VFBquery Performance Test Results

Test Date: 2026-10-18 02:12:15 UTC Git Commit: a9ffda77d68e368a5893f1b27c9aec8f75600100 Branch: main Workflow Run: 39088903481

Test Overview

This performance test measures the execution time of all implemented VFB queries organized by functionality:

1. Term Information Queries

Term Info: Comprehensive term information retrieval with preview data

2. Neuron Part & Synaptic Queries

NeuronsPartHere: Neurons with parts overlapping anatomical regions
NeuronsSynaptic: Neurons with synapses in a region
NeuronsPresynapticHere: Neurons with presynaptic terminals in a region
NeuronsPostsynapticHere: Neurons with postsynaptic terminals in a region

3. Anatomical Hierarchy Queries

ComponentsOf: Anatomical components of a structure
PartsOf: Parts of an anatomical structure
SubclassesOf: Subclasses of anatomical terms (can be very slow for complex terms)

4. Tract/Nerve & Lineage Queries

NeuronClassesFasciculatingHere: Neurons fasciculating with tracts
TractsNervesInnervatingHere: Tracts/nerves innervating neuropils
LineageClonesIn: Lineage clones in neuropils (complex OWL reasoning)

5. Image & Developmental Queries

ImagesNeurons: Neuron images in anatomical regions
ImagesThatDevelopFrom: Developmental lineage images
epFrag: Expression pattern fragments
ListAllAvailableImages: All available images for a term

6. Connectivity Queries

NeuronNeuronConnectivity: Neuron-to-neuron connectivity
NeuronRegionConnectivity: Neuron-to-region connectivity
NeuronInputsTo: Individual neuron inputs

7. Similarity Queries (NBLAST & NeuronBridge)

SimilarMorphologyTo: NBLAST morphological similarity
SimilarMorphologyToPartOf: NBLAST to expression patterns (NBLASTexp)
SimilarMorphologyToPartOfexp: Reverse NBLASTexp
SimilarMorphologyToNB: NeuronBridge matches
SimilarMorphologyToNBexp: NeuronBridge for expression patterns

8. Expression & Transcriptomics Queries

ExpressionOverlapsHere: Expression patterns overlapping regions
anatScRNAseqQuery: scRNAseq clusters in anatomy
clusterExpression: Genes expressed in clusters
expressionCluster: Clusters expressing genes
scRNAdatasetData: Cluster data from scRNAseq datasets

9. Dataset & Template Queries

PaintedDomains: Template painted anatomy domains
DatasetImages: Images in datasets
AllAlignedImages: Images aligned to templates
AlignedDatasets: Datasets aligned to templates
AllDatasets: All available datasets

10. Publication & Transgene Queries

TermsForPub: Terms referencing publications
TransgeneExpressionHere: Transgene expression patterns in regions

Performance Thresholds

Fast queries: < 1 second (SOLR lookups)
Medium queries: < 3 seconds (Owlery + SOLR)
Slow queries: < 10 seconds (Neo4j + complex processing)
Very Slow queries: < 31 seconds (Complex OWL reasoning - over 30 seconds)

Test Results

=== RETRY ATTEMPT (auto-retry on first failure) ===
VFBquery functions patched with caching support
VFBquery: SOLR caching enabled by default (3-month TTL)
         Disable with: export VFBQUERY_CACHE_ENABLED=false
============================= test session starts ==============================
platform linux -- Python 3.10.22, pytest-9.1.1, pluggy-1.7.0 -- /opt/hostedtoolcache/Python/3.10.22/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/VFBquery/VFBquery
configfile: pyproject.toml
plugins: platformdirs-4.12.4, timeout-2.4.0, xdist-3.8.0
timeout: 300.0s
timeout method: signal
timeout func_only: False
created: 4/4 workers
4 workers [18 items]

