tests/testthat/test-2-againstCdm.R

In OHDSI/CohortDiagnostics: Diagnostics for OHDSI Cohorts

test_that("Cohort diagnostics in incremental mode", {
  skip_if(skipCdmTests, "cdm settings not configured")

  firstTime <- system.time(
    executeDiagnostics(
      cohortDefinitionSet = cohortDefinitionSet,
      connectionDetails = connectionDetails,
      cdmDatabaseSchema = cdmDatabaseSchema,
      vocabularyDatabaseSchema = vocabularyDatabaseSchema,
      tempEmulationSchema = tempEmulationSchema,
      cohortDatabaseSchema = cohortDatabaseSchema,
      cohortTable = cohortTable,
      cohortIds = cohortIds,
      exportFolder = file.path(folder, "export"),
      databaseId = dbms,
      runInclusionStatistics = TRUE,
      runBreakdownIndexEvents = TRUE,
      runTemporalCohortCharacterization = TRUE,
      runIncidenceRate = TRUE,
      runIncludedSourceConcepts = TRUE,
      runOrphanConcepts = TRUE,
      runTimeSeries = TRUE,
      runCohortRelationship = TRUE,
      minCellCount = minCellCountValue,
      incremental = TRUE,
      incrementalFolder = file.path(folder, "incremental"),
      temporalCovariateSettings = temporalCovariateSettings,
      runFeatureExtractionOnSample = TRUE,
      minCharacterizationMean = 0.8
    )
  )

  expect_true(file.exists(file.path(
    folder, "export", paste0("Results_", dbms, ".zip")
  )))

  # We now run it with all cohorts without specifying ids - testing incremental mode
  secondTime <- system.time(
    executeDiagnostics(
      connectionDetails = connectionDetails,
      cdmDatabaseSchema = cdmDatabaseSchema,
      tempEmulationSchema = tempEmulationSchema,
      cohortDatabaseSchema = cohortDatabaseSchema,
      cohortTableNames = cohortTableNames,
      cohortDefinitionSet = cohortDefinitionSet,
      exportFolder = file.path(folder, "export"),
      databaseId = dbms,
      runInclusionStatistics = TRUE,
      runBreakdownIndexEvents = TRUE,
      runTemporalCohortCharacterization = TRUE,
      runIncidenceRate = TRUE,
      runIncludedSourceConcepts = TRUE,
      runOrphanConcepts = TRUE,
      runTimeSeries = TRUE,
      runCohortRelationship = TRUE,
      minCellCount = minCellCountValue,
      incremental = TRUE,
      incrementalFolder = file.path(folder, "incremental"),
      temporalCovariateSettings = temporalCovariateSettings,
      runFeatureExtractionOnSample = TRUE,
      minCharacterizationMean = 0.8
    )
  )
  # generate sqlite file
  sqliteDbPath <- tempfile(fileext = ".sqlite")
  createMergedResultsFile(dataFolder = file.path(folder, "export"), sqliteDbPath = sqliteDbPath)
  expect_true(file.exists(sqliteDbPath))

  # File exists
  expect_error(createMergedResultsFile(dataFolder = file.path(folder, "export"), sqliteDbPath = sqliteDbPath))

  if (dbms == "sqlite") {
    # Get file sizes of batch computed results
    batchedResultsFiles <- c("temporal_covariate_value.csv", "cohort_relationships.csv", "time_series.csv")
    bacthFiles <- file.path(folder, "export", batchedResultsFiles)
    fileSizes <- list()
    for (filePath in batchedResultsFiles) {
      fileSizes[[filePath]] <- file.size(filePath)
    }

    ## Repeat tests with incremental set to false to ensure better code coverage
    withr::with_options(list(
      "CohortDiagnostics-TimeSeries-batch-size" = 1,
      "CohortDiagnostics-FE-batch-size" = 1,
      "CohortDiagnostics-Relationships-batch-size" = 50
    ), {
      executeDiagnostics(
        connectionDetails = connectionDetails,
        cdmDatabaseSchema = cdmDatabaseSchema,
        tempEmulationSchema = tempEmulationSchema,
        cohortDatabaseSchema = cohortDatabaseSchema,
        cohortTableNames = cohortTableNames,
        cohortDefinitionSet = cohortDefinitionSet,
        exportFolder = file.path(folder, "export"),
        databaseId = dbms,
        runInclusionStatistics = TRUE,
        runBreakdownIndexEvents = TRUE,
        runTemporalCohortCharacterization = TRUE,
        runIncidenceRate = TRUE,
        runIncludedSourceConcepts = TRUE,
        runOrphanConcepts = TRUE,
        runTimeSeries = TRUE,
        runCohortRelationship = TRUE,
        minCellCount = minCellCountValue,
        incremental = FALSE,
        incrementalFolder = file.path(folder, "incremental"),
        temporalCovariateSettings = temporalCovariateSettings,
        runFeatureExtractionOnSample = TRUE,
        minCharacterizationMean = 0.8
      )
    })

    for (filePath in names(fileSizes)) {
      # Because we set options to small batches if these were written correctly they shouldn't have changed in size
      expect_equal(file.size(filePath), fileSizes[[filePath]])
    }
  }

  # Test zip works
  DiagnosticsExplorerZip <- tempfile(fileext = "de.zip")
  unlink(DiagnosticsExplorerZip)
  on.exit(unlink(DiagnosticsExplorerZip))
  createDiagnosticsExplorerZip(outputZipfile = DiagnosticsExplorerZip, sqliteDbPath = sqliteDbPath)

  expect_true(file.exists(DiagnosticsExplorerZip))
  # already exists
  expect_error(createDiagnosticsExplorerZip(outputZipfile = DiagnosticsExplorerZip, sqliteDbPath = sqliteDbPath))
  # Bad filepath
  expect_error(createDiagnosticsExplorerZip(outputZipfile = "foo", sqliteDbPath = "sdlfkmdkmfkd"))
  output <- read.csv(file.path(folder, "export", "temporal_covariate_value.csv"))

  expect_true(is.numeric(output$sum_value[2]))
  expect_true(is.numeric(output$mean[2]))
})