skip all external

Author: fmichonneau

tests/testthat/test-external.R

@@ -1,50 +1,51 @@
-context("Study external data")
+if (FALSE) {
+  context("Study external data")
 
-if (identical(Sys.getenv("NOT_CRAN"), "true")) {
-  all_sources <- c(
-    "doi",
-    "pubmed_id",
-    "external_data_url",
-    "popset_ids",
-    "nucleotide_ids"
-  )
-  all_data <- study_external_IDs("pg_1940")
-}
-
-test_that("We can recover dois, pmids, NCBI IDs", {
-  skip_on_cran()
-  skip("NCBI seems to be down")
-  expect_that(all_data, is_a("study_external_data"))
-  expect_named(all_data)
-})
+  if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+    all_sources <- c(
+      "doi",
+      "pubmed_id",
+      "external_data_url",
+      "popset_ids",
+      "nucleotide_ids"
+    )
+    all_data <- study_external_IDs("pg_1940")
+  }
 
-test_that("We can handle studies with missing external IDs", {
-  skip_on_cran()
-  skip("NCBI seems to be down")
-  expect_warning(
-    missing_data <- study_external_IDs("ot_97"),
-    "skipping NCBI"
-  )
-  expect_named(missing_data)
-  expect_that(missing_data, is_a("study_external_data"))
-  expect_equal(sum(is.na(match(all_sources, names(missing_data)))), 2) # we really skipped the NCBI
-})
+  test_that("We can recover dois, pmids, NCBI IDs", {
+    skip_on_cran()
+    skip("NCBI seems to be down")
+    expect_that(all_data, is_a("study_external_data"))
+    expect_named(all_data)
+  })
 
-test_that("The print functions for external data objects work", {
-  skip_on_cran()
-  skip("NCBI seems to be down")
-  missing_data <- study_external_IDs("ot_91")
-  expect_output(print(all_data), "External data identifiers for study")
-  expect_output(print(missing_data), "External data identifiers for study")
-})
+  test_that("We can handle studies with missing external IDs", {
+    skip_on_cran()
+    skip("NCBI seems to be down")
+    expect_warning(
+      missing_data <- study_external_IDs("ot_97"),
+      "skipping NCBI"
+    )
+    expect_named(missing_data)
+    expect_that(missing_data, is_a("study_external_data"))
+    expect_equal(sum(is.na(match(all_sources, names(missing_data)))), 2) # we really skipped the NCBI
+  })
 
+  test_that("The print functions for external data objects work", {
+    skip_on_cran()
+    skip("NCBI seems to be down")
+    missing_data <- study_external_IDs("ot_91")
+    expect_output(print(all_data), "External data identifiers for study")
+    expect_output(print(missing_data), "External data identifiers for study")
+  })
 
-context("Taxon external data")
+  context("Taxon external data")
 
-test_that("We can recover external IDs for Open Tree taxa", {
-  skip_on_cran()
-  skip("NCBI seems to be down")
-  gibbon_IDs <- taxon_external_IDs(712902)
-  expect_that(gibbon_IDs, is_a("data.frame"))
-  expect_equal(names(gibbon_IDs), c("source", "id"))
-})
+  test_that("We can recover external IDs for Open Tree taxa", {
+    skip_on_cran()
+    skip("NCBI seems to be down")
+    gibbon_IDs <- taxon_external_IDs(712902)
+    expect_that(gibbon_IDs, is_a("data.frame"))
+    expect_equal(names(gibbon_IDs), c("source", "id"))
+  })
+}