tests/testthat/test00-schema.R

In Paradigm4/revealgenomics: SciDB REVEAL/Genomics API

context("test00-schema")


test_that("get_base_idname(ENTITY) matches entity_id for metadata classes", {
  expect_base_idname = function(entity) {
    expect_equal(revealgenomics:::get_base_idname(entity), 
                 paste0(tolower(entity), "_id"))
  }
  expect_base_idname(entity = .ghEnv$meta$arrFeature)
  expect_base_idname(entity = .ghEnv$meta$arrFeatureSynonym)
  expect_base_idname(entity = .ghEnv$meta$arrFeatureset)
  expect_base_idname(entity = .ghEnv$meta$arrProject)
  expect_base_idname(entity = .ghEnv$meta$arrDataset)
  expect_base_idname(entity = .ghEnv$meta$arrIndividuals)
  expect_base_idname(entity = .ghEnv$meta$arrBiosample)
  expect_base_idname(entity = .ghEnv$meta$arrExperimentSet)
  expect_base_idname(entity = .ghEnv$meta$arrMeasurementSet)
  expect_base_idname(entity = .ghEnv$meta$arrGeneSymbol)
  expect_base_idname(entity = .ghEnv$meta$arrGenelist)
  expect_base_idname(entity = .ghEnv$meta$arrGenelist_gene)
  expect_base_idname(entity = .ghEnv$meta$arrDefinition)
})

test_that("dataset_id is a mandatory column for certain metadata entities", {
  expect_true('dataset_id' %in% mandatory_fields()[[.ghEnv$meta$arrIndividuals]])
  expect_true('dataset_id' %in% mandatory_fields()[[.ghEnv$meta$arrBiosample]])
  expect_true('dataset_id' %in% mandatory_fields()[[.ghEnv$meta$arrMeasurementSet]])
  expect_true('dataset_id' %in% mandatory_fields()[[.ghEnv$meta$arrMeasurement]])
  expect_true('dataset_id' %in% mandatory_fields()[[.ghEnv$meta$arrDefinition]])
  # add more
})

test_that("get list of arrays maintained by API works", {
  res = revealgenomics:::get_list_of_arrays()
  expect_equal(class(res), "character")
  # Check for some basic entity names
  expect_true(any(grepl("PROJECT", res)))
  expect_true(any(grepl("FEATURE", res)))
})