diff --git a/DESCRIPTION b/DESCRIPTION index e96c03e3c..c796cd682 100644 --- 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 = "gilbert@ohdsi.org", role = c("aut", "cre")), diff --git a/NEWS.md b/NEWS.md index ee210c5f8..e08c568b7 100644 --- 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 index 5fccc4d65..141a1e89c 100644 --- 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 index 8ebc11f53..6c7d9a483 100644 --- 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 index 2bd101099..f6686940d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/articles/CreatingAStudyPackage.html b/docs/articles/CreatingAStudyPackage.html index 7b55265a0..ed3ad29f6 100644 --- a/docs/articles/CreatingAStudyPackage.html +++ b/docs/articles/CreatingAStudyPackage.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -97,7 +97,7 @@

Creating a study package

Gowtham A. Rao

-

2023-05-16

+

2023-07-20

Source: vignettes/CreatingAStudyPackage.Rmd diff --git a/docs/articles/DatabaseModeInDiagnosticsExplorer.html b/docs/articles/DatabaseModeInDiagnosticsExplorer.html index e0607d13d..304db91eb 100644 --- a/docs/articles/DatabaseModeInDiagnosticsExplorer.html +++ b/docs/articles/DatabaseModeInDiagnosticsExplorer.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -97,7 +97,7 @@

Database mode in Diagnostics Explorer

Gowtham Rao

-

2023-05-16

+

2023-07-20

Source: vignettes/DatabaseModeInDiagnosticsExplorer.Rmd diff --git a/docs/articles/RunningCohortDiagnostics.html b/docs/articles/RunningCohortDiagnostics.html index 00543f3bd..8dabd7b81 100644 --- a/docs/articles/RunningCohortDiagnostics.html +++ b/docs/articles/RunningCohortDiagnostics.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -97,7 +97,7 @@

Running Cohort Diagnostics

Gowtham Rao and James P. Gilbert

-

2023-05-16

+

2023-07-20

Source: vignettes/RunningCohortDiagnostics.Rmd diff --git a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html index c892369ba..3a8a6831a 100644 --- a/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html +++ b/docs/articles/ViewingResultsUsingDiagnosticsExplorer.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -97,7 +97,7 @@

Viewing results using Diagnostics Explorer

Gowtham Rao

-

2023-05-16

+

2023-07-20

Source: vignettes/ViewingResultsUsingDiagnosticsExplorer.Rmd diff --git a/docs/articles/WhatIsCohortDiagnostics.html b/docs/articles/WhatIsCohortDiagnostics.html index 8fcb2a370..c046b6203 100644 --- a/docs/articles/WhatIsCohortDiagnostics.html +++ b/docs/articles/WhatIsCohortDiagnostics.html @@ -33,7 +33,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -97,7 +97,7 @@

What is Cohort Diagnostics?

Gowtham Rao

-

2023-05-16

+

2023-07-20

Source: vignettes/WhatIsCohortDiagnostics.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 8a7bae0fc..0e118f7d0 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/authors.html b/docs/authors.html index d7305286b..a3b2413dd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/index.html b/docs/index.html index 0f2b7125f..4380a75e0 100644 --- a/docs/index.html +++ b/docs/index.html @@ -39,7 +39,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/news/index.html b/docs/news/index.html index ef0f86f2c..eb69bb02f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 @@ -72,6 +72,10 @@

