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Workaround for changed column names in DQD 2.1
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See issue OHDSI#30.  The fix is borrowed from
OHDSI#35.
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xitology committed Apr 26, 2023
1 parent 8882e02 commit 6d8c4a2
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion R/AugmentConceptFiles.R
Original file line number Diff line number Diff line change
Expand Up @@ -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))
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