diff --git a/tests/testOracle.R b/tests/testOracle.R new file mode 100644 index 00000000..aeca4137 --- /dev/null +++ b/tests/testOracle.R @@ -0,0 +1,6 @@ +library(testthat) +options(dbms = "oracle") +runTestsOnOracle <- !(Sys.getenv("CDM5_ORACLE_USER") == "" & Sys.getenv("CDM5_ORACLE_PASSWORD") == "" & Sys.getenv("CDM5_ORACLE_SERVER") == "" & Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" & Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "") +if (runTestsOnOracle) { + test_check("FeatureExtraction") +} \ No newline at end of file diff --git a/tests/testPostgres.R b/tests/testPostgres.R new file mode 100644 index 00000000..f9ee8eb1 --- /dev/null +++ b/tests/testPostgres.R @@ -0,0 +1,6 @@ +library(testthat) +options(dbms = "postgresql") +runTestsOnPostgreSQL <- !(Sys.getenv("CDM5_POSTGRESQL_USER") == "" & Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" & Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" & Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" & Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "") +if (runTestsOnPostgreSQL) { + test_check("FeatureExtraction") +} \ No newline at end of file diff --git a/tests/testRedshift.R b/tests/testRedshift.R new file mode 100644 index 00000000..ef111c53 --- /dev/null +++ b/tests/testRedshift.R @@ -0,0 +1,6 @@ +library(testthat) +options(dbms = "redshift") +runTestsOnRedshift <- FALSE #!(Sys.getenv("CDM5_REDSHIFT_USER") == "" & Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" & Sys.getenv("CDM5_REDSHIFT_SERVER") == "" & Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" & Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "") +if (runTestsOnRedshift) { + test_check("FeatureExtraction") +} \ No newline at end of file diff --git a/tests/testSqlServer.R b/tests/testSqlServer.R new file mode 100644 index 00000000..76a295b2 --- /dev/null +++ b/tests/testSqlServer.R @@ -0,0 +1,6 @@ +library(testthat) +options(dbms = "sql server") +runTestsOnSQLServer <- !(Sys.getenv("CDM5_SQL_SERVER_USER") == "" & Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" & Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" & Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" & Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "") +if (runTestsOnSQLServer) { + test_check("FeatureExtraction") +} \ No newline at end of file diff --git a/tests/testSqlite.R b/tests/testSqlite.R new file mode 100644 index 00000000..2b7093e9 --- /dev/null +++ b/tests/testSqlite.R @@ -0,0 +1,6 @@ +library(testthat) +options(dbms = "sqlite") +runTestsOnEunomia <- TRUE +if (runTestsOnEunomia) { + test_check("FeatureExtraction") +} \ No newline at end of file diff --git a/tests/testthat.R b/tests/testthat.R deleted file mode 100644 index ace61c8d..00000000 --- a/tests/testthat.R +++ /dev/null @@ -1,3 +0,0 @@ -library(testthat) -library(FeatureExtraction) -test_check("FeatureExtraction") diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index c9e85158..f03782ed 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -2,6 +2,9 @@ library(testthat) library(FeatureExtraction) library(dplyr) +dbms <- getOption("dbms", default = "sqlite") +message("************* Testing on ", dbms, " *************\n") + # Unit Test Settings ------ # Set a directory for the JDBC drivers used in the tests oldJarFolder <- Sys.getenv("DATABASECONNECTOR_JAR_FOLDER") @@ -17,15 +20,6 @@ withr::defer( testthat::teardown_env() ) - -# Get all environment variables to determine which DBMS to use for testing -runTestsOnPostgreSQL <- !(Sys.getenv("CDM5_POSTGRESQL_USER") == "" & Sys.getenv("CDM5_POSTGRESQL_PASSWORD") == "" & Sys.getenv("CDM5_POSTGRESQL_SERVER") == "" & Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA") == "" & Sys.getenv("CDM5_POSTGRESQL_OHDSI_SCHEMA") == "") -runTestsOnSQLServer <- !(Sys.getenv("CDM5_SQL_SERVER_USER") == "" & Sys.getenv("CDM5_SQL_SERVER_PASSWORD") == "" & Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" & Sys.getenv("CDM5_SQL_SERVER_CDM_SCHEMA") == "" & Sys.getenv("CDM5_SQL_SERVER_OHDSI_SCHEMA") == "") -runTestsOnOracle <- !(Sys.getenv("CDM5_ORACLE_USER") == "" & Sys.getenv("CDM5_ORACLE_PASSWORD") == "" & Sys.getenv("CDM5_ORACLE_SERVER") == "" & Sys.getenv("CDM5_ORACLE_CDM_SCHEMA") == "" & Sys.getenv("CDM5_ORACLE_OHDSI_SCHEMA") == "") -runTestsOnImpala <- !(Sys.getenv("CDM5_IMPALA_USER") == "" & Sys.getenv("CDM5_IMPALA_PASSWORD") == "" & Sys.getenv("CDM5_IMPALA_SERVER") == "" & Sys.getenv("CDM5_IMPALA_CDM_SCHEMA") == "" & Sys.getenv("CDM5_IMPALA_OHDSI_SCHEMA") == "") -runTestsOnRedshift <- !