reverted call to closure

OHDSI · Jan 6, 2025 · 6ab78fb · 6ab78fb
1 parent 8b1c39a
commit 6ab78fb
Show file tree

Hide file tree

Showing 2 changed files with 19 additions and 11 deletions.
diff --git a/R/RunAnalyses.R b/R/RunAnalyses.R
@@ -49,7 +49,6 @@ runSccAnalyses <- function(connectionDetails,
                            computeThreads = 1) {
 
   # Get negative controls
-
   checkmate::assertChoice(controlType, c("outcome", "exposure"))
   negatives <- list()
   for (exposureOutcome in exposureOutcomeList) {
@@ -123,13 +122,18 @@ runSccAnalyses <- function(connectionDetails,
                  resultExportPath = file.path(outputFolder, paste0("A_", refRow$analysisId)),
                  computeThreads = computeThreads)
     args <- append(args, getrunSelfControlledCohortArgs)
-    executionArgList[[length(executionArgList) + 1]] <- args
+    executionArgList[[length(executionArgList) + 1]] <- list(args = args)
+  }
+
+  exececuteScc <- function(params) {
+    sccResults <- do.call("runSelfControlledCohort", params$args)
   }
 
   if (length(executionArgList) != 0) {
     cluster <- ParallelLogger::makeCluster(analysisThreads)
     ParallelLogger::clusterRequire(cluster, "SelfControlledCohort")
-    dummy <- ParallelLogger::clusterApply(cluster, executionArgList, runSelfControlledCohort)
+
+    dummy <- ParallelLogger::clusterApply(cluster, executionArgList, exececuteScc)
     ParallelLogger::stopCluster(cluster)
   }
 

diff --git a/R/SelfControlledCohort.R b/R/SelfControlledCohort.R
@@ -56,7 +56,6 @@ computeIrrs <- function(estimates) {
 }
 
 
-
 batchComputeEstimates <- function(connection,
                                   computeThreads,
                                   resultsTable,
@@ -79,12 +78,12 @@ batchComputeEstimates <- function(connection,
       rows <- split(rows, rep_len(1:batches, nrow(rows)))
       rows <- ParallelLogger::clusterApply(cluster, rows, computeIrrs, progressBar = FALSE)
       rows <- do.call(rbind, rows)
+    }
 
-      if (position == 1) {
-        andromeda$estimates <- rows
-      } else {
-        Andromeda::appendToTable(andromeda$estimates, rows)
-      }
+    if (position == 1) {
+      andromeda$estimates <- rows
+    } else {
+      Andromeda::appendToTable(andromeda$estimates, rows)
     }
 
     return(rows)
@@ -100,6 +99,11 @@ batchComputeEstimates <- function(connection,
                                   transformFunctionArgs = args,
                                   append = FALSE)
 
+  if (is.null(andromeda$estimates)) {
+    ParallelLogger::logInfo("No effect estimates produced")
+    return(NULL)
+  }
+
   if (length(negativeControlPairs) > 0) {
     ncPairsDf <- do.call(rbind, lapply(negativeControlPairs, function(eo) {
       data.frame(targetCohortId = eo[[1]], outcomeCohortId = eo[[2]])
@@ -131,7 +135,7 @@ batchComputeEstimates <- function(connection,
       ncPairsDf |>
         dplyr::group_by(.data$outcomeCohortId) |>
         dplyr::group_map(function(data, outcomeCohortId) {
-
+          browser()
           estimates <- andromeda$estimates |>
             dplyr::filter(.data$outcomeCohortId == outcomeCohortId)
 
@@ -472,7 +476,7 @@ runSelfControlledCohort <- function(connectionDetails = NULL,
   DatabaseConnector::executeSql(connection, sql)
 
   resultExportManager$writeManifest(packageName = utils::packageName(),
-                             packageVersion = packageVersion(utils::packageName()))
+                                    packageVersion = packageVersion(utils::packageName()))
 
   delta <- Sys.time() - start
   ParallelLogger::logInfo(paste("Performing SCC analysis took", signif(delta, 3), attr(delta, "units")))