Skip to content

performance.md

Latest commit

 

History

History
286 lines (230 loc) · 11.6 KB

performance.md

File metadata and controls

286 lines (230 loc) · 11.6 KB

VFBquery Performance Test Results

Test Date: 2026-04-23 04:46:48 UTC Git Commit: b3c4b23c4d65567248c7e18ac9115d7dab93087f Branch: main Workflow Run: 24817236881

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_01_term_info_queries (src.test.test_query_performance.QueryPerformanceTest)
Test term info query performance ... ok
test_02_neuron_part_queries (src.test.test_query_performance.QueryPerformanceTest)
Test neuron part overlap queries ... ok
test_03_synaptic_queries (src.test.test_query_performance.QueryPerformanceTest)
Test synaptic terminal queries ... ok
test_04_anatomy_hierarchy_queries (src.test.test_query_performance.QueryPerformanceTest)
Test anatomical hierarchy queries ... ok
test_05_tract_lineage_queries (src.test.test_query_performance.QueryPerformanceTest)
Test tract/nerve and lineage clone queries ... ok
test_05b_image_queries (src.test.test_query_performance.QueryPerformanceTest)
Test image and developmental lineage queries ... ok
test_06_instance_queries (src.test.test_query_performance.QueryPerformanceTest)
Test instance retrieval queries ... ok
test_07_connectivity_queries (src.test.test_query_performance.QueryPerformanceTest)
Test neuron connectivity queries ... ok
test_08_similarity_queries (src.test.test_query_performance.QueryPerformanceTest)
Test NBLAST similarity queries ... ok
test_09_neuron_input_queries (src.test.test_query_performance.QueryPerformanceTest)
Test neuron input/synapse queries ... ok
test_10_expression_queries (src.test.test_query_performance.QueryPerformanceTest)
Test expression pattern queries ... ok
test_11_transcriptomics_queries (src.test.test_query_performance.QueryPerformanceTest)
Test scRNAseq transcriptomics queries ... ok
test_12_nblast_queries (src.test.test_query_performance.QueryPerformanceTest)
Test NBLAST similarity queries ... ok
test_13_dataset_template_queries (src.test.test_query_performance.QueryPerformanceTest)
Test dataset and template queries ... ok
test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerformanceTest)
Test publication and transgene queries ... ok

----------------------------------------------------------------------
Ran 15 tests in 63.104s

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

🔥 SOLR caching enabled for performance tests

================================================================================
TERM INFO QUERIES
================================================================================
get_term_info (mushroom body): 2.8037s ✅
get_term_info (individual): 1.7955s ✅

================================================================================
NEURON PART OVERLAP QUERIES
================================================================================
NeuronsPartHere: 2.3884s ✅

================================================================================
SYNAPTIC TERMINAL QUERIES
================================================================================
NeuronsSynaptic: 2.1679s ✅
NeuronsPresynapticHere: 1.7512s ✅
NeuronsPostsynapticHere: 1.6045s ✅
NeuronNeuronConnectivity: 1.2606s ✅

================================================================================
ANATOMICAL HIERARCHY QUERIES
================================================================================
ComponentsOf: 1.2443s ✅
PartsOf: 1.3146s ✅
SubclassesOf: 1.2288s ✅

================================================================================
TRACT/NERVE AND LINEAGE QUERIES
================================================================================
NeuronClassesFasciculatingHere: 1.7945s ✅
TractsNervesInnervatingHere: 1.2854s ✅
LineageClonesIn: 1.2266s ✅

================================================================================
IMAGE AND DEVELOPMENTAL QUERIES
================================================================================
ImagesNeurons: 2.1640s ✅
ImagesThatDevelopFrom: 1.5883s ✅
epFrag: 1.4882s ✅

================================================================================
INSTANCE QUERIES
================================================================================
ListAllAvailableImages: 1.4578s ✅

================================================================================
CONNECTIVITY QUERIES
================================================================================
NeuronNeuronConnectivityQuery: 1.1956s ✅
NeuronRegionConnectivityQuery: 1.4489s ✅

================================================================================
SIMILARITY QUERIES (Neo4j NBLAST)
================================================================================
SimilarMorphologyTo: 0.6526s ✅

================================================================================
NEURON INPUT QUERIES (Neo4j)
================================================================================
NeuronInputsTo: 3.0078s ✅

================================================================================
EXPRESSION PATTERN QUERIES (Neo4j)
================================================================================
ExpressionOverlapsHere: 1.1738s ✅
  └─ Found 3922 total expression patterns, returned 10

================================================================================
TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)
================================================================================
anatScRNAseqQuery: 0.8738s ✅
  └─ Found 57 total clusters, returned 10
clusterExpression: 0.9782s ✅
  └─ Found 4588 genes expressed, returned 10
expressionCluster: 0.6463s ✅
  └─ Found 9 clusters expressing gene
scRNAdatasetData: 0.6403s ✅
  └─ Found 13 clusters in dataset, returned 10

================================================================================
NBLAST SIMILARITY QUERIES
================================================================================
SimilarMorphologyTo: 0.8850s ✅
  └─ Found 215 NBLAST matches, returned 10
SimilarMorphologyToPartOf: 0.6794s ✅
  └─ Found 0 NBLASTexp matches
SimilarMorphologyToPartOfexp: 0.6247s ✅
  └─ Found 0 reverse NBLASTexp matches
SimilarMorphologyToNB: 0.6738s ✅
  └─ Found 15 NeuronBridge matches, returned 10
SimilarMorphologyToNBexp: 0.6227s ✅
  └─ Found 15 NeuronBridge expression matches, returned 10
✅ All NBLAST similarity queries completed

================================================================================
DATASET/TEMPLATE QUERIES
================================================================================
PaintedDomains: 0.6116s ✅
  └─ Found 46 painted domains, returned 10
DatasetImages: 0.6611s ✅
  └─ Found 46 images in dataset, returned 10
AllAlignedImages: 2.5500s ✅
  └─ Found 527179 aligned images, returned 10
AlignedDatasets: 0.6054s ✅
  └─ Found 72 aligned datasets, returned 10
AllDatasets: 1.0051s ✅
  └─ Found 130 total datasets, returned 20
✅ All dataset/template queries completed

================================================================================
PUBLICATION/TRANSGENE QUERIES
================================================================================
TermsForPub: 0.5843s ✅
  └─ Found 2 terms for publication
TransgeneExpressionHere: 1.3415s ✅
  └─ Found 2340 transgene expressions, returned 10
✅ All publication/transgene queries completed

================================================================================
PERFORMANCE TEST SUMMARY
================================================================================
All performance tests completed!
================================================================================
test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
Performance test for specific term info queries. ... ok

----------------------------------------------------------------------
Ran 1 test in 2.435s

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: 1.2240 seconds
VFB_00101567 query took: 1.2104 seconds
Total time for both queries: 2.4343 seconds
Performance Level: 🟡 Good (1.5-3 seconds)
==================================================
Performance test completed successfully!

Summary

✅ Test Status: Performance tests completed

Historical Performance

Track performance trends across commits:

Last updated: 2026-04-23 04:46:48 UTC