Merge branch 'v1.0-main' into results-data-model

OHDSI · Sep 30, 2024 · 79c4e58 · 79c4e58
2 parents 44c51e3 + 45223f6
commit 79c4e58
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Showing 7 changed files with 415 additions and 134 deletions.
diff --git a/R/Execution.R b/R/Execution.R
@@ -80,6 +80,61 @@ execute <- function(analysisSpecifications,
     }
   }
 
+  # Determine if the user has opted to subset to specific modules
+  # in the analysis specification. If so, validate that the
+  # modulesToExecute are present in the analysis specification
+  # before attempting to subset the analyses to run.
+  if (length(executionSettings$modulesToExecute) > 0) {
+    # Get the modules in the analysis specification with their
+    # index in the array
+    modulesWithIndex <- lapply(
+      X = seq_along(analysisSpecifications$moduleSpecifications),
+      FUN = function(i) {
+        list(
+          idx = i,
+          module = analysisSpecifications$moduleSpecifications[[i]]$module
+        )
+      }
+    )
+    modulesInAnalysisSpecification <- sapply(
+      X = modulesWithIndex,
+      FUN = function(x) {
+        x$module
+      }
+    )
+
+    modulesToExecuteString <- paste(executionSettings$modulesToExecute, collapse = ", ")
+    modulesInAnalysisSpecificationString <- paste(modulesInAnalysisSpecification, collapse = ", ")
+
+    # Stop if we cannot find all of the requested modules
+    # to execute in the overall analysis specification
+    if(!all(tolower(executionSettings$modulesToExecute) %in% tolower(modulesInAnalysisSpecification))) {
+      errorMsg <- paste0(
+        "The executionSettings specified to run only the modules: ",
+        modulesToExecuteString,
+        ".\n However the analysis specification includes the following modules: ",
+        modulesInAnalysisSpecificationString
+      )
+      stop(errorMsg)
+    }
+
+    # Subset the analysis specifications to those modules
+    # specified by the user
+    cli::cli_alert_info(paste0("Runnning a subset of modules: ", modulesToExecuteString))
+    moduleSubset <- unlist(
+      lapply(
+        X = modulesWithIndex,
+        FUN = function(x) {
+          if (tolower(x$module) %in% tolower(executionSettings$modulesToExecute)) {
+            return(x$idx)
+          }
+        }
+      )
+    )
+    analysisSpecifications$moduleSpecifications <- analysisSpecifications$moduleSpecifications[moduleSubset]
+  }
+
+
   # Set up logging
   if (!dir.exists(dirname(executionSettings$logFileName))) {
     dir.create(dirname(executionSettings$logFileName), recursive = T)

diff --git a/R/Settings.R b/R/Settings.R
@@ -258,6 +258,8 @@ createEmptyAnalysisSpecificiations <- function() {
 #'                                   and attempt to pick up where they left off when this value is set to TRUE.
 #' @param maxCores                   The maximum number of processing cores to use for execution. The default is to
 #'                                   use all available cores on the machine.
+#' @param modulesToExecute           (Optional) A vector with the list of modules to execute. When an empty vector/NULL is supplied (default),
+#'                                   all modules in the analysis specification are executed.
 #'
 #' @return
 #' An object of type `ExecutionSettings`.
@@ -272,7 +274,8 @@ createCdmExecutionSettings <- function(workDatabaseSchema,
                                        logFileName = file.path(resultsFolder, "strategus-log.txt"),
                                        minCellCount = 5,
                                        incremental = TRUE,
-                                       maxCores = parallel::detectCores()) {
+                                       maxCores = parallel::detectCores(),
+                                       modulesToExecute = c()) {
   errorMessages <- checkmate::makeAssertCollection()
   checkmate::assertCharacter(workDatabaseSchema, len = 1, add = errorMessages)
   checkmate::assertCharacter(cdmDatabaseSchema, len = 1, add = errorMessages)
@@ -283,6 +286,7 @@ createCdmExecutionSettings <- function(workDatabaseSchema,
   checkmate::assertInt(minCellCount, add = errorMessages)
   checkmate::assertLogical(incremental, add = errorMessages)
   checkmate::assertInt(maxCores, add = errorMessages)
+  checkmate::assertVector(modulesToExecute, null.ok = TRUE, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
 
   # Normalize paths to convert relative paths to absolute paths
@@ -308,6 +312,9 @@ createCdmExecutionSettings <- function(workDatabaseSchema,
 #'                                   in results.
 #' @param maxCores                   The maximum number of processing cores to use for execution. The default is to
 #'                                   use all available cores on the machine.
+#' @param modulesToExecute           (Optional) A vector with the list of modules to execute. When an empty vector/NULL is supplied (default),
+#'                                   all modules in the analysis specification are executed.
+#'
 #' @return
 #' An object of type `ExecutionSettings`.
 #'
@@ -317,14 +324,16 @@ createResultsExecutionSettings <- function(resultsDatabaseSchema,
                                            resultsFolder,
                                            logFileName = file.path(resultsFolder, "strategus-log.txt"),
                                            minCellCount = 5,
-                                           maxCores = parallel::detectCores()) {
+                                           maxCores = parallel::detectCores(),
+                                           modulesToExecute = c()) {
   errorMessages <- checkmate::makeAssertCollection()
   checkmate::assertCharacter(resultsDatabaseSchema, len = 1, add = errorMessages)
   checkmate::assertCharacter(workFolder, len = 1, add = errorMessages)
   checkmate::assertCharacter(resultsFolder, len = 1, add = errorMessages)
   checkmate::assertCharacter(logFileName, len = 1, add = errorMessages)
   checkmate::assertInt(minCellCount, add = errorMessages)
   checkmate::assertInt(maxCores, add = errorMessages)
+  checkmate::assertVector(modulesToExecute, null.ok = TRUE, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
 
   # Normalize paths to convert relative paths to absolute paths

diff --git a/extras/PackageMaintenance.R b/extras/PackageMaintenance.R
@@ -116,8 +116,7 @@ cdModuleSpecifications <- cdModuleSettingsCreator$createModuleSpecifications(
   runBreakdownIndexEvents = TRUE,
   runIncidenceRate = TRUE,
   runCohortRelationship = TRUE,
-  runTemporalCohortCharacterization = TRUE,
-  incremental = FALSE
+  runTemporalCohortCharacterization = TRUE
 )
 
 # Cohort Generator -----------------
@@ -448,9 +447,8 @@ cdmModulesAnalysisSpecifications <- createEmptyAnalysisSpecificiations() |>
   addCharacterizationModuleSpecifications(cModuleSpecifications) |>
   addCohortDiagnosticsModuleSpecifications(cdModuleSpecifications) |>
   addCohortGeneratorModuleSpecifications(cgModuleSpecifications) |>
-  #addCohortIncidenceModuleSpecifications(ciModuleSpecifications) |>
+  addCohortIncidenceModuleSpecifications(ciModuleSpecifications) |>
   addCohortMethodeModuleSpecifications(cmModuleSpecifications) |>
-  #addEvidenceSynthesisModuleSpecifications(evidenceSynthesisAnalysisSpecifications) |>
   addSelfControlledCaseSeriesModuleSpecifications(sccsModuleSpecifications) |>
   addPatientLevelPredictionModuleSpecifications(plpModuleSpecifications)