fix to get_ols_ontology

Author: oerc0042

isatools/net/ols.py

@@ -23,7 +23,7 @@
 
 def get_ols_ontologies():
     """Returns a list of OntologySource objects according to what's in OLS"""
-    ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE)
+    ontologiesUri = OLS_API_BASE_URI + "/ontologies?" + str(OLS_PAGINATION_SIZE)
     log.debug(ontologiesUri)
     J = json.loads(urlopen(ontologiesUri).read().decode("utf-8"))
     ontology_sources = []
@@ -43,9 +43,9 @@ def get_ols_ontologies():
     return ontology_sources
 
 
-def get_ols_ontology(ontology_name):
+def get_ols_ontology(ontology_name, page: int):
     """Returns a single OntologySource objects according to what's in OLS"""
-    ontologiesUri = OLS_API_BASE_URI + "/ontologies?size=" + str(OLS_PAGINATION_SIZE)
+    ontologiesUri = OLS_API_BASE_URI + "/ontologies?page=" + str(page) + "&size=" + str(OLS_PAGINATION_SIZE)
     log.debug(ontologiesUri)
     J = json.loads(urlopen(ontologiesUri).read().decode("utf-8"))
     print("EMBEDDED: ", J["_embedded"]["ontologies"])
@@ -80,6 +80,8 @@ def search_ols(term, ontology_source):
 
     query = "{0}&queryFields=label&ontology={1}&exact=True".format(term, os_search)
     url += "?q={}".format(query)
+
+    print("OLS_URL", url)
     log.debug(url)
     import requests
 

tests/convert/test_isatab2sra.py

@@ -114,7 +114,7 @@ def test_isatab2sra_dump_submission_xml_biis7(self):
             actual_submission_xml_biis7 = etree.fromstring(submission_xml)
             self.assertTrue(utils.assert_xml_equal(self._expected_submission_xml_biis7, actual_submission_xml_biis7))
 
-    @unittest.skip("Not working yet")
+    # @unittest.skip("Not working yet")
     def test_isatab2sra_dump_project_set_xml_biis7(self):
         isatab2sra.convert(self._biis7_dir, self._tmp_dir, validate_first=False)
         with open(os.path.join(self._tmp_dir, "project_set.xml"), "rb") as ps_fp:

tests/isatab/test_isatab.py

@@ -2005,9 +2005,7 @@ def test_isatab_protocol_chain_parsing(self):
                 for proc in nucleotide_sequencing_assay.process_sequence
                 if proc.executes_protocol.name == "genomic DNA extraction - standard procedure 4"
             )
-            extract = next(
-                mat for mat in nucleotide_sequencing_assay.other_material if mat.name == "GSM255770.e1"
-            )
+            extract = next(mat for mat in nucleotide_sequencing_assay.other_material if mat.name == "GSM255770.e1")
             self.assertTrue(nucl_ac_extraction_process.next_process is gen_dna_extraction_process)
             self.assertEqual(len(gen_dna_extraction_process.outputs), 1)
             self.assertFalse(nucl_ac_extraction_process.outputs)

tests/utils/test_isatools_utils.py

@@ -139,26 +139,55 @@ def test_get_ontologies(self):
         self.assertIsInstance(ontology_sources, list)
         self.assertIsInstance(ontology_sources[0], OntologySource)
 
