Workaround for changed column names in DQD 2.1

See issue OHDSI#30. The fix is borrowed from OHDSI#35.
TuftsCTSI · Apr 26, 2023 · 6e0e034 · 6e0e034
1 parent 8882e02
commit 6e0e034
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/R/AugmentConceptFiles.R b/R/AugmentConceptFiles.R
@@ -36,7 +36,9 @@ augmentConceptFiles <- function(releaseFolder) {
   if (file.exists(dataQualityResultsFile)) {
     writeLines("updating concept files with data quality results")
     dataQualityResults <- jsonlite::fromJSON(dataQualityResultsFile)
-    results <- dataQualityResults$CheckResults
+    results <- dataQualityResults$CheckResults %>%
+      dplyr::rename_with(SqlRender::camelCaseToSnakeCase) %>%
+      dplyr::rename_with(toupper)
 
     # 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))

diff --git a/R/BuildNetworkPerformanceIndex.R b/R/BuildNetworkPerformanceIndex.R
@@ -66,7 +66,7 @@ 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") %>%
+                rename(TASK = CheckResults.checkId, TIMING = CheckResults.executionTime, CATEGORY = CheckResults.category) %>% mutate(PACKAGE = "DQD") %>%
                 mutate_at("TIMING", str_replace, " secs", "")
 
               mergedTable <- rbind(performanceTable, dqdTable)