vfbquery 0.3.2__py3-none-any.whl → 0.3.4__py3-none-any.whl

test/term_info_queries_test.py

@@ -12,7 +12,7 @@ class TermInfoQueriesTest(unittest.TestCase):
 
     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 mechanosensory 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": []}
+        {"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": []}
         """
 
         terminfo = deserialize_term_info(terminfo_json)
@@ -38,15 +38,21 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertEqual("", terminfo.pub_syn[0].pub.PubMed)
 
     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]
         start_time = time.time()
         terminfo = deserialize_term_info_from_dict(vfbTerm)
         print("--- %s seconds ---" % (time.time() - start_time))
-        print(vfbTerm)
-        print(terminfo)
+        print("vfbTerm:", vfbTerm)
+        print("terminfo:", terminfo)
+        # Add debug for unique_facets
+        if hasattr(terminfo.term.core, 'unique_facets'):
+            print("unique_facets:", terminfo.term.core.unique_facets)
+        else:
+            print("unique_facets attribute NOT present!")
 
         self.assertEqual("Get JSON for Neuron Class", terminfo.query)
-
         self.assertEqual("http://purl.obolibrary.org/obo/FBbt_00048514", terminfo.term.core.iri)
         self.assertEqual("BM-Taste", terminfo.term.core.symbol)
         # TODO: XXX unique facets are not in vfb_connect release
@@ -58,13 +64,24 @@ class TermInfoQueriesTest(unittest.TestCase):
 
         self.assertEqual(0, len(terminfo.xrefs))
 
-        self.assertEqual(6, len(terminfo.pub_syn))
-        # TODO: XXX check vfb_connect version
-        # self.assertEqual("labellar taste bristle mechanosensitive neuron", terminfo.pub_syn[0].synonym.label)
-        self.assertTrue("labellar taste bristle mechanosensory neuron" == terminfo.pub_syn[0].synonym.label or "labellar hMSN" == terminfo.pub_syn[0].synonym.label, "not matching synonym")
-        self.assertEqual("FBrf0248869", terminfo.pub_syn[0].pub.core.short_form)
-        # Update to expect the PubMed ID
-        self.assertEqual("33657409", terminfo.pub_syn[0].pub.PubMed)
+        self.assertEqual(7, 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]
+        expected_labels = ["labellar taste bristle mechanosensitive neuron", "labellar hMSN", "labial taste bristle mechanosensory neuron"]
+        
+        # Check that at least one of the expected labels exists
+        found_labels = [label for label in expected_labels if label in synonym_labels]
+        self.assertTrue(len(found_labels) > 0, f"None of the expected synonym labels found. Found: {synonym_labels}")
+        
+        # Check that entries with "Unattributed" pub exist (most entries should have this)
+        unattributed_entries = [entry for entry in terminfo.pub_syn if entry.pub.core.short_form == "Unattributed"]
+        self.assertTrue(len(unattributed_entries) > 0, "No entries with 'Unattributed' pub found")
+        
+        # Check for the PubMed ID in the correct synonym entry (labellar hMSN)
+        labellar_hmsn_entry = next((entry for entry in terminfo.pub_syn if entry.synonym.label == "labellar hMSN"), None)
+        self.assertIsNotNone(labellar_hmsn_entry, "labellar hMSN entry not found")
+        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]
@@ -128,7 +145,7 @@ 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([Spradling, 1993](FBrf0064777), [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([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])
@@ -149,13 +166,10 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertFalse("examples" in serialized)
         self.assertFalse("thumbnail" in serialized)
         self.assertTrue("references" in serialized)
-        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(1, len(serialized["references"]))
         self.assertEqual({'link': '[King, 1970, Ovarian Development in Drosophila melanogaster. ](FBrf0021038)',
                           'refs': ['http://flybase.org/reports/FBrf0021038'],
-                          'types': ' pub'}, serialized["references"][1])
+                          'types': ' pub'}, serialized["references"][0])
         self.assertFalse("targetingSplits" in serialized)
         self.assertFalse("targetingNeurons" in serialized)
 
@@ -244,7 +258,7 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertTrue("Turner-Evans et al., 2020" in description)
         
         self.assertTrue("synonyms" in serialized)
-        self.assertEqual(9, len(serialized["synonyms"]))
+        self.assertEqual(10, len(serialized["synonyms"]))
         print(serialized["synonyms"][0])
         self.assertTrue("has_exact_synonym: EB-PB 1 glomerulus-D/Vgall neuron" in serialized["synonyms"])
         self.assertFalse("source" in serialized)
@@ -276,7 +290,7 @@ class TermInfoQueriesTest(unittest.TestCase):
         self.assertFalse("thumbnail" in serialized)
 
         self.assertTrue("references" in serialized)
-        self.assertEqual(6, len(serialized["references"]))
+        self.assertEqual(7, len(serialized["references"]))
 
         self.assertTrue("targetingSplits" in serialized)
         self.assertEqual(6, len(serialized["targetingSplits"]))
@@ -329,7 +343,7 @@ class TermInfoQueriesTest(unittest.TestCase):
                                   '(http://splitgal4.janelia.org/cgi-bin/view_splitgal4_imagery.cgi?line=SS50574) '},
                          serialized["xrefs"][0])
 
