Workaround for changed column names in DQD 2.1

See issue OHDSI#30. The fix is borrowed from OHDSI#35.
TuftsCTSI · Apr 26, 2023 · 25b0957 · 25b0957
1 parent 8882e02
commit 25b0957
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/R/AugmentConceptFiles.R b/R/AugmentConceptFiles.R
@@ -39,7 +39,7 @@ augmentConceptFiles <- function(releaseFolder) {
     results <- dataQualityResults$CheckResults
 
     # augment achilles concept files with data quality failure count for relevant concept checks
-    conceptAggregates <- results %>% filter(!is.na(results$CONCEPT_ID) && results$FAILED==1) %>% count(CONCEPT_ID,tolower(CDM_TABLE_NAME))
+    conceptAggregates <- results %>% filter(!is.na(results$conceptId) && results$failed==1) %>% count(conceptId,tolower(cdmTableName))
     names(conceptAggregates) <- c("concept_id","cdm_table_name", "count_failed")
     writeLines(paste0(nrow(conceptAggregates), " concept level data quality issues found."))
     if (nrow(conceptAggregates) > 0) {

diff --git a/R/BuildNetworkPerformanceIndex.R b/R/BuildNetworkPerformanceIndex.R
@@ -65,8 +65,8 @@ buildNetworkPerformanceIndex <-
 
               performanceTable <- merge(x=performanceTable,y=analysisDetails,by="TASK",all.x=TRUE)
 
-              dqdTable <- dplyr::select(dqdData, c("CheckResults.checkId", "CheckResults.EXECUTION_TIME", "CheckResults.CATEGORY")) %>%
-                rename(TASK = CheckResults.checkId, TIMING = CheckResults.EXECUTION_TIME, CATEGORY = CheckResults.CATEGORY) %>% mutate(PACKAGE = "DQD") %>%
+              dqdTable <- dplyr::select(dqdData, c("CheckResults.checkId", "CheckResults.executionTime", "CheckResults.category")) %>%
+                rename(TASK = CheckResults.checkId, TIMING = CheckResults.executionTime, CATEGORY = CheckResults.category) %>% mutate(PACKAGE = "DQD") %>%
                 mutate_at("TIMING", str_replace, " secs", "")
 
               mergedTable <- rbind(performanceTable, dqdTable)