diff --git a/NAMESPACE b/NAMESPACE index 929c06a7..8fc8e256 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -41,8 +41,7 @@ import(ParallelLogger) import(SqlRender) import(dplyr) importFrom(data.table,fwrite) -importFrom(dplyr,desc) -importFrom(dplyr,ntile) +importFrom(dplyr,rename_with) importFrom(rlang,.data) importFrom(stats,aggregate) importFrom(stats,cycle) diff --git a/R/exportToAres.R b/R/exportToAres.R index 35ee5b71..081242bf 100644 --- a/R/exportToAres.R +++ b/R/exportToAres.R @@ -9,6 +9,11 @@ normalizeEmptyValue <- function(x) { } } +querySqlWithUpperCaseColumns <- function(...) { + DatabaseConnector::querySql(...) |> + dplyr::rename_with(toupper) +} + saveConceptsAsJson <- function( concept_id, reports, @@ -153,24 +158,24 @@ generateAOProcedureReports <- function(connectionDetails, proceduresData, cdmDat conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataProceduresByType <- - DatabaseConnector::querySql(conn, queryProceduresByType) %>% + querySqlWithUpperCaseColumns(conn, queryProceduresByType) %>% dplyr::select(c("CONCEPT_ID" = "PROCEDURE_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataAgeAtFirstOccurrence <- - DatabaseConnector::querySql(conn, queryAgeAtFirstOccurrence) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstOccurrence) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataProcedureFrequencyDistribution <- - DatabaseConnector::querySql(conn, queryProcedureFrequencyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryProcedureFrequencyDistribution) %>% dplyr::select(c("CONCEPT_ID", "Y_NUM_PERSONS", "X_COUNT")) @@ -260,7 +265,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results vocab_database_schema = vocabDatabaseSchema ) - personSummaryData <- DatabaseConnector::querySql(conn, renderedSql) + personSummaryData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$SUMMARY <- personSummaryData renderedSql <- SqlRender::loadRenderTranslateSql( @@ -272,7 +277,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - ageGenderData <- DatabaseConnector::querySql(conn, renderedSql) + ageGenderData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$AGE_GENDER_DATA <- ageGenderData renderedSql <- SqlRender::loadRenderTranslateSql( @@ -284,7 +289,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - genderData <- DatabaseConnector::querySql(conn, renderedSql) + genderData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$GENDER_DATA <- genderData renderedSql <- SqlRender::loadRenderTranslateSql( @@ -296,7 +301,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - raceData <- DatabaseConnector::querySql(conn, renderedSql) + raceData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$RACE_DATA <- raceData renderedSql <- SqlRender::loadRenderTranslateSql( @@ -308,7 +313,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - ethnicityData <- DatabaseConnector::querySql(conn, renderedSql) + ethnicityData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$ETHNICITY_DATA <- ethnicityData @@ -321,7 +326,7 @@ generateAOPersonReport <- function(connectionDetails, cdmDatabaseSchema, results results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - birthYearData <- DatabaseConnector::querySql(conn, renderedSql) + birthYearData <- querySqlWithUpperCaseColumns(conn, renderedSql) output$BIRTH_YEAR_DATA <- birthYearData return(output) } @@ -337,7 +342,7 @@ generateAOAchillesPerformanceReport <- function(connection, cdmDatabaseSchema, r vocab_database_schema = vocabDatabaseSchema ) - dataPerformance <- DatabaseConnector::querySql(connection, queryAchillesPerformance) + dataPerformance <- querySqlWithUpperCaseColumns(connection, queryAchillesPerformance) names(dataPerformance) <- c("analysis_id", "analysis_name", "category", "elapsed_seconds") dataPerformance$elapsed_seconds <- format(round(as.numeric(dataPerformance$elapsed_seconds), digits = 2), nsmall = 2) return(dataPerformance) @@ -374,10 +379,10 @@ generateAODeathReport <- function(connection, cdmDatabaseSchema, resultsDatabase results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - deathByTypeData <- DatabaseConnector::querySql(connection, queryDeathByType) - prevalenceByGenderAgeYearData <- DatabaseConnector::querySql(connection, queryPrevalenceByGenderAgeYear) - prevalenceByMonthData <- DatabaseConnector::querySql(connection, queryPrevalenceByMonth) - ageAtDeathData <- DatabaseConnector::querySql(connection, queryAgeAtDeath) + deathByTypeData <- querySqlWithUpperCaseColumns(connection, queryDeathByType) + prevalenceByGenderAgeYearData <- querySqlWithUpperCaseColumns(connection, queryPrevalenceByGenderAgeYear) + prevalenceByMonthData <- querySqlWithUpperCaseColumns(connection, queryPrevalenceByMonth) + ageAtDeathData <- querySqlWithUpperCaseColumns(connection, queryAgeAtDeath) output <- { } output$PREVALENCE_BY_GENDER_AGE_YEAR <- prevalenceByGenderAgeYearData @@ -395,7 +400,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - ageAtFirstObservationData <- DatabaseConnector::querySql(connection, renderedSql) + ageAtFirstObservationData <- querySqlWithUpperCaseColumns(connection, renderedSql) output$AGE_AT_FIRST_OBSERVATION <- ageAtFirstObservationData renderedSql <- SqlRender::loadRenderTranslateSql( @@ -405,7 +410,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - ageByGenderData <- DatabaseConnector::querySql(connection, renderedSql) + ageByGenderData <- querySqlWithUpperCaseColumns(connection, renderedSql) output$AGE_BY_GENDER <- ageByGenderData observationLengthHist <- { } @@ -415,7 +420,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - observationLengthStats <- DatabaseConnector::querySql(connection, renderedSql) + observationLengthStats <- querySqlWithUpperCaseColumns(connection, renderedSql) observationLengthHist$MIN <- observationLengthStats$MIN_VALUE observationLengthHist$MAX <- observationLengthStats$MAX_VALUE observationLengthHist$INTERVAL_SIZE <- observationLengthStats$INTERVAL_SIZE @@ -427,7 +432,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - observationLengthData <- DatabaseConnector::querySql(connection, renderedSql) + observationLengthData <- querySqlWithUpperCaseColumns(connection, renderedSql) output$OBSERVATION_LENGTH_HISTOGRAM <- observationLengthHist renderedSql <- SqlRender::loadRenderTranslateSql( @@ -436,7 +441,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - cumulativeDurationData <- DatabaseConnector::querySql(connection, renderedSql) + cumulativeDurationData <- querySqlWithUpperCaseColumns(connection, renderedSql) cumulativeDurationData$X_LENGTH_OF_OBSERVATION <- cumulativeDurationData$X_LENGTH_OF_OBSERVATION / 365.25 cumulativeDurationData$SERIES_NAME <- NULL names(cumulativeDurationData) <- c("YEARS", "PERCENT_PEOPLE") @@ -449,7 +454,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - opLengthByGenderData <- DatabaseConnector::querySql(connection, renderedSql) + opLengthByGenderData <- querySqlWithUpperCaseColumns(connection, renderedSql) opLengthByGenderData$MIN_VALUE <- opLengthByGenderData$MIN_VALUE / 365.25 opLengthByGenderData$P10_VALUE <- opLengthByGenderData$P10_VALUE / 365.25 opLengthByGenderData$P25_VALUE <- opLengthByGenderData$P25_VALUE / 365.25 @@ -466,7 +471,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - opLengthByAgeData <- DatabaseConnector::querySql(connection, renderedSql) + opLengthByAgeData <- querySqlWithUpperCaseColumns(connection, renderedSql) opLengthByAgeData$MIN_VALUE <- opLengthByAgeData$MIN_VALUE / 365.25 opLengthByAgeData$P10_VALUE <- opLengthByAgeData$P10_VALUE / 365.25 opLengthByAgeData$P25_VALUE <- opLengthByAgeData$P25_VALUE / 365.25 @@ -483,7 +488,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - observedByYearStats <- DatabaseConnector::querySql(connection, renderedSql) + observedByYearStats <- querySqlWithUpperCaseColumns(connection, renderedSql) observedByYearHist$MIN <- observedByYearStats$MIN_VALUE observedByYearHist$MAX <- observedByYearStats$MAX_VALUE