test-query-no-fail.R
In FeatureExtraction: Generating Features for a Cohort

library(testthat)

# runExtractionPerPerson -----------
runExtractionPerPerson <- function(connection, cdmDatabaseSchema, ohdsiDatabaseSchema, cohortTable) {
  settings <- createCovariateSettings(
    useDemographicsGender = TRUE,
    useDemographicsAge = TRUE,
    useDemographicsAgeGroup = TRUE,
    useDemographicsRace = TRUE,
    useDemographicsEthnicity = TRUE,
    useDemographicsIndexYear = TRUE,
    useDemographicsIndexMonth = TRUE,
    useDemographicsPriorObservationTime = TRUE,
    useDemographicsPostObservationTime = FALSE,
    useDemographicsTimeInCohort = FALSE,
    useDemographicsIndexYearMonth = TRUE,
    useCareSiteId = TRUE,
    useConditionOccurrenceAnyTimePrior = FALSE,
    useConditionOccurrenceLongTerm = FALSE,
    useConditionOccurrenceMediumTerm = FALSE,
    useConditionOccurrenceShortTerm = TRUE,
    useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
    useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
    useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
    useConditionOccurrencePrimaryInpatientShortTerm = TRUE,
    useConditionEraAnyTimePrior = FALSE,
    useConditionEraLongTerm = FALSE,
    useConditionEraMediumTerm = FALSE,
    useConditionEraShortTerm = TRUE,
    useConditionEraOverlapping = FALSE,
    useConditionEraStartLongTerm = FALSE,
    useConditionEraStartMediumTerm = FALSE,
    useConditionEraStartShortTerm = TRUE,
    useConditionGroupEraAnyTimePrior = FALSE,
    useConditionGroupEraLongTerm = FALSE,
    useConditionGroupEraMediumTerm = FALSE,
    useConditionGroupEraShortTerm = TRUE,
    useConditionGroupEraOverlapping = FALSE,
    useConditionGroupEraStartLongTerm = FALSE,
    useConditionGroupEraStartMediumTerm = FALSE,
    useConditionGroupEraStartShortTerm = FALSE,
    useDrugExposureAnyTimePrior = FALSE,
    useDrugExposureLongTerm = FALSE,
    useDrugExposureMediumTerm = FALSE,
    useDrugExposureShortTerm = TRUE,
    useDrugEraAnyTimePrior = FALSE,
    useDrugEraLongTerm = FALSE,
    useDrugEraMediumTerm = FALSE,
    useDrugEraShortTerm = TRUE,
    useDrugEraOverlapping = FALSE,
    useDrugEraStartLongTerm = FALSE,
    useDrugEraStartMediumTerm = FALSE,
    useDrugEraStartShortTerm = TRUE,
    useDrugGroupEraAnyTimePrior = FALSE,
    useDrugGroupEraLongTerm = FALSE,
    useDrugGroupEraMediumTerm = FALSE,
    useDrugGroupEraShortTerm = TRUE,
    useDrugGroupEraOverlapping = FALSE,
    useDrugGroupEraStartLongTerm = FALSE,
    useDrugGroupEraStartMediumTerm = FALSE,
    useDrugGroupEraStartShortTerm = TRUE,
    useProcedureOccurrenceAnyTimePrior = FALSE,
    useProcedureOccurrenceLongTerm = FALSE,
    useProcedureOccurrenceMediumTerm = FALSE,
    useProcedureOccurrenceShortTerm = TRUE,
    useDeviceExposureAnyTimePrior = FALSE,
    useDeviceExposureLongTerm = FALSE,
    useDeviceExposureMediumTerm = FALSE,
    useDeviceExposureShortTerm = TRUE,
    useMeasurementAnyTimePrior = FALSE,
    useMeasurementLongTerm = FALSE,
    useMeasurementMediumTerm = FALSE,
    useMeasurementShortTerm = TRUE,
    useMeasurementValueAnyTimePrior = FALSE,
    useMeasurementValueLongTerm = FALSE,
    useMeasurementValueMediumTerm = FALSE,
    useMeasurementValueShortTerm = TRUE,
    useMeasurementRangeGroupAnyTimePrior = FALSE,
    useMeasurementRangeGroupLongTerm = FALSE,
    useMeasurementRangeGroupMediumTerm = FALSE,
    useMeasurementRangeGroupShortTerm = TRUE,
    useMeasurementValueAsConceptAnyTimePrior = FALSE,
    useMeasurementValueAsConceptLongTerm = FALSE,
    useMeasurementValueAsConceptMediumTerm = FALSE,
    useMeasurementValueAsConceptShortTerm = TRUE,
    useObservationAnyTimePrior = FALSE,
    useObservationLongTerm = FALSE,
    useObservationMediumTerm = FALSE,
    useObservationShortTerm = TRUE,
    useObservationValueAsConceptAnyTimePrior = FALSE,
    useObservationValueAsConceptLongTerm = FALSE,
    useObservationValueAsConceptMediumTerm = FALSE,
    useObservationValueAsConceptShortTerm = TRUE,
    useCharlsonIndex = TRUE,
    useDcsi = TRUE,
    useChads2 = TRUE,
    useChads2Vasc = TRUE,
    useHfrs = TRUE,
    useDistinctConditionCountLongTerm = FALSE,
    useDistinctConditionCountMediumTerm = FALSE,
    useDistinctConditionCountShortTerm = TRUE,
    useDistinctIngredientCountLongTerm = FALSE,
    useDistinctIngredientCountMediumTerm = FALSE,
    useDistinctIngredientCountShortTerm = TRUE,
    useDistinctProcedureCountLongTerm = FALSE,
    useDistinctProcedureCountMediumTerm = FALSE,
    useDistinctProcedureCountShortTerm = TRUE,
    useDistinctMeasurementCountLongTerm = FALSE,
    useDistinctMeasurementCountMediumTerm = FALSE,
    useDistinctMeasurementCountShortTerm = TRUE,
    useDistinctObservationCountLongTerm = FALSE,
    useDistinctObservationCountMediumTerm = FALSE,
    useDistinctObservationCountShortTerm = TRUE,
    useVisitCountLongTerm = FALSE,
    useVisitCountMediumTerm = FALSE,
    useVisitCountShortTerm = TRUE,
    useVisitConceptCountLongTerm = FALSE,
    useVisitConceptCountMediumTerm = FALSE,
    useVisitConceptCountShortTerm = TRUE,
    longTermStartDays = -365,
    mediumTermStartDays = -180,
    shortTermStartDays = -30,
    endDays = 0,
    includedCovariateConceptIds = c(),
    addDescendantsToInclude = FALSE,
    excludedCovariateConceptIds = c(),
    addDescendantsToExclude = FALSE,
    includedCovariateIds = c()
  )