-        self.assertFalse("examples" in serialized)
+        self.assertTrue("examples" in serialized)
         self.assertFalse("thumbnail" in serialized)
         self.assertFalse("references" in serialized)
         self.assertFalse("targetingSplits" in serialized)

vfbquery/__init__.py

@@ -1 +1,4 @@
 from .vfb_queries import *
+
+# Version information
+__version__ = "0.3.4"

vfbquery/solr_fetcher.py

@@ -3,7 +3,6 @@ import json
 import logging
 import pandas as pd
 from typing import List, Dict, Any, Optional, Union
-from vfb_connect import vfb
 
 class SolrTermInfoFetcher:
     """Fetches term information directly from the Solr server instead of using VfbConnect"""
@@ -12,7 +11,19 @@ class SolrTermInfoFetcher:
         """Initialize with the Solr server URL"""
         self.solr_url = solr_url
         self.logger = logging.getLogger(__name__)
-        self.vfb = vfb
+        self._vfb = None  # Lazy load vfb_connect
+    
+    @property
+    def vfb(self):
+        """Lazy load vfb_connect to avoid import issues during testing"""
+        if self._vfb is None:
+            try:
+                from vfb_connect import vfb
+                self._vfb = vfb
+            except ImportError as e:
+                self.logger.error(f"Could not import vfb_connect: {e}")
+                raise ImportError("vfb_connect is required but could not be imported")
+        return self._vfb
     
     def get_TermInfo(self, short_forms: List[str], 
                     return_dataframe: bool = False, 

vfbquery/term_info_queries.py

@@ -1,5 +1,21 @@
 import re
 import json
+import numpy as np
+
+# Custom JSON encoder to handle NumPy and pandas types
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.integer):
+            return int(obj)
+        elif isinstance(obj, np.floating):
+            return float(obj)
+        elif isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, np.bool_):
+            return bool(obj)
+        elif hasattr(obj, 'item'):  # Handle pandas scalar types
+            return obj.item()
+        return super(NumpyEncoder, self).default(obj)
 import requests
 from dataclasses import dataclass
 from dataclasses_json import dataclass_json
@@ -15,7 +31,7 @@ class Coordinates:
     Z: float
 
     def __str__(self):
-        return json.dumps([str(self.X), str(self.Y), str(self.Z)])
+        return json.dumps([str(self.X), str(self.Y), str(self.Z)], cls=NumpyEncoder)
 
 
 class CoordinatesFactory:
@@ -1062,7 +1078,7 @@ def serialize_term_info_to_json(vfb_term: VfbTerminfo, show_types=False) -> str:
     :return: json string representation of the term info object
     """
     term_info_dict = serialize_term_info_to_dict(vfb_term, show_types)
-    return json.dumps(term_info_dict, indent=4)
+    return json.dumps(term_info_dict, indent=4, cls=NumpyEncoder)
 
 
 def process(term_info_response: dict, variable, loaded_template: Optional[str] = None, show_types=False) -> dict:

vfbquery/test_utils.py

@@ -1,6 +1,41 @@
 import pandas as pd
+import json
+import numpy as np
 from typing import Any, Dict, Union
 
+# Custom JSON encoder to handle NumPy and pandas types
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.integer):
+            return int(obj)
+        elif isinstance(obj, np.floating):
+            return float(obj)
+        elif isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, np.bool_):
+            return bool(obj)
+        elif hasattr(obj, 'item'):  # Handle pandas scalar types
+            return obj.item()
+        return super(NumpyEncoder, self).default(obj)
+
+def safe_to_dict(df, sort_by_id=True):
+    """Convert DataFrame to dict with numpy types converted to native Python types"""
+    if isinstance(df, pd.DataFrame):
+        # Convert numpy dtypes to native Python types
+        df_copy = df.copy()
+        for col in df_copy.columns:
+            if df_copy[col].dtype.name.startswith('int'):
+                df_copy[col] = df_copy[col].astype('object')
+            elif df_copy[col].dtype.name.startswith('float'):
+                df_copy[col] = df_copy[col].astype('object')
+        
+        # Sort by id column in descending order if it exists and sort_by_id is True
+        if sort_by_id and 'id' in df_copy.columns:
+            df_copy = df_copy.sort_values('id', ascending=False)
+        
+        return df_copy.to_dict("records")
+    return df
+
 def safe_extract_row(result: Any, index: int = 0) -> Dict:
     """
     Safely extract a row from a pandas DataFrame or return the object itself if not a DataFrame.
@@ -11,11 +46,83 @@ def safe_extract_row(result: Any, index: int = 0) -> Dict:
     """
     if isinstance(result, pd.DataFrame):
         if not result.empty and len(result.index) > index:
-            return result.iloc[index].to_dict()
+            # Convert to dict using safe method to handle numpy types
+            row_series = result.iloc[index]
+            return {col: (val.item() if hasattr(val, 'item') else val) for col, val in row_series.items()}
         else:
             return {}
     return result
 
