add online tests for Reference Genome Endpoints functions

rmgpanw · Jun 25, 2024 · 308b760 · 308b760
1 parent e1cbd40
commit 308b760
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diff --git a/tests/testthat/test-get_exons.R b/tests/testthat/test-get_exons.R
@@ -0,0 +1,26 @@
+test_that("`get_exons()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- get_exons(gencodeId = "ENSG00000203782.5", itemsPerPage = 1) |>
+    suppressWarnings()
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "featureType",
+      "end",
+      "genomeBuild",
+      "start",
+      "exonId",
+      "source",
+      "chromosome",
+      "gencodeId",
+      "transcriptId",
+      "geneSymbol",
+      "gencodeVersion",
+      "strand",
+      "exonNumber"
+    )
+  )
+})
diff --git a/tests/testthat/test-get_gene_search.R b/tests/testthat/test-get_gene_search.R
@@ -0,0 +1,27 @@
+test_that("`get_gene_search()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- get_gene_search("CRP")
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "chromosome",
+      "dataSource",
+      "description",
+      "end",
+      "gencodeId",
+      "gencodeVersion",
+      "geneStatus",
+      "geneSymbol",
+      "geneSymbolUpper",
+      "geneType",
+      "genomeBuild",
+      "start",
+      "strand",
+      "tss",
+      "entrezGeneId"
+    )
+  )
+})
diff --git a/tests/testthat/test-get_genes.R b/tests/testthat/test-get_genes.R
@@ -0,0 +1,27 @@
+test_that("`get_genes()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- get_genes("CRP")
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "chromosome",
+      "dataSource",
+      "description",
+      "end",
+      "entrezGeneId",
+      "gencodeId",
+      "gencodeVersion",
+      "geneStatus",
+      "geneSymbol",
+      "geneSymbolUpper",
+      "geneType",
+      "genomeBuild",
+      "start",
+      "strand",
+      "tss"
+    )
+  )
+})
diff --git a/tests/testthat/test-get_genomic_features.R b/tests/testthat/test-get_genomic_features.R
@@ -41,3 +41,34 @@ test_that("`process_get_genomic_features_resp_json()` handles non-empty response
               )
             )
           })
+
+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"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_gwas_catalog_by_location.R b/tests/testthat/test-get_gwas_catalog_by_location.R
@@ -0,0 +1,29 @@
+test_that("`get_gwas_catalog_by_location()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- get_gwas_catalog_by_location(
+              start = 1,
+              end = 10000000,
+              chromosome = "chr1",
+              itemsPerPage = 1
+            ) |>
+              suppressWarnings()
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "chromosome",
+                "start",
+                "end",
+                "phenotype",
+                "pValue",
+                "beta",
+                "pubmedId",
+                "snpId",
+                "riskAllele",
+                "genomeBuild"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_neighbor_gene.R b/tests/testthat/test-get_neighbor_gene.R
@@ -0,0 +1,33 @@
+test_that("`get_gwas_catalog_by_location()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- get_neighbor_gene(
+              pos = 1000000,
+              chromosome = "chr1",
+              bp_window = 10000,
+              itemsPerPage = 1
+            ) |>
+              suppressWarnings()
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "chromosome",
+                "dataSource",
+                "description",
+                "end",
+                "gencodeId",
+                "gencodeVersion",
+                "geneStatus",
+                "geneSymbol",
+                "geneSymbolUpper",
+                "geneType",
+                "genomeBuild",
+                "start",
+                "strand",
+                "tss"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_transcripts.R b/tests/testthat/test-get_transcripts.R
@@ -0,0 +1,24 @@
+test_that("`get_gwas_catalog_by_location()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- get_transcripts(gencodeId = "ENSG00000203782.5")
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "start",
+                "end",
+                "featureType",
+                "genomeBuild",
+                "transcriptId",
+                "source",
+                "chromosome",
+                "gencodeId",
+                "geneSymbol",
+                "gencodeVersion",
+                "strand"
+              )
+            )
+          })