  suppressWarnings(covariateData <- getDbCovariateData(
    connection = connection,
    cdmDatabaseSchema = cdmDatabaseSchema,
    tempEmulationSchema = ohdsiDatabaseSchema,
    cohortDatabaseSchema = ohdsiDatabaseSchema,
    cohortTable = cohortTable,
    cohortTableIsTemp = TRUE,
    cohortIds = c(1124300),
    rowIdField = "subject_id",
    covariateSettings = settings
  ))
  return(covariateData)
}

test_that("Run all analysis at per-person level on PostgreSQL", {
  skip_if_not(dbms == "postgresql")
  pgConnection <- createUnitTestData(pgConnectionDetails, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(pgConnection, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionPerPerson(pgConnection, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at per-person level on SQL Server", {
  skip_if_not(dbms == "sql server")
  sqlServerConnection <- createUnitTestData(sqlServerConnectionDetails, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(sqlServerConnection, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionPerPerson(sqlServerConnection, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at per-person level on Oracle", {
  skip_if_not(dbms == "oracle")
  oracleConnection <- createUnitTestData(oracleConnectionDetails, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(oracleConnection, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionPerPerson(oracleConnection, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at per-person level on Redshift", {
  skip_if_not(dbms == "redshift")
  redshiftConnection <- createUnitTestData(redshiftConnectionDetails, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(redshiftConnection, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionPerPerson(redshiftConnection, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at per-person level on Eunomia", {
  skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
  covariateData <- runExtractionPerPerson(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