+def sanitize_for_json(obj: Any) -> Any:
+    """
+    Recursively sanitize any data structure to make it JSON serializable.
+    Converts numpy types, pandas types, and other non-serializable types to native Python types.
+    
+    :param obj: Object to sanitize
+    :return: JSON-serializable version of the object
+    """
+    if isinstance(obj, dict):
+        return {key: sanitize_for_json(value) for key, value in obj.items()}
+    elif isinstance(obj, (list, tuple)):
+        return [sanitize_for_json(item) for item in obj]
+    elif isinstance(obj, np.integer):
+        return int(obj)
+    elif isinstance(obj, np.floating):
+        return float(obj)
+    elif isinstance(obj, np.ndarray):
+        return obj.tolist()
+    elif isinstance(obj, np.bool_):
+        return bool(obj)
+    elif hasattr(obj, 'item'):  # Handle pandas scalar types
+        return obj.item()
+    elif isinstance(obj, pd.DataFrame):
+        return safe_to_dict(obj)
+    elif hasattr(obj, '__dict__'):  # Handle custom objects
+        return sanitize_for_json(obj.__dict__)
+    else:
+        return obj
+
+def safe_json_dumps(obj: Any, **kwargs) -> str:
+    """
+    Safely serialize any object to JSON string, handling numpy and pandas types.
+    
+    :param obj: Object to serialize
+    :param kwargs: Additional arguments to pass to json.dumps
+    :return: JSON string
+    """
+    # Set default arguments
+    default_kwargs = {'indent': 2, 'ensure_ascii': False, 'cls': NumpyEncoder}
+    default_kwargs.update(kwargs)
+    
+    try:
+        # First try with the NumpyEncoder
+        return json.dumps(obj, **default_kwargs)
+    except (TypeError, ValueError):
+        # If that fails, sanitize the object first
+        sanitized_obj = sanitize_for_json(obj)
+        return json.dumps(sanitized_obj, **default_kwargs)
+
+def pretty_print_vfb_result(result: Any, max_length: int = 1000) -> None:
+    """
+    Pretty print any VFB query result in a safe, readable format.
+    
+    :param result: Result from any VFB query function
+    :param max_length: Maximum length of output (truncates if longer)
+    """
+    try:
+        json_str = safe_json_dumps(result)
+        if len(json_str) > max_length:
+            print(json_str[:max_length] + f'\n... (truncated, full length: {len(json_str)} characters)')
+        else:
+            print(json_str)
+    except Exception as e:
+        print(f'Error printing result: {e}')
+        print(f'Result type: {type(result)}')
+        if hasattr(result, '__dict__'):
+            print(f'Result attributes: {list(result.__dict__.keys())}')
+        else:
+            print(f'Result: {str(result)[:max_length]}...')
+
 def patch_vfb_connect_query_wrapper():
     """
     Apply monkey patches to VfbConnect.neo_query_wrapper to make it handle DataFrame results safely.
@@ -28,8 +135,8 @@ def patch_vfb_connect_query_wrapper():
         def patched_get_term_info(self, terms, *args, **kwargs):
             result = original_get_term_info(self, terms, *args, **kwargs)
             if isinstance(result, pd.DataFrame):
-                # Return list of row dictionaries instead of DataFrame
-                return [row.to_dict() for i, row in result.iterrows()]
+                # Return list of row dictionaries instead of DataFrame using safe conversion
+                return safe_to_dict(result)
             return result
             
         NeoQueryWrapper._get_TermInfo = patched_get_term_info

vfbquery/vfb_queries.py

@@ -2,13 +2,55 @@ import pysolr
 from .term_info_queries import deserialize_term_info
 # Replace VfbConnect import with our new SolrTermInfoFetcher
 from .solr_fetcher import SolrTermInfoFetcher
-# Keep dict_cursor if it's used elsewhere
-from vfb_connect.cross_server_tools import dict_cursor
+# Keep dict_cursor if it's used elsewhere - lazy import to avoid GUI issues
 from marshmallow import Schema, fields, post_load
 from typing import List, Tuple, Dict, Any, Union
 import pandas as pd
 from marshmallow import ValidationError
 import json
+import numpy as np
+
+# Custom JSON encoder to handle NumPy and pandas types
+class NumpyEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.integer):
+            return int(obj)
+        elif isinstance(obj, np.floating):
+            return float(obj)
+        elif isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, np.bool_):
+            return bool(obj)
+        elif hasattr(obj, 'item'):  # Handle pandas scalar types
+            return obj.item()
+        return super(NumpyEncoder, self).default(obj)
+
+def safe_to_dict(df, sort_by_id=True):
+    """Convert DataFrame to dict with numpy types converted to native Python types"""
+    if isinstance(df, pd.DataFrame):
+        # Convert numpy dtypes to native Python types
+        df_copy = df.copy()
+        for col in df_copy.columns:
+            if df_copy[col].dtype.name.startswith('int'):
+                df_copy[col] = df_copy[col].astype('object')
+            elif df_copy[col].dtype.name.startswith('float'):
+                df_copy[col] = df_copy[col].astype('object')
+        
+        # Sort by id column in descending order if it exists and sort_by_id is True
+        if sort_by_id and 'id' in df_copy.columns:
+            df_copy = df_copy.sort_values('id', ascending=False)
+        
+        return df_copy.to_dict("records")
+    return df
+
+# Lazy import for dict_cursor to avoid GUI library issues
+def get_dict_cursor():
+    """Lazy import dict_cursor to avoid import issues during testing"""
+    try:
+        from vfb_connect.cross_server_tools import dict_cursor
+        return dict_cursor
+    except ImportError as e:
+        raise ImportError(f"vfb_connect is required but could not be imported: {e}")
 
