From 0809aced8602745a066fabb20dce6ea7af27d378 Mon Sep 17 00:00:00 2001
From: keesvanbochove <kees@thehyve.nl>
Date: Fri, 1 Oct 2021 23:38:13 +0200
Subject: [PATCH] A few additional fixes for data.table usage

---
 R/FeatureConstruction.R                            |  4 ++--
 R/ResourceFiles.R                                  | 12 ++++++------
 R/RunStudy.R                                       |  4 ++--
 inst/shiny/PioneerWatchfulWaitingExplorer/server.R |  1 -
 4 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/R/FeatureConstruction.R b/R/FeatureConstruction.R
index 3687d2f77..489f3c0de 100644
--- a/R/FeatureConstruction.R
+++ b/R/FeatureConstruction.R
@@ -107,9 +107,9 @@ featureWindowsTempTableSql <- function(connection, featureWindows, oracleTempSch
 getAllFeatures <- function() {
   colNames <- c("name", "cohortId") # Use this to subset to the columns of interest
   cohortBasedStrata <- getCohortBasedStrata()
-  cohortBasedStrata <- cohortBasedStrata[, match(colNames, names(cohortBasedStrata))]
+  cohortBasedStrata <- cohortBasedStrata[, ..colNames]
   cohortBasedFeatures <- getFeatures()
-  cohortBasedFeatures <- cohortBasedFeatures[, match(colNames, names(cohortBasedFeatures))]
+  cohortBasedFeatures <- cohortBasedFeatures[, ..colNames]
   features <- rbind(cohortBasedStrata, cohortBasedFeatures)
   return(features)  
 }
diff --git a/R/ResourceFiles.R b/R/ResourceFiles.R
index 0470479ab..3c6183c72 100644
--- a/R/ResourceFiles.R
+++ b/R/ResourceFiles.R
@@ -52,10 +52,10 @@ getCohortsToCreate <- function(cohortGroups = getCohortGroups()) {
 getAllStrata <- function() {
   colNames <- c("name", "cohortId", "generationScript") # Use this to subset to the columns of interest
   bulkStrata <- getBulkStrata()
-  bulkStrata <- bulkStrata[, match(colNames, names(bulkStrata))]
+  bulkStrata <- bulkStrata[, ..colNames]
   atlasCohortStrata <- getCohortBasedStrata()
   atlasCohortStrata$generationScript <- paste0(atlasCohortStrata$cohortId, ".sql")
-  atlasCohortStrata <- atlasCohortStrata[, match(colNames, names(atlasCohortStrata))]
+  atlasCohortStrata <- atlasCohortStrata[, ..colNames]
   strata <- rbind(bulkStrata, atlasCohortStrata)
   return(strata)  
 }
@@ -64,8 +64,8 @@ getAllStudyCohorts <- function() {
   cohortsToCreate <- getCohortsToCreate()
   targetStrataXref <- getTargetStrataXref()
   colNames <- c("name", "cohortId")
-  cohortsToCreate <- cohortsToCreate[, match(colNames, names(cohortsToCreate))]
-  targetStrataXref <- targetStrataXref[, match(colNames, names(targetStrataXref))]
+  cohortsToCreate <- cohortsToCreate[, ..colNames]
+  targetStrataXref <- targetStrataXref[, ..colNames]
   allCohorts <- rbind(cohortsToCreate, targetStrataXref)
   return(allCohorts)
 }
@@ -82,12 +82,12 @@ getAllStudyCohortsWithDetails <- function() {
   cohortsToCreate$strataCohortId <- 0
   cohortsToCreate$strataCohortName <- "All"
   cohortsToCreate <- dplyr::rename(cohortsToCreate, cohortName = "name")
-  cohortsToCreate <- cohortsToCreate[, match(colNames, names(cohortsToCreate))]
+  cohortsToCreate <- cohortsToCreate[, ..colNames]
   # Format - targetStrataXref
   stratifiedCohorts <- dplyr::inner_join(targetStrataXref, cohortsToCreate[,c("targetCohortId", "targetCohortName")], by = c("targetId" = "targetCohortId"))
   stratifiedCohorts <- dplyr::inner_join(stratifiedCohorts, allStrata[,c("cohortId", "name")], by=c("strataId" = "cohortId"))
   stratifiedCohorts <- dplyr::rename(stratifiedCohorts, targetCohortId="targetId",strataCohortId="strataId",cohortName="name.x",strataCohortName="name.y")
-  stratifiedCohorts <- stratifiedCohorts[,match(colNames, names(stratifiedCohorts))]
+  stratifiedCohorts <- stratifiedCohorts[,..colNames]
   # Bind
   allCohorts <- rbind(cohortsToCreate, stratifiedCohorts)
   return(allCohorts)
diff --git a/R/RunStudy.R b/R/RunStudy.R
index e662cb2cd..69643badb 100644
--- a/R/RunStudy.R
+++ b/R/RunStudy.R
@@ -225,7 +225,7 @@ runStudy <- function(connectionDetails = NULL,
   for(analysis in DistribAnalyses){
     outcome <- gsub("TimeTo", "", analysis)
     outcome <- substring(SqlRender::camelCaseToTitleCase(outcome), 2)
-    outcomeId <- outcomes[tolower(outcomes$name) == tolower(outcome), "cohortId"]
+    outcomeId <- outcomes[tolower(outcomes$name) == tolower(outcome), "cohortId"][[1]]
     
     if (length(outcomeId) == 0 & analysis %in% outcomeBasedAnalyses){
       next
@@ -537,7 +537,7 @@ loadCohortsForExportFromPackage <- function(cohortIds) {
                   strataId = NULL)
   
   cols <- names(cohorts)
-  cohorts <- rbind(cohorts, targetStrataXref[cols])
+  cohorts <- rbind(cohorts, targetStrataXref[,..cols])
   
   if (!is.null(cohortIds)) {
     cohorts <- cohorts[cohorts$cohortId %in% cohortIds, ]
diff --git a/inst/shiny/PioneerWatchfulWaitingExplorer/server.R b/inst/shiny/PioneerWatchfulWaitingExplorer/server.R
index 11a41072a..f5b47a86c 100644
--- a/inst/shiny/PioneerWatchfulWaitingExplorer/server.R
+++ b/inst/shiny/PioneerWatchfulWaitingExplorer/server.R
@@ -354,7 +354,6 @@ shinyServer(function(input, output, session) {
   
   
   getMetricsTable <- reactive ({
-    browser()
     target_id <- cohortCount[cohortCount$databaseId %in% input$databasesMetricsDistribution 
                              & cohortCount$cohortId %in% cohortIdMetricsDistribution(), ][[1]]
     metricsTable <- metricsDistribution %>% dplyr::filter(cohortDefinitionId == target_id,