Merge pull request #268 from OHDSI/cran

skip some tests on CRAN

tests/testthat/setup.R

@@ -133,7 +133,7 @@ if (dbms == "bigquery" && .Platform$OS.type == "windows") {
 # oracle
 if (dbms == "oracle") {
   DatabaseConnector::downloadJdbcDrivers(dbms)
-  oracleConnectionDetails <- createConnectionDetails(
+  oracleConnectionDetails <- DatabaseConnector::createConnectionDetails(
     dbms = dbms,
     user = Sys.getenv("CDM5_ORACLE_USER"),
     password = URLdecode(Sys.getenv("CDM5_ORACLE_PASSWORD")),
@@ -148,7 +148,7 @@ if (dbms == "oracle") {
 # postgres
 if (dbms == "postgresql") {
   DatabaseConnector::downloadJdbcDrivers(dbms)
-  pgConnectionDetails <- createConnectionDetails(
+  pgConnectionDetails <- DatabaseConnector::createConnectionDetails(
     dbms = dbms,
     user = Sys.getenv("CDM5_POSTGRESQL_USER"),
     password = URLdecode(Sys.getenv("CDM5_POSTGRESQL_PASSWORD")),
@@ -161,7 +161,7 @@ if (dbms == "postgresql") {
 # redshift
 if (dbms == "redshift") {
   DatabaseConnector::downloadJdbcDrivers(dbms)
-  redshiftConnectionDetails <- createConnectionDetails(
+  redshiftConnectionDetails <- DatabaseConnector::createConnectionDetails(
     dbms = dbms,
     user = Sys.getenv("CDM5_REDSHIFT_USER"),
     password = URLdecode(Sys.getenv("CDM5_REDSHIFT_PASSWORD")),
@@ -204,7 +204,7 @@ if (dbms == "spark") {
 # sql server
 if (dbms == "sql server") {
   DatabaseConnector::downloadJdbcDrivers("sql server")
-  sqlServerConnectionDetails <- createConnectionDetails(
+  sqlServerConnectionDetails <- DatabaseConnector::createConnectionDetails(
     dbms = "sql server",
     user = Sys.getenv("CDM5_SQL_SERVER_USER"),
     password = URLdecode(Sys.getenv("CDM5_SQL_SERVER_PASSWORD")),

tests/testthat/test-Aggregation.R

@@ -3,6 +3,7 @@
 # covr::file_report(covr::file_coverage("R/Aggregation.R", "tests/testthat/test-Aggregation.R"))
 
 test_that("aggregateCovariates works", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   settings <- createCovariateSettings(useDemographicsAgeGroup = TRUE, useChads2Vasc = TRUE)
   covariateData <- getDbCovariateData(

tests/testthat/test-CompareCohorts.R

@@ -39,6 +39,7 @@ test_that("Test stdDiff continuous variable computation", {
 })
 
 test_that("Test stdDiff binary variable computation", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   connectionDetails <- Eunomia::getEunomiaConnectionDetails()
   Eunomia::createCohorts(connectionDetails)

tests/testthat/test-CovariateData.R

@@ -52,6 +52,7 @@ test_that("test CovariateData Class on Empty", {
 })
 
 test_that("test saveCovariateData error cases", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   saveFileTest <- tempfile("covDatSave")
   settings <- createDefaultCovariateSettings()
@@ -95,6 +96,7 @@ test_that("test summary call for covariateData class", {
 })
 
 test_that("test filtering of covariates based on minCharacterizationMean", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   settings <- createDefaultCovariateSettings()
   covariateData <- getDbCovariateData(
@@ -155,6 +157,7 @@ test_that("Test show method", {
 })
 
 test_that("getDbCovariateData cohortId warning", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   settings <- createDefaultCovariateSettings()
   expect_warning(getDbCovariateData(
@@ -168,6 +171,7 @@ test_that("getDbCovariateData cohortId warning", {
 })
 
 test_that("getDbCovariateData settings list - check metaData", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   looCovSet <- FeatureExtraction:::.createLooCovariateSettings(useLengthOfObs = TRUE)
   covariateSettingsList <- list(looCovSet, looCovSet)

tests/testthat/test-GetCohortBasedCovariates.R

@@ -486,6 +486,7 @@ test_that("Cohort-based covariates: binary, non-aggregated on Eunomia", {
 })
 
 test_that("Cohort-based covariates: binary, aggregated on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedBinaryAggTest(
     connection = eunomiaConnection,
@@ -496,6 +497,7 @@ test_that("Cohort-based covariates: binary, aggregated on Eunomia", {
 })
 
 test_that("Cohort-based covariates: binary, non-aggregated, temporal on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedBinaryNonAggTemporalTest(
     connection = eunomiaConnection,
@@ -506,6 +508,7 @@ test_that("Cohort-based covariates: binary, non-aggregated, temporal on Eunomia"
 })
 
 test_that("Cohort-based covariates: binary, aggregated, temporal on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedBinaryAggTemporalTest(
     connection = eunomiaConnection,
@@ -516,6 +519,7 @@ test_that("Cohort-based covariates: binary, aggregated, temporal on Eunomia", {
 })
 
 test_that("Cohort-based covariates: counts, non-aggregated on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedCountsNonAggTest(
     connection = eunomiaConnection,
@@ -526,6 +530,7 @@ test_that("Cohort-based covariates: counts, non-aggregated on Eunomia", {
 })
 