Changelog

Source: NEWS.md +
+

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
    2. +

CohortDiagnostics 3.2.2

  1. Fixes to unit tests breaking with R 4.3 due to change of Sys.time function
    2. diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 152527a25..3c6a48ff7 100644 --- 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 index 6d88eca12..99f516b39 100644 --- a/docs/reference/CohortDiagnostics-package.html +++ b/docs/reference/CohortDiagnostics-package.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3
diff --git a/docs/reference/checkInputFileEncoding.html b/docs/reference/checkInputFileEncoding.html index 9aedb15b3..ee14f4df2 100644 --- a/docs/reference/checkInputFileEncoding.html +++ b/docs/reference/checkInputFileEncoding.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/createDiagnosticsExplorerZip.html b/docs/reference/createDiagnosticsExplorerZip.html index e2505526a..517f638dc 100644 --- a/docs/reference/createDiagnosticsExplorerZip.html +++ b/docs/reference/createDiagnosticsExplorerZip.html @@ -20,7 +20,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/createMergedResultsFile.html b/docs/reference/createMergedResultsFile.html index 85bce13af..fb18655aa 100644 --- a/docs/reference/createMergedResultsFile.html +++ b/docs/reference/createMergedResultsFile.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/createResultsDataModel.html b/docs/reference/createResultsDataModel.html index 73bb4cfff..2fda86eda 100644 --- a/docs/reference/createResultsDataModel.html +++ b/docs/reference/createResultsDataModel.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/executeDiagnostics.html b/docs/reference/executeDiagnostics.html index e4b0e33f8..e180d7729 100644 --- a/docs/reference/executeDiagnostics.html +++ b/docs/reference/executeDiagnostics.html @@ -22,7 +22,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getCdmDataSourceInformation.html b/docs/reference/getCdmDataSourceInformation.html index d974d3a20..92d84898c 100644 --- a/docs/reference/getCdmDataSourceInformation.html +++ b/docs/reference/getCdmDataSourceInformation.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getCohortCounts.html b/docs/reference/getCohortCounts.html index 0f706fc11..80462ee55 100644 --- a/docs/reference/getCohortCounts.html +++ b/docs/reference/getCohortCounts.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getDataMigrator.html b/docs/reference/getDataMigrator.html index 9bb95f853..95285fc78 100644 --- a/docs/reference/getDataMigrator.html +++ b/docs/reference/getDataMigrator.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getDefaultCovariateSettings.html b/docs/reference/getDefaultCovariateSettings.html index 3ed887e77..9b6b65e83 100644 --- a/docs/reference/getDefaultCovariateSettings.html +++ b/docs/reference/getDefaultCovariateSettings.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getDefaultVocabularyTableNames.html b/docs/reference/getDefaultVocabularyTableNames.html index 054c701aa..0bddbef0b 100644 --- a/docs/reference/getDefaultVocabularyTableNames.html +++ b/docs/reference/getDefaultVocabularyTableNames.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/getResultsDataModelSpecifications.html b/docs/reference/getResultsDataModelSpecifications.html index 3077b5bfb..a57f85df5 100644 --- a/docs/reference/getResultsDataModelSpecifications.html +++ b/docs/reference/getResultsDataModelSpecifications.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/index.html b/docs/reference/index.html index 1bb95a5d5..72c5309bd 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/launchDiagnosticsExplorer.html b/docs/reference/launchDiagnosticsExplorer.html index a301ea0f4..19e961251 100644 --- a/docs/reference/launchDiagnosticsExplorer.html +++ b/docs/reference/launchDiagnosticsExplorer.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/migrateDataModel.html b/docs/reference/migrateDataModel.html index 94b1fdd41..56c9d7bf8 100644 --- a/docs/reference/migrateDataModel.html +++ b/docs/reference/migrateDataModel.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/runCohortRelationshipDiagnostics.html b/docs/reference/runCohortRelationshipDiagnostics.html index b97d6a929..c2ffd3a16 100644 --- a/docs/reference/runCohortRelationshipDiagnostics.html +++ b/docs/reference/runCohortRelationshipDiagnostics.html @@ -18,7 +18,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/runCohortTimeSeriesDiagnostics.html b/docs/reference/runCohortTimeSeriesDiagnostics.html index 08e26c84d..548fea1f0 100644 --- a/docs/reference/runCohortTimeSeriesDiagnostics.html +++ b/docs/reference/runCohortTimeSeriesDiagnostics.html @@ -25,7 +25,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/timeExecution.html b/docs/reference/timeExecution.html index e12731389..d97c95661 100644 --- a/docs/reference/timeExecution.html +++ b/docs/reference/timeExecution.html @@ -17,7 +17,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/docs/reference/uploadResults.html b/docs/reference/uploadResults.html index 709bd53b6..86fec260b 100644 --- a/docs/reference/uploadResults.html +++ b/docs/reference/uploadResults.html @@ -19,7 +19,7 @@ CohortDiagnostics - 3.2.2 + 3.2.3 diff --git a/inst/doc/RunningCohortDiagnostics.pdf b/inst/doc/RunningCohortDiagnostics.pdf index 140ad3cdb..4c9145da3 100644 Binary files a/inst/doc/RunningCohortDiagnostics.pdf and b/inst/doc/RunningCohortDiagnostics.pdf differ diff --git a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf index 5fb69e696..2fa37e58a 100644 Binary files a/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf and b/inst/doc/ViewingResultsUsingDiagnosticsExplorer.pdf differ diff --git a/inst/doc/WhatIsCohortDiagnostics.pdf b/inst/doc/WhatIsCohortDiagnostics.pdf index 3e933e8c1..c43cf304f 100644 Binary files a/inst/doc/WhatIsCohortDiagnostics.pdf and b/inst/doc/WhatIsCohortDiagnostics.pdf differ diff --git a/inst/shiny/DiagnosticsExplorer/global.R b/inst/shiny/DiagnosticsExplorer/global.R index 05cf5dfba..61f05f31a 100644 --- a/inst/shiny/DiagnosticsExplorer/global.R +++ b/inst/shiny/DiagnosticsExplorer/global.R @@ -90,3 +90,4 @@ dataSource <- + diff --git a/inst/sql/sql_server/UpdateVersionNumber.sql b/inst/sql/sql_server/UpdateVersionNumber.sql index 52f21b19b..7cada8199 100644 --- a/inst/sql/sql_server/UpdateVersionNumber.sql +++ b/inst/sql/sql_server/UpdateVersionNumber.sql @@ -1,5 +1,5 @@ {DEFAULT @package_version = package_version} -{DEFAULT @version_number = '3.2.2'} +{DEFAULT @version_number = '3.2.3'} DELETE FROM @database_schema.@table_prefix@package_version; INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALUES ('@version_number'); @@ -8,3 +8,4 @@ INSERT INTO @database_schema.@table_prefix@package_version (version_number) VALU +