Merge pull request #599 from ISA-tools/ols_fix

fix to get_ols_ontology

Author: proccaserra

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 = []
@@ -43,28 +43,24 @@ 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"])
     ontology_sources = []
     for ontology_source_json in J["_embedded"]["ontologies"]:
-        ontology_sources.append(
-            OntologySource(
-                name=ontology_source_json["ontologyId"],
-                version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "",
-                description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "",
-                file=ontology_source_json["_links"]["self"]["href"],
+        if ontology_source_json["ontologyId"] == ontology_name:
+            ontology_sources.append(
+                OntologySource(
+                    name=ontology_source_json["ontologyId"],
+                    version=ontology_source_json["config"]["version"] if ontology_source_json["config"]["version"] else "",
+                    description=ontology_source_json["config"]["title"] if ontology_source_json["config"]["title"] else "",
+                    file=ontology_source_json["_links"]["self"]["href"],
+                )
             )
-        )
-    print("NAME: ", ontology_name)
-    print("SOURCES: ", [o.name for o in ontology_sources])
-    hits = [o for o in ontology_sources if o.name == ontology_name]
-    print("HITS: ", hits)
-    if len(hits) == 1:
-        return hits[0]
+    if len(ontology_sources) == 1:
+        return ontology_sources[0]
     return None
 
 
@@ -80,6 +76,8 @@ 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)