tests/testthat/test-get_genomic_features.R

In gtexr: Query the GTEx Portal API

test_that("`validate_featureId()` detects invalid `.featureId` arguments",
          {
            # wrong class
            expect_error(validate_featureId(1L), "integer of length 1")

            # wrong length
            expect_error(validate_featureId(1:2), "integer of length 2")

            expect_error(validate_featureId(letters), "character of length 26")

            # invalid characters
            expect_error(validate_featureId("%"), "1 invalid character")

            expect_error(validate_featureId("% ,"), "3 invalid characters")

            expect_error(validate_featureId("%%  ,,"), "3 invalid characters")
          })

test_that("`process_get_genomic_features_resp_json()` handles empty responses",
          {
            expect_equal(
              process_get_genomic_features_resp_json(list(
                features = list(), assembly = "HG38"
              )),
              tibble::tibble(assembly = "HG38")
            )
          })

test_that("`process_get_genomic_features_resp_json()` handles non-empty responses",
          {
            expect_equal(
              process_get_genomic_features_resp_json(list(
                features = list(list(
                  gencodeVersion = "v26", geneSymbol = "CRP"
                )), assembly = "HG38"
              )),
              tibble::tibble(
                gencodeVersion = "v26",
                geneSymbol = "CRP",
                assembly = "HG38"
              )
            )
          })

test_that("`get_genomic_features()` returns tibble with expected colnames",
          {
            skip_if_offline()
            result <- get_genomic_features("brca1")

            expect_s3_class(result, "tbl_df")

            expect_identical(
              names(result),
              c(
                "gencodeVersion",
                "end",
                "description",
                "geneSymbolUpper",
                "genomeBuild",
                "geneStatus",
                "strand",
                "entrezGeneId",
                "geneType",
                "start",
                "dataSource",
                "gencodeId",
                "geneSymbol",
                "tss",
                "chromosome",
                "featureType",
                "assembly"
              )
            )
          })