Sos challenge

R/DatabaseMetaData.R

@@ -42,7 +42,7 @@ createDatabaseMetaData <- function(executionSettings, keyringName = NULL) {
     connection = connection,
     databaseSchema = executionSettings$cdmDatabaseSchema
   )
-  cdmTableList <- tolower(cdmTableList)
+  cdmTableList <- unique(tolower(cdmTableList))
 
   if (!length(cdmTableList[which(x = cdmTableList %in% requiredTables)]) == length(requiredTables)) {
     missingCdmTables <- requiredTables[!(requiredTables %in% cdmTableList)]

R/Execution.R

@@ -53,6 +53,17 @@ execute <- function(analysisSpecifications,
   checkmate::assertChoice(x = keyringName, choices = keyringList$keyring, null.ok = TRUE, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
 
+  # Assert that the temp emulation schema is set if required for the dbms
+  # specified by the executionSettings
+  connectionDetails <- retrieveConnectionDetails(
+    connectionDetailsReference = executionSettings$connectionDetailsReference,
+    keyringName = keyringName
+  )
+  DatabaseConnector::assertTempEmulationSchemaSet(
+    dbms = connectionDetails$dbms,
+    tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
+  )
+
   modules <- ensureAllModulesInstantiated(analysisSpecifications)
 
   if (is.null(executionScriptFolder)) {

R/ModuleInstantiation.R

@@ -191,15 +191,15 @@ instantiateModule <- function(module, version, remoteRepo, remoteUsername, modul
     stop(message)
   }
 
-  script <- "
-      renv::restore(prompt = FALSE)
-      if (!require('ParallelLogger', quietly = TRUE)) {
-        install.packages('ParallelLogger')
-      }
-      if (!require('keyring', quietly = TRUE)) {
-        install.packages('keyring')
-      }
-    "
+  script <- paste(
+    c(
+      "renv::install(c('ParallelLogger', 'keyring'), prompt = FALSE)",
+      sprintf("ParallelLogger::addDefaultFileLogger(file.path('%s', 'moduleInitLog.txt'))", moduleFolder),
+      sprintf("ParallelLogger::addDefaultErrorReportLogger(fileName = file.path('%s', 'moduleInitErrorReport.R'))", moduleFolder),
+      "renv::restore(prompt = FALSE)"
+     ),
+    collapse = "\n"
+  )
   tempScriptFile <- tempfile(fileext = ".R")
   fileConn <- file(tempScriptFile)
   writeLines(script, fileConn)

R/RunModule.R

@@ -88,6 +88,8 @@ runModule <- function(analysisSpecifications, keyringSettings, moduleIndex, exec
 
       options(andromedaTempFolder = file.path(jobContext$moduleExecutionSettings$workFolder, 'andromedaTemp'))
 
+      options(tempEmulationSchema = jobContext$moduleExecutionSettings$tempEmulationSchema)
+
        if (Sys.getenv('FORCE_RENV_USE', '') == 'TRUE') {
          renv::use(lockfile = 'renv.lock')
        }

R/Settings.R

@@ -103,6 +103,7 @@ createCdmExecutionSettings <- function(connectionDetailsReference,
                                        workDatabaseSchema,
                                        cdmDatabaseSchema,
                                        cohortTableNames = CohortGenerator::getCohortTableNames(cohortTable = "cohort"),
+                                       tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
                                        workFolder,
                                        resultsFolder,
                                        minCellCount = 5,
@@ -125,6 +126,7 @@ createCdmExecutionSettings <- function(connectionDetailsReference,
     workDatabaseSchema = workDatabaseSchema,
     cdmDatabaseSchema = cdmDatabaseSchema,
     cohortTableNames = cohortTableNames,
+    tempEmulationSchema = tempEmulationSchema,
     workFolder = workFolder,
     resultsFolder = resultsFolder,
     minCellCount = minCellCount,
@@ -214,7 +216,7 @@ storeConnectionDetails <- function(connectionDetails, connectionDetailsReference
     if (is.function(connectionDetails[[i]])) {
       detail <- connectionDetails[[i]]()
       if (is.null(detail)) {
-        connectionDetails[[i]] <- ""
+        connectionDetails[[i]] <- list(NULL) # Fixes Issue #74
       } else {
         connectionDetails[[i]] <- connectionDetails[[i]]()
       }

inst/testdata/analysisSpecification.json

@@ -223,7 +223,7 @@
   "moduleSpecifications": [
     {
       "module": "CohortGeneratorModule",
-      "version": "0.1.0",
+      "version": "0.1.1-1",
       "remoteRepo": "github.com",
       "remoteUsername": "ohdsi",
       "settings": {