vfbquery 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

test/term_info_queries_test.py

@@ -70,7 +70,7 @@ class TermInfoQueriesTest(unittest.TestCase):
 
         self.assertEqual(0, len(terminfo.xrefs))
 
-        self.assertEqual(7, len(terminfo.pub_syn))
+        self.assertEqual(8, len(terminfo.pub_syn))
         
         # Check that we have the expected synonym labels (order-independent)
         synonym_labels = [entry.synonym.label for entry in terminfo.pub_syn]
@@ -151,7 +151,7 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertFalse("link" in serialized)
         self.assertEqual(4, len(serialized["types"]))
         self.assertTrue("Anatomy" in serialized["types"])
-        self.assertEqual("Cyst composed of two cyst cells following the division of a newly-formed cystoblast in the germarium. The two cells are connected by a cytoplasmic bridge.\n([King, 1970](FBrf0021038))", serialized["description"])
+        self.assertEqual("Cyst composed of two cyst cells following the division of a newly-formed cystoblast in the germarium. The two cells are connected by a cytoplasmic bridge.\n([Spradling, 1993](FBrf0064777), [King, 1970](FBrf0021038))", serialized["description"])
         self.assertTrue("synonyms" in serialized)
         self.assertEqual(1, len(serialized["synonyms"]))
         self.assertEqual("has_exact_synonym: germarial 2-cell cluster ([King, 1970](FBrf0021038))", serialized["synonyms"][0])
@@ -172,10 +172,13 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertFalse("examples" in serialized)
         self.assertFalse("thumbnail" in serialized)
         self.assertTrue("references" in serialized)
-        self.assertEqual(1, len(serialized["references"]))
+        self.assertEqual(2, len(serialized["references"]))
+        self.assertEqual({'link': '[Spradling, 1993, Bate, Martinez Arias, 1993: 1--70](FBrf0064777)',
+                          'refs': ['http://flybase.org/reports/FBrf0064777'],
+                          'types': ' pub'}, serialized["references"][0])
         self.assertEqual({'link': '[King, 1970, Ovarian Development in Drosophila melanogaster. ](FBrf0021038)',
                           'refs': ['http://flybase.org/reports/FBrf0021038'],
-                          'types': ' pub'}, serialized["references"][0])
+                          'types': ' pub'}, serialized["references"][1])
         self.assertFalse("targetingSplits" in serialized)
         self.assertFalse("targetingNeurons" in serialized)
 

vfbquery/__init__.py

@@ -95,4 +95,4 @@ except ImportError:
     __solr_caching_available__ = False
 
 # Version information
-__version__ = "0.5.1"
+__version__ = "0.5.3"

vfbquery/vfb_queries.py

@@ -2698,7 +2698,7 @@ def get_neuron_neuron_connectivity(short_form: str, return_dataframe=True, limit
     }
     return {
         'headers': headers,
-        'data': rows,
+        'rows': rows,
         'count': len(rows)
     }
 
@@ -2756,7 +2756,7 @@ def get_neuron_region_connectivity(short_form: str, return_dataframe=True, limit
     }
     return {
         'headers': headers,
-        'data': rows,
+        'rows': rows,
         'count': len(rows)
     }
 
@@ -3087,19 +3087,37 @@ def _owlery_query_to_results(owl_query_string: str, short_form: str, return_data
         owlery_url = f"{owlery_base}{endpoint}?{urlencode(params)}"
         
         import sys
-        print(f"ERROR: Owlery {'instances' if query_instances else 'subclasses'} query failed: {e}", file=sys.stderr)
-        print(f"       Full URL: {owlery_url}", file=sys.stderr)
-        print(f"       Query string: {owl_query_string}", file=sys.stderr)
-        import traceback
-        traceback.print_exc()
-        # Return error indication with count=-1
-        if return_dataframe:
-            return pd.DataFrame()
-        return {
-            "headers": _get_standard_query_headers(),
-            "rows": [],
-            "count": -1
-        }
+        import requests
+        
+        # Check if this is a 400 Bad Request (invalid query) vs other errors
+        is_bad_request = isinstance(e, requests.exceptions.HTTPError) and hasattr(e, 'response') and e.response.status_code == 400
+        
+        if is_bad_request:
+            # 400 Bad Request means the term isn't valid for this type of query (e.g., anatomical query on expression pattern)
+            # Return 0 results instead of error
+            print(f"INFO: Owlery query returned 400 Bad Request (invalid for this term type): {owl_query_string}", file=sys.stderr)
+            if return_dataframe:
+                return pd.DataFrame()
+            return {
+                "headers": _get_standard_query_headers(),
+                "rows": [],
+                "count": 0
+            }
+        else:
+            # Other errors (500, network issues, etc.) - return error indication
+            print(f"ERROR: Owlery {'instances' if query_instances else 'subclasses'} query failed: {e}", file=sys.stderr)
+            print(f"       Full URL: {owlery_url}", file=sys.stderr)
+            print(f"       Query string: {owl_query_string}", file=sys.stderr)
+            import traceback
+            traceback.print_exc()
+            # Return error indication with count=-1
+            if return_dataframe:
+                return pd.DataFrame()
+            return {
+                "headers": _get_standard_query_headers(),
+                "rows": [],
+                "count": -1
+            }
 
 
 def get_anatomy_scrnaseq(anatomy_short_form: str, return_dataframe=True, limit: int = -1):
@@ -3906,6 +3924,20 @@ def fill_query_results(term_info):
                             filtered_item = item
                         filtered_result.append(filtered_item)
                         
