Fix cmd checks and revise test

R/Execution.R

@@ -158,9 +158,7 @@ generateTargetsScript <- function(analysisSpecifications, executionSettings, dep
           )
         }
       }
-    }
-
-    targetList
+      targetList
   }, script = fileName)
 
   #Store settings objects in the temp folder so they are available in targets

R/ModuleEnv.R

@@ -44,9 +44,11 @@
 #'
 #' @param code              code block to execute
 #' @param moduleFolder      Instantiated Strategus module folder
-#' @param injectVars         list of var names list(name=value) to replace (e.g. replace list(foo = "some string") will
+#' @param injectVars        list of var names list(name=value) to replace (e.g. replace list(foo = "some string") will
 #'                          find the pattern foo and replace it with the string some string - be careful!
-#' @param tempScriptFile    tempFile to write script to (ret
+#' @param tempScriptFile    tempFile to write script to
+#' @param useLocalStrategusLibrary Use the locally installed Strategus library? TRUE will use the Strategus
+#'                          installation from the calling R process.
 #' @param job               run as rstudio job
 #' @param processName       String name for process
 #' @returns NULL invisibly

R/Settings.R

@@ -87,6 +87,7 @@ addModuleSpecifications <- function(analysisSpecifications, moduleSpecifications
 #' @param cohortTableNames           An object identifying the various cohort table names that will be created in the
 #'                                   `workDatabaseSchema`. This object can be created using the
 #'                                   [CohortGenerator::getCohortTableNames()] function.
+#' @param tempEmulationSchema        Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.
 #' @param workFolder                 A folder in the local file system where intermediate results can be written.
 #' @param resultsFolder              A folder in the local file system where the module output will be written.
 #' @param minCellCount               The minimum number of subjects contributing to a count before it can be included

