Disable Mac Rv4.2.3 tests and small revision to unit tests (#115)

* Disable Mac 4.2.3 tests for now
OHDSI · Jan 17, 2024 · 9735a19 · 9735a19
1 parent 13d020e
commit 9735a19
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Showing 3 changed files with 9 additions and 8 deletions.
diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
@@ -21,7 +21,7 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
+          #- {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
@@ -68,15 +68,15 @@ withr::defer(
 cdmDatabaseSchema <- "main"
 workDatabaseSchema <- "main"
 vocabularyDatabaseSchema <- workDatabaseSchema
-cohortTable <- "cohort"
+cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = paste0("s", tableSuffix))
 tempEmulationSchema <- NULL
 
 connectionDetailsList[[length(connectionDetailsList) + 1]] <- list(
   connectionDetails = connectionDetails,
   cdmDatabaseSchema = "main",
   workDatabaseSchema = "main",
   vocabularyDatabaseSchema = "main",
-  cohortTable = "cohort",
+  cohortTableNames = cohortTableNames,
   tempEmulationSchema = NULL
 )
 
@@ -99,7 +99,7 @@ if (!(Sys.getenv("CDM5_POSTGRESQL_USER") == "" &
     cdmDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
     workDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA"),
     vocabularyDatabaseSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"),
-    cohortTable = "cohort",
+    cohortTableNames = cohortTableNames,
     tempEmulationSchema = NULL
   )
 }
@@ -123,7 +123,7 @@ if (!(Sys.getenv("CDM5_ORACLE_USER") == "" &
     cdmDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
     workDatabaseSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA"),
     vocabularyDatabaseSchema = Sys.getenv("CDM5_ORACLE_CDM_SCHEMA"),
-    cohortTable = "cohort",
+    cohortTableNames = cohortTableNames,
     tempEmulationSchema = Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA")
   )
 }
@@ -147,7 +147,7 @@ if (!(Sys.getenv("CDM5_REDSHIFT_USER") == "" &
     cdmDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
     workDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA"),
     vocabularyDatabaseSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
-    cohortTable = "cohort",
+    cohortTableNames = cohortTableNames,
     tempEmulationSchema = NULL
   )
 }
@@ -171,7 +171,7 @@ if (!(Sys.getenv("CDM5_SQL_SERVER_USER") == "" &
     cdmDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
     workDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA"),
     vocabularyDatabaseSchema = Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA"),
-    cohortTable = "cohort",
+    cohortTableNames = cohortTableNames,
     tempEmulationSchema = NULL
   )
 }

diff --git a/tests/testthat/test-Strategus.R b/tests/testthat/test-Strategus.R
@@ -28,6 +28,7 @@ test_that("Run unit test study", {
     workDatabaseSchema <- connectionDetailsList[[i]]$workDatabaseSchema
     cdmDatabaseSchema <- connectionDetailsList[[i]]$cdmDatabaseSchema
     tempEmulationSchema <- connectionDetailsList[[i]]$tempEmulationSchema
+    cohortTableNames <- connectionDetailsList[[i]]$cohortTableNames
     studyRootFolder <- file.path(tempDir, "EunomiaTestStudy", dbms)
     workFolder <- file.path(studyRootFolder, "work_folder")
     resultsFolder <- file.path(studyRootFolder, "results_folder")
@@ -72,7 +73,7 @@ test_that("Run unit test study", {
       workDatabaseSchema = workDatabaseSchema,
       cdmDatabaseSchema = cdmDatabaseSchema,
       tempEmulationSchema = tempEmulationSchema,
-      cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = paste0("s", tableSuffix)),
+      cohortTableNames = cohortTableNames,
       workFolder = workFolder,
       resultsFolder = resultsFolder,
       minCellCount = 5,