Release v0.0.3

.github/workflows/R_CMD_check_Hades.yaml

@@ -67,7 +67,6 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get install -y libssh-dev
-          Rscript -e 'install.packages("remotes")'
           while read -r cmd
           do
             eval sudo $cmd
@@ -140,33 +139,34 @@ jobs:
           draft: false
           prerelease: false
 
-      - uses: r-lib/actions/setup-r@v2
-        if: ${{ env.new_version != '' }}
-
-      - name: Install drat
-        if: ${{ env.new_version != '' }}
-        run: |
-          install.packages('drat')
-        shell: Rscript {0}
-
-      - name: Remove any tarballs that already exists
-        if: ${{ env.new_version != '' }}
-        run: |
-          rm -f *.tar.gz
-
-      - name: Download package tarball
-        if: ${{ env.new_version != '' }}
-        uses: actions/download-artifact@v2
-        with:
-          name: package_tarball
-
-      - name: Push to drat
-        if: ${{ env.new_version != '' }}
-        run: |
-          bash deploy.sh
-
-      - name: Push to BroadSea
-        if: ${{ env.new_version != '' }}
-        run: |
-          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
-
+      # AGS: Commenting out until Strategus is in HADES
+      # - uses: r-lib/actions/setup-r@v2
+      #   if: ${{ env.new_version != '' }}
+      #
+      # - name: Install drat
+      #   if: ${{ env.new_version != '' }}
+      #   run: |
+      #     install.packages('drat')
+      #   shell: Rscript {0}
+      #
+      # - name: Remove any tarballs that already exists
+      #   if: ${{ env.new_version != '' }}
+      #   run: |
+      #     rm -f *.tar.gz
+      #
+      # - name: Download package tarball
+      #   if: ${{ env.new_version != '' }}
+      #   uses: actions/download-artifact@v2
+      #   with:
+      #     name: package_tarball
+      #
+      # - name: Push to drat
+      #   if: ${{ env.new_version != '' }}
+      #   run: |
+      #     bash deploy.sh
+      #
+      # - name: Push to BroadSea
+      #   if: ${{ env.new_version != '' }}
+      #   run: |
+      #     curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
+      #

DESCRIPTION

@@ -1,43 +1,48 @@
 Package: Strategus
 Type: Package
 Title: Coordinating and Executing Analytics Using HADES Modules
-Version: 0.0.2
-Date: 2022-03-25
+Version: 0.0.3
+Date: 2023-03-10
 Authors@R: c(
-	person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre"))
-	)
-Maintainer: Martijn Schuemie <[email protected]>
+	person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
+	person("Anthony", "Sena", email = "[email protected]", role = c("aut")),
+	person("Observational Health Data Science and Informatics", role = c("cph"))
+  )
+Maintainer: Anthony Sena <[email protected]>
 Description: An R package for coordinating and executing analytics using HADES modules.
 License: Apache License 2.0
 URL: https://ohdsi.github.io/Strategus, https://github.com/OHDSI/Strategus
 BugReports: https://github.com/OHDSI/Strategus/issues
 Depends:
 	R (>= 4.0.0),
-	CohortGenerator (>= 0.5.0),
-	DatabaseConnector (>= 5.0.4)
+	CohortGenerator (>= 0.7.0),
+	DatabaseConnector (>= 5.1.0)
 Imports:
-	targets,
-	renv (>= 0.15.5),
-	ParallelLogger,
-	dplyr,
-	checkmate,
-	keyring,
-	rlang,
-	utils,
-	R.utils,
-	digest,
-	SqlRender,
-	readr
+  targets,
+  renv (>= 0.15.5),
+  ParallelLogger (>= 3.1.0),
+  dplyr,
+  checkmate,
+  keyring,
+  rlang,
+  utils,
+  R.utils,
+  digest,
+  methods,
+  tibble,
+  SqlRender (>= 1.11.0)
 Suggests:
-	testthat,
-	fs,
-	knitr,
-	rmarkdown
+    testthat (>= 3.0.0),
+    fs,
+    knitr,
+    rmarkdown,
+    Eunomia
 Remotes:
   ohdsi/CohortGenerator,
-  ohdsi/DatabaseConnector
+  ohdsi/Eunomia
 VignetteBuilder: knitr
 NeedsCompilation: no
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
+Config/testthat/edition: 3

NAMESPACE

@@ -2,13 +2,17 @@
 
 export(addModuleSpecifications)
 export(addSharedResources)
+export(createCdmExecutionSettings)
 export(createEmptyAnalysisSpecificiations)
-export(createExecutionSettings)
+export(createResultsExecutionSettings)
 export(ensureAllModulesInstantiated)
 export(execute)
+export(getModuleList)
 export(retrieveConnectionDetails)
 export(storeConnectionDetails)
+export(unlockKeyring)
 import(CohortGenerator)
 import(DatabaseConnector)
 import(dplyr)
+importFrom(methods,is)
 importFrom(rlang,.data)

NEWS.md

@@ -1,4 +1,24 @@
+Strategus 0.0.3
+===============
+
+- Breaking change: removed function `createExecutionSettings()` and replaced with 2 new functions: `createCdmExecutionSettings()` and `createResultsExecutionSettings()`. (#19)
+- Added Vignettes (#23)
+- Provide better support for `keyring` to handle named/locked keyrings (#24)
+- Add function to list Strategus modules (#30)
+- Fixes from testing (#36)
+- Enforce module structure for proper use with renv (#37)
+- Support CDM 5.4 source table format (#41)
+- Add unit tests (#47)
+
+
+Strategus 0.0.2
+===============
+
+- Updates renv to 0.15.5
+- Call renv::use() for each module
+
+
 Strategus 0.0.1
 ===============
 
-Initial version
+Initial version

R/DatabaseMetaData.R

@@ -1,4 +1,4 @@
-# Copyright 2022 Observational Health Data Sciences and Informatics
+# Copyright 2023 Observational Health Data Sciences and Informatics
 #
 # This file is part of Strategus
 #
@@ -21,48 +21,79 @@
 # carefully consider serialization and deserialization to JSON, which currently
 # uses custom functionality in ParallelLogger to maintain object attributes.
 