# runExtractionAggregated -----------
runExtractionAggregated <- function(connection, cdmDatabaseSchema, ohdsiDatabaseSchema, cohortTable) {
  settings <- createCovariateSettings(
    useDemographicsGender = TRUE,
    useDemographicsAge = TRUE,
    useDemographicsAgeGroup = TRUE,
    useDemographicsRace = TRUE,
    useDemographicsEthnicity = TRUE,
    useDemographicsIndexYear = TRUE,
    useDemographicsIndexMonth = TRUE,
    useDemographicsPriorObservationTime = TRUE,
    useDemographicsPostObservationTime = FALSE,
    useDemographicsTimeInCohort = FALSE,
    useDemographicsIndexYearMonth = TRUE,
    useCareSiteId = TRUE,
    useConditionOccurrenceAnyTimePrior = FALSE,
    useConditionOccurrenceLongTerm = FALSE,
    useConditionOccurrenceMediumTerm = FALSE,
    useConditionOccurrenceShortTerm = TRUE,
    useConditionOccurrencePrimaryInpatientAnyTimePrior = FALSE,
    useConditionOccurrencePrimaryInpatientLongTerm = FALSE,
    useConditionOccurrencePrimaryInpatientMediumTerm = FALSE,
    useConditionOccurrencePrimaryInpatientShortTerm = TRUE,
    useConditionEraAnyTimePrior = FALSE,
    useConditionEraLongTerm = FALSE,
    useConditionEraMediumTerm = FALSE,
    useConditionEraShortTerm = TRUE,
    useConditionEraOverlapping = FALSE,
    useConditionEraStartLongTerm = FALSE,
    useConditionEraStartMediumTerm = FALSE,
    useConditionEraStartShortTerm = TRUE,
    useConditionGroupEraAnyTimePrior = FALSE,
    useConditionGroupEraLongTerm = FALSE,
    useConditionGroupEraMediumTerm = FALSE,
    useConditionGroupEraShortTerm = TRUE,
    useConditionGroupEraOverlapping = FALSE,
    useConditionGroupEraStartLongTerm = FALSE,
    useConditionGroupEraStartMediumTerm = FALSE,
    useConditionGroupEraStartShortTerm = FALSE,
    useDrugExposureAnyTimePrior = FALSE,
    useDrugExposureLongTerm = FALSE,
    useDrugExposureMediumTerm = FALSE,
    useDrugExposureShortTerm = TRUE,
    useDrugEraAnyTimePrior = FALSE,
    useDrugEraLongTerm = FALSE,
    useDrugEraMediumTerm = FALSE,
    useDrugEraShortTerm = TRUE,
    useDrugEraOverlapping = FALSE,
    useDrugEraStartLongTerm = FALSE,
    useDrugEraStartMediumTerm = FALSE,
    useDrugEraStartShortTerm = TRUE,
    useDrugGroupEraAnyTimePrior = FALSE,
    useDrugGroupEraLongTerm = FALSE,
    useDrugGroupEraMediumTerm = FALSE,
    useDrugGroupEraShortTerm = TRUE,
    useDrugGroupEraOverlapping = FALSE,
    useDrugGroupEraStartLongTerm = FALSE,
    useDrugGroupEraStartMediumTerm = FALSE,
    useDrugGroupEraStartShortTerm = FALSE,
    useProcedureOccurrenceAnyTimePrior = FALSE,
    useProcedureOccurrenceLongTerm = FALSE,
    useProcedureOccurrenceMediumTerm = FALSE,
    useProcedureOccurrenceShortTerm = TRUE,
    useDeviceExposureAnyTimePrior = FALSE,
    useDeviceExposureLongTerm = FALSE,
    useDeviceExposureMediumTerm = FALSE,
    useDeviceExposureShortTerm = TRUE,
    useMeasurementAnyTimePrior = FALSE,
    useMeasurementLongTerm = FALSE,
    useMeasurementMediumTerm = FALSE,
    useMeasurementShortTerm = TRUE,
    useMeasurementValueAnyTimePrior = FALSE,
    useMeasurementValueLongTerm = FALSE,
    useMeasurementValueMediumTerm = FALSE,
    useMeasurementValueShortTerm = TRUE,
    useMeasurementRangeGroupAnyTimePrior = FALSE,
    useMeasurementRangeGroupLongTerm = FALSE,
    useMeasurementRangeGroupMediumTerm = FALSE,
    useMeasurementRangeGroupShortTerm = TRUE,
    useMeasurementValueAsConceptAnyTimePrior = FALSE,
    useMeasurementValueAsConceptLongTerm = FALSE,
    useMeasurementValueAsConceptMediumTerm = FALSE,
    useMeasurementValueAsConceptShortTerm = TRUE,
    useObservationAnyTimePrior = FALSE,
    useObservationLongTerm = FALSE,
    useObservationMediumTerm = FALSE,
    useObservationShortTerm = TRUE,
    useObservationValueAsConceptAnyTimePrior = FALSE,
    useObservationValueAsConceptLongTerm = FALSE,
    useObservationValueAsConceptMediumTerm = FALSE,
    useObservationValueAsConceptShortTerm = TRUE,
    useCharlsonIndex = TRUE,
    useDcsi = TRUE,
    useChads2 = TRUE,
    useChads2Vasc = TRUE,
    useHfrs = TRUE,
    useDistinctConditionCountLongTerm = FALSE,
    useDistinctConditionCountMediumTerm = FALSE,
    useDistinctConditionCountShortTerm = TRUE,
    useDistinctIngredientCountLongTerm = FALSE,
    useDistinctIngredientCountMediumTerm = FALSE,
    useDistinctIngredientCountShortTerm = TRUE,
    useDistinctProcedureCountLongTerm = FALSE,
    useDistinctProcedureCountMediumTerm = FALSE,
    useDistinctProcedureCountShortTerm = TRUE,
    useDistinctMeasurementCountLongTerm = FALSE,
    useDistinctMeasurementCountMediumTerm = FALSE,
    useDistinctMeasurementCountShortTerm = TRUE,
    useDistinctObservationCountLongTerm = FALSE,
    useDistinctObservationCountMediumTerm = FALSE,
    useDistinctObservationCountShortTerm = TRUE,
    useVisitCountLongTerm = FALSE,
    useVisitCountMediumTerm = FALSE,
    useVisitCountShortTerm = TRUE,
    useVisitConceptCountLongTerm = FALSE,
    useVisitConceptCountMediumTerm = FALSE,
    useVisitConceptCountShortTerm = TRUE,
    longTermStartDays = -365,
    mediumTermStartDays = -180,
    shortTermStartDays = -30,
    endDays = 0,
    includedCovariateConceptIds = c(),
    addDescendantsToInclude = FALSE,
    excludedCovariateConceptIds = c(),
    addDescendantsToExclude = FALSE,
    includedCovariateIds = c()
  )

