From cf07b9fe59324c99da6d3fc05f374f930815a8ab Mon Sep 17 00:00:00 2001
From: rmgpanw <rmgpanw@ucl.ac.uk>
Date: Tue, 25 Jun 2024 22:06:02 +0100
Subject: [PATCH] add online tests for static association endpoint functions

---
 .../get_significant_single_tissue_isqtls.R    | 40 +++++++++++++++++++
 tests/testthat/test-get_eqtl_genes.R          | 22 ++++++++++
 tests/testthat/test-get_fine_mapping.R        | 21 ++++++++++
 tests/testthat/test-get_independent_eqtl.R    | 27 +++++++++++++
 tests/testthat/test-get_multi_tissue_eqtls.R  | 10 +++++
 ...test-get_significant_single_tissue_eqtls.R | 28 +++++++++++++
 ...nificant_single_tissue_eqtls_by_location.R | 32 +++++++++++++++
 ...est-get_significant_single_tissue_ieqtls.R | 39 ++++++++++++++++++
 ...test-get_significant_single_tissue_sqtls.R | 28 +++++++++++++
 tests/testthat/test-get_sqtl_genes.R          | 23 +++++++++++
 10 files changed, 270 insertions(+)
 create mode 100644 tests/testthat/get_significant_single_tissue_isqtls.R
 create mode 100644 tests/testthat/test-get_eqtl_genes.R
 create mode 100644 tests/testthat/test-get_fine_mapping.R
 create mode 100644 tests/testthat/test-get_independent_eqtl.R
 create mode 100644 tests/testthat/test-get_multi_tissue_eqtls.R
 create mode 100644 tests/testthat/test-get_significant_single_tissue_eqtls.R
 create mode 100644 tests/testthat/test-get_significant_single_tissue_eqtls_by_location.R
 create mode 100644 tests/testthat/test-get_significant_single_tissue_ieqtls.R
 create mode 100644 tests/testthat/test-get_significant_single_tissue_sqtls.R
 create mode 100644 tests/testthat/test-get_sqtl_genes.R

diff --git a/tests/testthat/get_significant_single_tissue_isqtls.R b/tests/testthat/get_significant_single_tissue_isqtls.R
new file mode 100644
index 0000000..48fd1ac
--- /dev/null
+++ b/tests/testthat/get_significant_single_tissue_isqtls.R
@@ -0,0 +1,40 @@
+test_that("`get_significant_single_tissue_isqtls()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <-
+              get_significant_single_tissue_isqtls(gencodeIds = "ENSG00000203782.5", itemsPerPage = 1) |>
+              suppressWarnings()
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "snpId",
+                "bGISE",
+                "pos",
+                "snpIdUpper",
+                "pValueG",
+                "pValueGI",
+                "geneSymbol",
+                "geneSymbolUpper",
+                "pValueI",
+                "bGI",
+                "tissueSiteDetailId",
+                "ontologyId",
+                "chromosome",
+                "tissueCellType",
+                "tssDistance",
+                "bGSE",
+                "variantId",
+                "maf",
+                "bISE",
+                "datasetId",
+                "bG",
+                "pValueAdjustedBH",
+                "bI",
+                "gencodeId",
+                "phenotypeId"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_eqtl_genes.R b/tests/testthat/test-get_eqtl_genes.R
new file mode 100644
index 0000000..c513610
--- /dev/null
+++ b/tests/testthat/test-get_eqtl_genes.R
@@ -0,0 +1,22 @@
+test_that("`get_eqtl_genes()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- suppressWarnings(get_eqtl_genes("Whole_Blood", itemsPerPage = 1))
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "tissueSiteDetailId",
+      "ontologyId",
+      "datasetId",
+      "empiricalPValue",
+      "gencodeId",
+      "geneSymbol",
+      "log2AllelicFoldChange",
+      "pValue",
+      "pValueThreshold",
+      "qValue"
+    )
+  )
+})
diff --git a/tests/testthat/test-get_fine_mapping.R b/tests/testthat/test-get_fine_mapping.R
new file mode 100644
index 0000000..185ea40
--- /dev/null
+++ b/tests/testthat/test-get_fine_mapping.R
@@ -0,0 +1,21 @@
+test_that("`get_fine_mapping()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- suppressWarnings(get_fine_mapping(gencodeIds = "ENSG00000203782.5", itemsPerPage = 1))
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "datasetId",
+      "gencodeId",
+      "method",
+      "pip",
+      "setId",
+      "setSize",
+      "tissueSiteDetailId",
+      "ontologyId",
+      "variantId"
+    )
+  )
+})
diff --git a/tests/testthat/test-get_independent_eqtl.R b/tests/testthat/test-get_independent_eqtl.R
new file mode 100644
index 0000000..48641a7
--- /dev/null
+++ b/tests/testthat/test-get_independent_eqtl.R
@@ -0,0 +1,27 @@
+test_that("`get_independent_eqtl()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- suppressWarnings(get_independent_eqtl(gencodeIds = "ENSG00000203782.5", itemsPerPage = 1))
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "gencodeId",
+                "geneSymbol",
+                "variantId",
+                "snpId",
+                "tissueSiteDetailId",
+                "ontologyId",
+                "rank",
+                "tssDistance",
+                "maf",
+                "pValue",
+                "nes",
+                "chromosome",
+                "pos",
+                "datasetId"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_multi_tissue_eqtls.R b/tests/testthat/test-get_multi_tissue_eqtls.R
new file mode 100644
index 0000000..8bfb2b7
--- /dev/null
+++ b/tests/testthat/test-get_multi_tissue_eqtls.R
@@ -0,0 +1,10 @@