 # Connect to the VFB SOLR server
 vfb_solr = pysolr.Solr('http://solr.virtualflybrain.org/solr/vfb_json/', always_commit=False, timeout=990)
@@ -481,6 +523,11 @@ def term_info_parse_object(results, short_form):
                     if "image_" in key and not ("thumbnail" in key or "folder" in key) and len(vars(image.channel_image.image)[key]) > 1:
                         record[key.replace("image_","")] = vars(image.channel_image.image)[key].replace("http://","https://")
                 images[image.channel_image.image.template_anatomy.short_form].append(record)
+            
+            # Sort each template's images by id in descending order (newest first)
+            for template_key in images:
+                images[template_key] = sorted(images[template_key], key=lambda x: x["id"], reverse=True)
+            
             termInfo["Examples"] = images
             # add a query to `queries` list for listing all available images
             q = ListAllAvailableImages_to_schema(termInfo["Name"], {"short_form":vfbTerm.term.core.short_form})
@@ -504,6 +551,11 @@ def term_info_parse_object(results, short_form):
                     if "image_" in key and not ("thumbnail" in key or "folder" in key) and len(vars(image.image)[key]) > 1:
                         record[key.replace("image_","")] = vars(image.image)[key].replace("http://","https://")
                 images[image.image.template_anatomy.short_form].append(record)
+            
+            # Sort each template's images by id in descending order (newest first)
+            for template_key in images:
+                images[template_key] = sorted(images[template_key], key=lambda x: x["id"], reverse=True)
+            
             # Add the thumbnails to the term info
             termInfo["Images"] = images
 
@@ -525,13 +577,29 @@ def term_info_parse_object(results, short_form):
             images = {}
             image = vfbTerm.template_channel
             record = {}
-            record["id"] = vfbTerm.template_channel.channel.short_form
-            label = vfbTerm.template_channel.channel.label
+            
+            # Validate that the channel ID matches the template ID (numeric part should be the same)
+            template_id = vfbTerm.term.core.short_form
+            channel_id = vfbTerm.template_channel.channel.short_form
+            
+            # Extract numeric parts for validation
+            if template_id and channel_id:
+                template_numeric = template_id.replace("VFB_", "") if template_id.startswith("VFB_") else ""
+                channel_numeric = channel_id.replace("VFBc_", "") if channel_id.startswith("VFBc_") else ""
+                
+                if template_numeric != channel_numeric:
+                    print(f"Warning: Template ID {template_id} does not match channel ID {channel_id}")
+                    label = vfbTerm.template_channel.channel.label
+                    record["id"] = channel_id
+                else:
+                    label = vfbTerm.term.core.label
+                    record["id"] = template_id
+            
             if vfbTerm.template_channel.channel.symbol != "" and len(vfbTerm.template_channel.channel.symbol) > 0:
                 label = vfbTerm.template_channel.channel.symbol
             record["label"] = label
-            if not vfbTerm.template_channel.channel.short_form in images.keys():
-                images[vfbTerm.template_channel.channel.short_form]=[]
+            if not template_id in images.keys():
+                images[template_id]=[]
             record["thumbnail"] = image.image_thumbnail.replace("http://","https://").replace("thumbnailT.png","thumbnail.png")
             record["thumbnail_transparent"] = image.image_thumbnail.replace("http://","https://").replace("thumbnail.png","thumbnailT.png")
             for key in vars(image).keys():
@@ -549,7 +617,7 @@ def term_info_parse_object(results, short_form):
                 record['voxel'] = image.get_voxel()
             if 'orientation' in image_vars.keys():
                 record['orientation'] = image.orientation
-            images[vfbTerm.template_channel.channel.short_form].append(record)
+            images[template_id].append(record)
 
             # Add the thumbnails to the term info
             termInfo["Images"] = images
@@ -756,8 +824,13 @@ def ListAllAvailableImages_to_schema(name, take_default):
     return Query(query=query, label=label, function=function, takes=takes, preview=preview, preview_columns=preview_columns)
 
 def serialize_solr_output(results):
-    # Serialize the sanitized dictionary to JSON
-    json_string = json.dumps(results.docs[0], ensure_ascii=False)
+    # Create a copy of the document and remove Solr-specific fields
+    doc = dict(results.docs[0])
+    # Remove the _version_ field which can cause serialization issues with large integers
+    doc.pop('_version_', None)
+    
+    # Serialize the sanitized dictionary to JSON using NumpyEncoder
+    json_string = json.dumps(doc, ensure_ascii=False, cls=NumpyEncoder)
     json_string = json_string.replace('\\', '')
     json_string = json_string.replace('"{', '{')
     json_string = json_string.replace('}"', '}')
@@ -822,7 +895,7 @@ def get_instances(short_form: str, return_dataframe=True, limit: int = -1):
     RETURN COUNT(r) AS total_count
     """
     count_results = vc.nc.commit_list([count_query])
-    count_df = pd.DataFrame.from_records(dict_cursor(count_results))
+    count_df = pd.DataFrame.from_records(get_dict_cursor()(count_results))
     total_count = count_df['total_count'][0] if not count_df.empty else 0
 