  suppressWarnings(covariateData <- getDbCovariateData(
    connection = connection,
    cdmDatabaseSchema = cdmDatabaseSchema,
    tempEmulationSchema = ohdsiDatabaseSchema,
    cohortDatabaseSchema = ohdsiDatabaseSchema,
    cohortTable = cohortTable,
    cohortTableIsTemp = TRUE,
    cohortIds = c(1124300),
    rowIdField = "subject_id",
    covariateSettings = settings,
    aggregated = TRUE,
    minCharacterizationMean = 0.001
  ))
  return(covariateData)
}

test_that("Run all analysis at aggregated level on PostgreSQL", {
  skip_if_not(dbms == "postgresql")
  pgConnection <- createUnitTestData(pgConnectionDetails, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(pgConnection, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionAggregated(pgConnection, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at aggregated level on SQL Server", {
  skip_if_not(dbms == "sql server")
  sqlServerConnection <- createUnitTestData(sqlServerConnectionDetails, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(sqlServerConnection, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionAggregated(sqlServerConnection, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at aggregated level on Oracle", {
  skip_if_not(dbms == "oracle")
  oracleConnection <- createUnitTestData(oracleConnectionDetails, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(oracleConnection, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionAggregated(oracleConnection, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at aggregated level on Redshift", {
  skip_if_not(dbms == "redshift")
  redshiftConnection <- createUnitTestData(redshiftConnectionDetails, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(redshiftConnection, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionAggregated(redshiftConnection, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all analysis at aggregated level on Eunomia", {
  skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
  covariateData <- runExtractionAggregated(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