(Sys.getenv("CDM5_REDSHIFT_USER") == "" & Sys.getenv("CDM5_REDSHIFT_PASSWORD") == "" & Sys.getenv("CDM5_REDSHIFT_SERVER") == "" & Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA") == "" & Sys.getenv("CDM5_REDSHIFT_OHDSI_SCHEMA") == "") -runTestsOnEunomia <- TRUE - # The cohort table is a temp table but uses the same platform/datetime suffix to avoid collisions when running # tests in parallel tableSuffix <- paste0(substr(.Platform$OS.type, 1, 3), format(Sys.time(), "%y%m%d%H%M%S"), sample(1:100, 1)) @@ -81,7 +75,7 @@ dropUnitTestData <- function(connection, ohdsiDatabaseSchema, cohortTable, cohor # Database Test Settings ----------- # postgres -if (runTestsOnPostgreSQL) { +if (dbms == "postgresql") { DatabaseConnector::downloadJdbcDrivers("postgresql") pgConnectionDetails <- createConnectionDetails( dbms = "postgresql", @@ -94,7 +88,7 @@ if (runTestsOnPostgreSQL) { } # sql server -if (runTestsOnSQLServer) { +if (dbms == "sql server") { DatabaseConnector::downloadJdbcDrivers("sql server") sqlServerConnectionDetails <- createConnectionDetails( dbms = "sql server", @@ -107,7 +101,7 @@ if (runTestsOnSQLServer) { } # oracle -if (runTestsOnOracle) { +if (dbms == "oracle") { DatabaseConnector::downloadJdbcDrivers("oracle") oracleConnectionDetails <- createConnectionDetails( dbms = "oracle", @@ -121,22 +115,8 @@ if (runTestsOnOracle) { options(sqlRenderTempEmulationSchema = oracleOhdsiDatabaseSchema) } -# impala -if (runTestsOnImpala) { - # NOTE: Driver for IMPALA requires manual installation - impalaConnectionDetails <- createConnectionDetails( - dbms = "impala", - user = Sys.getenv("CDM5_IMPALA_USER"), - password = URLdecode(Sys.getenv("CDM5_IMPALA_PASSWORD")), - server = Sys.getenv("CDM5_IMPALA_SERVER"), - pathToDriver = Sys.getenv("CDM5_IMPALA_PATH_TO_DRIVER") - ) - impalaCdmDatabaseSchema <- Sys.getenv("CDM5_IMPALA_CDM_SCHEMA") - impalaOhdsiDatabaseSchema <- Sys.getenv("CDM5_IMPALA_OHDSI_SCHEMA") -} - # redshift -if (runTestsOnRedshift) { +if (dbms == "redshift") { DatabaseConnector::downloadJdbcDrivers("redshift") redshiftConnectionDetails <- createConnectionDetails( dbms = "redshift", @@ -149,7 +129,7 @@ if (runTestsOnRedshift) { } # eunomia -if (runTestsOnEunomia) { +if (dbms == "sqlite") { eunomiaConnectionDetails <- Eunomia::getEunomiaConnectionDetails(databaseFile = "testEunomia.sqlite") eunomiaCdmDatabaseSchema <- "main" eunomiaOhdsiDatabaseSchema <- "main" diff --git a/tests/testthat/test-Aggregation.R b/tests/testthat/test-Aggregation.R index 24059a99..2dbd1314 100644 --- a/tests/testthat/test-Aggregation.R +++ b/tests/testthat/test-Aggregation.R @@ -3,7 +3,7 @@ # covr::file_report(covr::file_coverage("R/Aggregation.R", "tests/testthat/test-Aggregation.R")) test_that("aggregateCovariates works", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createCovariateSettings(useDemographicsAgeGroup = TRUE, useChads2Vasc = TRUE) covariateData <- getDbCovariateData(connectionDetails = eunomiaConnectionDetails, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -27,7 +27,7 @@ test_that("aggregateCovariates works", { }) test_that("aggregateCovariates handles temporalCovariates", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createTemporalCovariateSettings(useDemographicsGender = TRUE) covariateData <- getDbCovariateData(connectionDetails = eunomiaConnectionDetails, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, diff --git a/tests/testthat/test-CovariateData.R b/tests/testthat/test-CovariateData.R index 46ca1608..7b90064e 100644 --- a/tests/testthat/test-CovariateData.R +++ b/tests/testthat/test-CovariateData.R @@ -3,7 +3,7 @@ # covr::file_report(covr::file_coverage("R/CovariateData.R", "tests/testthat/test-CovariateData.R")) test_that("test CovariateData Class on Empty", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # create 4 scenarios of Covariate Data # 1) error (non class), 2) covariate data, 3) aggregatedCovariate Data, # 4) temporalCovariate Data @@ -46,7 +46,7 @@ test_that("test CovariateData Class on Empty", { }) test_that("test saveCovariateData error cases", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") saveFileTest <- tempfile("covDatSave") settings <- createDefaultCovariateSettings() covariateData <- getDbCovariateData(connectionDetails = eunomiaConnectionDetails, @@ -70,7 +70,7 @@ test_that("test saveCovariateData error cases", { }) test_that("test summary call for covariateData class", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createDefaultCovariateSettings() covariateData <- getDbCovariateData(connectionDetails = eunomiaConnectionDetails, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -110,7 +110,7 @@ test_that("Test show method", { on.exit(rm(cvData)) }) test_that("getDbCovariateData cohortId warning", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createDefaultCovariateSettings() expect_warning(getDbCovariateData(connectionDetails = eunomiaConnectionDetails, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, diff --git a/tests/testthat/test-GetCohortBasedCovariates.R b/tests/testthat/test-GetCohortBasedCovariates.R index e9a6cad6..743cdf1f 100644 --- a/tests/testthat/test-GetCohortBasedCovariates.R +++ b/tests/testthat/test-GetCohortBasedCovariates.R @@ -476,7 +476,7 @@ runCohortBasedCountsAggMultiCohortTest <- function(connection, cdmDatabaseSchema # Eunomia tests ------------ test_that("Cohort-based covariates: binary, non-aggregated on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedBinaryNonAggTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -486,7 +486,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on Eunomia", { }) test_that("Cohort-based covariates: binary, aggregated on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedBinaryAggTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -496,7 +496,7 @@ test_that("Cohort-based covariates: binary, aggregated on Eunomia", { }) test_that("Cohort-based covariates: binary, non-aggregated, temporal on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedBinaryNonAggTemporalTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -506,7 +506,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on Eunomia" }) test_that("Cohort-based covariates: binary, aggregated, temporal on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedBinaryAggTemporalTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -516,7 +516,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on Eunomia", { }) test_that("Cohort-based covariates: counts, non-aggregated on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedCountsNonAggTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -526,7 +526,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on Eunomia", { }) test_that("Cohort-based covariates: counts, aggregated on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedCountsAggTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -536,7 +536,7 @@ test_that("Cohort-based covariates: counts, aggregated on Eunomia", { }) test_that("Cohort-based covariates: counts, non-aggregated, temporal on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedCountsNonAggTemporalTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -546,7 +546,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on Eunomia" }) test_that("Cohort-based covariates: counts, aggregated, temporal on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedCountsAggTemporalTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -556,7 +556,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on Eunomia", { }) test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runCohortBasedCountsAggMultiCohortTest( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -567,7 +567,7 @@ test_that("Cohort-based covariates: counts, aggregated, using multiple cohort ID # Postgres tests ------------ test_that("Cohort-based covariates: binary, non-aggregated on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTest( @@ -579,7 +579,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on Postgres", { }) test_that("Cohort-based covariates: binary, aggregated on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTest( @@ -591,7 +591,7 @@ test_that("Cohort-based covariates: binary, aggregated on Postgres", { }) test_that("Cohort-based covariates: binary, non-aggregated, temporal on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTemporalTest( @@ -603,7 +603,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on Postgres }) test_that("Cohort-based covariates: binary, aggregated, temporal on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTemporalTest( @@ -615,7 +615,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on Postgres", { }) test_that("Cohort-based covariates: counts, non-aggregated on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTest( @@ -627,7 +627,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on Postgres", { }) test_that("Cohort-based covariates: counts, aggregated on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTest( @@ -639,7 +639,7 @@ test_that("Cohort-based covariates: counts, aggregated on Postgres", { }) test_that("Cohort-based covariates: counts, non-aggregated, temporal on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTemporalTest( @@ -651,7 +651,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on Postgres }) test_that("Cohort-based covariates: counts, aggregated, temporal on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTemporalTest( @@ -663,7 +663,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on Postgres", { }) test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on Postgres", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") connection <- DatabaseConnector::connect(pgConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggMultiCohortTest( @@ -676,7 +676,7 @@ test_that("Cohort-based covariates: counts, aggregated, using multiple cohort ID # SQL Server tests ------------ test_that("Cohort-based covariates: binary, non-aggregated on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTest( @@ -688,7 +688,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on SQL Server", { }) test_that("Cohort-based covariates: binary, aggregated on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTest( @@ -700,7 +700,7 @@ test_that("Cohort-based covariates: binary, aggregated on SQL Server", { }) test_that("Cohort-based covariates: binary, non-aggregated, temporal on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTemporalTest( @@ -712,7 +712,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on SQL Serv }) test_that("Cohort-based covariates: binary, aggregated, temporal