Skip tests that may require internet

neurogenomics · Dec 18, 2024 · 7ca2469 · 7ca2469
1 parent de63e02
commit 7ca2469
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Showing 8 changed files with 18 additions and 9 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -80,7 +80,8 @@ Suggests:
   tidyr,
   DiagrammeR,
   forcats,
-  arrow
+  arrow,
+  curl
 Remotes:
   github::monarch-initiative/monarchr,
   github::phenoscape/rphenoscape,

diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,8 @@
 ## Bug fixes
 * `DESCRIPTION`
   - Update remote for `monarchr`.
+* Tests
+  - Add `skip_if_offline` to tests that (may) require internet access.
 * `ontology_to`
   - `igraph::as_adj` (deprecated) -> `igraph::as_adjacency_matrix`.
 

diff --git a/tests/testthat/test-filter_ontology.R b/tests/testthat/test-filter_ontology.R
@@ -1,3 +1,4 @@
+skip_if_offline()
 test_that("filter_ontology works", {
 
   ont <- get_ontology("hp")

diff --git a/tests/testthat/test-get_monarch_models.R b/tests/testthat/test-get_monarch_models.R
@@ -1,3 +1,4 @@
+skip_if_offline()
 test_that("get_monarch_models works", {
 
   models <- get_monarch_models()

diff --git a/tests/testthat/test-get_ontology_levels.R b/tests/testthat/test-get_ontology_levels.R
@@ -1,3 +1,4 @@
+skip_if_offline()
 test_that("get_ontology_levels works", {
 
   hpo <- get_ontology("hp")

diff --git a/tests/testthat/test-map_mondo.R b/tests/testthat/test-map_mondo.R
@@ -1,5 +1,6 @@
+skip_if_offline()
 test_that("map_mondo works", {
-  
+
   dat <- example_dat(rm_types="gene")
   dat2 <- map_mondo(dat = dat, map_to = "hpo")
   testthat::expect_true(methods::is(dat2,"data.table"))

diff --git a/tests/testthat/test-map_ontology_terms.R b/tests/testthat/test-map_ontology_terms.R
@@ -1,3 +1,4 @@
+skip_if_offline()
 test_that("map_ontology_terms works", {
 
   ont <- get_ontology("hp")
@@ -6,8 +7,8 @@ test_that("map_ontology_terms works", {
               "HP:0000002","HP:0000003")
   term_names <- map_ontology_terms(ont=ont, terms=terms)
   term_ids <- map_ontology_terms(ont=ont, terms=terms, to="id")
-  
-  
+
+
   testthat::expect_true(
     length(term_names)==length(terms)
   )
@@ -16,8 +17,8 @@ test_that("map_ontology_terms works", {
   )
   testthat::expect_true(
     all(names(term_names)==terms)
-  ) 
+  )
   testthat::expect_true(
     all(names(term_ids)==terms)
-  ) 
+  )
 })
diff --git a/tests/testthat/test-map_upheno.R b/tests/testthat/test-map_upheno.R
@@ -1,7 +1,8 @@
+skip_if_offline()
 test_that("map_upheno works", {
-  
+
   testthat::skip()
-  
+
   run_tests <- function(res){
     testthat::expect_true(methods::is(res$data,"data.table"))
     for(x in res$plots){
@@ -15,7 +16,7 @@ test_that("map_upheno works", {
                     # pheno_map_method="upheno",
                     terms = terms)
   run_tests(res)
-  
+
   #### Use cached data and filter by HPO terms
   res <- map_upheno(force_new = FALSE,
                     terms = terms)