Merge branch 'main' of https://github.com/VirtualFlyBrain/VFBquery

Author: Robbie1977

performance.md

@@ -1,9 +1,9 @@
 # VFBquery Performance Test Results
 
-**Test Date:** 2026-02-02 04:17:08 UTC
-**Git Commit:** 149ffe79fba63cfa149929f34dbd46fd54136621
+**Test Date:** 2026-02-04 04:26:45 UTC
+**Git Commit:** 6bc4d6ca382711555b357a9dff702dc182fffb6b
 **Branch:** main
-**Workflow Run:** [21577138574](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/21577138574)
+**Workflow Run:** [21658000888](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/21658000888)
 
 ## Test Overview
 
@@ -91,7 +91,7 @@ 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 anatomical hierarchy queries ... FAIL
 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)
@@ -103,22 +103,85 @@ 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 neuron input/synapse queries ... FAIL
 test_10_expression_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test expression pattern queries ... ok
+Test expression pattern queries ... FAIL
 test_11_transcriptomics_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test scRNAseq transcriptomics queries ... ok
+Test scRNAseq transcriptomics queries ... FAIL
 test_12_nblast_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test NBLAST similarity queries ... ok
+Test NBLAST similarity queries ... FAIL
 test_13_dataset_template_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test dataset and template queries ... ok
+Test dataset and template queries ... FAIL
 test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerformanceTest)
-Test publication and transgene queries ... ok
+Test publication and transgene queries ... FAIL
 
+======================================================================
+FAIL: test_04_anatomy_hierarchy_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test anatomical hierarchy queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 206, in test_04_anatomy_hierarchy_queries
+    self.assertLess(duration, self.THRESHOLD_SLOW, "ComponentsOf exceeded threshold")
+AssertionError: 15.446540832519531 not less than 15.0 : ComponentsOf exceeded threshold
+
+======================================================================
+FAIL: test_09_neuron_input_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test neuron input/synapse queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 386, in test_09_neuron_input_queries
+    self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronInputsTo exceeded threshold")
+AssertionError: 405.9274363517761 not less than 15.0 : NeuronInputsTo exceeded threshold
+
+======================================================================
+FAIL: test_10_expression_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test expression pattern queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 405, in test_10_expression_queries
+    self.assertLess(duration, self.THRESHOLD_SLOW, "ExpressionOverlapsHere exceeded threshold")
+AssertionError: 137.50752902030945 not less than 15.0 : ExpressionOverlapsHere exceeded threshold
+
+======================================================================
+FAIL: test_11_transcriptomics_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test scRNAseq transcriptomics queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 428, in test_11_transcriptomics_queries
+    self.assertLess(duration, self.THRESHOLD_SLOW, "anatScRNAseqQuery exceeded threshold")
+AssertionError: 134.93782830238342 not less than 15.0 : anatScRNAseqQuery exceeded threshold
+
+======================================================================
+FAIL: test_12_nblast_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test NBLAST similarity queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 539, in test_12_nblast_queries
+    self.assertLess(duration, self.THRESHOLD_MEDIUM, "SimilarMorphologyToPartOfexp exceeded threshold")
+AssertionError: 133.54691076278687 not less than 3.0 : SimilarMorphologyToPartOfexp exceeded threshold
+
+======================================================================
+FAIL: test_13_dataset_template_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test dataset and template queries
 ----------------------------------------------------------------------
-Ran 15 tests in 64.275s
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 602, in test_13_dataset_template_queries
+    self.assertLess(duration, self.THRESHOLD_MEDIUM, "PaintedDomains exceeded threshold")
+AssertionError: 135.85583353042603 not less than 3.0 : PaintedDomains exceeded threshold
+
+======================================================================
+FAIL: test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerformanceTest)
+Test publication and transgene queries
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/test_query_performance.py", line 689, in test_14_publication_transgene_queries
+    self.assertLess(duration, self.THRESHOLD_MEDIUM, "TermsForPub exceeded threshold")
+AssertionError: 134.45622777938843 not less than 3.0 : TermsForPub exceeded threshold
+
+----------------------------------------------------------------------
+Ran 15 tests in 1242.656s
 