-createDatabaseMetaData <- function(executionSettings) {
+createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
   databaseMetaDataFolder <- file.path(executionSettings$resultsFolder, "DatabaseMetaData")
   if (!dir.exists(databaseMetaDataFolder)) {
     dir.create(databaseMetaDataFolder, recursive = TRUE)
   }
 
-  connectionDetails <- retrieveConnectionDetails(executionSettings$connectionDetailsReference)
+  connectionDetails <- retrieveConnectionDetails(
+    connectionDetailsReference = executionSettings$connectionDetailsReference,
+    keyringName = keyringName
+  )
   connection <- DatabaseConnector::connect(connectionDetails)
   on.exit(DatabaseConnector::disconnect(connection))
 
+  resultsDataModel <- CohortGenerator::readCsv(
+    file = system.file("databaseMetaDataRdms.csv", package = "Strategus"),
+    warnOnCaseMismatch = FALSE
+  )
+
   sql <- "SELECT TOP 1 * FROM @cdm_database_schema.cdm_source;"
-  cdmSource <- renderTranslateQuerySql(connection = connection,
-                                       sql = sql,
-                                       snakeCaseToCamelCase = TRUE,
-                                       cdm_database_schema = executionSettings$cdmDatabaseSchema)
+  cdmSource <- renderTranslateQuerySql(
+    connection = connection,
+    sql = sql,
+    snakeCaseToCamelCase = TRUE,
+    cdm_database_schema = executionSettings$cdmDatabaseSchema
+  )
+
+  # Restrict the cdmSource columns to those that are
+  # expected in the resultsDataModel
+  cdmSource <- cdmSource[, which(names(cdmSource) %in% SqlRender::snakeCaseToCamelCase(resultsDataModel$columnName))]
+
+  # In the case that the CDM is pre v5.4, it will lack the new
+  # cdm_version_concept_id column. In this case, we'll default it to
+  # concept_id == 1147638 which is CDM v5.3.1
+  # Ref: https://ohdsi.github.io/CommonDataModel/cdm54Changes.html
+  if (!"cdmVersionConceptId" %in% names(cdmSource)) {
+    cdmSource$cdmVersionConceptId <- 1147638
+  }
 
   sql <- "SELECT TOP 1 vocabulary_version  FROM @cdm_database_schema.vocabulary WHERE vocabulary_id = 'None';"
-  vocabVersion <- renderTranslateQuerySql(connection = connection,
-                                          sql = sql,
-                                          snakeCaseToCamelCase = TRUE,
-                                          cdm_database_schema = executionSettings$cdmDatabaseSchema)
+  vocabVersion <- renderTranslateQuerySql(
+    connection = connection,
+    sql = sql,
+    snakeCaseToCamelCase = TRUE,
+    cdm_database_schema = executionSettings$cdmDatabaseSchema
+  )
 
   sql <- "SELECT MAX(observation_period_end_date) as max_obs_period_end_date
   FROM @cdm_database_schema.observation_period;"
-  observationPeriodMax <- renderTranslateQuerySql(connection = connection,
-                                                  sql = sql,
-                                                  snakeCaseToCamelCase = TRUE,
-                                                  cdm_database_schema = executionSettings$cdmDatabaseSchema)
+  observationPeriodMax <- renderTranslateQuerySql(
+    connection = connection,
+    sql = sql,
+    snakeCaseToCamelCase = TRUE,
+    cdm_database_schema = executionSettings$cdmDatabaseSchema
+  )
 
   databaseId <- digest::digest2int(paste(cdmSource$cdmSourceName, cdmSource$cdmReleaseDate))
   database <- cdmSource %>%
-    mutate(vocabularyVersion = vocabVersion$vocabularyVersion,
-           databaseId = !!databaseId) %>%
+    mutate(
+      vocabularyVersion = vocabVersion$vocabularyVersion,
+      databaseId = !!databaseId
+    ) %>%
     bind_cols(observationPeriodMax)
 
   # Export the csv files:
-  CohortGenerator::writeCsv(x = database,
-                            file = file.path(databaseMetaDataFolder, "database_meta_data.csv"))
+  CohortGenerator::writeCsv(
+    x = database,
+    file = file.path(databaseMetaDataFolder, "database_meta_data.csv")
+  )
 
-  resultsDataModel <- readr::read_csv(file = system.file("databaseMetaDataRdms.csv", package = "Strategus"),
-                                      show_col_types = FALSE)
-  CohortGenerator::writeCsv(x = resultsDataModel,
-                            file = file.path(databaseMetaDataFolder, "resultsDataModelSpecification.csv"))
+  CohortGenerator::writeCsv(
+    x = resultsDataModel,
+    file = file.path(databaseMetaDataFolder, "resultsDataModelSpecification.csv"),
+    warnOnFileNameCaseMismatch = FALSE
+  )
   return(databaseId)
 }