diff --git a/DESCRIPTION b/DESCRIPTION index 95f7a27..af636e5 100644 --- 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 index 6cf44ce..569e822 100644 --- 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 index eb1886b..19a0117 100644 --- 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 index 1e6c3f2..e999415 100644 --- 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 index c3b5f61..1ddfcc5 100644 --- 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 index d5ba38c..ce3f989 100644 --- 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 index a8a21be..81d9659 100644 --- 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 index 9d260d6..0ae72d7 100644 --- 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)