Merge pull request #221 from OHDSI/unitTests

Modify unit tests structure

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")
+}

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")
+}

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")
+}

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")
+}

tests/testSqlite.R

@@ -0,0 +1,6 @@
+library(testthat)
+options(dbms = "sqlite")
+runTestsOnEunomia <- TRUE
+if (runTestsOnEunomia) {
+  test_check("FeatureExtraction")
+}

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"

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,

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,