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VFBquery Performance Test Results

Test Date: 2026-06-04 16:16:36 UTC Git Commit: 54e9559ae8f507090941f21e6ccd567ddd6f7423 Branch: main Workflow Run: 26964062416

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

============================= test session starts ==============================
platform linux -- Python 3.10.20, pytest-9.0.3, pluggy-1.6.0 -- /opt/hostedtoolcache/Python/3.10.20/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/VFBquery/VFBquery
configfile: pyproject.toml
plugins: xdist-3.8.0
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_01_term_info_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_03_synaptic_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_06_instance_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 
[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 
[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_07_connectivity_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_07b_downstream_class_connectivity 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07b_upstream_class_connectivity 
src/test/test_query_performance.py::QueryPerformanceTest::test_08_similarity_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07b_downstream_class_connectivity 
src/test/test_query_performance.py::QueryPerformanceTest::test_09_neuron_input_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 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_08_similarity_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_10_expression_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_10_expression_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_13_dataset_template_queries 
[gw1] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_04_anatomy_hierarchy_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_12_nblast_queries 
[gw2] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_05b_image_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_07c_cross_dataset_connectivity 
[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 
[gw2] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_07c_cross_dataset_connectivity 
[gw1] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_12_nblast_queries 
[gw3] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_11_transcriptomics_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_13_dataset_template_queries 
src/test/test_query_performance.py::QueryPerformanceTest::test_14_publication_transgene_queries 
[gw0] PASSED src/test/test_query_performance.py::QueryPerformanceTest::test_14_publication_transgene_queries 

============================= 18 passed in 31.52s ==============================
=== LEGACY RETRY ATTEMPT ===
test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
Performance test for specific term info queries. ... ok

----------------------------------------------------------------------
Ran 1 test in 3.862s

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: 1.9059 seconds
VFB_00101567 query took: 1.9558 seconds
Total time for both queries: 3.8617 seconds
Performance Level: 🟠 Acceptable (3-6 seconds)
==================================================
Performance test completed successfully!
============================= test session starts ==============================
platform linux -- Python 3.10.20, pytest-9.0.3, pluggy-1.6.0 -- /opt/hostedtoolcache/Python/3.10.20/x64/bin/python
cachedir: .pytest_cache
rootdir: /home/runner/work/VFBquery/VFBquery
configfile: pyproject.toml
plugins: xdist-3.8.0
created: 8/8 workers
8 workers [55 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_headers_present 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_upstream 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_returns_dataframe 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_headers_present 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_returns_results 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_returns_dataframe 
[gw6] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_headers_present 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_limit_respected 
[gw1] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_headers_present 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_limit_respected 
[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 
[gw4] 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 
[gw6] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_limit_respected 
[gw1] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_limit_respected 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivitySchema::test_schema_generation 
[gw7] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_returns_dataframe 
src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw3] 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 
[gw5] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_limit_respected 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivitySchema::test_schema_generation 
[gw5] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivitySchema::test_schema_generation 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw4] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDict::test_row_has_expected_keys 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_row_has_expected_keys 
[gw0] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_row_has_expected_keys 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_returns_results 
[gw7] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_empty_class_returns_zero 
[gw6] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivityDataFrame::test_limit_respected 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_headers_present 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_upstream 
src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_downstream 
[gw3] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_returns_dataframe 
[gw2] PASSED src/test/test_neuron_neuron_connectivity.py::TestNeuronNeuronConnectivityDict::test_direction_downstream 
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_row_has_expected_keys 
[gw7] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_empty_class_returns_zero 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_total_n_is_constant_across_rows 
[gw1] PASSED src/test/test_neuron_region_connectivity.py::TestNeuronRegionConnectivitySchema::test_schema_generation 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_limit_respected 
[gw3] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_returns_dataframe 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_returns_results 
[gw5] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_limit_respected 
[gw4] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_row_has_expected_keys 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
[gw2] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_row_has_expected_keys 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_headers_present 
[gw4] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_limit_respected 
[gw6] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_headers_present 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
[gw0] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::test_returns_results 
src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
[gw7] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_total_n_is_constant_across_rows 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_limit_respected 
[gw1] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDict::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_vfb_connectivity.py::TestListConnectomeDatasets::test_returns_datasets 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_returns_datasets 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_datasets_have_label_and_symbol 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_datasets_have_label_and_symbol 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_hemibrain_present 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_hemibrain_present 
src/test/test_vfb_connectivity.py::TestListConnectomeDatasets::test_every_dataset_has_symbol 
[gw1] 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 
[gw1] 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 
[gw1] 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 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityGroupByClass::test_group_by_class 
src/test/test_vfb_connectivity.py::TestQueryConnectivityWeightFiltering::test_higher_weight_fewer_results 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityWeightFiltering::test_higher_weight_fewer_results 
src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbs::test_exclude_all_returns_no_results 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityExcludeDbs::test_exclude_all_returns_no_results 
src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_nonexistent_type_returns_warning 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_nonexistent_type_returns_warning 
src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_no_types_raises_error 
[gw1] PASSED src/test/test_vfb_connectivity.py::TestQueryConnectivityEdgeCases::test_no_types_raises_error 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_returns_results 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_returns_dataframe 
[gw5] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityDataFrame::test_limit_respected 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw2] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_headers_present 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
[gw4] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_limit_respected 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
[gw2] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_empty_class_returns_empty_dataframe 
[gw0] PASSED 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 
[gw7] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDict::test_limit_respected 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivitySchema::test_schema_generation 
[gw7] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivitySchema::test_schema_generation 
[gw6] PASSED src/test/test_upstream_class_connectivity.py::TestUpstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_total_n_is_constant_across_rows 
[gw5] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_dataframe_has_expected_columns 
[gw3] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityDataFrame::test_returns_dataframe 
[gw4] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_parent_class_appears_with_sensible_counts 
[gw0] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_no_rows_above_neuron_root 
[gw6] PASSED src/test/test_downstream_class_connectivity.py::TestDownstreamClassConnectivityHierarchyRollup::test_total_n_is_constant_across_rows 

======================== 55 passed in 327.92s (0:05:27) ========================

Summary

✅ Test Status: Performance tests completed

Test Statistics

  • Total Tests: 74
  • Passed: 74 ✅
  • Failed: 0 ❌
  • Errors: 0 ⚠️

Query Performance Details

Query Duration Status

🎉 Result: All performance thresholds met!

Historical Performance

Track performance trends across commits:

Last updated: 2026-06-04 16:16:36 UTC