Support for BIGINT person_id

.github/workflows/R_CMD_check_Hades.yaml

@@ -53,7 +53,7 @@ jobs:
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -86,22 +86,37 @@ jobs:
 
       - name: Upload source package
         if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: package_tarball
           path: check/*.tar.gz
 
       - name: Install covr
-        if: runner.os == 'macOS'
+        if: runner.os == 'Linux'
         run: |
-          install.packages("covr")
+          remotes::install_cran("covr")
+          remotes::install_cran("xml2")
         shell: Rscript {0}
-
+        
       - name: Test coverage
-        if: runner.os == 'macOS'
-        run: covr::codecov()
+        if: runner.os == 'Linux'
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        if: runner.os == 'Linux'
+        with:
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
   Release:
     needs: R-CMD-Check
 

NEWS.md

@@ -2,6 +2,7 @@ CohortExplorer 0.1.1
 ======================
 Improve test coverage to 100%
 Force creation of .Rproj file for shiny app.
+Support BIGINT person IDs.
 
 
 CohortExplorer 0.1.0

R/CreateCohortExplorerApp.R

@@ -172,23 +172,14 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
     add = errorMessage
   )
 
-  if (is.null(personIds)) {
-    checkmate::assertIntegerish(
-      x = sampleSize,
-      lower = 0,
-      len = 1,
-      null.ok = TRUE,
+  # personIds can be interger, numeric, or character to allow bigint (R does not
+  # support 64-bit integers):
+  if (!is.null(personIds)) {
+    checkmate::assertTRUE(
+      all(grepl("[0-9]+", as.character(personIds))), 
       add = errorMessage
     )
-  } else {
-    checkmate::assertIntegerish(
-      x = personIds,
-      lower = 0,
-      min.len = 1,
-      null.ok = TRUE
-    )
   }
-
   exportFolder <- normalizePath(exportFolder, mustWork = FALSE)
 
   dir.create(
@@ -331,7 +322,7 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
       progressBar = TRUE,
       bulkLoad = (Sys.getenv("bulkLoad") == TRUE),
       camelCaseToSnakeCase = TRUE,
-      data = dplyr::tibble(subjectId = as.double(personIds) |> unique())
+      data = dplyr::tibble(subjectId = as.character(personIds) |> unique())
     )
 
     DatabaseConnector::renderTranslateExecuteSql(
@@ -341,7 +332,7 @@ createCohortExplorerApp <- function(connectionDetails = NULL,
                   INTO #person_id_data2
                   FROM #person_id_data a
                   INNER JOIN #persons_to_filter b
-                  ON a.subject_id = b.subject_id;
+                  ON CAST(a.subject_id AS BIGINT) = CAST(b.subject_id AS BIGINT);
 
                   DROP TABLE IF EXISTS #person_id_data;
                   SELECT DISTINCT subject_id