tests/testthat/test_Dictionary.R

In hms-dbmi/pic-sure-biodatacatalyst-r-adapter-hpds: Simplified R library to communicate with HPDS-hosted services on the BioData Catalyst network

library(jsonlite)

describe("PicSureHpdsDictionaryBdc", {
  testProfile = jsonlite::toJSON(list(
    queryScopes = list("\\DCC Harmonized data set\\", "\\phs000001\\")
  ), auto_unbox=TRUE)
  api_results = function(uuid, query) jsonlite::toJSON(list(
    results = list(
      phenotypes = list(
        `\\phs000001\\pht000001\\phv00000001\\test\\` = list(
          min = 0,
          max = 5,
          categorical = FALSE,
          name = "\\phs000001\\pht000001\\phv00000001\\test\\"
        )
      ),
      info = list(
        A_Variant = list(
          description = "Description=\"A proper testing description.\"",
          values = c("ABC", "DEF"),
          continuous = FALSE
        )
      )
    )
  ), auto_unbox=TRUE)
  loadDictionary = function(profile, search) {
    connection = MockConnection$new(profile, search)
    resource = PicSureHpdsResourceConnectionBdc$new(connection, resource_uuid_list[[1]])
    return(resource$dictionary())
  }
  describe("getKeyInfo()", {
    it("should return FALSE if path does not exist", {
      dictionary = loadDictionary(testProfile, api_results)
      result = dictionary$getKeyInfo("unknown_path")
      expect_equal(result, FALSE)
    })
    it("should return a list of data if path exists", {
      dictionary = loadDictionary(testProfile, api_results)
      result = dictionary$getKeyInfo("\\phs000001\\pht000001\\phv00000001\\test\\")
      expect_class(result, 'list')
    })
    it("should return correctly formatted list of phenotype data", {
      dictionary = loadDictionary(testProfile, api_results)
      result = dictionary$getKeyInfo("\\phs000001\\pht000001\\phv00000001\\test\\")
      expect_snapshot(result)
    })
    it("should return correctly formatted list of genotype data", {
      dictionary = loadDictionary(testProfile, api_results)
      result = dictionary$getKeyInfo("A_Variant")
      expect_snapshot(result)
    })
  })
  describe("genotypeAnnotations()", {
    it("should return a data.frame object", {
      dictionary = loadDictionary(testProfile, api_results)
      annotations = dictionary$genotypeAnnotations()
      expect_class(annotations, 'data.frame')
    })
    it("should return correctly formatted genomic annotations", {
      dictionary = loadDictionary(testProfile, api_results)
      annotations = dictionary$genotypeAnnotations()
      expect_snapshot(annotations)
    })
    it("should send api call with blank query", {
      api_results = function(uuid, query) {
        expect_snapshot(toString(query))
        return("{}")
      }
      dictionary = loadDictionary(testProfile, api_results)
      expect_success(dictionary$genotypeAnnotations())
    })
  })
  describe("find()", {
    it("should return a dictionary result object", {
      api_results = function(uuid, query) "{}"
      dictionary = loadDictionary(testProfile, api_results)
      capture.output(result <- dictionary$find('clouds'))
      expect_class(result, 'PicSureHpdsDictionaryBdcResult')
    })
    it("should send correctly formatted json api call", {
      api_results = function(uuid, query) {
        expect_snapshot(toString(query))
        return("{}")
      }
      dictionary = loadDictionary(testProfile, api_results)
      expect_success(capture.output(dictionary$find('clouds', 10)))
    })
  })
})