Merge branch 'develop' into installable-modules

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 +53,18 @@ 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
+  if (is(executionSettings, "CdmExecutionSettings")) {
+    connectionDetails <- retrieveConnectionDetails(
+      connectionDetailsReference = executionSettings$connectionDetailsReference,
+      keyringName = keyringName
+    )
+    DatabaseConnector::assertTempEmulationSchemaSet(
+      dbms = connectionDetails$dbms,
+      tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")
+    )
+  }
   modules <- ensureAllModulesInstantiated(analysisSpecifications)
 
   if (is.null(executionScriptFolder)) {
@@ -170,7 +182,7 @@ generateTargetsScript <- function(analysisSpecifications, executionSettings, dep
 
   dependenciesFileName <- gsub("\\\\", "/", file.path(executionScriptFolder, "dependencies.rds"))
   saveRDS(dependencies, dependenciesFileName)
-  
+
   execResultsUpload <- all(c(is(executionSettings, "CdmExecutionSettings"),
                              !is.null(executionSettings$resultsConnectionDetailsReference),
                              !is.null(executionSettings$resultsDatabaseSchema)))

R/ModuleEnv.R

@@ -70,6 +70,19 @@ withModuleRenv <- function(code,
     libPath <- file.path(find.package("Strategus"), "../")
     script <- c(sprintf("library(Strategus, lib.loc = '%s')", libPath),
                 script)
+    # Adding Strategus dependencies to the script
+    libPath <- file.path(find.package("CohortGenerator"), "../")
+    script <- c(sprintf("library(CohortGenerator, lib.loc = '%s')", libPath),
+                script)
+    libPath <- file.path(find.package("DatabaseConnector"), "../")
+    script <- c(sprintf("library(DatabaseConnector, lib.loc = '%s')", libPath),
+                script)
+    libPath <- file.path(find.package("keyring"), "../")
+    script <- c(sprintf("library(keyring, lib.loc = '%s')", libPath),
+                script)
+    libPath <- file.path(find.package("openssl"), "../")
+    script <- c(sprintf("library(openssl, lib.loc = '%s')", libPath),
+                script)
   }
 
   # Write file and execute script inside an renv
@@ -83,4 +96,4 @@ withModuleRenv <- function(code,
     project = moduleFolder
   )
   return(invisible(NULL))
-}
+}

R/ModuleInstantiation.R

@@ -193,15 +193,15 @@ 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.txt'))", moduleFolder),
+      "renv::restore(prompt = FALSE)"
+     ),
+    collapse = "\n"
+  )
   tempScriptFile <- tempfile(fileext = ".R")
   fileConn <- file(tempScriptFile)
   writeLines(script, fileConn)

R/RunModule.R

@@ -87,21 +87,24 @@ runModule <- function(analysisSpecifications, keyringSettings, moduleIndex, exec
       ParallelLogger::addDefaultErrorReportLogger(file.path(jobContext$moduleExecutionSettings$resultsSubFolder, 'errorReport.R'))
 
       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')
        }
 
        # NOTE injected variable isResultsExecution - will look strange outside of Strategus definition
        if (isCdmExecution) {
-         connectionDetails <- keyring::key_get(jobContext$moduleExecutionSettings$connectionDetailsReference, keyring = keyringName)
-         connectionDetails <- ParallelLogger::convertJsonToSettings(connectionDetails)
-         connectionDetails <- do.call(DatabaseConnector::createConnectionDetails, connectionDetails)
+         connectionDetails <- Strategus::retrieveConnectionDetails(
+           connectionDetailsReference = jobContext$moduleExecutionSettings$connectionDetailsReference,
+           keyringName = keyringName
+         )
          jobContext$moduleExecutionSettings$connectionDetails <- connectionDetails
        } else {
-         resultsConnectionDetails <- keyring::key_get(jobContext$moduleExecutionSettings$resultsConnectionDetailsReference, keyring = keyringName)
-         resultsConnectionDetails <- ParallelLogger::convertJsonToSettings(resultsConnectionDetails)
-         resultsConnectionDetails <- do.call(DatabaseConnector::createConnectionDetails, resultsConnectionDetails)
+         resultsConnectionDetails <- Strategus::retrieveConnectionDetails(
+           connectionDetailsReference = jobContext$moduleExecutionSettings$resultsConnectionDetailsReference,
+           keyringName = keyringName
+         )
          jobContext$moduleExecutionSettings$resultsConnectionDetails <- resultsConnectionDetails
        }
        if (keyringLocked) {

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]]()
       }
@@ -255,6 +257,15 @@ retrieveConnectionDetails <- function(connectionDetailsReference, keyringName =
 
   connectionDetails <- keyring::key_get(connectionDetailsReference, keyring = keyringName)
   connectionDetails <- ParallelLogger::convertJsonToSettings(connectionDetails)
+
+  # Ensure that NA values are converted to NULL prior to calling
+  # DatabaseConnector
+  for (i in 1:length(connectionDetails)) {
+    if (isTRUE(is.na(connectionDetails[[i]]))) {
+      connectionDetails[[i]] <- list(NULL) # Fixes Issue #74
+    }
+  }
+
   connectionDetails <- do.call(DatabaseConnector::createConnectionDetails, connectionDetails)
 
   if (keyringLocked) {

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": {