observedByYearHist$INTERVAL_SIZE <- observedByYearStats$INTERVAL_SIZE @@ -495,7 +500,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - observedByYearData <- DatabaseConnector::querySql(connection, renderedSql) + observedByYearData <- querySqlWithUpperCaseColumns(connection, renderedSql) observedByYearHist$DATA <- observedByYearData output$OBSERVED_BY_YEAR_HISTOGRAM <- observedByYearHist @@ -506,7 +511,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - observedByMonth <- DatabaseConnector::querySql(connection, renderedSql) + observedByMonth <- querySqlWithUpperCaseColumns(connection, renderedSql) output$OBSERVED_BY_MONTH <- observedByMonth renderedSql <- SqlRender::loadRenderTranslateSql( @@ -515,7 +520,7 @@ generateAOObservationPeriodReport <- function(connection, cdmDatabaseSchema, res dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - personPeriodsData <- DatabaseConnector::querySql(connection, renderedSql) + personPeriodsData <- querySqlWithUpperCaseColumns(connection, renderedSql) output$PERSON_PERIODS_DATA <- personPeriodsData return(output) } @@ -563,7 +568,7 @@ generateAOVisitReports <- function(connectionDetails, cdmDatabaseSchema, results conn <- DatabaseConnector::connect(connectionDetails) dataVisits <- - DatabaseConnector::querySql(conn, queryVisits) %>% + querySqlWithUpperCaseColumns(conn, queryVisits) %>% dplyr::rename(dplyr::all_of(c("CONCEPT_NAME" = "CONCEPT_PATH"))) %>% dplyr::select( "CONCEPT_ID", @@ -577,16 +582,16 @@ generateAOVisitReports <- function(connectionDetails, cdmDatabaseSchema, results } dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataVisitDurationByType <- - DatabaseConnector::querySql(conn, queryVisitDurationByType) %>% + querySqlWithUpperCaseColumns(conn, queryVisitDurationByType) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataAgeAtFirstOccurrence <- - DatabaseConnector::querySql(conn, queryAgeAtFirstOccurrence) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstOccurrence) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) uniqueConcepts <- data.frame( @@ -695,7 +700,7 @@ generateAOVisitDetailReports <- function(connectionDetails, cdmDatabaseSchema, r conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataVisitDetails <- - DatabaseConnector::querySql(conn, queryVisitDetails) %>% + querySqlWithUpperCaseColumns(conn, queryVisitDetails) %>% dplyr::rename(dplyr::all_of(c("CONCEPT_NAME" = "CONCEPT_PATH"))) %>% dplyr::select( "CONCEPT_ID", @@ -710,16 +715,16 @@ generateAOVisitDetailReports <- function(connectionDetails, cdmDatabaseSchema, r } dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataVisitDetailDurationByType <- - DatabaseConnector::querySql(conn, queryVisitDetailDurationByType) %>% + querySqlWithUpperCaseColumns(conn, queryVisitDetailDurationByType) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataAgeAtFirstOccurrence <- - DatabaseConnector::querySql(conn, queryAgeAtFirstOccurrence) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstOccurrence) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) uniqueConcepts <- data.frame( @@ -785,7 +790,7 @@ generateAOMetadataReport <- function(connection, cdmDatabaseSchema, outputPath) dbms = connection@dbms, cdm_database_schema = cdmDatabaseSchema ) - dataMetadata <- DatabaseConnector::querySql(connection, queryMetadata) + dataMetadata <- querySqlWithUpperCaseColumns(connection, queryMetadata) return(dataMetadata) } } @@ -838,19 +843,19 @@ generateAOObservationReports <- function(connectionDetails, observationsData, cd conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataObservationsByType <- - DatabaseConnector::querySql(conn, queryObservationsByType) %>% + querySqlWithUpperCaseColumns(conn, queryObservationsByType) %>% dplyr::select(c("CONCEPT_ID" = "OBSERVATION_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataAgeAtFirstOccurrence <- - DatabaseConnector::querySql(conn, queryAgeAtFirstOccurrence) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstOccurrence) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataObsFrequencyDistribution <- - DatabaseConnector::querySql(conn, queryObsFrequencyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryObsFrequencyDistribution) %>% dplyr::select(c("CONCEPT_ID", "Y_NUM_PERSONS", "X_COUNT")) uniqueConcepts <- data.frame( @@ -933,7 +938,7 @@ generateAOCdmSourceReport <- function(connection, cdmDatabaseSchema, outputPath) cdm_database_schema = cdmDatabaseSchema ) - dataCdmSource <- DatabaseConnector::querySql(connection, queryCdmSource) + dataCdmSource <- querySqlWithUpperCaseColumns(connection, queryCdmSource) return(dataCdmSource) } } @@ -1037,38 +1042,38 @@ generateAOMeasurementReports <- function(connectionDetails, dataMeasurements, cd conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) if (nrow(dataPrevalenceByMonth) == 0) { return(NULL) } dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataMeasurementsByType <- - DatabaseConnector::querySql(conn, queryMeasurementsByType) %>% + querySqlWithUpperCaseColumns(conn, queryMeasurementsByType) %>% dplyr::select(c("CONCEPT_ID" = "MEASUREMENT_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataAgeAtFirstOccurrence <- - DatabaseConnector::querySql(conn, queryAgeAtFirstOccurrence) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstOccurrence) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataRecordsByUnit <- - DatabaseConnector::querySql(conn, queryRecordsByUnit) %>% + querySqlWithUpperCaseColumns(conn, queryRecordsByUnit) %>% dplyr::select(c("CONCEPT_ID" = "MEASUREMENT_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE", "UNIT_CONCEPT_ID")) dataMeasurementValueDistribution <- - DatabaseConnector::querySql(conn, queryMeasurementValueDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryMeasurementValueDistribution) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE", "UNIT_CONCEPT_ID")) dataLowerLimitDistribution <- - DatabaseConnector::querySql(conn, queryLowerLimitDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryLowerLimitDistribution) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataUpperLimitDistribution <- - DatabaseConnector::querySql(conn, queryUpperLimitDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryUpperLimitDistribution) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataValuesRelativeToNorm <- - DatabaseConnector::querySql(conn, queryValuesRelativeToNorm) %>% + querySqlWithUpperCaseColumns(conn, queryValuesRelativeToNorm) %>% dplyr::select(c("CONCEPT_ID" = "MEASUREMENT_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataFrequencyDistribution <- - DatabaseConnector::querySql(conn, queryFrequencyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryFrequencyDistribution) %>% dplyr::select(c("CONCEPT_ID", "Y_NUM_PERSONS", "X_COUNT")) uniqueConcepts <- data.frame( @@ -1223,16 +1228,16 @@ generateAODrugEraReports <- function(connectionDetails, dataDrugEra, cdmDatabase conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataAgeAtFirstExposure <- - DatabaseConnector::querySql(conn, queryAgeAtFirstExposure) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstExposure) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataLengthOfEra <- - DatabaseConnector::querySql(conn, queryLengthOfEra) %>% + querySqlWithUpperCaseColumns(conn, queryLengthOfEra) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) uniqueConcepts <- data.frame( @@ -1367,32 +1372,32 @@ generateAODrugReports <- function(connectionDetails, dataDrugs, cdmDatabaseSchem conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) if (nrow(dataPrevalenceByMonth) == 0) { return(NULL) } dataAgeAtFirstExposure <- - DatabaseConnector::querySql(conn, queryAgeAtFirstExposure) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstExposure) %>% dplyr::select(c("CONCEPT_ID" = "DRUG_CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataDaysSupplyDistribution <- - DatabaseConnector::querySql(conn, queryDaysSupplyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryDaysSupplyDistribution) %>% dplyr::select(c("CONCEPT_ID" = "DRUG_CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataDrugsByType <- - DatabaseConnector::querySql(conn, queryDrugsByType) %>% + querySqlWithUpperCaseColumns(conn, queryDrugsByType) %>% dplyr::select(c("CONCEPT_ID" = "DRUG_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataQuantityDistribution <- - DatabaseConnector::querySql(conn, queryQuantityDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryQuantityDistribution) %>% dplyr::select(c("CONCEPT_ID" = "DRUG_CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataRefillsDistribution <- - DatabaseConnector::querySql(conn, queryRefillsDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryRefillsDistribution) %>% dplyr::select(c("CONCEPT_ID" = "DRUG_CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataDrugFrequencyDistribution <- - DatabaseConnector::querySql(conn, queryDrugFrequencyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryDrugFrequencyDistribution) %>% dplyr::select(c("CONCEPT_ID", "Y_NUM_PERSONS", "X_COUNT")) uniqueConcepts <- data.frame( @@ -1539,19 +1544,19 @@ generateAODeviceReports <- function(connectionDetails, dataDevices, cdmDatabaseS conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataAgeAtFirstExposure <- - DatabaseConnector::querySql(conn, queryAgeAtFirstExposure) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstExposure) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataDevicesByType <- - DatabaseConnector::querySql(conn, queryDevicesByType) %>% + querySqlWithUpperCaseColumns(conn, queryDevicesByType) %>% dplyr::select(c("CONCEPT_ID" = "DEVICE_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataDeviceFrequencyDistribution <- - DatabaseConnector::querySql(conn, queryDeviceFrequencyDistribution) %>% + querySqlWithUpperCaseColumns(conn, queryDeviceFrequencyDistribution) %>% dplyr::select(c("CONCEPT_ID", "Y_NUM_PERSONS", "X_COUNT")) uniqueConcepts <- data.frame( @@ -1670,20 +1675,20 @@ generateAOConditionReports <- function(connectionDetails, dataConditions, cdmDat conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) if (nrow(dataPrevalenceByMonth) == 0) { return(NULL) } dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataConditionsByType <- - DatabaseConnector::querySql(conn, queryConditionsByType) %>% + querySqlWithUpperCaseColumns(conn, queryConditionsByType) %>% dplyr::select(c("CONCEPT_ID" = "CONDITION_CONCEPT_ID", "CONCEPT_NAME", "COUNT_VALUE")) dataAgeAtFirstDiagnosis <- - DatabaseConnector::querySql(conn, queryAgeAtFirstDiagnosis) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstDiagnosis) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) uniqueConcepts <- data.frame( @@ -1798,16 +1803,16 @@ generateAOConditionEraReports <- function(connectionDetails, dataConditionEra, c conn <- DatabaseConnector::connect(connectionDetails) on.exit(DatabaseConnector::disconnect(connection = conn)) dataPrevalenceByGenderAgeYear <- - DatabaseConnector::querySql(conn, queryPrevalenceByGenderAgeYear) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByGenderAgeYear) %>% dplyr::select(c("CONCEPT_ID", "TRELLIS_NAME", "SERIES_NAME", "X_CALENDAR_YEAR", "Y_PREVALENCE_1000PP")) dataPrevalenceByMonth <- - DatabaseConnector::querySql(conn, queryPrevalenceByMonth) %>% + querySqlWithUpperCaseColumns(conn, queryPrevalenceByMonth) %>% dplyr::select(c("CONCEPT_ID", "X_CALENDAR_MONTH", "Y_PREVALENCE_1000PP")) dataLengthOfEra <- - DatabaseConnector::querySql(conn, queryLengthOfEra) %>% + querySqlWithUpperCaseColumns(conn, queryLengthOfEra) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) dataAgeAtFirstDiagnosis <- - DatabaseConnector::querySql(conn, queryAgeAtFirstDiagnosis) %>% + querySqlWithUpperCaseColumns(conn, queryAgeAtFirstDiagnosis) %>% dplyr::select(c("CONCEPT_ID", "CATEGORY", "MIN_VALUE", "P10_VALUE", "P25_VALUE", "MEDIAN_VALUE", "P75_VALUE", "P90_VALUE", "MAX_VALUE")) uniqueConcepts <- data.frame( @@ -1883,7 +1888,7 @@ generateDataDensityTotal <- function(connection, resultsDatabaseSchema) { results_database_schema = resultsDatabaseSchema ) - totalRecordsData <- DatabaseConnector::querySql(connection, renderedSql) + totalRecordsData <- querySqlWithUpperCaseColumns(connection, renderedSql) colnames(totalRecordsData) <- c("domain", "date", "records") totalRecordsData$date <- lubridate::parse_date_time(totalRecordsData$date, "ym") @@ -1901,7 +1906,7 @@ generateLocationData <- function(connection, resultsDatabaseSchema) { results_database_schema = resultsDatabaseSchema ) - locationData <- DatabaseConnector::querySql(connection, renderedSql) + locationData <- querySqlWithUpperCaseColumns(connection, renderedSql) return(locationData) } @@ -1913,7 +1918,7 @@ generateDataDensityRecordsPerPerson <- function(connection, resultsDatabaseSchem results_database_schema = resultsDatabaseSchema ) - recordsPerPerson <- DatabaseConnector::querySql(connection, renderedSql) + recordsPerPerson <- querySqlWithUpperCaseColumns(connection, renderedSql) colnames(recordsPerPerson) <- c("domain", "date", "records") recordsPerPerson$date <- lubridate::parse_date_time(recordsPerPerson$date, "ym") recordsPerPerson$records <- round(recordsPerPerson$records, 2) @@ -1927,7 +1932,7 @@ generateDataDensityConceptsPerPerson <- function(connection, resultsDatabaseSche dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - conceptsPerPerson <- DatabaseConnector::querySql(connection, renderedSql) + conceptsPerPerson <- querySqlWithUpperCaseColumns(connection, renderedSql) return(conceptsPerPerson) # data.table::fwrite(conceptsPerPerson, file=paste0(sourceOutputPath, "/datadensity-concepts-per-person.csv")) # dbWriteTable(duckdbCon, "concepts_per_person", conceptsPerPerson) @@ -1940,7 +1945,7 @@ generateDataDensityDomainsPerPerson <- function(connection, resultsDatabaseSchem dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - domainsPerPerson <- DatabaseConnector::querySql(connection, renderedSql) + domainsPerPerson <- querySqlWithUpperCaseColumns(connection, renderedSql) domainsPerPerson$PERCENT_VALUE <- round(as.numeric(domainsPerPerson$PERCENT_VALUE), 2) return(domainsPerPerson) # data.table::fwrite(domainsPerPerson, file=paste0(sourceOutputPath, "/datadensity-domains-per-person.csv")) @@ -1955,7 +1960,7 @@ generateDomainSummaryConditions <- function(connection, resultsDatabaseSchema, v results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataConditions <- DatabaseConnector::querySql(connection, queryConditions) + dataConditions <- querySqlWithUpperCaseColumns(connection, queryConditions) dataConditions$PERCENT_PERSONS <- format(round(dataConditions$PERCENT_PERSONS, 4), nsmall = 4) dataConditions$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataConditions$PERCENT_PERSONS), 10) dataConditions$RECORDS_PER_PERSON <- format(round(dataConditions$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -1973,7 +1978,7 @@ generateDomainSummaryConditionEras <- function(connection, resultsDatabaseSchema results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataConditionEra <- DatabaseConnector::querySql(connection, queryConditionEra) + dataConditionEra <- querySqlWithUpperCaseColumns(connection, queryConditionEra) dataConditionEra$PERCENT_PERSONS <- format(round(dataConditionEra$PERCENT_PERSONS, 4), nsmall = 4) dataConditionEra$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataConditionEra$PERCENT_PERSONS), 10) dataConditionEra$RECORDS_PER_PERSON <- format(round(dataConditionEra$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -1990,7 +1995,7 @@ generateDomainSummaryDrugs <- function(connection, resultsDatabaseSchema, vocabD results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataDrugs <- DatabaseConnector::querySql(connection, queryDrugs) + dataDrugs <- querySqlWithUpperCaseColumns(connection, queryDrugs) dataDrugs$PERCENT_PERSONS <- format(round(dataDrugs$PERCENT_PERSONS, 