     # Define the main Cypher query
@@ -852,7 +925,7 @@ def get_instances(short_form: str, return_dataframe=True, limit: int = -1):
     results = vc.nc.commit_list([query])
 
     # Convert the results to a DataFrame
-    df = pd.DataFrame.from_records(dict_cursor(results))
+    df = pd.DataFrame.from_records(get_dict_cursor()(results))
 
     columns_to_encode = ['label', 'parent', 'source', 'source_id', 'template', 'dataset', 'license', 'thumbnail']
     df = encode_markdown_links(df, columns_to_encode)
@@ -890,7 +963,7 @@ def get_instances(short_form: str, return_dataframe=True, limit: int = -1):
                     "thumbnail"
                 ]
             }
-            for row in df.to_dict("records")
+            for row in safe_to_dict(df)
         ],
         "count": total_count
     }
@@ -910,7 +983,7 @@ def get_templates(limit: int = -1, return_dataframe: bool = False):
                 RETURN COUNT(DISTINCT t) AS total_count"""
 
     count_results = vc.nc.commit_list([count_query])
-    count_df = pd.DataFrame.from_records(dict_cursor(count_results))
+    count_df = pd.DataFrame.from_records(get_dict_cursor()(count_results))
     total_count = count_df['total_count'][0] if not count_df.empty else 0
 
     # Define the main Cypher query
@@ -935,7 +1008,7 @@ def get_templates(limit: int = -1, return_dataframe: bool = False):
     results = vc.nc.commit_list([query])
 
     # Convert the results to a DataFrame
-    df = pd.DataFrame.from_records(dict_cursor(results))
+    df = pd.DataFrame.from_records(get_dict_cursor()(results))
 
     columns_to_encode = ['name', 'dataset', 'license', 'thumbnail']
     df = encode_markdown_links(df, columns_to_encode)
@@ -978,7 +1051,7 @@ def get_templates(limit: int = -1, return_dataframe: bool = False):
                         "license"
                     ]
                 }
-                for row in df.to_dict("records")
+                for row in safe_to_dict(df)
             ],
             "count": total_count
         }
@@ -1037,7 +1110,7 @@ def get_similar_neurons(neuron, similarity_score='NBLAST_score', return_datafram
                 RETURN COUNT(DISTINCT n2) AS total_count"""
 
     count_results = vc.nc.commit_list([count_query])
-    count_df = pd.DataFrame.from_records(dict_cursor(count_results))
+    count_df = pd.DataFrame.from_records(get_dict_cursor()(count_results))
     total_count = count_df['total_count'][0] if not count_df.empty else 0
 
     main_query = f"""MATCH (c1:Class)<-[:INSTANCEOF]-(n1)-[r:has_similar_morphology_to]-(n2)-[:INSTANCEOF]->(c2:Class) 
@@ -1063,7 +1136,7 @@ def get_similar_neurons(neuron, similarity_score='NBLAST_score', return_datafram
     results = vc.nc.commit_list([main_query])
 
     # Convert the results to a DataFrame
-    df = pd.DataFrame.from_records(dict_cursor(results))
+    df = pd.DataFrame.from_records(get_dict_cursor()(results))
 
     columns_to_encode = ['name', 'source', 'source_id', 'thumbnail']
     df = encode_markdown_links(df, columns_to_encode)
@@ -1094,7 +1167,7 @@ def get_similar_neurons(neuron, similarity_score='NBLAST_score', return_datafram
                         "thumbnail"
                     ]
                 }
-                for row in df.to_dict("records")
+                for row in safe_to_dict(df)
             ],
             "count": total_count
         }
@@ -1127,7 +1200,7 @@ def get_individual_neuron_inputs(neuron_short_form: str, return_dataframe=True,
                     RETURN COUNT(DISTINCT c) AS total_count"""
 
     count_results = vc.nc.commit_list([count_query])
-    count_df = pd.DataFrame.from_records(dict_cursor(count_results))
+    count_df = pd.DataFrame.from_records(get_dict_cursor()(count_results))
     total_count = count_df['total_count'][0] if not count_df.empty else 0
 
     # Define the part of the query for normal mode
@@ -1166,7 +1239,7 @@ def get_individual_neuron_inputs(neuron_short_form: str, return_dataframe=True,
     results = vc.nc.commit_list([query])
 
