Merge pull request #1065 from OHDSI/develop

Release 3.2.3
OHDSI · Jul 20, 2023 · 73120fe · 73120fe
2 parents ea6b5f8 + 777f68a
commit 73120fe
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 3.2.2
+Version: 3.2.3
 Date: 2022-12-19
 Authors@R: c(
     person("Jamie", "Gilbert", email = "[email protected]", role = c("aut", "cre")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+CohortDiagnostics 3.2.3
+=======================
+
+1. Resolved issue where concept sets were only exported when diagnostics for them were executed. All concept sets are
+now always exported into results csv and imported into databases
+
 CohortDiagnostics 3.2.2
 =======================
 

diff --git a/R/ConceptSets.R b/R/ConceptSets.R
@@ -325,6 +325,29 @@ getCodeSetIds <- function(criterionList) {
   }
 }
 
+exportConceptSets <- function(cohortDefinitionSet, exportFolder, minCellCount, databaseId) {
+  ParallelLogger::logInfo("Exporting cohort concept sets to csv")
+  # We need to get concept sets from all cohorts in case subsets are present and
+  # Added incrementally after cohort generation
+  conceptSets <- combineConceptSetsFromCohorts(cohortDefinitionSet)
+  # Save concept set metadata ---------------------------------------
+  conceptSetsExport <- makeDataExportable(
+    x = conceptSets %>%
+      dplyr::select(-uniqueConceptSetId) %>%
+      dplyr::distinct(),
+    tableName = "concept_sets",
+    minCellCount = minCellCount,
+    databaseId = databaseId
+  )
+
+  # Always write all concept sets for all cohorts as they are always needed
+  writeToCsv(
+    data = conceptSetsExport,
+    fileName = file.path(exportFolder, "concept_sets.csv"),
+    incremental = FALSE,
+    cohortId = conceptSetsExport$cohortId
+  )
+}
 
 runConceptSetDiagnostics <- function(connection,
                                      tempEmulationSchema,
@@ -395,22 +418,6 @@ runConceptSetDiagnostics <- function(connection,
     )
     return(NULL)
   }
-  # Save concept set metadata ---------------------------------------
-  conceptSetsExport <- makeDataExportable(
-    x = conceptSets %>%
-      dplyr::select(-uniqueConceptSetId) %>%
-      dplyr::distinct(),
-    tableName = "concept_sets",
-    minCellCount = minCellCount,
-    databaseId = databaseId
-  )
-
-  writeToCsv(
-    data = conceptSetsExport,
-    fileName = file.path(exportFolder, "concept_sets.csv"),
-    incremental = incremental,
-    cohortId = conceptSetsExport$cohortId
-  )
 
   uniqueConceptSets <-
     conceptSets[!duplicated(conceptSets$uniqueConceptSetId), ] %>%

diff --git a/R/RunDiagnostics.R b/R/RunDiagnostics.R
@@ -670,6 +670,14 @@ executeDiagnostics <- function(cohortDefinitionSet,
     )
   }
 
+  # Always export concept sets to csv
+  exportConceptSets(
+    cohortDefinitionSet = cohortDefinitionSet,
+    exportFolder = exportFolder,
+    minCellCount = minCellCount,
+    databaseId = databaseId
+  )
+
   # Concept set diagnostics -----------------------------------------------
   if (runIncludedSourceConcepts ||
     runOrphanConcepts ||

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html
diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html
diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html
diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html
diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -7,5 +7,5 @@ articles:
   RunningCohortDiagnostics: RunningCohortDiagnostics.html
   ViewingResultsUsingDiagnosticsExplorer: ViewingResultsUsingDiagnosticsExplorer.html
   WhatIsCohortDiagnostics: WhatIsCohortDiagnostics.html
-last_built: 2023-05-16T17:32Z
+last_built: 2023-07-20T14:57Z
 
diff --git a/docs/reference/CohortDiagnostics-package.html b/docs/reference/CohortDiagnostics-package.html
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html
diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html
diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html
diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html
diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html
diff --git a/docs/reference/getCdmDataSourceInformation.html b/docs/reference/getCdmDataSourceInformation.html
diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html
diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html
diff --git a/docs/reference/getDefaultCovariateSettings.html b/docs/reference/getDefaultCovariateSettings.html
diff --git a/docs/reference/getDefaultVocabularyTableNames.html b/docs/reference/getDefaultVocabularyTableNames.html
diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html
diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html
diff --git a/docs/reference/runCohortRelationshipDiagnostics.html b/docs/reference/runCohortRelationshipDiagnostics.html
diff --git a/docs/reference/runCohortTimeSeriesDiagnostics.html b/docs/reference/runCohortTimeSeriesDiagnostics.html