+                    if 'headers' in result:
+                        if 'preview_columns' in query.keys() and len(query['preview_columns']) > 0:
+                            filtered_headers = {col: result['headers'][col] for col in query['preview_columns']}
+                        else:
+                            filtered_headers = result['headers']
+                elif isinstance(result, dict) and 'data' in result:
+                    # Handle legacy 'data' key as alias for 'rows'
+                    for item in result['data']:
+                        if 'preview_columns' in query.keys() and len(query['preview_columns']) > 0:
+                            filtered_item = {col: item[col] for col in query['preview_columns']}
+                        else:
+                            filtered_item = item
+                        filtered_result.append(filtered_item)
+                        
                     if 'headers' in result:
                         if 'preview_columns' in query.keys() and len(query['preview_columns']) > 0:
                             filtered_headers = {col: result['headers'][col] for col in query['preview_columns']}

{vfbquery-0.5.1.dist-info → vfbquery-0.5.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vfbquery
-Version: 0.5.1
+Version: 0.5.3
 Summary: Wrapper for querying VirtualFlyBrain knowledge graph.
 Home-page: https://github.com/VirtualFlyBrain/VFBquery
 Author: VirtualFlyBrain

{vfbquery-0.5.1.dist-info → vfbquery-0.5.3.dist-info}/RECORD

@@ -1,6 +1,6 @@
 test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 test/readme_parser.py,sha256=Y5cGYaFaTBfUflpQFZh-zMpRFpYu78wUawIjwmFfBp4,5485
-test/term_info_queries_test.py,sha256=ZVx2yrdbU-7SDfPSD0EADkw-_N4zIPUT0N_zDl_qQpk,37036
+test/term_info_queries_test.py,sha256=MTp9FnGZWMT0ak49lPqOGhYYIja19m5xtaHFlt-Aw20,37322
 test/test_dataset_template_queries.py,sha256=rRKcgYn8elNfHI0SQBzvCJwkSw4bhoqKrEf3cUjsggg,5291
 test/test_default_caching.py,sha256=rr6LLHiGjUHOtqNpFYXjCzJKjed8iavjYrjWycef5oI,6963
 test/test_examples_code.py,sha256=CCX9aYGofopjTdrrfPrx0sSLB2ZKJCrEp6bJcGx35ew,293
@@ -22,7 +22,7 @@ test/test_query_performance.py,sha256=0T4qybM2GRInUmpKCQV4Q-cl6sCfxi6PjIodpirQtf
 test/test_similar_morphology.py,sha256=SRtr1Zj2_RW55Qe8O6m6SCvb9QfltWgAmxPEzMX-7hg,7390
 test/test_tracts_nerves_innervating.py,sha256=k9l-XlrvLfqzKJNyPhuJq8qBfhhrU5b8QLRnAPv1LMI,8077
 test/test_transcriptomics.py,sha256=VZf3Tgh2XgyGZpojM87j04y42RT2Dbca6xP46h_fQHg,9969
-vfbquery/__init__.py,sha256=KHVZvzikqG2YWbHbhVRV61yO0dtse-MrhhU6_k134ks,3754
+vfbquery/__init__.py,sha256=pesugXM2yE-UKr9uC0zj5xOjjLUUlMYWFP3Dr6rvpGE,3754
 vfbquery/cache_enhancements.py,sha256=-PCM0YZHPjwUJwJODZLgmz91sDyFGuYz_QRph_kTbB8,17341
 vfbquery/cached_functions.py,sha256=P0YMkKxqWsB7ZNW2AZ8uCoPlD6dMNqh9foqiYiXv1QM,45067
 vfbquery/neo4j_client.py,sha256=zyekidmosybvR5_Qcf18W4rLJt16d-kYMojbeOEkZWY,3904
@@ -32,9 +32,9 @@ vfbquery/solr_fetcher.py,sha256=_6Cb6W7JmMwZxytDPwB8ydUqZ7MNN7j2YmaF6gpBn0Y,5696
 vfbquery/solr_result_cache.py,sha256=sR17d-0V7-TfVf9b0MFmJORXginfg3rDb0mFS-yy8iI,50441
 vfbquery/term_info_queries.py,sha256=GHf1nFFJ32be7-h26EBgE8gRrfIN0XRR5qSlgDxUD9w,42010
 vfbquery/test_utils.py,sha256=7wUA3xgaGu3eLnjC98msNYt1wL538nOimVJjkC0ZLjU,5791
-vfbquery/vfb_queries.py,sha256=N6nnGzwoa7O7Y3eCUQ784Xpfw-3QhOWBXN3jotzqg14,198076
-vfbquery-0.5.1.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-vfbquery-0.5.1.dist-info/METADATA,sha256=3yiBH1v45FQqE2lDoJ4fVwNn5xYT66PtCKUtTToFxnQ,114719
-vfbquery-0.5.1.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
-vfbquery-0.5.1.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
-vfbquery-0.5.1.dist-info/RECORD,,
+vfbquery/vfb_queries.py,sha256=zM7e1nwk0iXZ1kp68zjRXrkxha6j0Z5WBX_h6Divql8,199924
+vfbquery-0.5.3.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+vfbquery-0.5.3.dist-info/METADATA,sha256=mn1jsDexJ0NPUSXhVWiC0zWwZWyD8UVQ_lLNXMacgUc,114719
+vfbquery-0.5.3.dist-info/WHEEL,sha256=hPN0AlP2dZM_3ZJZWP4WooepkmU9wzjGgCLCeFjkHLA,92
+vfbquery-0.5.3.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
+vfbquery-0.5.3.dist-info/RECORD,,

{vfbquery-0.5.1.dist-info → vfbquery-0.5.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.45.1)
+Generator: bdist_wheel (0.46.3)
 Root-Is-Purelib: true
 Tag: py3-none-any