tests/testthat/test-Strategus.R

@@ -1,73 +1,73 @@
-# test_that("Run Eunomia study", {
-#   # NOTE: Need to set this in each test otherwise it goes out of scope
-#   renv:::renv_scope_envvars(RENV_PATHS_CACHE = renvCachePath)
-#
-#   # Setup keyring for the test
-#   Sys.setenv("STRATEGUS_KEYRING_PASSWORD" = keyringPassword)
-#   createKeyringForUnitTest(selectedKeyring = keyringName, selectedKeyringPassword = keyringPassword)
-#   on.exit(deleteKeyringForUnitTest())
-#
-#   # Using a named and secured keyring
-#   Strategus::storeConnectionDetails(
-#     connectionDetails = connectionDetails,
-#     connectionDetailsReference = dbms,
-#     keyringName = keyringName
-#   )
-#
-#   analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
-#     fileName = system.file("testdata/analysisSpecification.json",
-#       package = "Strategus"
-#     )
-#   )
-#
-#   # Create a unique set of cohort tables for this test run and
-#   # ensure they are removed when complete
-#   cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = paste0("s", tableSuffix))
-#
-#   # Use this line to limit to only running the CohortGeneratorModule
-#   # for testing purposes.
-#   analysisSpecifications$moduleSpecifications <- analysisSpecifications$moduleSpecifications[-c(2:length(analysisSpecifications$moduleSpecifications))]
-#   executionSettings <- createCdmExecutionSettings(
-#     connectionDetailsReference = dbms,
-#     workDatabaseSchema = workDatabaseSchema,
-#     cdmDatabaseSchema = cdmDatabaseSchema,
-#     cohortTableNames = cohortTableNames,
-#     workFolder = file.path(tempDir, "EunomiaTestStudy/work_folder"),
-#     resultsFolder = file.path(tempDir, "EunomiaTestStudy/results_folder"),
-#     minCellCount = 5
-#   )
-#
-#   if (!dir.exists(file.path(tempDir, "EunomiaTestStudy"))) {
-#     dir.create(file.path(tempDir, "EunomiaTestStudy"), recursive = TRUE)
-#   }
-#   ParallelLogger::saveSettingsToJson(
-#     object = executionSettings,
-#     file.path(tempDir, "EunomiaTestStudy/eunomiaExecutionSettings.json")
-#   )
-#
-#   executionSettings <- ParallelLogger::loadSettingsFromJson(
-#     fileName = file.path(tempDir, "EunomiaTestStudy/eunomiaExecutionSettings.json")
-#   )
-#
-#   Strategus::execute(
-#     analysisSpecifications = analysisSpecifications,
-#     executionSettings = executionSettings,
-#     executionScriptFolder = file.path(tempDir, "EunomiaTestStudy/script_folder"),
-#     keyringName = keyringName
-#   )
-#
-#   expect_true(file.exists(file.path(tempDir, "EunomiaTestStudy/results_folder/CohortGeneratorModule_1/done")))
-#
-#   withr::defer(
-#     {
-#       CohortGenerator::dropCohortStatsTables(
-#         connectionDetails = connectionDetails,
-#         cohortDatabaseSchema = workDatabaseSchema,
-#         cohortTableNames = cohortTableNames,
-#         dropCohortTable = TRUE
-#       )
-#       unlink(file.path(tempDir, "EunomiaTestStudy"), recursive = TRUE, force = TRUE)
-#     },
-#     testthat::teardown_env()
-#   )
-# })
+test_that("Run Eunomia study", {
+  # NOTE: Need to set this in each test otherwise it goes out of scope
+  renv:::renv_scope_envvars(RENV_PATHS_CACHE = renvCachePath)
+
+  # Setup keyring for the test
+  Sys.setenv("STRATEGUS_KEYRING_PASSWORD" = keyringPassword)
+  createKeyringForUnitTest(selectedKeyring = keyringName, selectedKeyringPassword = keyringPassword)
+  on.exit(deleteKeyringForUnitTest())
+
+  # Using a named and secured keyring
+  Strategus::storeConnectionDetails(
+    connectionDetails = connectionDetails,
+    connectionDetailsReference = dbms,
+    keyringName = keyringName
+  )
+
+  analysisSpecifications <- ParallelLogger::loadSettingsFromJson(
+    fileName = system.file("testdata/analysisSpecification.json",
+      package = "Strategus"
+    )
+  )
+
+  # Create a unique set of cohort tables for this test run and
+  # ensure they are removed when complete
+  cohortTableNames <- CohortGenerator::getCohortTableNames(cohortTable = paste0("s", tableSuffix))
+
+  # Use this line to limit to only running the CohortGeneratorModule
+  # for testing purposes.
+  analysisSpecifications$moduleSpecifications <- analysisSpecifications$moduleSpecifications[-c(2:length(analysisSpecifications$moduleSpecifications))]
+  executionSettings <- createCdmExecutionSettings(
+    connectionDetailsReference = dbms,
+    workDatabaseSchema = workDatabaseSchema,
+    cdmDatabaseSchema = cdmDatabaseSchema,
+    cohortTableNames = cohortTableNames,
+    workFolder = file.path(tempDir, "EunomiaTestStudy/work_folder"),
+    resultsFolder = file.path(tempDir, "EunomiaTestStudy/results_folder"),
+    minCellCount = 5
+  )
+
+  if (!dir.exists(file.path(tempDir, "EunomiaTestStudy"))) {
+    dir.create(file.path(tempDir, "EunomiaTestStudy"), recursive = TRUE)
+  }
+  ParallelLogger::saveSettingsToJson(
+    object = executionSettings,
+    file.path(tempDir, "EunomiaTestStudy/eunomiaExecutionSettings.json")
+  )
+
+  executionSettings <- ParallelLogger::loadSettingsFromJson(
+    fileName = file.path(tempDir, "EunomiaTestStudy/eunomiaExecutionSettings.json")
+  )
+
+  Strategus::execute(
+    analysisSpecifications = analysisSpecifications,
+    executionSettings = executionSettings,
+    executionScriptFolder = file.path(tempDir, "EunomiaTestStudy/script_folder"),
+    keyringName = keyringName
+  )
+
+  expect_true(file.exists(file.path(tempDir, "EunomiaTestStudy/results_folder/CohortGeneratorModule_1/done")))
+
+  withr::defer(
+    {
+      CohortGenerator::dropCohortStatsTables(
+        connectionDetails = connectionDetails,
+        cohortDatabaseSchema = workDatabaseSchema,
+        cohortTableNames = cohortTableNames,
+        dropCohortTable = TRUE
+      )
+      unlink(file.path(tempDir, "EunomiaTestStudy"), recursive = TRUE, force = TRUE)
+    },
+    testthat::teardown_env()
+  )
+})