-OK
+FAILED (failures=7)
 VFBquery functions patched with caching support
 VFBquery: SOLR caching enabled by default (3-month TTL)
          Disable with: export VFBQUERY_CACHE_ENABLED=false
@@ -128,146 +191,129 @@ VFBquery: SOLR caching enabled by default (3-month TTL)
 ================================================================================
 TERM INFO QUERIES
 ================================================================================
-get_term_info (mushroom body): 2.3683s ✅
-get_term_info (individual): 2.5339s ✅
+get_term_info (mushroom body): 6.9956s ✅
+get_term_info (individual): 8.5556s ✅
 
 ================================================================================
 NEURON PART OVERLAP QUERIES
 ================================================================================
-NeuronsPartHere: 2.3378s ✅
+NeuronsPartHere: 15.9128s ✅
 
 ================================================================================
 SYNAPTIC TERMINAL QUERIES
 ================================================================================
-NeuronsSynaptic: 2.2107s ✅
-NeuronsPresynapticHere: 2.1013s ✅
-NeuronsPostsynapticHere: 2.1857s ✅
-NeuronNeuronConnectivity: 1.9037s ✅
+NeuronsSynaptic: 8.7726s ✅
+NeuronsPresynapticHere: 15.6042s ✅
+NeuronsPostsynapticHere: 6.5888s ✅
+NeuronNeuronConnectivity: 1.8051s ✅
 
 ================================================================================
 ANATOMICAL HIERARCHY QUERIES
 ================================================================================
-ComponentsOf: 1.7692s ✅
-PartsOf: 1.7630s ✅
-SubclassesOf: 1.7574s ✅
+ComponentsOf: 15.4465s ✅
 
 ================================================================================
 TRACT/NERVE AND LINEAGE QUERIES
 ================================================================================
-NeuronClassesFasciculatingHere: 1.7693s ✅
-TractsNervesInnervatingHere: 1.7604s ✅
-LineageClonesIn: 1.7664s ✅
+NeuronClassesFasciculatingHere: 10.2345s ✅
+TractsNervesInnervatingHere: 6.3050s ✅
+LineageClonesIn: 8.3160s ✅
 
 ================================================================================
 IMAGE AND DEVELOPMENTAL QUERIES
 ================================================================================
-ImagesNeurons: 1.7720s ✅
-ImagesThatDevelopFrom: 1.7838s ✅
-epFrag: 1.7635s ✅
+ImagesNeurons: 12.4778s ✅
+ImagesThatDevelopFrom: 11.0662s ✅
+epFrag: 10.2089s ✅
 
 ================================================================================
 INSTANCE QUERIES
 ================================================================================
-ListAllAvailableImages: 1.7647s ✅
+ListAllAvailableImages: 13.2370s ✅
 
 ================================================================================
 CONNECTIVITY QUERIES
 ================================================================================
-NeuronNeuronConnectivityQuery: 1.7660s ✅
-NeuronRegionConnectivityQuery: 1.7998s ✅
+NeuronNeuronConnectivityQuery: 3.2010s ✅
+NeuronRegionConnectivityQuery: 3.4581s ✅
 
 ================================================================================
 SIMILARITY QUERIES (Neo4j NBLAST)
 ================================================================================
-SimilarMorphologyTo: 1.0433s ✅
+SimilarMorphologyTo: 0.6568s ✅
 
 ================================================================================
 NEURON INPUT QUERIES (Neo4j)
 ================================================================================
-NeuronInputsTo: 3.4916s ✅
+NeuronInputsTo: 405.9274s ✅
 
 ================================================================================
 EXPRESSION PATTERN QUERIES (Neo4j)
 ================================================================================
-ExpressionOverlapsHere: 3.9390s ✅
+ExpressionOverlapsHere: 137.5075s ✅
   └─ Found 3922 total expression patterns, returned 10
 
