Remove local library attachment in module run script

OHDSI · Dec 14, 2023 · ed310f2 · ed310f2
1 parent 00d0c00
commit ed310f2
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Showing 5 changed files with 666 additions and 1,123 deletions.
diff --git a/R/ModuleEnv.R b/R/ModuleEnv.R
@@ -47,16 +47,13 @@
 #' @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
-#' @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
 withModuleRenv <- function(code,
                            moduleFolder,
                            injectVars = list(),
                            tempScriptFile = tempfile(fileext = ".R"),
-                           useLocalStrategusLibrary = TRUE,
                            job = FALSE,
                            processName = paste(moduleFolder, "_renv_run")) {
   # convert human readable code to a string for writing
@@ -81,18 +78,9 @@ withModuleRenv <- function(code,
     }
   }
 
-  # Enforce attachment of Strategus from calling process - note one inside the renv
-  if (useLocalStrategusLibrary) {
-    script <- c(.getLocalLibraryScipt("Strategus"), script)
-    # Adding Strategus dependencies to the script
-    script <- c(.getLocalLibraryScipt("ParallelLogger"), script)
-    script <- c(.getLocalLibraryScipt("CohortGenerator"), script)
-    script <- c(.getLocalLibraryScipt("DatabaseConnector"), script)
-    script <- c(.getLocalLibraryScipt("keyring"), script)
-    script <- c(.getLocalLibraryScipt("openssl"), script)
-    script <- c(.getLocalLibraryScipt("dplyr"), script)
-    script <- c(.getLocalLibraryScipt("R6"), script)
-  }
+  # Import the Strategus function we need to retrieve the
+  # connection details and embed it into the module script
+  script <- c("retrieveConnectionDetails <- ", base::deparse(Strategus::retrieveConnectionDetails), script)
 
   # Write file and execute script inside an renv
   fileConn <- file(tempScriptFile)

diff --git a/R/RunModule.R b/R/RunModule.R
@@ -97,13 +97,13 @@ runModule <- function(analysisSpecifications, keyringSettings, moduleIndex, exec
 
       # NOTE injected variable isResultsExecution - will look strange outside of Strategus definition
       if (isCdmExecution) {
-        connectionDetails <- Strategus::retrieveConnectionDetails(
+        connectionDetails <- retrieveConnectionDetails(
           connectionDetailsReference = jobContext$moduleExecutionSettings$connectionDetailsReference,
           keyringName = keyringName
         )
         jobContext$moduleExecutionSettings$connectionDetails <- connectionDetails
       } else {
-        resultsConnectionDetails <- Strategus::retrieveConnectionDetails(
+        resultsConnectionDetails <- retrieveConnectionDetails(
           connectionDetailsReference = jobContext$moduleExecutionSettings$resultsConnectionDetailsReference,
           keyringName = keyringName
         )