     # Convert the results to a DataFrame
-    df = pd.DataFrame.from_records(dict_cursor(results))
+    df = pd.DataFrame.from_records(get_dict_cursor()(results))
 
     columns_to_encode = ['Neurotransmitter', 'Type', 'Name', 'Template_Space', 'Imaging_Technique', 'thumbnail']
     df = encode_markdown_links(df, columns_to_encode)
@@ -1204,7 +1277,7 @@ def get_individual_neuron_inputs(neuron_short_form: str, return_dataframe=True,
                         "Images"
                     ]
                 }
-                for row in df.to_dict("records")
+                for row in safe_to_dict(df)
             ],
             "count": total_count
         }
@@ -1224,7 +1297,7 @@ def get_individual_neuron_inputs(neuron_short_form: str, return_dataframe=True,
                         "Weight",
                     ]
                 }
-                for row in df.to_dict("records")
+                for row in safe_to_dict(df)
             ],
             "count": total_count
         }
@@ -1289,7 +1362,7 @@ def fill_query_results(term_info):
                             filtered_item = item
                         filtered_result.append(filtered_item)
                 elif isinstance(result, pd.DataFrame):
-                    filtered_result = result[query['preview_columns']].to_dict('records')
+                    filtered_result = safe_to_dict(result[query['preview_columns']])
                 else:
                     print(f"Unsupported result format for filtering columns in {query['function']}")
                 