scheduling tests via LoadScheduling

src/test/test_query_performance.py::QueryPerformanceTest::test_05_tract_lineage_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_03_synaptic_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_06_instance_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_01_term_info_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_06_instance_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_07_connectivity_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_01_term_info_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_02_neuron_part_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07_connectivity_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_07b_downstream_class_connectivity 
[gw2] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_05_tract_lineage_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_05b_image_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07b_downstream_class_connectivity 
src/test/test_query_performance.py::QueryPerformanceTest::test_07c_cross_dataset_connectivity 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_02_neuron_part_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_07b_upstream_class_connectivity 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07c_cross_dataset_connectivity 
src/test/test_query_performance.py::QueryPerformanceTest::test_09_neuron_input_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07b_upstream_class_connectivity 
src/test/test_query_performance.py::QueryPerformanceTest::test_10_expression_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_09_neuron_input_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_11_transcriptomics_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_10_expression_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_12_nblast_queries 
[gw1] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_03_synaptic_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_04_anatomy_hierarchy_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_11_transcriptomics_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_13_dataset_template_queries 
[gw2] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_05b_image_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_08_similarity_queries 
[gw2] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_08_similarity_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_12_nblast_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_14_publication_transgene_queries 
[gw1] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_04_anatomy_hierarchy_queries 
[gw0] FAILED src/test/test_query_performance.py::QueryPerformanceTest::test_14_publication_transgene_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_13_dataset_template_queries 

=================================== FAILURES ===================================
__________ QueryPerformanceTest.test_14_publication_transgene_queries __________
[gw0] linux -- Python 3.10.22 /opt/hostedtoolcache/Python/3.10.22/x64/bin/python

self = <src.test.test_query_performance.QueryPerformanceTest testMethod=test_14_publication_transgene_queries>

    def test_14_publication_transgene_queries(self):
        """Test publication and transgene queries"""
        print("\n" + "="*80)
        print("PUBLICATION/TRANSGENE QUERIES")
        print("="*80)
    
        # Import the new query functions
        from vfbquery.vfb_queries import (
            get_terms_for_pub,
            get_transgene_expression_here
        )
    
        # Test terms
        pub_term = 'FBrf0224194'  # Example publication with results
        anatomy_term = self.test_terms['mushroom_body']  # mushroom body
    
        # TermsForPub - Terms referencing a publication
        # Warm up cache with full results
        try:
            get_terms_for_pub(pub_term, return_dataframe=False, limit=-1)
        except Exception:
            pass  # Ignore warm-up failures
    
        result, duration, success = self._time_query(
            "TermsForPub",
            get_terms_for_pub,
            pub_term,
            return_dataframe=False,
            limit=10
        )
        print(f"TermsForPub: {duration:.4f}s {'✅' if success else '❌'}")
        if success and result:
            count = result.get('count', 0)
            print(f"  └─ Found {count} terms for publication" + (", returned 10" if count > 10 else ""))
        self.assertLess(duration, self.THRESHOLD_MEDIUM, "TermsForPub exceeded threshold")
    
        # TransgeneExpressionHere - Complex transgene expression query
>       result, duration, success = self._time_query(
            "TransgeneExpressionHere",
            get_transgene_expression_here,
            anatomy_term,
            return_dataframe=False,
            limit=10
        )

src/test/test_query_performance.py:835: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
src/test/test_query_performance.py:109: in _time_query
    self.assertGreater(self._result_size(result), 0,
E   AssertionError: 0 not greater than 0 : TransgeneExpressionHere returned no rows
=========================== short test summary info ============================
FAILED src/test/test_query_performance.py::QueryPerformanceTest::test_14_publication_transgene_queries - AssertionError: 0 not greater than 0 : TransgeneExpressionHere returned no rows
======================== 1 failed, 17 passed in 11.15s =========================
test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
Performance test for specific term info queries. ... ok

----------------------------------------------------------------------
Ran 1 test in 1.164s

OK
VFBquery functions patched with caching support
VFBquery: SOLR caching enabled by default (3-month TTL)
         Disable with: export VFBQUERY_CACHE_ENABLED=false

