From c1a46ced1f01787d33510c8ccb497965e36458c8 Mon Sep 17 00:00:00 2001
From: Jamie Gilbert <JGilber2@its.jnj.com>
Date: Thu, 4 Jan 2024 13:54:56 -0800
Subject: [PATCH] Fixes to support big int cohorts ids

---
 R/Analyses.R          | 11 +++++------
 R/DataLoadingSaving.R |  6 +++---
 R/RunAnalyses.R       |  4 ++--
 3 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/R/Analyses.R b/R/Analyses.R
index 539a1204..cd2f7a64 100644
--- a/R/Analyses.R
+++ b/R/Analyses.R
@@ -210,19 +210,18 @@ createOutcome <- function(outcomeId,
                           riskWindowEnd = NULL,
                           endAnchor = NULL) {
   errorMessages <- checkmate::makeAssertCollection()
-  checkmate::assertInt(outcomeId, add = errorMessages)
+  checkmate::assertNumeric(outcomeId, add = errorMessages)
   checkmate::assertLogical(outcomeOfInterest, add = errorMessages)
   checkmate::assertNumeric(trueEffectSize, len = 1, null.ok = TRUE, add = errorMessages)
   checkmate::assertInt(riskWindowStart, null.ok = TRUE, add = errorMessages)
   checkmate::assertInt(riskWindowEnd, null.ok = TRUE, add = errorMessages)
   checkmate::reportAssertions(collection = errorMessages)
   if (!is.null(startAnchor) && !grepl("start$|end$", startAnchor, ignore.case = TRUE)) {
-    stop("startAnchor should have value 'cohort start' or 'cohort end'")
+    stop("startAnchor should have value \'cohort start\' or \'cohort end\'")
   }
   if (!is.null(riskWindowEnd) && !grepl("start$|end$", endAnchor, ignore.case = TRUE)) {
-    stop("endAnchor should have value 'cohort start' or 'cohort end'")
+    stop("endAnchor should have value \'cohort start\' or \'cohort end\'")
   }
-
   outcome <- list()
   for (name in names(formals(createOutcome))) {
     outcome[[name]] <- get(name)
@@ -259,8 +258,8 @@ createTargetComparatorOutcomes <- function(targetId,
                                            excludedCovariateConceptIds = c(),
                                            includedCovariateConceptIds = c()) {
   errorMessages <- checkmate::makeAssertCollection()
-  checkmate::assertInt(targetId, add = errorMessages)
-  checkmate::assertInt(comparatorId, add = errorMessages)
+  checkmate::assertNumeric(targetId, add = errorMessages)
+  checkmate::assertNumeric(comparatorId, add = errorMessages)
   checkmate::assertList(outcomes, min.len = 1, add = errorMessages)
   for (i in seq_along(outcomes)) {
     checkmate::assertClass(outcomes[[i]], "outcome", add = errorMessages)
diff --git a/R/DataLoadingSaving.R b/R/DataLoadingSaving.R
index a8f690c3..3c031d80 100644
--- a/R/DataLoadingSaving.R
+++ b/R/DataLoadingSaving.R
@@ -127,9 +127,9 @@ getDbCohortMethodData <- function(connectionDetails,
   checkmate::assertClass(connectionDetails, "ConnectionDetails", add = errorMessages)
   checkmate::assertCharacter(cdmDatabaseSchema, len = 1, add = errorMessages)
   checkmate::assertCharacter(tempEmulationSchema, len = 1, null.ok = TRUE, add = errorMessages)
-  checkmate::assertInt(targetId, add = errorMessages)
-  checkmate::assertInt(comparatorId, add = errorMessages)
-  checkmate::assertIntegerish(outcomeIds, add = errorMessages)
+  checkmate::assertNumeric(targetId, add = errorMessages)
+  checkmate::assertNumeric(comparatorId, add = errorMessages)
+  checkmate::assertNumeric(outcomeIds, add = errorMessages)
   checkmate::assertCharacter(studyStartDate, len = 1, add = errorMessages)
   checkmate::assertCharacter(studyEndDate, len = 1, add = errorMessages)
   checkmate::assertCharacter(exposureDatabaseSchema, len = 1, add = errorMessages)
diff --git a/R/RunAnalyses.R b/R/RunAnalyses.R
index 3b9f90ff..1c133c74 100644
--- a/R/RunAnalyses.R
+++ b/R/RunAnalyses.R
@@ -749,7 +749,7 @@ getPs <- function(psFile) {
 }
 
 doCreateCmDataObject <- function(params) {
-  ParallelLogger::logDebug(sprintf("Calling getDbCohortMethodData() for targetId %d, comparatorId %d",
+  ParallelLogger::logDebug(sprintf("Calling getDbCohortMethodData() for targetId %s, comparatorId %s",
                                    params$args$targetId,
                                    params$args$comparatorId))
   cohortMethodData <- do.call("getDbCohortMethodData", params$args)
@@ -761,7 +761,7 @@ doCreateStudyPopObject <- function(params) {
   cohortMethodData <- getCohortMethodData(params$cohortMethodDataFile)
   args <- params$args
   args$cohortMethodData <- cohortMethodData
-  ParallelLogger::logDebug(sprintf("Calling createStudyPopulation() using %s for outcomeId %d",
+  ParallelLogger::logDebug(sprintf("Calling createStudyPopulation() using %s for outcomeId %s",
                                    params$cohortMethodDataFile,
                                    args$outcomeId))
   studyPop <- do.call("createStudyPopulation", args)