tests/testthat/test-query-no-fail.R
In OHDSI/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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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,
oracleTempSchema = 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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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,
oracleTempSchema = ohdsiDatabaseSchema,
cohortDatabaseSchema = ohdsiDatabaseSchema,
cohortTable = cohortTable,
cohortTableIsTemp = TRUE,
cohortIds = c(1124300),
rowIdField = "subject_id",
covariateSettings = settings,
aggregated = TRUE
))
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,
useObservation = 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,
oracleTempSchema = 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,
useObservation = 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,
oracleTempSchema = ohdsiDatabaseSchema,
cohortDatabaseSchema = ohdsiDatabaseSchema,
cohortTable = cohortTable,
cohortTableIsTemp = TRUE,
cohortIds = c(1124300),
rowIdField = "subject_id",
covariateSettings = settings,
aggregated = TRUE
))
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"))
})
OHDSI/FeatureExtraction documentation built on May 2, 2024, 11:30 p.m.
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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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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,
oracleTempSchema = 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,
useObservationAnyTimePrior = FALSE,
useObservationLongTerm = FALSE,
useObservationMediumTerm = FALSE,
useObservationShortTerm = 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,
oracleTempSchema = ohdsiDatabaseSchema,
cohortDatabaseSchema = ohdsiDatabaseSchema,
cohortTable = cohortTable,
cohortTableIsTemp = TRUE,
cohortIds = c(1124300),
rowIdField = "subject_id",
covariateSettings = settings,
aggregated = TRUE
))
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,
useObservation = 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,
oracleTempSchema = 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,
useObservation = 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,
oracleTempSchema = ohdsiDatabaseSchema,
cohortDatabaseSchema = ohdsiDatabaseSchema,
cohortTable = cohortTable,
cohortTableIsTemp = TRUE,
cohortIds = c(1124300),
rowIdField = "subject_id",
covariateSettings = settings,
aggregated = TRUE
))
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"))
})
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