on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTemporalTest( @@ -724,7 +724,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on SQL Server", }) test_that("Cohort-based covariates: counts, non-aggregated on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTest( @@ -736,7 +736,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on SQL Server", { }) test_that("Cohort-based covariates: counts, aggregated on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTest( @@ -748,7 +748,7 @@ test_that("Cohort-based covariates: counts, aggregated on SQL Server", { }) test_that("Cohort-based covariates: counts, non-aggregated, temporal on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTemporalTest( @@ -760,7 +760,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on SQL Serv }) test_that("Cohort-based covariates: counts, aggregated, temporal on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTemporalTest( @@ -772,7 +772,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on SQL Server", }) test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") connection <- DatabaseConnector::connect(sqlServerConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggMultiCohortTest( @@ -785,7 +785,7 @@ test_that("Cohort-based covariates: counts, aggregated, using multiple cohort ID # Oracle tests ------------ test_that("Cohort-based covariates: binary, non-aggregated on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTest( @@ -797,7 +797,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on Oracle", { }) test_that("Cohort-based covariates: binary, aggregated on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTest( @@ -809,7 +809,7 @@ test_that("Cohort-based covariates: binary, aggregated on Oracle", { }) test_that("Cohort-based covariates: binary, non-aggregated, temporal on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTemporalTest( @@ -821,7 +821,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on Oracle", }) test_that("Cohort-based covariates: binary, aggregated, temporal on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTemporalTest( @@ -833,7 +833,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on Oracle", { }) test_that("Cohort-based covariates: counts, non-aggregated on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTest( @@ -845,7 +845,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on Oracle", { }) test_that("Cohort-based covariates: counts, aggregated on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTest( @@ -857,7 +857,7 @@ test_that("Cohort-based covariates: counts, aggregated on Oracle", { }) test_that("Cohort-based covariates: counts, non-aggregated, temporal on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTemporalTest( @@ -869,7 +869,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on Oracle", }) test_that("Cohort-based covariates: counts, aggregated, temporal on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTemporalTest( @@ -881,7 +881,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on Oracle", { }) test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") connection <- DatabaseConnector::connect(oracleConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggMultiCohortTest( @@ -894,7 +894,7 @@ test_that("Cohort-based covariates: counts, aggregated, using multiple cohort ID # RedShift tests ------------ test_that("Cohort-based covariates: binary, non-aggregated on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTest( @@ -906,7 +906,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on RedShift", { }) test_that("Cohort-based covariates: binary, aggregated on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTest( @@ -918,7 +918,7 @@ test_that("Cohort-based covariates: binary, aggregated on RedShift", { }) test_that("Cohort-based covariates: binary, non-aggregated, temporal on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryNonAggTemporalTest( @@ -930,7 +930,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on RedShift }) test_that("Cohort-based covariates: binary, aggregated, temporal on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedBinaryAggTemporalTest( @@ -942,7 +942,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on RedShift", { }) test_that("Cohort-based covariates: counts, non-aggregated on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTest( @@ -954,7 +954,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on RedShift", { }) test_that("Cohort-based covariates: counts, aggregated on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTest( @@ -966,7 +966,7 @@ test_that("Cohort-based covariates: counts, aggregated on RedShift", { }) test_that("Cohort-based covariates: counts, non-aggregated, temporal on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsNonAggTemporalTest( @@ -978,7 +978,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on RedShift }) test_that("Cohort-based covariates: counts, aggregated, temporal on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggTemporalTest( @@ -990,7 +990,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on RedShift", { }) test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on RedShift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") connection <- DatabaseConnector::connect(redshiftConnectionDetails) on.exit(DatabaseConnector::disconnect(connection)) runCohortBasedCountsAggMultiCohortTest( diff --git a/tests/testthat/test-GetCovariates.R b/tests/testthat/test-GetCovariates.R index b37f2274..a55eac52 100644 --- a/tests/testthat/test-GetCovariates.R +++ b/tests/testthat/test-GetCovariates.R @@ -34,7 +34,7 @@ getCovariateSettings <- function() { # } test_that("getDbCovariateData enforces specification of database details", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # No database details specified expect_error(getDbCovariateData( connectionDetails = NULL, @@ -60,7 +60,7 @@ test_that("getDbCovariateData enforces specification of database details", { }) test_that("getDbCovariateData CDM v4 not supported", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") expect_error(getDbCovariateData( connectionDetails = eunomiaConnectionDetails, connection = NULL, @@ -71,7 +71,7 @@ test_that("getDbCovariateData CDM v4 not supported", { }) test_that("getDbCovariateData cohortTableIsTemp tests when table name lacks # symbol", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") result <- getDbCovariateData( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -83,7 +83,7 @@ test_that("getDbCovariateData cohortTableIsTemp tests when table name lacks # sy }) test_that("getDbCovariateData cohortTableIsTemp tests when table name contains # symbol", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") result <- getDbCovariateData( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -95,7 +95,7 @@ test_that("getDbCovariateData cohortTableIsTemp tests when table name contains # }) test_that("getDbCovariateData populationSize == 0 tests", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") expect_warning(getDbCovariateData(connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, cohortTableIsTemp = FALSE, @@ -106,7 +106,7 @@ test_that("getDbCovariateData populationSize == 0 tests", { test_that("Custom covariate builder", { # TODO: This test is probably good to run on all DB platforms - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateSettings <- createCovariateSettings( useDemographicsGender = TRUE, useDemographicsAgeGroup = TRUE, @@ -126,7 +126,7 @@ test_that("Custom covariate builder", { test_that("getDbCovariateData care site from person tests", { # TODO: This test is probably good to run on all DB platforms - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # Add care site IDs to person table person <- DatabaseConnector::querySql(eunomiaConnection, "SELECT * FROM main.person;", snakeCaseToCamelCase = TRUE) @@ -164,7 +164,7 @@ test_that("getDbCovariateData care site from person tests", { test_that("getDbCovariateData care site from visit_occurrence tests", { # TODO: This test is probably good to run on all DB platforms - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # Add care site IDs to visit occurrence table visitOccurrence <- DatabaseConnector::querySql(eunomiaConnection, "SELECT * FROM main.visit_occurrence;", snakeCaseToCamelCase = TRUE) diff --git a/tests/testthat/test-GetCovariatesFromCohortAttributes.R b/tests/testthat/test-GetCovariatesFromCohortAttributes.R index 6c0f8bfc..eb86db96 100644 --- a/tests/testthat/test-GetCovariatesFromCohortAttributes.R +++ b/tests/testthat/test-GetCovariatesFromCohortAttributes.R @@ -7,7 +7,7 @@ # covr::file_report(covr::file_coverage("R/GetCovariatesFromCohortAttributes.R", "tests/testthat/test-GetCovariatesFromCohortAttributes.R")) test_that("getDbCohortAttrCovariatesData aggregation not supported check", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") expect_error(getDbCohortAttrCovariatesData( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -17,7 +17,7 @@ test_that("getDbCohortAttrCovariatesData aggregation not supported check", { }) test_that("getDbCohortAttrCovariatesData CDM v4 not supported check", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") expect_error(getDbCohortAttrCovariatesData( connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, @@ -28,7 +28,7 @@ test_that("getDbCohortAttrCovariatesData CDM v4 not supported check", { test_that("getDbCohortAttrCovariatesData hasIncludedAttributes == 0", { # TODO: This test is probably good to run on all DB platforms - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateSettings <- createCohortAttrCovariateSettings( attrDatabaseSchema = eunomiaOhdsiDatabaseSchema, cohortAttrTable = cohortAttributeTable, @@ -48,7 +48,7 @@ test_that("getDbCohortAttrCovariatesData hasIncludedAttributes == 0", { test_that("getDbCohortAttrCovariatesData hasIncludedAttributes > 0", { # TODO: This test is probably good to run on all DB platforms - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateSettings <- createCohortAttrCovariateSettings( attrDatabaseSchema = eunomiaOhdsiDatabaseSchema, cohortAttrTable = cohortAttributeTable, @@ -68,13 +68,13 @@ test_that("getDbCohortAttrCovariatesData hasIncludedAttributes > 0", { }) test_that("createCohortAttrCovariateSettings check", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") result <- createCohortAttrCovariateSettings(attrDatabaseSchema = "main") expect_equal(class(result), "covariateSettings") }) test_that("getDbCohortAttrCovariatesData cohortId warning", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateSettings <- createCohortAttrCovariateSettings( attrDatabaseSchema = eunomiaOhdsiDatabaseSchema, cohortAttrTable = cohortAttributeTable, diff --git a/tests/testthat/test-GetCovariatesTemporalSequence.R b/tests/testthat/test-GetCovariatesTemporalSequence.R index 33a1de47..4b20024c 100644 --- a/tests/testthat/test-GetCovariatesTemporalSequence.R +++ b/tests/testthat/test-GetCovariatesTemporalSequence.R @@ -46,7 +46,7 @@ test_that("createTemporalSequenceCovariateSettings correctly sets function", { # check extraction test_that("getDbCovariateData works with createTemporalSequenceCovariateSettings", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covSet <- createTemporalSequenceCovariateSettings(useDemographicsGender = T, useDemographicsAge = T, useDemographicsRace = T, @@ -74,7 +74,7 @@ test_that("getDbCovariateData works with createTemporalSequenceCovariateSettings # Check backwards compatibility test_that("Temporal Covariate Settings are backwards compatible", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # Temporal covariate settings created previously will not have # the temporalSequence property diff --git a/tests/testthat/test-GetDefaultCovariates.R b/tests/testthat/test-GetDefaultCovariates.R index ab149785..8570920b 100644 --- a/tests/testthat/test-GetDefaultCovariates.R +++ b/tests/testthat/test-GetDefaultCovariates.R @@ -3,7 +3,7 @@ # covr::file_report(covr::file_coverage("R/GetDefaultCovariates.R", "tests/testthat/test-GetDefaultCovariates.R")) test_that("Test exit conditions", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") # covariateSettings object type expect_error(getDbDefaultCovariateData( diff --git a/tests/testthat/test-HelperFunctions.R b/tests/testthat/test-HelperFunctions.R index c53f7c5a..f0881e78 100644 --- a/tests/testthat/test-HelperFunctions.R +++ b/tests/testthat/test-HelperFunctions.R @@ -3,7 +3,7 @@ # covr::file_report(covr::file_coverage("R/HelperFunctions.R", "tests/testthat/test-HelperFunctions.R")) test_that("Test helper functions for non-aggregated covariate data", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") expect_error(filterByRowId("blah", 1), "not of class CovariateData") covariateData <- getDbCovariateData(connection = eunomiaConnection, @@ -26,9 +26,9 @@ test_that("Test helper functions for non-aggregated covariate data", { }) test_that("Test helper functions for aggregated covariate data", { - skip_if_not(runTestsOnEunomia) - expect_error(filterByCohortDefinitionIds("blah", cohortIds = c(1)), "not of class CovariateData") - + skip_if_not(dbms == "sqlite") + expect_error(filterByCohortDefinitionIds("blah", 1), "not of class CovariateData") + aggregatedCovariateData <- getDbCovariateData(connection = eunomiaConnection, cdmDatabaseSchema = eunomiaCdmDatabaseSchema, cohortDatabaseSchema = eunomiaOhdsiDatabaseSchema, @@ -37,6 +37,7 @@ test_that("Test helper functions for aggregated covariate data", { aggregated = TRUE) aggCovariateDataFiltered <- filterByCohortDefinitionIds(aggregatedCovariateData, cohortIds = c(1)) + expect_equal(unique(pull(aggCovariateDataFiltered$covariates, cohortDefinitionId)), 1) expect_error(filterByRowId(aggregatedCovariateData, 1), "Cannot filter aggregated") Andromeda::close(aggregatedCovariateData) diff --git a/tests/testthat/test-Table1.R b/tests/testthat/test-Table1.R index f1eb5204..1b9b7613 100644 --- a/tests/testthat/test-Table1.R +++ b/tests/testthat/test-Table1.R @@ -10,7 +10,7 @@ test_that("getDefaultTable1Specifications works", { test_that("createTable1 works with categorical covariates", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createCovariateSettings(useDemographicsAgeGroup = TRUE, useDemographicsGender = TRUE, @@ -66,7 +66,7 @@ test_that("createTable1 works with categorical covariates", { test_that("createTable1 works with continuous covariates", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createCovariateSettings(useDemographicsAgeGroup = TRUE, useDemographicsGender = TRUE, @@ -116,7 +116,7 @@ test_that("createTable1 works with continuous covariates", { test_that("createTable1 works with other covariates", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") settings <- createCovariateSettings( useDemographicsAgeGroup = TRUE, useChads2Vasc = TRUE diff --git a/tests/testthat/test-query-no-fail.R b/tests/testthat/test-query-no-fail.R index 115ed358..1b9a6584 100644 --- a/tests/testthat/test-query-no-fail.R +++ b/tests/testthat/test-query-no-fail.R @@ -133,7 +133,7 @@ runExtractionPerPerson <- function(connection, cdmDatabaseSchema, ohdsiDatabaseS } test_that("Run all analysis at per-person level on PostgreSQL", { - skip_if_not(runTestsOnPostgreSQL) + 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) @@ -141,7 +141,7 @@ test_that("Run all analysis at per-person level on PostgreSQL", { }) test_that("Run all analysis at per-person level on SQL Server", { - skip_if_not(runTestsOnSQLServer) + 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) @@ -149,23 +149,15 @@ test_that("Run all analysis at per-person level on SQL Server", { }) test_that("Run all analysis at per-person level on Oracle", { - skip_if_not(runTestsOnOracle) + 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 Impala", { - skip_if_not(runTestsOnImpala) - impalaConnection <- createUnitTestData(impalaConnectionDetails, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) - on.exit(dropUnitTestData(impalaConnection, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) - covariateData <- runExtractionPerPerson(impalaConnection, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable) - expect_true(is(covariateData, "CovariateData")) -}) - test_that("Run all analysis at per-person level on Redshift", { - skip_if_not(runTestsOnRedshift) + 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) @@ -173,7 +165,7 @@ test_that("Run all analysis at per-person level on Redshift", { }) test_that("Run all analysis at per-person level on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateData <- runExtractionPerPerson(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable) expect_true(is(covariateData, "CovariateData")) }) @@ -312,7 +304,7 @@ runExtractionAggregated <- function(connection, cdmDatabaseSchema, ohdsiDatabase } test_that("Run all analysis at aggregated level on PostgreSQL", { - skip_if_not(runTestsOnPostgreSQL) + 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) @@ -320,7 +312,7 @@ test_that("Run all analysis at aggregated level on PostgreSQL", { }) test_that("Run all analysis at aggregated level on SQL Server", { - skip_if_not(runTestsOnSQLServer) + 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) @@ -328,23 +320,15 @@ test_that("Run all analysis at aggregated level on SQL Server", { }) test_that("Run all analysis at aggregated level on Oracle", { - skip_if_not(runTestsOnOracle) + 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 Impala", { - skip_if_not(runTestsOnImpala) - impalaConnection <- createUnitTestData(impalaConnectionDetails, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) - on.exit(dropUnitTestData(impalaConnection, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) - covariateData <- runExtractionAggregated(impalaConnection, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable) - expect_true(is(covariateData, "CovariateData")) -}) - test_that("Run all analysis at aggregated level on Redshift", { - skip_if_not(runTestsOnRedshift) + 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) @@ -352,7 +336,7 @@ test_that("Run all analysis at aggregated level on Redshift", { }) test_that("Run all analysis at aggregated level on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateData <- runExtractionAggregated(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable) expect_true(is(covariateData, "CovariateData")) }) @@ -420,7 +404,7 @@ runExtractionTemporalPerPerson <- function(connection, cdmDatabaseSchema, ohdsiD } test_that("Run all temporalanalysis at per-person level on PostgreSQL", { - skip_if_not(runTestsOnPostgreSQL) + 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) @@ -428,7 +412,7 @@ test_that("Run all temporalanalysis at per-person level on PostgreSQL", { }) test_that("Run all temporalanalysis at per-person level on SQL Server", { - skip_if_not(runTestsOnSQLServer) + 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) @@ -436,23 +420,15 @@ test_that("Run all temporalanalysis at per-person level on SQL Server", { }) test_that("Run all temporalanalysis at per-person level on Oracle", { - skip_if_not(runTestsOnOracle) + 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 Impala", { - skip_if_not(runTestsOnImpala) - impalaConnection <- createUnitTestData(impalaConnectionDetails, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) - on.exit(dropUnitTestData(impalaConnection, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) - covariateData <- runExtractionTemporalPerPerson(impalaConnection, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable) - expect_true(is(covariateData, "CovariateData")) -}) - test_that("Run all temporalanalysis at per-person level on Redshift", { - skip_if_not(runTestsOnRedshift) + 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) @@ -460,7 +436,7 @@ test_that("Run all temporalanalysis at per-person level on Redshift", { }) test_that("Run all temporalanalysis at per-person level on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateData <- runExtractionTemporalPerPerson(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable) expect_true(is(covariateData, "CovariateData")) }) @@ -529,7 +505,7 @@ runExtractionTemporalAggregated <- function(connection, cdmDatabaseSchema, ohdsi } test_that("Run all temporalanalysis at aggregated level on PostgreSQL", { - skip_if_not(runTestsOnPostgreSQL) + 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) @@ -537,7 +513,7 @@ test_that("Run all temporalanalysis at aggregated level on PostgreSQL", { }) test_that("Run all temporalanalysis at aggregated level on SQL Server", { - skip_if_not(runTestsOnSQLServer) + 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) @@ -545,23 +521,15 @@ test_that("Run all temporalanalysis at aggregated level on SQL Server", { }) test_that("Run all temporalanalysis at aggregated level on Oracle", { - skip_if_not(runTestsOnOracle) + 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 Impala", { - skip_if_not(runTestsOnImpala) - impalaConnection <- createUnitTestData(impalaConnectionDetails, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) - on.exit(dropUnitTestData(impalaConnection, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) - covariateData <- runExtractionTemporalAggregated(impalaConnection, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable) - expect_true(is(covariateData, "CovariateData")) -}) - test_that("Run all temporalanalysis at aggregated level on Redshift", { - skip_if_not(runTestsOnRedshift) + 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) @@ -569,7 +537,7 @@ test_that("Run all temporalanalysis at aggregated level on Redshift", { }) test_that("Run all temporalanalysis at aggregated level on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateData <- runExtractionTemporalAggregated(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable) expect_true(is(covariateData, "CovariateData")) }) diff --git a/tests/testthat/test-spot-checks.R b/tests/testthat/test-spot-checks.R index d120988a..7b7f431a 100644 --- a/tests/testthat/test-spot-checks.R +++ b/tests/testthat/test-spot-checks.R @@ -181,41 +181,34 @@ runSpotChecks <- function(connection, cdmDatabaseSchema, ohdsiDatabaseSchema, co } test_that("Run spot-checks at per-person level on PostgreSQL", { - skip_if_not(runTestsOnPostgreSQL) + skip_if_not(dbms == "postgresql") pgConnection <- createUnitTestData(pgConnectionDetails, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) on.exit(dropUnitTestData(pgConnection, pgOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) runSpotChecks(pgConnection, pgCdmDatabaseSchema, pgOhdsiDatabaseSchema, cohortTable) }) test_that("Run spot-checks at per-person level on SQL Server", { - skip_if_not(runTestsOnSQLServer) + skip_if_not(dbms == "sql server") sqlServerConnection <- createUnitTestData(sqlServerConnectionDetails, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) on.exit(dropUnitTestData(sqlServerConnection, sqlServerOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) runSpotChecks(sqlServerConnection, sqlServerCdmDatabaseSchema, sqlServerOhdsiDatabaseSchema, cohortTable) }) test_that("Run spot-checks at per-person level on Oracle", { - skip_if_not(runTestsOnOracle) + skip_if_not(dbms == "oracle") oracleConnection <- createUnitTestData(oracleConnectionDetails, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) on.exit(dropUnitTestData(oracleConnection, oracleOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) runSpotChecks(oracleConnection, oracleCdmDatabaseSchema, oracleOhdsiDatabaseSchema, cohortTable) }) -test_that("Run spot-checks at per-person level on Impala", { - skip_if_not(runTestsOnImpala) - impalaConnection <- createUnitTestData(impalaConnectionDetails, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) - on.exit(dropUnitTestData(impalaConnection, impalaOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) - runSpotChecks(impalaConnection, impalaCdmDatabaseSchema, impalaOhdsiDatabaseSchema, cohortTable) -}) - test_that("Run spot-checks at per-person level on Redshift", { - skip_if_not(runTestsOnRedshift) + skip_if_not(dbms == "redshift") redshiftConnection <- createUnitTestData(redshiftConnectionDetails, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable) on.exit(dropUnitTestData(redshiftConnection, redshiftOhdsiDatabaseSchema, cohortTable, cohortAttributeTable, attributeDefinitionTable)) runSpotChecks(redshiftConnection, redshiftCdmDatabaseSchema, redshiftOhdsiDatabaseSchema, cohortTable) }) test_that("Run spot-checks at per-person level on Eunomia", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") runSpotChecks(eunomiaConnection, eunomiaCdmDatabaseSchema, eunomiaOhdsiDatabaseSchema, cohortTable) }) diff --git a/tests/testthat/test-tidyCovariates.R b/tests/testthat/test-tidyCovariates.R index f76c6ab2..4b26cd40 100644 --- a/tests/testthat/test-tidyCovariates.R +++ b/tests/testthat/test-tidyCovariates.R @@ -72,7 +72,7 @@ test_that("tidyCovariates works", { }) test_that("tidyCovariateData on Temporal Data", { - skip_if_not(runTestsOnEunomia) + skip_if_not(dbms == "sqlite") covariateSettings <- createTemporalCovariateSettings(useDrugExposure = TRUE, temporalStartDays = -2:-1, temporalEndDays = -2:-1)