{vfbquery-0.3.2.dist-info → vfbquery-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vfbquery
-Version: 0.3.2
+Version: 0.3.4
 Summary: Wrapper for querying VirtualFlyBrain knowledge graph.
 Home-page: https://github.com/VirtualFlyBrain/VFBquery
 Author: VirtualFlyBrain
@@ -53,7 +53,7 @@ vfb.get_term_info('FBbt_00003748')
    "Meta": {
       "Name": "[medulla](FBbt_00003748)",
       "Description": "The second optic neuropil, sandwiched between the lamina and the lobula complex. It is divided into 10 layers: 1-6 make up the outer (distal) medulla, the seventh (or serpentine) layer exhibits a distinct architecture and layers 8-10 make up the inner (proximal) medulla (Ito et al., 2014).",
-      "Comment": "",
+      "Comment": "Nern et al. (2025) - doi:10.1038/s41586-025-08746-0 say distal is M1-5 and M6-7 is central medulla.",
       "Types": "[anterior ectoderm derivative](FBbt_00025991); [synaptic neuropil domain](FBbt_00040007)",
       "Relationships": "[develops from](RO_0002202): [medulla anlage](FBbt_00001935); [is part of](BFO_0000050): [adult optic lobe](FBbt_00003701)"
    },
@@ -143,19 +143,18 @@ vfb.get_term_info('FBbt_00003748')
          "count": 4
       }
    ],
-   "IsIndividual": False,
-   "Images": {},
-   "IsClass": True,
+   "IsIndividual": false,
+   "IsClass": true,
    "Examples": {
-      "VFB_00030786": [
+      "VFB_00101384": [
          {
-            "id": "VFB_00030810",
-            "label": "medulla on adult brain template Ito2014",
-            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png",
-            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnailT.png",
-            "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/volume.nrrd",
-            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/volume.wlz",
-            "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/volume_man.obj"
+            "id": "VFB_00101385",
+            "label": "ME(R) on JRC_FlyEM_Hemibrain",
+            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png",
+            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnailT.png",
+            "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.nrrd",
+            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.wlz",
+            "obj": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume_man.obj"
          }
       ],
       "VFB_00101567": [
@@ -180,22 +179,19 @@ vfb.get_term_info('FBbt_00003748')
             "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/volume_man.obj"
          }
       ],
-      "VFB_00101384": [
+      "VFB_00030786": [
          {
-            "id": "VFB_00101385",
-            "label": "ME(R) on JRC_FlyEM_Hemibrain",
-            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png",
-            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnailT.png",
-            "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.nrrd",
-            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume.wlz",
-            "obj": "https://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/volume_man.obj"
+            "id": "VFB_00030810",
+            "label": "medulla on adult brain template Ito2014",
+            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png",
+            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnailT.png",
+            "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume.nrrd",
+            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume.wlz",
+            "obj": "https://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/volume_man.obj"
          }
       ]
    },
-   "IsTemplate": False,
-   "Domains": {},
-   "Licenses": {},
-   "Publications": [],
+   "IsTemplate": false,
    "Synonyms": [
       {
          "label": "ME",
@@ -203,12 +199,6 @@ vfb.get_term_info('FBbt_00003748')
          "type": "",
          "publication": "[Ito et al., 2014](FBrf0224194)"
       },
-      {
-         "label": "m",
-         "scope": "has_related_synonym",
-         "type": "",
-         "publication": ""
-      },
       {
          "label": "Med",
          "scope": "has_exact_synonym",
@@ -220,6 +210,12 @@ vfb.get_term_info('FBbt_00003748')
          "scope": "has_exact_synonym",
          "type": "",
          "publication": "[Venkatesh and Shyamala, 2010](FBrf0212889)"
+      },
+      {
+         "label": "m",
+         "scope": "has_related_synonym",
+         "type": "",
+         "publication": ""
       }
    ]
 }
@@ -259,7 +255,8 @@ vfb.get_term_info('VFB_00000001')
    "Tags": [
       "Adult",
       "Expression_pattern_fragment",
-      "Neuron"
+      "Neuron",
+      "lineage_CM3"
    ],
    "Queries": [
       {
@@ -325,41 +322,41 @@ vfb.get_term_info('VFB_00000001')
                   "id": "VFB_00000333",
                   "score": "0.61",
                   "name": "[fru-M-000204](VFB_00000333)",
-                  "tags": "Expression_pattern_fragment|Neuron|Adult",
-                  "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://virtualflybrain.org/reports/VFB_00000333/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
+                  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
+                  "thumbnail": "[![fru-M-000204 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00017894/thumbnail.png 'fru-M-000204 aligned to JFRC2')](VFB_00017894,VFB_00000333)"
                },
                {
                   "id": "VFB_00000333",
                   "score": "0.61",
                   "name": "[fru-M-000204](VFB_00000333)",
-                  "tags": "Expression_pattern_fragment|Neuron|Adult",
-                  "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://virtualflybrain.org/reports/VFB_00000333/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
+                  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
+                  "thumbnail": "[![fru-M-000204 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0333/VFB_00101567/thumbnail.png 'fru-M-000204 aligned to JRC2018U')](VFB_00101567,VFB_00000333)"
                },
                {
                   "id": "VFB_00002439",
                   "score": "0.6",
                   "name": "[fru-M-900020](VFB_00002439)",
-                  "tags": "Expression_pattern_fragment|Neuron|Adult",
-                  "thumbnail": "[![fru-M-900020 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00017894/thumbnail.png 'fru-M-900020 aligned to JFRC2')](VFB_00017894,VFB_00002439)"
+                  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
+                  "thumbnail": "[![fru-M-900020 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00101567/thumbnail.png 'fru-M-900020 aligned to JRC2018U')](VFB_00101567,VFB_00002439)"
                },
                {
                   "id": "VFB_00002439",
                   "score": "0.6",
                   "name": "[fru-M-900020](VFB_00002439)",
-                  "tags": "Expression_pattern_fragment|Neuron|Adult",
-                  "thumbnail": "[![fru-M-900020 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00101567/thumbnail.png 'fru-M-900020 aligned to JRC2018U')](VFB_00101567,VFB_00002439)"
+                  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
+                  "thumbnail": "[![fru-M-900020 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/2439/VFB_00017894/thumbnail.png 'fru-M-900020 aligned to JFRC2')](VFB_00017894,VFB_00002439)"
                },
                {
-                  "id": "VFB_00001880",
+                  "id": "VFB_00000845",
                   "score": "0.59",
-                  "name": "[fru-M-100041](VFB_00001880)",
-                  "tags": "Expression_pattern_fragment|Neuron|Adult",
-                  "thumbnail": "[![fru-M-100041 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0000/1880/VFB_00017894/thumbnail.png 'fru-M-100041 aligned to JFRC2')](VFB_00017894,VFB_00001880)"
+                  "name": "[fru-M-100191](VFB_00000845)",
+                  "tags": "Expression_pattern_fragment|Neuron|Adult|lineage_CM3",
+                  "thumbnail": "[![fru-M-100191 aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0000/0845/VFB_00101567/thumbnail.png 'fru-M-100191 aligned to JRC2018U')](VFB_00101567,VFB_00000845)"
                }
             ]
          },
          "output_format": "table",
-         "count": 46
+         "count": 60
       }
    ],
    "IsIndividual": True,
@@ -368,11 +365,11 @@ vfb.get_term_info('VFB_00000001')
          {
             "id": "VFB_00000001",
             "label": "fru-M-200266",
-            "thumbnail": "https://virtualflybrain.org/reports/VFB_00000001/thumbnail.png",
-            "thumbnail_transparent": "https://virtualflybrain.org/reports/VFB_00000001/thumbnailT.png",
+            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/thumbnail.png",
+            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/thumbnailT.png",
             "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.nrrd",
-            "wlz": "https://virtualflybrain.org/reports/VFB_00000001/volume.wlz",
-            "obj": "https://virtualflybrain.org/reports/VFB_00000001/volume.obj",
+            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.wlz",
+            "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.obj",
             "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00017894/volume.swc"
          }
       ],
@@ -380,19 +377,17 @@ vfb.get_term_info('VFB_00000001')
          {
             "id": "VFB_00000001",
             "label": "fru-M-200266",
-            "thumbnail": "https://virtualflybrain.org/reports/VFB_00000001/thumbnail.png",
-            "thumbnail_transparent": "https://virtualflybrain.org/reports/VFB_00000001/thumbnailT.png",
+            "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnail.png",
+            "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/thumbnailT.png",
             "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.nrrd",
-            "wlz": "https://virtualflybrain.org/reports/VFB_00000001/volume.wlz",
-            "obj": "https://virtualflybrain.org/reports/VFB_00000001/volume.obj",
+            "wlz": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.wlz",
+            "obj": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.obj",
             "swc": "https://www.virtualflybrain.org/data/VFB/i/0000/0001/VFB_00101567/volume.swc"
          }
       ]
    },
    "IsClass": False,
-   "Examples": {},
    "IsTemplate": False,
-   "Domains": {},
    "Licenses": {
       "0": {
          "iri": "http://virtualflybrain.org/reports/VFBlicense_FlyCircuit_License",
@@ -402,9 +397,7 @@ vfb.get_term_info('VFB_00000001')
          "source": "FlyCircuit 1.0 - single neurons (Chiang2010)",
          "source_iri": "http://virtualflybrain.org/reports/Chiang2010"
       }
-   },
-   "Publications": [],
-   "Synonyms": []
+   }
 }
 ```
 
@@ -412,7 +405,6 @@ Template example:
 ```python
 vfb.get_term_info('VFB_00101567')
 ```
-
 ```json
 {
    "Name": "JRC2018U",
@@ -441,10 +433,10 @@ vfb.get_term_info('VFB_00101567')
    "Queries": [],
    "IsIndividual": True,
    "Images": {
-      "VFBc_00101567": [
+      "VFB_00101567": [
          {
-            "id": "VFBc_00101567",
-            "label": "JRC2018Unisex_c",
+            "id": "VFB_00101567",
+            "label": "JRC2018Unisex",
             "thumbnail": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnail.png",
             "thumbnail_transparent": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/thumbnailT.png",
             "nrrd": "https://www.virtualflybrain.org/data/VFB/i/0010/1567/VFB_00101567/volume.nrrd",

