70,7 @@ dput(result) #################### DeleteGroup #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_group_name <- "group_name_example" # character | name of group to delete. @@ -82,7 +82,7 @@ api_instance$tags_api$DeleteGroup(var_project_id, var_group_name) #################### DeleteTag #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to delete from. var_tag_name <- "tag_name_example" # character | name of the tag definition to delete. @@ -94,7 +94,7 @@ api_instance$tags_api$DeleteTag(var_project_id, var_tag_name) #################### GetGroupByName #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_group_name <- "group_name_example" # character | name of the group @@ -109,7 +109,7 @@ dput(result) #################### GetGroups #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_group_type <- "group_type_example" # character | type of the group (Optional) @@ -124,7 +124,7 @@ dput(result) #################### GetTag #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_tag_name <- "tag_name_example" # character | name of the tag @@ -139,7 +139,7 @@ dput(result) #################### GetTags #################### -library(Rsirius) +library(RSirius) var_project_id <- "project_id_example" # character | project-space to read from. var_tag_type <- "tag_type_example" # character | scope of the tag (optional) (Optional) diff --git a/client-api_r/generated/man/rsirius_api.Rd b/client-api_r/generated/man/rsirius_api.Rd index 9f838a18..10d0e0a7 100644 --- a/client-api_r/generated/man/rsirius_api.Rd +++ b/client-api_r/generated/man/rsirius_api.Rd @@ -18,9 +18,9 @@ REST API that provides the full functionality of SIRIUS and its web services as The version of the OpenAPI document: 3.1 Generated by: https://openapi-generator.tech -Rsirius API Class +RSirius API Class -A single point of access to the Rsirius API. +A single point of access to the RSirius API. NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech). Ref: https://openapi-generator.tech @@ -68,7 +68,7 @@ Do not edit the class manually. \if{html}{\out{}} \if{latex}{\out{\hypertarget{method-rsirius_api-new}{}}} \subsection{Method \code{new()}}{ -Initialize a new Rsirius API Class. +Initialize a new RSirius API Class. \subsection{Usage}{ \if{html}{\out{

}}\preformatted{rsirius_api$new(api_client)}\if{html}{\out{
}} }