# runExtractionTemporalPerPerson -----------
runExtractionTemporalPerPerson <- function(connection, cdmDatabaseSchema, ohdsiDatabaseSchema, cohortTable) {
  settings <- createTemporalCovariateSettings(
    useDemographicsGender = TRUE,
    useDemographicsAge = TRUE,
    useDemographicsAgeGroup = TRUE,
    useDemographicsRace = TRUE,
    useDemographicsEthnicity = TRUE,
    useDemographicsIndexYear = TRUE,
    useDemographicsIndexMonth = TRUE,
    useDemographicsIndexYearMonth = TRUE,
    useDemographicsPriorObservationTime = TRUE,
    useDemographicsPostObservationTime = TRUE,
    useDemographicsTimeInCohort = TRUE,
    useCareSiteId = TRUE,
    useConditionOccurrence = TRUE,
    useConditionOccurrencePrimaryInpatient = TRUE,
    useConditionEraStart = TRUE,
    useConditionEraOverlap = TRUE,
    useConditionEraGroupStart = FALSE,
    useConditionEraGroupOverlap = FALSE,
    useDrugExposure = TRUE,
    useDrugEraStart = TRUE,
    useDrugEraOverlap = TRUE,
    useDrugEraGroupStart = FALSE,
    useDrugEraGroupOverlap = FALSE,
    useProcedureOccurrence = TRUE,
    useDeviceExposure = TRUE,
    useMeasurement = TRUE,
    useMeasurementValue = TRUE,
    useMeasurementRangeGroup = TRUE,
    useMeasurementValueAsConcept = TRUE,
    useObservation = TRUE,
    useObservationValueAsConcept = TRUE,
    useCharlsonIndex = TRUE,
    useDcsi = TRUE,
    useChads2 = TRUE,
    useChads2Vasc = TRUE,
    useHfrs = TRUE,
    useDistinctConditionCount = TRUE,
    useDistinctIngredientCount = TRUE,
    useDistinctProcedureCount = TRUE,
    useDistinctMeasurementCount = TRUE,
    useDistinctObservationCount = TRUE,
    useVisitCount = TRUE,
    useVisitConceptCount = TRUE,
    temporalStartDays = -365:-1,
    temporalEndDays = -365:-1,
    includedCovariateConceptIds = c(),
    addDescendantsToInclude = FALSE,
    excludedCovariateConceptIds = c(),
    addDescendantsToExclude = FALSE,
    includedCovariateIds = c()
  )
  suppressWarnings(covariateData <- getDbCovariateData(
    connection = connection,
    cdmDatabaseSchema = cdmDatabaseSchema,
    tempEmulationSchema = ohdsiDatabaseSchema,
    cohortDatabaseSchema = ohdsiDatabaseSchema,
    cohortTable = cohortTable,
    cohortTableIsTemp = TRUE,
    cohortIds = c(1124300),
    rowIdField = "subject_id",
    covariateSettings = settings
  ))
  return(covariateData)
}

test_that("Run all temporalanalysis at per-person level on PostgreSQL", {
  skip_if_not(dbms == "postgresql")
  pgConnection <- createUnitTestData(pgConnectionDetails, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(pgConnection, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalPerPerson(pgConnection, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at per-person level on SQL Server", {
  skip_if_not(dbms == "sql server")
  sqlServerConnection <- createUnitTestData(sqlServerConnectionDetails, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(sqlServerConnection, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalPerPerson(sqlServerConnection, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at per-person level on Oracle", {
  skip_if_not(dbms == "oracle")
  oracleConnection <- createUnitTestData(oracleConnectionDetails, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(oracleConnection, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalPerPerson(oracleConnection, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at per-person level on Redshift", {
  skip_if_not(dbms == "redshift")
  redshiftConnection <- createUnitTestData(redshiftConnectionDetails, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(redshiftConnection, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalPerPerson(redshiftConnection, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at per-person level on Eunomia", {
  skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
  covariateData <- runExtractionTemporalPerPerson(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

