From 4ee8a011d61cf800224bb44c658ec91715048e52 Mon Sep 17 00:00:00 2001 From: Rafael Goncalves Date: Tue, 1 Oct 2024 17:47:27 -0400 Subject: [PATCH] Remove GO as purl.obolib links are often problematic --- test/simple_tests.py | 6 ++++-- text2term/resources/ontologies.csv | 1 - 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/test/simple_tests.py b/test/simple_tests.py index 25dfb60..4e3f373 100644 --- a/test/simple_tests.py +++ b/test/simple_tests.py @@ -46,9 +46,11 @@ def test_caching_ontology_from_acronym(self): assert clo_cache.cache_exists() is True def test_caching_ontology_set(self): - nr_ontologies_in_registry = 8 + ontology_registry_filepath = os.path.join("..", "text2term", "resources", "ontologies.csv") + nr_ontologies_in_registry = len(pd.read_csv(ontology_registry_filepath)) + # Test caching the set of ontologies specified in resources/ontologies.csv - caches = text2term.cache_ontology_set(os.path.join("..", "text2term", "resources", "ontologies.csv")) + caches = text2term.cache_ontology_set(ontology_registry_filepath) assert len(caches) == nr_ontologies_in_registry def test_mapping_to_cached_ontology(self): diff --git a/text2term/resources/ontologies.csv b/text2term/resources/ontologies.csv index 910acbd..1f6e269 100644 --- a/text2term/resources/ontologies.csv +++ b/text2term/resources/ontologies.csv @@ -2,7 +2,6 @@ acronym,version,url CL,2023-09-21,https://github.com/obophenotype/cell-ontology/releases/download/v2023-09-21/cl.owl EFO,3.57.0,https://github.com/EBISPOT/efo/releases/download/v3.57.0/efo.owl FOODON,0.6.0,https://github.com/FoodOntology/foodon/raw/v0.6.0/foodon.owl -GO,2023-07-27,http://purl.obolibrary.org/obo/go/releases/2023-07-27/go.owl HPO,2023-09-01,https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-09-01/hp.owl MONDO,2023-09-12,https://github.com/monarch-initiative/mondo/releases/download/v2023-08-02/mondo.owl NCIT,2022-08-19,https://github.com/NCI-Thesaurus/thesaurus-obo-edition/releases/download/v2022-08-19/ncit.owl