==================================================
Performance Test Results:
==================================================
FBbt_00003748 query took: 0.6725 seconds
VFB_00101567 query took: 0.4912 seconds
Total time for both queries: 1.1637 seconds
Performance Level: 🟢 Excellent (< 1.5 seconds)
==================================================
Performance test completed successfully!
============================= test session starts ==============================
platform linux -- Python 3.10.22, pytest-9.1.1, pluggy-1.7.0 -- /opt/hostedtoolcache/Python/3.10.22/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/VFBquery/VFBquery
configfile: pyproject.toml
plugins: platformdirs-4.12.4, timeout-2.4.0, xdist-3.8.0
timeout: 300.0s
timeout method: signal
timeout func_only: False
created: 4/4 workers
4 workers [78 items]

scheduling tests via LoadScheduling

src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_returns_results 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_upstream 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_headers_present 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_limit_respected 
[gw3] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_headers_present 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_count_columns_populated 
[gw0] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_returns_results 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_row_has_expected_keys 
[gw3] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_count_columns_populated 
[gw1] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_limit_respected 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivitySchema::test_schema_generation 
[gw1] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivitySchema::test_schema_generation 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_returns_results 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_returns_results 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_row_has_expected_keys 
[gw3] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_returns_dataframe 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_upstream 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_downstream 
[gw0] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_row_has_expected_keys 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_headers_present 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_row_has_expected_keys 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw3] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_returns_dataframe 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_row_has_expected_keys 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_limit_respected 
[gw0] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_headers_present 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_limit_respected 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivitySchema::test_schema_generation 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_downstream 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_returns_dataframe 
[gw0] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_limit_respected 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_limit_respected 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_returns_dataframe 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivitySchema::test_schema_generation 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityAttachment::test_query_attached_to_term_info 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityAttachment::test_query_attached_to_term_info 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_returns_results 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_row_has_expected_keys 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_headers_present 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_headers_present 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_limit_respected 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_limit_respected 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_empty_class_returns_zero 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_empty_class_returns_zero 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_returns_dataframe 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_returns_dataframe 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw2] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivitySchema::test_schema_generation 
[gw2] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivitySchema::test_schema_generation 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_returns_results 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_limit_respected 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_total_n_is_per_partner 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_total_n_is_per_partner 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_includes_subclass_breakdown 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_includes_subclass_breakdown 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
[gw1] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_returns_results 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_headers_present 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_limit_respected 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_limit_respected 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
[gw2] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_returns_results 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_row_has_expected_keys 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
[gw2] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_row_has_expected_keys 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_datasets_have_label_and_symbol 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_datasets_have_label_and_symbol 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_hemibrain_present 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_hemibrain_present 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_every_dataset_has_symbol 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_every_dataset_has_symbol 
src/test/test_vfb_connectivity.py::TestQueryConnectivityKnown::test_known_connection_both_types 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityKnown::test_known_connection_both_types 
src/test/test_vfb_connectivity.py::TestQueryConnectivityKnown::test_both_types_subset_of_either_alone 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivitySchema::test_schema_generation 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivitySchema::test_schema_generation 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_returns_datasets 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_returns_datasets 
src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_top_level_query_term_row_present 
[gw0] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_total_n_constant_within_each_query_class 
[gw0] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_total_n_constant_within_each_query_class 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_includes_subclass_breakdown 
[gw0] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_includes_subclass_breakdown 
src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_parent_row_dominates_its_children 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_top_level_query_term_row_present 
src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_finer_levels_also_present 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_finer_levels_also_present 
src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbs::test_exclude_all_returns_no_results 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbs::test_exclude_all_returns_no_results 
src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_parent_class_with_no_direct_instances_returns_results 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_parent_row_dominates_its_children 
src/test/test_vfb_connectivity.py::TestQueryConnectivityWeightFiltering::test_higher_weight_fewer_results 
[gw1] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_headers_present 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_limit_respected 
[gw1] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_limit_respected 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_empty_class_returns_zero 
[gw1] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_empty_class_returns_zero 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_returns_dataframe 
[gw1] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_returns_dataframe 
src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_ambiguous_label_lists_candidates 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_ambiguous_label_lists_candidates 
src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbsDefault::test_default_excludes_are_a_strict_subset_of_everything 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityWeightFiltering::test_higher_weight_fewer_results 
src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_anchor_side_does_not_change_the_answer 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_parent_class_with_no_direct_instances_returns_results 
src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_resolved_reports_how_a_label_was_read 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_resolved_reports_how_a_label_was_read 
src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_no_types_raises_error 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_no_types_raises_error 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_tm9_is_predominantly_cholinergic 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivitySubclassExpansion::test_anchor_side_does_not_change_the_answer 
src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_nonexistent_type_returns_warning 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_tm9_is_predominantly_cholinergic 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_aggregate_row_shape 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_aggregate_row_shape 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_split_by_dataset_adds_dataset_column 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_nonexistent_type_returns_warning 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_per_instance_shape 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_split_by_dataset_adds_dataset_column 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_min_confidence_filters 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_per_instance_shape 
src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_nonexistent_type_returns_warning 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_nonexistent_type_returns_warning 
src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_includes_subclasses 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestPredictedNeurotransmitters::test_min_confidence_filters 
src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_tm9_known_cholinergic 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_includes_subclasses 
src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_row_shape 
[gw0] PASSED src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_row_shape 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_tm9_known_cholinergic 
src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_nonexistent_type_returns_warning 
[gw3] PASSED src/test/test_vfb_connectivity.py::TestKnownNeurotransmitters::test_nonexistent_type_returns_warning 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbsDefault::test_default_excludes_are_a_strict_subset_of_everything 
src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbsDefault::test_default_matches_passing_it_explicitly 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbsDefault::test_default_matches_passing_it_explicitly 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityKnown::test_both_types_subset_of_either_alone 
src/test/test_vfb_connectivity.py::TestQueryConnectivityGroupByClass::test_group_by_class 
[gw2] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityGroupByClass::test_group_by_class 