# runExtractionTemporalPerPerson -----------
runExtractionTemporalAggregated <- function(connection, cdmDatabaseSchema, ohdsiDatabaseSchema, cohortTable) {
  settings <- createTemporalCovariateSettings(
    useDemographicsGender = TRUE,
    useDemographicsAge = TRUE,
    useDemographicsAgeGroup = TRUE,
    useDemographicsRace = TRUE,
    useDemographicsEthnicity = TRUE,
    useDemographicsIndexYear = TRUE,
    useDemographicsIndexMonth = TRUE,
    useDemographicsIndexYearMonth = TRUE,
    useDemographicsPriorObservationTime = TRUE,
    useDemographicsPostObservationTime = TRUE,
    useDemographicsTimeInCohort = TRUE,
    useCareSiteId = TRUE,
    useConditionOccurrence = TRUE,
    useConditionOccurrencePrimaryInpatient = TRUE,
    useConditionEraStart = TRUE,
    useConditionEraOverlap = TRUE,
    useConditionEraGroupStart = FALSE,
    useConditionEraGroupOverlap = FALSE,
    useDrugExposure = TRUE,
    useDrugEraStart = TRUE,
    useDrugEraOverlap = TRUE,
    useDrugEraGroupStart = FALSE,
    useDrugEraGroupOverlap = FALSE,
    useProcedureOccurrence = TRUE,
    useDeviceExposure = TRUE,
    useMeasurement = TRUE,
    useMeasurementValue = TRUE,
    useMeasurementRangeGroup = TRUE,
    useMeasurementValueAsConcept = TRUE,
    useObservation = TRUE,
    useObservationValueAsConcept = TRUE,
    useCharlsonIndex = TRUE,
    useDcsi = TRUE,
    useChads2 = TRUE,
    useChads2Vasc = TRUE,
    useHfrs = TRUE,
    useDistinctConditionCount = TRUE,
    useDistinctIngredientCount = TRUE,
    useDistinctProcedureCount = TRUE,
    useDistinctMeasurementCount = TRUE,
    useDistinctObservationCount = TRUE,
    useVisitCount = TRUE,
    useVisitConceptCount = TRUE,
    temporalStartDays = -365:-1,
    temporalEndDays = -365:-1,
    includedCovariateConceptIds = c(),
    addDescendantsToInclude = FALSE,
    excludedCovariateConceptIds = c(),
    addDescendantsToExclude = FALSE,
    includedCovariateIds = c()
  )
  suppressWarnings(covariateData <- getDbCovariateData(
    connection = connection,
    cdmDatabaseSchema = cdmDatabaseSchema,
    tempEmulationSchema = ohdsiDatabaseSchema,
    cohortDatabaseSchema = ohdsiDatabaseSchema,
    cohortTable = cohortTable,
    cohortTableIsTemp = TRUE,
    cohortIds = c(1124300),
    rowIdField = "subject_id",
    covariateSettings = settings,
    aggregated = TRUE,
    minCharacterizationMean = 0.001
  ))
  return(covariateData)
}

test_that("Run all temporalanalysis at aggregated level on PostgreSQL", {
  skip_if_not(dbms == "postgresql")
  pgConnection <- createUnitTestData(pgConnectionDetails, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(pgConnection, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalAggregated(pgConnection, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at aggregated level on SQL Server", {
  skip_if_not(dbms == "sql server")
  sqlServerConnection <- createUnitTestData(sqlServerConnectionDetails, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(sqlServerConnection, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalAggregated(sqlServerConnection, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at aggregated level on Oracle", {
  skip_if_not(dbms == "oracle")
  oracleConnection <- createUnitTestData(oracleConnectionDetails, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(oracleConnection, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalAggregated(oracleConnection, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at aggregated level on Redshift", {
  skip_if_not(dbms == "redshift")
  redshiftConnection <- createUnitTestData(redshiftConnectionDetails, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)
  on.exit(dropUnitTestData(redshiftConnection, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable))
  covariateData <- runExtractionTemporalAggregated(redshiftConnection, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})

test_that("Run all temporalanalysis at aggregated level on Eunomia", {
  skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
  covariateData <- runExtractionTemporalAggregated(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable)
  expect_true(is(covariateData, "CovariateData"))
})