tests/testthat/test-GetDefaultCovariates.R

In quinterpriest/FeatureExtraction: Generating Features for a Cohort

# This file covers the code in GetDefaultCovariates.R. View coverage for this file using
#library(testthat); library(FeatureExtraction)
#covr::file_report(covr::file_coverage("R/GetDefaultCovariates.R", "tests/testthat/test-GetDefaultCovariates.R"))

connectionDetails <- Eunomia::getEunomiaConnectionDetails()

test_that("Test exit conditions", {
  connection <- DatabaseConnector::connect(connectionDetails)
  
  # covariateSettings object type
  expect_error(getDbDefaultCovariateData(connection = connection,
                                         cdmDatabaseSchema = "main",
                                         covariateSettings = list(),
                                         targetDatabaseSchema = "main",
                                         targetCovariateTable = "cov",
                                         targetCovariateRefTable = "cov_ref",
                                         targetAnalysisRefTable = "cov_analysis_ref"))
  # CDM 4 not supported
  expect_error(getDbDefaultCovariateData(connection = connection,
                                         cdmDatabaseSchema = "main",
                                         cdmVersion = "4",
                                         covariateSettings = createDefaultCovariateSettings(),
                                         targetDatabaseSchema = "main",
                                         targetCovariateTable = "cov",
                                         targetCovariateRefTable = "cov_ref",
                                         targetAnalysisRefTable = "cov_analysis_ref"))
  
  # targetCovariateTable and aggregated not supported
  expect_error(getDbDefaultCovariateData(connection = connection,
                                         cdmDatabaseSchema = "main",
                                         covariateSettings = createDefaultCovariateSettings(),
                                         targetDatabaseSchema = "main",
                                         targetCovariateTable = "cov",
                                         targetCovariateRefTable = "cov_ref",
                                         targetAnalysisRefTable = "cov_analysis_ref",
                                         aggregated = TRUE))
  
  on.exit(DatabaseConnector::disconnect(connection))  
})

# AGS - This test fails and is likely due to a bug when using SqlLite
# test_that("Test target table", {
#   connection <- DatabaseConnector::connect(connectionDetails)
#   Eunomia::createCohorts(connectionDetails)
#   
#   results <- getDbDefaultCovariateData(connection = connection,
#                                        cdmDatabaseSchema = "main",
#                                        cohortTable = "cohort",
#                                        covariateSettings = createDefaultCovariateSettings(),
#                                        targetDatabaseSchema = "main",
#                                        targetCovariateTable = "ut_cov",
#                                        targetCovariateRefTable = "ut_cov_ref",
#                                        targetAnalysisRefTable = "ut_cov_analysis_ref")
# 
#   on.exit(DatabaseConnector::disconnect(connection))  
# })

unlink(connectionDetails$server())