+test_that("`get_multi_tissue_eqtls()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- suppressWarnings(get_multi_tissue_eqtls(gencodeIds = "ENSG00000203782.5", itemsPerPage = 1))
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(names(result),
+                             c("gencodeId", "datasetId", "metaP", "variantId", "tissues"))
+          })
diff --git a/tests/testthat/test-get_significant_single_tissue_eqtls.R b/tests/testthat/test-get_significant_single_tissue_eqtls.R
new file mode 100644
index 0000000..600b5ac
--- /dev/null
+++ b/tests/testthat/test-get_significant_single_tissue_eqtls.R
@@ -0,0 +1,28 @@
+test_that("`get_significant_single_tissue_eqtls()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <- suppressWarnings(
+              get_significant_single_tissue_eqtls(gencodeIds = "ENSG00000132693.12", itemsPerPage = 1)
+            )
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "snpId",
+                "pos",
+                "snpIdUpper",
+                "variantId",
+                "geneSymbol",
+                "pValue",
+                "geneSymbolUpper",
+                "datasetId",
+                "tissueSiteDetailId",
+                "ontologyId",
+                "chromosome",
+                "gencodeId",
+                "nes"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_significant_single_tissue_eqtls_by_location.R b/tests/testthat/test-get_significant_single_tissue_eqtls_by_location.R
new file mode 100644
index 0000000..a0ebe99
--- /dev/null
+++ b/tests/testthat/test-get_significant_single_tissue_eqtls_by_location.R
@@ -0,0 +1,32 @@
+test_that(
+  "`get_significant_single_tissue_eqtls_by_location()` returns tibble with expected colnames",
+  {
+    skip_if_offline()
+    result <-
+      get_significant_single_tissue_eqtls_by_location(
+        tissueSiteDetailId = "Artery_Aorta",
+        start = 240000,
+        end = 250000,
+        chromosome = "chr11"
+      )
+
+    expect_s3_class(result, "tbl_df")
+
+    expect_identical(
+      names(result),
+      c(
+        "chromosome",
+        "datasetId",
+        "gencodeId",
+        "geneSymbol",
+        "geneSymbolUpper",
+        "nes",
+        "pValue",
+        "pos",
+        "snpId",
+        "tissueSiteDetailId",
+        "variantId"
+      )
+    )
+  }
+)
diff --git a/tests/testthat/test-get_significant_single_tissue_ieqtls.R b/tests/testthat/test-get_significant_single_tissue_ieqtls.R
new file mode 100644
index 0000000..44daaa4
--- /dev/null
+++ b/tests/testthat/test-get_significant_single_tissue_ieqtls.R
@@ -0,0 +1,39 @@
+test_that("`get_significant_single_tissue_ieqtls()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <-
+              get_significant_single_tissue_ieqtls(gencodeIds = "ENSG00000203782.5", itemsPerPage = 1) |>
+              suppressWarnings()
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "snpId",
+                "bGISE",
+                "pos",
+                "snpIdUpper",
+                "pValueG",
+                "pValueGI",
+                "geneSymbol",
+                "geneSymbolUpper",
+                "pValueI",
+                "bGI",
+                "tissueSiteDetailId",
+                "ontologyId",
+                "chromosome",
+                "tissueCellType",
+                "tssDistance",
+                "bGSE",
+                "variantId",
+                "maf",
+                "bISE",
+                "datasetId",
+                "bG",
+                "pValueAdjustedBH",
+                "bI",
+                "gencodeId"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_significant_single_tissue_sqtls.R b/tests/testthat/test-get_significant_single_tissue_sqtls.R
new file mode 100644
index 0000000..380c53a
--- /dev/null
+++ b/tests/testthat/test-get_significant_single_tissue_sqtls.R
@@ -0,0 +1,28 @@
+test_that("`get_significant_single_tissue_sqtls()` returns tibble with expected colnames",
+          {
+            skip_if_offline()
+            result <-
+              get_significant_single_tissue_sqtls(gencodeIds = "ENSG00000203782.5")
+
+            expect_s3_class(result, "tbl_df")
+
+            expect_identical(
+              names(result),
+              c(
+                "snpId",
+                "pos",
+                "snpIdUpper",
+                "variantId",
+                "geneSymbol",
+                "pValue",
+                "geneSymbolUpper",
+                "datasetId",
+                "tissueSiteDetailId",
+                "ontologyId",
+                "chromosome",
+                "gencodeId",
+                "nes",
+                "phenotypeId"
+              )
+            )
+          })
diff --git a/tests/testthat/test-get_sqtl_genes.R b/tests/testthat/test-get_sqtl_genes.R
new file mode 100644
index 0000000..824c183
--- /dev/null
+++ b/tests/testthat/test-get_sqtl_genes.R
@@ -0,0 +1,23 @@
+test_that("`get_sqtl_genes()` returns tibble with expected colnames", {
+  skip_if_offline()
+  result <- suppressWarnings(get_sqtl_genes("Whole_Blood", itemsPerPage = 1))
+
+  expect_s3_class(result, "tbl_df")
+
+  expect_identical(
+    names(result),
+    c(
+      "nPhenotypes",
+      "pValueThreshold",
+      "phenotypeId",
+      "geneSymbol",
+      "pValue",
+      "datasetId",
+      "empiricalPValue",
+      "tissueSiteDetailId",
+      "ontologyId",
+      "qValue",
+      "gencodeId"
+    )
+  )
+})