Add helper method to skip tests if SOLR server is unavailable

Author: Robbie1977

src/test/term_info_queries_test.py

@@ -10,6 +10,12 @@ def setUp(self):
         self.vc = SolrTermInfoFetcher()
         self.variable = TestVariable("my_id", "my_name")
 
+    def get_term_info_or_skip(self, term_id):
+        try:
+            return self.vc.get_TermInfo([term_id], return_dataframe=False, summary=False)[0]
+        except Exception as e:
+            self.skipTest(f"SOLR server not available: {e}")
+
     def test_term_info_deserialization(self):
         terminfo_json = """
         {"term": {"core": {"iri": "http://purl.obolibrary.org/obo/FBbt_00048514", "symbol": "BM-Taste", "types": ["Entity", "Adult", "Anatomy", "Cell", "Class", "Mechanosensory_system", "Nervous_system", "Neuron", "Sensory_neuron"], "short_form": "FBbt_00048514", "unique_facets": ["Adult", "Mechanosensory_system", "Nervous_system", "Sensory_neuron"], "label": "labial taste bristle mechanosensory neuron"}, "description": ["Any mechanosensory neuron (FBbt:00005919) that has sensory dendrite in some labellar taste bristle (FBbt:00004162)."], "comment": []}, "query": "Get JSON for Neuron Class", "version": "3d2a474", "parents": [{"symbol": "", "iri": "http://purl.obolibrary.org/obo/FBbt_00048508", "types": ["Entity", "Anatomy", "Cell", "Class", "Mechanosensory_system", "Nervous_system", "Neuron", "Sensory_neuron"], "short_form": "FBbt_00048508", "unique_facets": ["Mechanosensory_system", "Nervous_system", "Sensory_neuron"], "label": "mechanosensory neuron of chaeta"}, {"symbol": "", "iri": "http://purl.obolibrary.org/obo/FBbt_00051420", "types": ["Entity", "Adult", "Anatomy", "Cell", "Class", "Mechanosensory_system", "Nervous_system", "Neuron", "Sensory_neuron"], "short_form": "FBbt_00051420", "unique_facets": ["Adult", "Mechanosensory_system", "Nervous_system", "Sensory_neuron"], "label": "adult mechanosensory neuron"}, {"symbol": "", "iri": "http://purl.obolibrary.org/obo/FBbt_00048029", "types": ["Entity", "Adult", "Anatomy", "Cell", "Class", "Nervous_system", "Neuron", "Sensory_neuron"], "short_form": "FBbt_00048029", "unique_facets": ["Adult", "Nervous_system", "Sensory_neuron"], "label": "labellar taste bristle sensory neuron"}], "relationships": [{"relation": {"iri": "http://purl.obolibrary.org/obo/BFO_0000050", "label": "is part of", "type": "part_of"}, "object": {"symbol": "", "iri": "http://purl.obolibrary.org/obo/FBbt_00005892", "types": ["Entity", "Adult", "Anatomy", "Class", "Nervous_system"], "short_form": "FBbt_00005892", "unique_facets": ["Adult", "Nervous_system"], "label": "adult peripheral nervous system"}}], "xrefs": [], "anatomy_channel_image": [], "pub_syn": [{"synonym": {"scope": "has_exact_synonym", "label": "labellar taste bristle mechanosensitive neuron", "type": ""}, "pub": {"core": {"symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": ["Entity", "Individual", "pub"], "short_form": "Unattributed", "unique_facets": ["pub"], "label": ""}, "FlyBase": "", "PubMed": "", "DOI": ""}}, {"synonym": {"scope": "has_exact_synonym", "label": "labellar taste bristle mechanosensitive neuron", "type": ""}, "pub": {"core": {"symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": ["Entity", "Individual", "pub"], "short_form": "Unattributed", "unique_facets": ["pub"], "label": ""}, "FlyBase": "", "PubMed": "", "DOI": ""}}, {"synonym": {"scope": "has_exact_synonym", "label": "labial taste bristle mechanosensitive neuron", "type": ""}, "pub": {"core": {"symbol": "", "iri": "http://flybase.org/reports/Unattributed", "types": ["Entity", "Individual", "pub"], "short_form": "Unattributed", "unique_facets": ["pub"], "label": ""}, "FlyBase": "", "PubMed": "", "DOI": ""}}], "def_pubs": [{"core": {"symbol": "", "iri": "http://flybase.org/reports/FBrf0242472", "types": ["Entity", "Individual", "pub"], "short_form": "FBrf0242472", "unique_facets": ["pub"], "label": "Zhou et al., 2019, Sci. Adv. 5(5): eaaw5141"}, "FlyBase": "", "PubMed": "31131327", "DOI": "10.1126/sciadv.aaw5141"}], "targeting_splits": []}
@@ -40,7 +46,7 @@ def test_term_info_deserialization(self):
     def test_term_info_deserialization_from_dict(self):
         import pkg_resources
         print("vfb_connect version:", pkg_resources.get_distribution("vfb_connect").version)
-        vfbTerm = self.vc.get_TermInfo(['FBbt_00048514'], return_dataframe=False, summary=False)[0]
+        vfbTerm = self.get_term_info_or_skip('FBbt_00048514')
         start_time = time.time()
         terminfo = deserialize_term_info_from_dict(vfbTerm)
         print("--- %s seconds ---" % (time.time() - start_time))
@@ -84,7 +90,7 @@ def test_term_info_deserialization_from_dict(self):
         self.assertEqual("33657409", labellar_hmsn_entry.pub.PubMed)
 