 ================================================================================
 TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)
 ================================================================================
-anatScRNAseqQuery: 0.7731s ✅
+anatScRNAseqQuery: 134.9378s ✅
   └─ Found 0 total clusters
-clusterExpression: 1.4449s ✅
-  └─ Found 0 genes expressed
-expressionCluster: 0.7145s ✅
-  └─ Found 0 clusters expressing gene
-scRNAdatasetData: 0.9069s ✅
-  └─ Found 0 clusters in dataset
 
 ================================================================================
 NBLAST SIMILARITY QUERIES
 ================================================================================
-SimilarMorphologyTo: 5.0523s ✅
+SimilarMorphologyTo: 0.9747s ✅
   └─ Found 215 NBLAST matches, returned 10
-SimilarMorphologyToPartOf: 0.8313s ✅
+SimilarMorphologyToPartOf: 0.6012s ✅
   └─ Found 0 NBLASTexp matches
-SimilarMorphologyToPartOfexp: 0.8272s ✅
+SimilarMorphologyToPartOfexp: 133.5469s ✅
   └─ Found 0 reverse NBLASTexp matches
-SimilarMorphologyToNB: 0.6831s ✅
-  └─ Found 15 NeuronBridge matches, returned 10
-SimilarMorphologyToNBexp: 0.7038s ✅
-  └─ Found 15 NeuronBridge expression matches, returned 10
-✅ All NBLAST similarity queries completed
 
 ================================================================================
 DATASET/TEMPLATE QUERIES
 ================================================================================
-PaintedDomains: 0.7336s ✅
+PaintedDomains: 135.8558s ✅
   └─ Found 0 painted domains
-DatasetImages: 0.6871s ✅
-  └─ Found 0 images in dataset
-AllAlignedImages: 1.2738s ✅
-  └─ Found 0 aligned images
-AlignedDatasets: 0.9392s ✅
-  └─ Found 0 aligned datasets
-AllDatasets: 1.0711s ✅
-  └─ Found 116 total datasets, returned 20
-✅ All dataset/template queries completed
 
 ================================================================================
 PUBLICATION/TRANSGENE QUERIES
 ================================================================================
-TermsForPub: 0.6462s ✅
+TermsForPub: 134.4562s ✅
   └─ Found 0 terms for publication
-TransgeneExpressionHere: 1.6328s ✅
-  └─ Found 2346 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
+Performance test for specific term info queries. ... FAIL
+
+======================================================================
+FAIL: test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
+Performance test for specific term info queries.
+----------------------------------------------------------------------
+Traceback (most recent call last):
+  File "/home/runner/work/VFBquery/VFBquery/src/test/term_info_queries_test.py", line 590, in test_term_info_performance
+    self.assertLess(duration_1, max_single_query_time,
+AssertionError: 15.537221193313599 not less than 5.0 : FBbt_00003748 query took 15.5372s, exceeding 5.0s threshold
 
 ----------------------------------------------------------------------
-Ran 1 test in 3.597s
+Ran 1 test in 17.063s
 
-OK
+FAILED (failures=1)
 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: 1.8087 seconds
-VFB_00101567 query took: 1.7878 seconds
-Total time for both queries: 3.5965 seconds
-Performance Level: 🟠 Acceptable (3-6 seconds)
+FBbt_00003748 query took: 15.5372 seconds
+VFB_00101567 query took: 1.5246 seconds
+Total time for both queries: 17.0618 seconds
+Performance Level: 🔴 Slow (> 6 seconds)
 ==================================================
-Performance test completed successfully!
 ```
 
 ## Summary
@@ -283,4 +329,4 @@ Track performance trends across commits:
 - [GitHub Actions History](https://github.com/VirtualFlyBrain/VFBquery/actions/workflows/performance-test.yml)
 
 ---
-*Last updated: 2026-02-02 04:17:08 UTC*
+*Last updated: 2026-02-04 04:26:45 UTC*