=============================== warnings summary ===============================
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts
src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_top_level_query_term_row_present
src/test/test_vfb_connectivity.py::TestQueryConnectivityRollup::test_parent_row_dominates_its_children
  /opt/hostedtoolcache/Python/3.10.22/x64/lib/python3.10/site-packages/_pytest/fixtures.py:1313: PytestRemovedIn10Warning: Class-scoped fixture defined as instance method is deprecated.
  Instance attributes set in this fixture will NOT be visible to test methods,
  as each test gets a new instance while the fixture runs only once per class.
  Use @classmethod decorator and set attributes on cls instead.
  See https://docs.pytest.org/en/stable/deprecations.html#class-scoped-fixture-as-instance-method
    fixturefunc = resolve_fixture_function(fixturedef, request)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================== 78 passed, 6 warnings in 274.86s (0:04:34) ==================

Summary

❌ Test Status: Performance tests ran but reported failures

Test Statistics

Total Tests: 97
Passed: 96 ✅
Failed: 1 ❌
Errors: 0 ⚠️

Query Performance Details

Query	Duration	Status

⚠️ Result: Some performance thresholds exceeded or tests failed

Please review the failed tests above. Common causes:

Network latency to VFB services
SOLR/Neo4j/Owlery server load
First-time cache population (expected to be slower)

Historical Performance

Track performance trends across commits:

GitHub Actions History

Last updated: 2026-10-18 02:12:15 UTC

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performance.md

performance.md

VFBquery Performance Test Results

Test Overview

1. Term Information Queries

2. Neuron Part & Synaptic Queries

3. Anatomical Hierarchy Queries

4. Tract/Nerve & Lineage Queries

5. Image & Developmental Queries

6. Connectivity Queries

7. Similarity Queries (NBLAST & NeuronBridge)

8. Expression & Transcriptomics Queries

9. Dataset & Template Queries

10. Publication & Transgene Queries

Performance Thresholds

Test Results

Summary

Test Statistics

Query Performance Details

Historical Performance

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VFBquery Performance Test Results

Test Overview

1. Term Information Queries

2. Neuron Part & Synaptic Queries

3. Anatomical Hierarchy Queries

4. Tract/Nerve & Lineage Queries

5. Image & Developmental Queries

6. Connectivity Queries

7. Similarity Queries (NBLAST & NeuronBridge)

8. Expression & Transcriptomics Queries

9. Dataset & Template Queries

10. Publication & Transgene Queries

Performance Thresholds

Test Results

Summary

Test Statistics

Query Performance Details

Historical Performance