Merge pull request #5 from OHDSI/develop

Develop

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
@@ -43,75 +43,46 @@ jobs:
       CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
       CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
       CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-tinytex@v1
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-tinytex@v2
 
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install system dependencies
+      - name: Install system requirements
         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
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
-      - name: Install libssh
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get install libssh-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Install covr
-        if: runner.os == 'macOS'
-        run: |
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Remove check folder if exists
-        if: runner.os == 'macOS'
-        run: unlink("check", recursive = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@v2
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          check-dir: '"check"'
 
       - name: Upload source package
         if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
@@ -120,6 +91,12 @@ jobs:
           name: package_tarball
           path: check/*.tar.gz
 
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          install.packages("covr")
+        shell: Rscript {0}
+
       - name: Test coverage
         if: runner.os == 'macOS'
         run: covr::codecov()
@@ -163,7 +140,7 @@ jobs:
           draft: false
           prerelease: false
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         if: ${{ env.new_version != '' }}
 
       - name: Install drat
@@ -192,3 +169,4 @@ jobs:
         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/
+

.github/workflows/R_CMD_check_main_weekly.yaml

@@ -0,0 +1,67 @@
+on:
+  schedule:
+    - cron: '0 14 * * 0' # every Sunday at 2pm UTC
+
+name: 'R check'
+
+jobs:
+  R-CMD-check-main:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          check-dir: '"check"'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Characterization
 Type: Package
 Title: Characterizations of Cohorts
-Version: 0.0.4
-Date: 2022-12-14
+Version: 0.0.5
+Date: 2023-01-12
 Authors@R: c(
 	person("Jenna", "Reps", , "reps@ohdsi.org", role = c("aut", "cre")),
 	person("Patrick", "Ryan", , "ryan@ohdsi.org", role = c("aut"))
@@ -32,7 +32,6 @@ Suggests:
 	markdown,
 	withr
 Remotes:
-  ohdsi/Andromeda,
 	ohdsi/FeatureExtraction,
 	ohdsi/Eunomia
 NeedsCompilation: no

R/AggregateCovariates.R

@@ -35,11 +35,36 @@ createAggregateCovariateSettings <- function(
   covariateSettings
 ){
 
-  # check cohortIds is a vector of int/double
-
+  errorMessages <- checkmate::makeAssertCollection()
+  # check targetIds is a vector of int/double
+  .checkCohortIds(
+    cohortIds = targetIds,
+    type = 'target',
+    errorMessages = errorMessages
+  )
   # check outcomeIds is a vector of int/double
+  .checkCohortIds(
+    cohortIds = outcomeIds,
+    type = 'outcome',
+    errorMessages = errorMessages
+  )
+
+  # check TAR
+  .checkTimeAtRisk(
+    riskWindowStart = riskWindowStart,
+    startAnchor = startAnchor,
+    riskWindowEnd = riskWindowEnd,
+    endAnchor = endAnchor,
+    errorMessages = errorMessages
+  )
+
+  # check covariateSettings
+  .checkCovariateSettings(
+    covariateSettings = covariateSettings,
+    errorMessages = errorMessages
+  )
 
-  #check TAR
+  checkmate::reportAssertions(errorMessages)
 
   # create list
   result <- list(
@@ -86,6 +111,7 @@ computeAggregateCovariateAnalyses <- function(
 ) {
 
   # check inputs
+
   start <- Sys.time()
 
   connection <- DatabaseConnector::connect(
@@ -150,80 +176,43 @@ computeAggregateCovariateAnalyses <- function(
         )
   }
 
-  # settings:
-  # run_id, database_id, covariate_setting_json,
-  # riskWindowStart, startAnchor, riskWindowEnd, endAnchor
-  # combined_cohort_id, target_cohort_id, outcome_cohort_id,
-  # type
-
+# cohort details:
 
-  result$settings <- DatabaseConnector::querySql(
+  result$cohortDetails <- DatabaseConnector::querySql(
     connection = connection,
     sql = SqlRender::translate(
-    sql = "
-    select distinct
-    cohort_definition_id as combined_cohort_id,
-    target_id as target_cohort_id,
-    outcome_id as outcome_cohort_id,
-    cohort_type
-    from #target_with_outcome
-
-    union
-
-    select distinct
-    cohort_definition_id as combined_cohort_id,
-    target_id as target_cohort_id,
-    outcome_id as outcome_cohort_id,
-    cohort_type
-    from #target_nooutcome
-
-    union
-
-    select distinct
-    cohort_definition_id + 2 as combined_cohort_id,
-    target_id as target_cohort_id,
-    outcome_id as outcome_cohort_id,
-    'OnT' as cohort_type
-    from #target_with_outcome
-
-    union
-
-    select distinct
-    cohort_definition_id*100000 as combined_cohort_id,
-    cohort_definition_id as target_cohort_id,
-    0 as outcome_cohort_id,
-    'T' as cohort_type
-    from #targets_agg
-
- union
-
- select distinct
-    cohort_definition_id*100000 as combined_cohort_id,
-    0 as target_cohort_id,
-    cohort_definition_id as outcome_cohort_id,
-    'O' as cohort_type
-    from #outcomes_agg
-    ;",
+    sql = " select * from #cohort_details;",
     targetDialect = connectionDetails$dbms
     ),
     snakeCaseToCamelCase = T
-  )
+  ) %>%
+    dplyr::mutate(
+      runId = !!runId,
+      databaseId = !!databaseId
+    ) %>%
+    dplyr::relocate(
+      "databaseId",
+      "runId"
+    )
+
+  # settings:
+  # run_id, database_id, covariate_setting_json,
+  # riskWindowStart, startAnchor, riskWindowEnd, endAnchor
 
   covariateSettingsJson <- as.character(
     ParallelLogger::convertSettingsToJson(
       aggregateCovariateSettings$covariateSettings
     )
   )
 
-  result$settings <- result$settings %>%
-    dplyr::mutate(
-      runId = !!runId,
-      databaseId = !!databaseId,
-      covariateSettingJson = !!covariateSettingsJson,
-      riskWindowStart = !!aggregateCovariateSettings$riskWindowStart,
-      startAnchor = !!aggregateCovariateSettings$startAnchor,
-      riskWindowEnd = !!aggregateCovariateSettings$riskWindowEnd ,
-      endAnchor = !!aggregateCovariateSettings$endAnchor
+  result$settings <- data.frame(
+      runId = runId,
+      databaseId = databaseId,
+      covariateSettingJson = covariateSettingsJson,
+      riskWindowStart = aggregateCovariateSettings$riskWindowStart,
+      startAnchor = aggregateCovariateSettings$startAnchor,
+      riskWindowEnd = aggregateCovariateSettings$riskWindowEnd ,
+      endAnchor = aggregateCovariateSettings$endAnchor
     )
 
   sql <- SqlRender::loadRenderTranslateSql(