4), nsmall = 4) dataDrugs$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataDrugs$PERCENT_PERSONS), 10) dataDrugs$RECORDS_PER_PERSON <- format(round(dataDrugs$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2007,7 +2012,7 @@ generateDomainDrugStratification <- function(connection, resultsDatabaseSchema, results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataDrugType <- DatabaseConnector::querySql(connection, queryDrugType) + dataDrugType <- querySqlWithUpperCaseColumns(connection, queryDrugType) return(dataDrugType) # data.table::fwrite(dataDrugType, file=paste0(sourceOutputPath, "/domain-drug-stratification.csv")) } @@ -2020,7 +2025,7 @@ generateDomainSummaryDrugEra <- function(connection, resultsDatabaseSchema, voca results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataDrugEra <- DatabaseConnector::querySql(connection, queryDrugEra) + dataDrugEra <- querySqlWithUpperCaseColumns(connection, queryDrugEra) dataDrugEra$PERCENT_PERSONS <- format(round(dataDrugEra$PERCENT_PERSONS, 4), nsmall = 4) dataDrugEra$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataDrugEra$PERCENT_PERSONS), 10) dataDrugEra$RECORDS_PER_PERSON <- format(round(dataDrugEra$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2037,7 +2042,7 @@ generateDomainSummaryMeasurements <- function(connection, resultsDatabaseSchema, results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataMeasurements <- DatabaseConnector::querySql(connection, queryMeasurements) + dataMeasurements <- querySqlWithUpperCaseColumns(connection, queryMeasurements) dataMeasurements$PERCENT_PERSONS <- format(round(dataMeasurements$PERCENT_PERSONS, 4), nsmall = 4) dataMeasurements$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataMeasurements$PERCENT_PERSONS), 10) dataMeasurements$RECORDS_PER_PERSON <- format(round(dataMeasurements$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2054,7 +2059,7 @@ generateDomainSummaryObservations <- function(connection, resultsDatabaseSchema, results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataObservations <- DatabaseConnector::querySql(connection, queryObservations) + dataObservations <- querySqlWithUpperCaseColumns(connection, queryObservations) dataObservations$PERCENT_PERSONS <- format(round(dataObservations$PERCENT_PERSONS, 4), nsmall = 4) dataObservations$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataObservations$PERCENT_PERSONS), 10) dataObservations$RECORDS_PER_PERSON <- format(round(dataObservations$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2071,7 +2076,7 @@ generateDomainSummaryVisitDetails <- function(connection, resultsDatabaseSchema, results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataVisitDetails <- DatabaseConnector::querySql(connection, queryVisitDetails) + dataVisitDetails <- querySqlWithUpperCaseColumns(connection, queryVisitDetails) dataVisitDetails$PERCENT_PERSONS <- format(round(dataVisitDetails$PERCENT_PERSONS, 4), nsmall = 4) dataVisitDetails$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataVisitDetails$PERCENT_PERSONS), 10) dataVisitDetails$RECORDS_PER_PERSON <- format(round(dataVisitDetails$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2089,7 +2094,7 @@ generateDomainSummaryVisits <- function(connection, resultsDatabaseSchema, vocab results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataVisits <- DatabaseConnector::querySql(connection, queryVisits) + dataVisits <- querySqlWithUpperCaseColumns(connection, queryVisits) dataVisits$PERCENT_PERSONS <- format(round(dataVisits$PERCENT_PERSONS, 4), nsmall = 4) dataVisits$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataVisits$PERCENT_PERSONS), 10) dataVisits$RECORDS_PER_PERSON <- format(round(dataVisits$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2107,7 +2112,7 @@ generateDomainVisitStratification <- function(connection, resultsDatabaseSchema, results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataVisits <- DatabaseConnector::querySql(connection, queryVisits) + dataVisits <- querySqlWithUpperCaseColumns(connection, queryVisits) return(dataVisits) # data.table::fwrite(dataVisits, file=paste0(sourceOutputPath, "/domain-visit-stratification.csv")) } @@ -2120,7 +2125,7 @@ generateDomainSummaryProcedures <- function(connection, resultsDatabaseSchema, v results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataProcedures <- DatabaseConnector::querySql(connection, queryProcedures) + dataProcedures <- querySqlWithUpperCaseColumns(connection, queryProcedures) dataProcedures$PERCENT_PERSONS <- format(round(dataProcedures$PERCENT_PERSONS, 4), nsmall = 4) dataProcedures$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataProcedures$PERCENT_PERSONS), 10) dataProcedures$RECORDS_PER_PERSON <- format(round(dataProcedures$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2137,7 +2142,7 @@ generateDomainSummaryDevices <- function(connection, resultsDatabaseSchema, voca results_database_schema = resultsDatabaseSchema, vocab_database_schema = vocabDatabaseSchema ) - dataDevices <- DatabaseConnector::querySql(connection, queryDevices) + dataDevices <- querySqlWithUpperCaseColumns(connection, queryDevices) dataDevices$PERCENT_PERSONS <- format(round(dataDevices$PERCENT_PERSONS, 4), nsmall = 4) dataDevices$PERCENT_PERSONS_NTILE <- dplyr::ntile(dplyr::desc(dataDevices$PERCENT_PERSONS), 10) dataDevices$RECORDS_PER_PERSON <- format(round(dataDevices$RECORDS_PER_PERSON, 1), nsmall = 1) @@ -2155,7 +2160,7 @@ generateDomainSummaryProvider <- function(connection, resultsDatabaseSchema, voc vocab_database_schema = vocabDatabaseSchema ) writeLines("Generating provider reports") - dataProviders <- DatabaseConnector::querySql(connection, queryProviders) + dataProviders <- querySqlWithUpperCaseColumns(connection, queryProviders) dataProviders$PERCENT_PERSONS <- format(round(dataProviders$PERCENT_PERSONS, 4), nsmall = 4) return(dataProviders) # data.table::fwrite(dataProviders, file=paste0(sourceOutputPath, "/domain-summary-provider.csv")) @@ -2169,7 +2174,7 @@ generateQualityCompleteness <- function(connection, resultsDatabaseSchema) { dbms = connection@dbms, results_database_schema = resultsDatabaseSchema ) - dataCompleteness <- DatabaseConnector::querySql(connection, queryCompleteness) + dataCompleteness <- querySqlWithUpperCaseColumns(connection, queryCompleteness) dataCompleteness <- dataCompleteness[order(-dataCompleteness$RECORD_COUNT), ] # prevent downstream crashes with large files if (nrow(dataCompleteness) > 100000) { @@ -2201,7 +2206,6 @@ generateQualityCompleteness <- function(connection, resultsDatabaseSchema) { #' #' @import DBI #' @importFrom data.table fwrite -#' @importFrom dplyr ntile desc #' @export exportToAres <- function( connectionDetails, @@ -2217,7 +2221,7 @@ exportToAres <- function( # generate a folder name for this release of the cdm characterization sql <- SqlRender::render(sql = "select * from @cdmDatabaseSchema.cdm_source;", cdmDatabaseSchema = cdmDatabaseSchema) sql <- SqlRender::translate(sql = sql, targetDialect = connectionDetails$dbms) - metadata <- DatabaseConnector::querySql(conn, sql) + metadata <- querySqlWithUpperCaseColumns(conn, sql) sourceKey <- gsub(" ", "_", metadata$CDM_SOURCE_ABBREVIATION) releaseDateKey <- format(lubridate::ymd(metadata$CDM_RELEASE_DATE), "%Y%m%d") sourceOutputPath <- file.path(outputPath, sourceKey, releaseDateKey) diff --git a/R/getTemporalData.r b/R/getTemporalData.r index bc5b0c6a..95e802c2 100644 --- a/R/getTemporalData.r +++ b/R/getTemporalData.r @@ -68,6 +68,7 @@ #' ) #' } #' +#' @importFrom dplyr rename_with #' @export @@ -115,7 +116,7 @@ getTemporalData <- function(connectionDetails, conn <- DatabaseConnector::connect(connectionDetails) - queryResults <- DatabaseConnector::querySql(conn, translatedSql) + queryResults <- DatabaseConnector::querySql(conn, translatedSql) |> dplyr::rename_with(toupper) on.exit(DatabaseConnector::disconnect(conn))