update documentation. Only download gibleed eunomia dataset if it doe…

…s not already exist. Skip results datamode test if SKIP_DB_TESTS is TRUE.
mi-erasmusmc · Sep 19, 2024 · abae4f1 · abae4f1
1 parent e1dec96
commit abae4f1
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Showing 4 changed files with 33 additions and 18 deletions.
diff --git a/man/createConceptCountsTable.Rd b/man/createConceptCountsTable.Rd
diff --git a/man/executeDiagnostics.Rd b/man/executeDiagnostics.Rd
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -31,9 +31,8 @@ minCellCountValue <- 5
 skipCdmTests <- FALSE
 
 if (dbms == "sqlite") {
-  databaseFile <- paste0(Sys.getpid(), "testEunomia.sqlite")
-
-  connectionDetails <- Eunomia::getEunomiaConnectionDetails(databaseFile = databaseFile)
+  databaseFile <- Eunomia::getDatabaseFile("GiBleed", overwrite = FALSE)
+  connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = databaseFile)
   withr::defer(
     {
       unlink(databaseFile, recursive = TRUE, force = TRUE)

diff --git a/tests/testthat/test-1-ResultsDataModel.R b/tests/testthat/test-1-ResultsDataModel.R
@@ -1,5 +1,5 @@
 skipResultsDm <- FALSE
-if (Sys.getenv("CDM5_POSTGRESQL_SERVER") == "") {
+if (Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" || Sys.getenv("SKIP_DB_TESTS") == "TRUE") {
   skipResultsDm <- TRUE
 } else {
   postgresConnectionDetails <- DatabaseConnector::createConnectionDetails(
@@ -179,6 +179,7 @@ VALUES ('Synthea','Synthea','OHDSI Community','SyntheaTM is a Synthetic Patient
 })
 
 test_that("Sqlite results data model", {
+  skip_if(skipResultsDm)
   dbFile <- tempfile(fileext = ".sqlite")
   createMergedResultsFile(dataFolder = file.path(folder, "export"), sqliteDbPath = dbFile, overwrite = TRUE, tablePrefix = "cd_")
   connectionDetailsSqlite <- DatabaseConnector::createConnectionDetails(dbms = "sqlite", server = dbFile)