vfbquery 0.5.1__tar.gz → 0.5.3__tar.gz

{vfbquery-0.5.1/src/vfbquery.egg-info → vfbquery-0.5.3}/PKG-INFO

@@ -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 → vfbquery-0.5.3}/setup.py

@@ -3,7 +3,7 @@ from os import path
 
 here = path.abspath(path.dirname(__file__))
 
-__version__ = "0.5.1"
+__version__ = "0.5.3"
 
 # Get the long description from the README file
 with open(path.join(here, 'README.md')) as f:

{vfbquery-0.5.1 → vfbquery-0.5.3}/src/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-0.5.1 → vfbquery-0.5.3}/src/vfbquery/__init__.py

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

{vfbquery-0.5.1 → vfbquery-0.5.3}/src/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 → vfbquery-0.5.3/src/vfbquery.egg-info}/PKG-INFO

@@ -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