 test_that("Cohort-based covariates: counts, aggregated on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedCountsAggTest(
     connection = eunomiaConnection,
@@ -536,6 +541,7 @@ test_that("Cohort-based covariates: counts, aggregated on Eunomia", {
 })
 
 test_that("Cohort-based covariates: counts, non-aggregated, temporal on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedCountsNonAggTemporalTest(
     connection = eunomiaConnection,
@@ -546,6 +552,7 @@ test_that("Cohort-based covariates: counts, non-aggregated, temporal on Eunomia"
 })
 
 test_that("Cohort-based covariates: counts, aggregated, temporal on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedCountsAggTemporalTest(
     connection = eunomiaConnection,
@@ -556,6 +563,7 @@ test_that("Cohort-based covariates: counts, aggregated, temporal on Eunomia", {
 })
 
 test_that("Cohort-based covariates: counts, aggregated, using multiple cohort IDs on Eunomia", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   runCohortBasedCountsAggMultiCohortTest(
     connection = eunomiaConnection,

tests/testthat/test-GetCovariates.R

@@ -60,6 +60,7 @@ test_that("getDbCovariateData enforces specification of database details", {
 })
 
 test_that("getDbCovariateData CDM v4 not supported", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   expect_error(getDbCovariateData(
     connectionDetails = eunomiaConnectionDetails,
@@ -83,6 +84,7 @@ test_that("getDbCovariateData cohortTableIsTemp tests when table name lacks # sy
 })
 
 test_that("getDbCovariateData cohortTableIsTemp tests when table name contains # symbol", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   result <- getDbCovariateData(
     connection = eunomiaConnection,
@@ -95,6 +97,7 @@ test_that("getDbCovariateData cohortTableIsTemp tests when table name contains #
 })
 
 test_that("getDbCovariateData populationSize == 0 tests", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   expect_warning(getDbCovariateData(
     connection = eunomiaConnection,
@@ -107,6 +110,7 @@ test_that("getDbCovariateData populationSize == 0 tests", {
 })
 
 test_that("Custom covariate builder", {
+  skip_on_cran()
   # TODO: This test is probably good to run on all DB platforms
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   covariateSettings <- createCovariateSettings(
@@ -129,6 +133,7 @@ test_that("Custom covariate builder", {
 })
 
 test_that("getDbCovariateData care site from person tests", {
+  skip_on_cran()
   # TODO: This test is probably good to run on all DB platforms
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
 
@@ -171,6 +176,7 @@ test_that("getDbCovariateData care site from person tests", {
 })
 
 test_that("getDbCovariateData care site from visit_occurrence tests", {
+  skip_on_cran()
   # TODO: This test is probably good to run on all DB platforms
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
 

tests/testthat/test-GetCovariatesFromCohortAttributes.R

@@ -27,6 +27,7 @@ test_that("getDbCohortAttrCovariatesData CDM v4 not supported check", {
 })
 
 test_that("getDbCohortAttrCovariatesData hasIncludedAttributes == 0", {
+  skip_on_cran()
   # TODO: This test is probably good to run on all DB platforms
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   covariateSettings <- createCohortAttrCovariateSettings(
@@ -47,6 +48,7 @@ test_that("getDbCohortAttrCovariatesData hasIncludedAttributes == 0", {
 })
 
 test_that("getDbCohortAttrCovariatesData hasIncludedAttributes > 0", {
+  skip_on_cran()
   # TODO: This test is probably good to run on all DB platforms
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   covariateSettings <- createCohortAttrCovariateSettings(
@@ -74,6 +76,7 @@ test_that("createCohortAttrCovariateSettings check", {
 })
 
 test_that("getDbCohortAttrCovariatesData cohortId warning", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   covariateSettings <- createCohortAttrCovariateSettings(
     attrDatabaseSchema = eunomiaOhdsiDatabaseSchema,

tests/testthat/test-GetCovariatesTemporalSequence.R

@@ -78,6 +78,7 @@ test_that("getDbCovariateData works with createTemporalSequenceCovariateSettings
 
 # Check backwards compatibility
 test_that("Temporal Covariate Settings are backwards compatible", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
 
   # Temporal covariate settings created previously will not have

tests/testthat/test-GetDefaultCovariates.R

@@ -3,6 +3,7 @@
 # covr::file_report(covr::file_coverage("R/GetDefaultCovariates.R", "tests/testthat/test-GetDefaultCovariates.R"))
 
 test_that("Test exit conditions", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
 
   # covariateSettings object type

tests/testthat/test-HelperFunctions.R

@@ -28,6 +28,7 @@ test_that("Test helper functions for non-aggregated covariate data", {
 })
 
 test_that("Test helper functions for aggregated covariate data", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   expect_error(filterByCohortDefinitionId("blah", 1), "not of class CovariateData")
 

tests/testthat/test-Table1.R

@@ -82,6 +82,7 @@ test_that("createTable1 works with categorical covariates", {
 
 
 test_that("createTable1 works with continuous covariates", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
 
   settings <- createCovariateSettings(
@@ -142,6 +143,7 @@ test_that("createTable1 works with continuous covariates", {
 
 
 test_that("createTable1 works with other covariates", {
+  skip_on_cran()
   skip_if_not(dbms == "sqlite" && exists("eunomiaConnection"))
   settings <- createCovariateSettings(
     useDemographicsAgeGroup = TRUE,