Workaround for changed column names in DQD 2.1

See issue OHDSI#30. The fix is borrowed from OHDSI#35.
TuftsCTSI · Apr 26, 2023 · 68bf19b · 68bf19b
1 parent 8882e02
commit 68bf19b
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Showing 3 changed files with 9 additions and 9 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/BuildDataQualityHistoryIndex.R b/R/BuildDataQualityHistoryIndex.R
@@ -32,18 +32,18 @@ buildDataQualityHistoryIndex <-
     stratified_index <- data.table::data.table()
 
     addResultsToIndex <- function(json) {
-      cdm_source_name <- json$Metadata[1,"CDM_SOURCE_NAME"]
-      cdm_source_abbreviation <- json$Metadata[1,"CDM_SOURCE_ABBREVIATION"]
-      vocabulary_version <- json$Metadata[1,"VOCABULARY_VERSION"]
-      cdm_release_date <- format(lubridate::ymd(json$Metadata[1,"CDM_RELEASE_DATE"]),"%Y-%m-%d")
+      cdm_source_name <- json$Metadata[1,"cdmSourceName"]
+      cdm_source_abbreviation <- json$Metadata[1,"cdmSourceAbbreviation"]
+      vocabulary_version <- json$Metadata[1,"vocabularyVersion"]
+      cdm_release_date <- format(lubridate::ymd(json$Metadata[1,"cdmReleaseDate"]),"%Y-%m-%d")
       count_passed <- as.numeric(json$Overview$countPassed)
       count_failed <- as.numeric(json$Overview$countOverallFailed)
       count_total <- count_passed + count_failed
       dqd_execution_date <- format(lubridate::ymd_hms(json$endTimestamp),"%Y-%m-%d")
 
       stratifiedAggregates <- json$CheckResults %>%
-        filter(FAILED==1) %>%
-        group_by(CATEGORY, toupper(CDM_TABLE_NAME)) %>%
+        filter(failed==1) %>%
+        group_by(category, toupper(cdmTableName)) %>%
         summarise(count_value=n())
       names(stratifiedAggregates) <- c("category", "cdm_table_name", "count_value")
       stratifiedAggregates$dqd_execution_date <- dqd_execution_date

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)