-    @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
-    def test_get_ontology(self):
-        ontology_source = ols.get_ols_ontology("efo")
+    # @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
+    def test_get_ontology0(self):
+        ontology_source = ols.get_ols_ontology("ado", 0)
+        self.assertIsInstance(ontology_source, OntologySource)
+        self.assertEqual(ontology_source.name, "ado")
+        self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file)
+        self.assertIn("/api/ontologies/ado?lang=en", ontology_source.file)
+        self.assertIsInstance(ontology_source.version, str)
+        self.assertEqual(ontology_source.description, "Alzheimer's Disease Ontology (ADO)")
+
+    def test_get_ontology1(self):
+        ontology_source = ols.get_ols_ontology("stato", 1)
+        self.assertIsInstance(ontology_source, OntologySource)
+        self.assertEqual(ontology_source.name, "stato")
+        self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file)
+        self.assertIn("/api/ontologies/stato?lang=en", ontology_source.file)
+        self.assertIsInstance(ontology_source.version, str)
+        self.assertEqual(ontology_source.description, "STATO: the statistical methods ontology")
+
+    def test_get_ontology2(self):
+        ontology_source = ols.get_ols_ontology("efo", 2)
         self.assertIsInstance(ontology_source, OntologySource)
         self.assertEqual(ontology_source.name, "efo")
         self.assertIn("://www.ebi.ac.uk/ols", ontology_source.file)
         self.assertIn("/api/ontologies/efo?lang=en", ontology_source.file)
         self.assertIsInstance(ontology_source.version, str)
         self.assertEqual(ontology_source.description, "Experimental Factor Ontology")
 
-    @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
-    def test_search_for_term(self):
-        ontology_source = ols.get_ols_ontology("efo")
-        ontology_annotations = ols.search_ols("cell type", ontology_source)
+    # @unittest.skip("efo is not available from https://www.ebi.ac.uk/ols4/api/ontologies")
+    def test_search_for_term_p0(self):
+        ontology_source = ols.get_ols_ontology("chmo", 0)
+        ontology_annotations = ols.search_ols("mobile phase", ontology_source)
+        self.assertIsInstance(ontology_annotations, list)
+        self.assertGreater(len(ontology_annotations), 0)
+        ontology_annotations = [oa for oa in ontology_annotations if oa.term == "mobile phase"]
+        self.assertIsInstance(ontology_annotations[-1], OntologyAnnotation)
+        self.assertEqual(ontology_annotations[-1].term, "mobile phase")
+        self.assertIn("http://purl.obolibrary.org/obo/CHMO_0000995", [oa.term_accession for oa in ontology_annotations])
+        self.assertEqual(ontology_annotations[-1].term_source, ontology_source)
+
+    def test_search_for_term_p1(self):
+        ontology_source = ols.get_ols_ontology("efo", 2)
+        ontology_annotations = ols.search_ols("time", ontology_source)
         self.assertIsInstance(ontology_annotations, list)
         self.assertGreater(len(ontology_annotations), 0)
-        ontology_annotations = [oa for oa in ontology_annotations if oa.term == "cell type"]
+        ontology_annotations = [oa for oa in ontology_annotations if oa.term == "time"]
         self.assertIsInstance(ontology_annotations[-1], OntologyAnnotation)
-        self.assertEqual(ontology_annotations[-1].term, "cell type")
-        self.assertIn("http://www.ebi.ac.uk/efo/EFO_0000324", [oa.term_accession for oa in ontology_annotations])
+        self.assertEqual(ontology_annotations[-1].term, "time")
+        self.assertIn("http://www.ebi.ac.uk/efo/EFO_0000721", [oa.term_accession for oa in ontology_annotations])
         self.assertEqual(ontology_annotations[-1].term_source, ontology_source)
 
 

tests/validators/test_validate_test_data.py

@@ -404,7 +404,7 @@ def test_validate_testdata_treatment_sequence_json(self):
         with open(os.path.join(utils.JSON_DATA_DIR, "create", "treatment_sequence_test.json")) as test_case_fp:
             with open(os.path.join(self.v2_create_schemas_path, "treatment_sequence_schema.json")) as fp:
                 treatment_sequence_schema = json.load(fp)
-            #res_path = pathlib.Path("file://", self.v2_create_schemas_path, "treatment_sequence_schema.json").as_uri()
+            # res_path = pathlib.Path("file://", self.v2_create_schemas_path, "treatment_sequence_schema.json").as_uri()
             # resolver = RefResolver(res_path, treatment_sequence_schema)
             # validator = Draft4Validator(treatment_sequence_schema, resolver=resolver)
             resources = []