vfbquery-0.3.4.dist-info/RECORD

@@ -0,0 +1,14 @@
+test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+test/readme_parser.py,sha256=puvcq4_oEltjx_faw1kQJ8mmIWiQU-40oLJjtJBQCsQ,4170
+test/term_info_queries_test.py,sha256=EiL6Od5L9W6Xm6MPRMU4V_4TfoVsSSWjO0wh0F2ITH0,34242
+test/test_examples_diff.py,sha256=ep_BzA-7az2OUPxUIsS3ReFV8LwuzGv8yIL0HirOGsc,15699
+vfbquery/__init__.py,sha256=ZirzaFa-rgWYvqvK08rwxachUEz_qjhKrm3C8s3tlZY,76
+vfbquery/solr_fetcher.py,sha256=U8mHaBJrwjncl1eU_gnNj5CGhEb-s9dCpcUTXTifQOY,3984
+vfbquery/term_info_queries.py,sha256=oE-Ogm7jCPPlKtD3W3EtttYZcHnInwDOpOj-phAEOaI,42009
+vfbquery/test_utils.py,sha256=7wUA3xgaGu3eLnjC98msNYt1wL538nOimVJjkC0ZLjU,5791
+vfbquery/vfb_queries.py,sha256=NnkWB3shgnv2ovG-WimcuzXZtQCjRzIqdWPnQvoY4Hs,66014
+vfbquery-0.3.4.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+vfbquery-0.3.4.dist-info/METADATA,sha256=T4Kxnz0tLOR_hmgIc-ZwfNWbkW_twWUYnMsy9t5jmzc,63097
+vfbquery-0.3.4.dist-info/WHEEL,sha256=tZoeGjtWxWRfdplE7E3d45VPlLNQnvbKiYnx7gwAy8A,92
+vfbquery-0.3.4.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
+vfbquery-0.3.4.dist-info/RECORD,,

{vfbquery-0.3.2.dist-info → vfbquery-0.3.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.3.2)
+Generator: bdist_wheel (0.45.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

vfbquery-0.3.2.dist-info/RECORD

@@ -1,14 +0,0 @@
-test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-test/readme_parser.py,sha256=puvcq4_oEltjx_faw1kQJ8mmIWiQU-40oLJjtJBQCsQ,4170
-test/term_info_queries_test.py,sha256=Rd7KeS6dVLjIB74s3poj5jr7h5s_DIViVpuEWnhzBB4,33423
-test/test_examples_diff.py,sha256=ep_BzA-7az2OUPxUIsS3ReFV8LwuzGv8yIL0HirOGsc,15699
-vfbquery/__init__.py,sha256=KPkQWJsiUtew3IrygX17djJJfCxJtqw3cy3rB-e3cL4,28
-vfbquery/solr_fetcher.py,sha256=_e0W87_tLwGeXSmok0FfBnpjIiM2lqTelKNkpdzxL1k,3529
-vfbquery/term_info_queries.py,sha256=79Bm2RJzAZyVPQE5HWhsvybeBYrz2AbFgbM0ympIxao,41399
-vfbquery/test_utils.py,sha256=HKFsQ2wqZYxR_wS9V6RIM3SguIi9kX5kyYDAXgpfp1A,1623
-vfbquery/vfb_queries.py,sha256=VE5-RBzgVMdadcWTjSmF5oQxefQ3fEDNwaQevG69Img,62760
-vfbquery-0.3.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-vfbquery-0.3.2.dist-info/METADATA,sha256=xllJx3ZOH91sagWa-_2O6_DI86wAjs0TQt8xsuEoUXA,62863
-vfbquery-0.3.2.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-vfbquery-0.3.2.dist-info/top_level.txt,sha256=UgaRTTOy4JBdKbkr_gkeknT4eaibm3ztF520G4NTQZs,14
-vfbquery-0.3.2.dist-info/RECORD,,