     def test_term_info_serialization_individual_anatomy(self):
-        term_info_dict = self.vc.get_TermInfo(['VFB_00010001'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('VFB_00010001')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -133,7 +139,7 @@ def test_term_info_serialization_individual_anatomy(self):
                          'reference': '[VFB_00017894,VFB_00010001]'} in serialized["thumbnail"])
 
     def test_term_info_serialization_class(self):
-        term_info_dict = self.vc.get_TermInfo(['FBbt_00048531'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('FBbt_00048531')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -176,7 +182,7 @@ def test_term_info_serialization_class(self):
         self.assertFalse("downloads_label" in serialized)
 
     def test_term_info_serialization_neuron_class(self):
-        term_info_dict = self.vc.get_TermInfo(['FBbt_00048999'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('FBbt_00048999')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -234,7 +240,7 @@ def test_term_info_serialization_neuron_class(self):
         self.assertFalse("template" in serialized)
 
     def test_term_info_serialization_neuron_class2(self):
-        term_info_dict = self.vc.get_TermInfo(['FBbt_00047030'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('FBbt_00047030')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -303,7 +309,7 @@ def test_term_info_serialization_neuron_class2(self):
         self.assertFalse("template" in serialized)
 
     def test_term_info_serialization_split_class(self):
-        term_info_dict = self.vc.get_TermInfo(['VFBexp_FBtp0124468FBtp0133404'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('VFBexp_FBtp0124468FBtp0133404')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -357,7 +363,7 @@ def test_term_info_serialization_split_class(self):
         self.assertFalse("template" in serialized)
 
     def test_term_info_serialization_dataset(self):
-        term_info_dict = self.vc.get_TermInfo(['Ito2013'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('Ito2013')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -395,7 +401,7 @@ def test_term_info_serialization_dataset(self):
         self.assertTrue("clone of Ito 2013" in sample_example["name"])
 
     def test_term_info_serialization_license(self):
-        term_info_dict = self.vc.get_TermInfo(['VFBlicense_CC_BY_NC_3_0'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('VFBlicense_CC_BY_NC_3_0')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -430,7 +436,7 @@ def test_term_info_serialization_license(self):
         self.assertFalse("template" in serialized)
 
     def test_term_info_serialization_template(self):
-        term_info_dict = self.vc.get_TermInfo(['VFB_00200000'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('VFB_00200000')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -486,7 +492,7 @@ def test_term_info_serialization_template(self):
         self.assertEqual("[JRC2018UnisexVNC](VFB_00200000)", serialized["template"])
 
     def test_term_info_serialization_pub(self):
-        term_info_dict = self.vc.get_TermInfo(['FBrf0243986'], return_dataframe=False, summary=False)[0]
+        term_info_dict = self.get_term_info_or_skip('FBrf0243986')
         print(term_info_dict)
         start_time = time.time()
         serialized = process(term_info_dict, self.variable)
@@ -531,15 +537,18 @@ def test_term_info_performance(self):
         """
         import vfbquery as vfb
 
-        # Test performance for FBbt_00003748 (mushroom body)
-        start_time = time.time()
-        result_1 = vfb.get_term_info('FBbt_00003748')
-        duration_1 = time.time() - start_time
-        
-        # Test performance for VFB_00101567 (individual anatomy)
-        start_time = time.time()
-        result_2 = vfb.get_term_info('VFB_00101567')
-        duration_2 = time.time() - start_time
+        try:
+            # Test performance for FBbt_00003748 (mushroom body)
+            start_time = time.time()
+            result_1 = vfb.get_term_info('FBbt_00003748')
+            duration_1 = time.time() - start_time
+            
+            # Test performance for VFB_00101567 (individual anatomy)
+            start_time = time.time()
+            result_2 = vfb.get_term_info('VFB_00101567')
+            duration_2 = time.time() - start_time
+        except Exception as e:
+            self.skipTest(f"SOLR server not available: {e}")
 
         # Print performance metrics for GitHub Actions logs
         print(f"\n" + "="*50)