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

Author: Robbie1977

performance.md

@@ -1,9 +1,9 @@
 # VFBquery Performance Test Results
 
-**Test Date:** 2025-11-18 06:01:43 UTC
-**Git Commit:** b9775161864d83b06e52027b9a31f0f39445e25e
+**Test Date:** 2025-11-18 06:08:22 UTC
+**Git Commit:** eefbc5673b3b6b310e00251f3c6d95beb471ba1b
 **Branch:** dev
-**Workflow Run:** [19455863324](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19455863324)
+**Workflow Run:** [19456000514](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19456000514)
 
 ## Test Overview
 
@@ -119,127 +119,126 @@ TERM INFO QUERIES
 DEBUG: Checking cache for term_info, term_id=FBbt_00003748, cache_term_id=FBbt_00003748_preview_True, should_cache=True
 DEBUG: Attempting cache lookup for term_info(FBbt_00003748_preview_True) with full results
 DEBUG: Cache lookup result: True
-get_term_info (mushroom body): 1.9338s ✅
+get_term_info (mushroom body): 2.6225s ✅
 DEBUG: Checking cache for term_info, term_id=VFB_00101567, cache_term_id=VFB_00101567_preview_True, should_cache=True
 DEBUG: Attempting cache lookup for term_info(VFB_00101567_preview_True) with full results
 DEBUG: Cache lookup result: True
-get_term_info (individual): 1.6916s ✅
+get_term_info (individual): 2.3024s ✅
 
 ================================================================================
 NEURON PART OVERLAP QUERIES
 ================================================================================
 DEBUG: Checking cache for neurons_part_here, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for neurons_part_here(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-NeuronsPartHere: 1.4204s ✅
+NeuronsPartHere: 2.2821s ✅
 
 ================================================================================
 SYNAPTIC TERMINAL QUERIES
 ================================================================================
 DEBUG: Checking cache for neurons_synaptic, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for neurons_synaptic(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-NeuronsSynaptic: 1.6820s ✅
+NeuronsSynaptic: 2.2283s ✅
 DEBUG: Checking cache for neurons_presynaptic, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for neurons_presynaptic(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-NeuronsPresynapticHere: 1.3561s ✅
+NeuronsPresynapticHere: 1.9719s ✅
 DEBUG: Checking cache for neurons_postsynaptic, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for neurons_postsynaptic(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-NeuronsPostsynapticHere: 1.4006s ✅
+NeuronsPostsynapticHere: 1.9266s ✅
 DEBUG: Checking cache for neuron_neuron_connectivity_query, term_id=VFB_jrchk00s, cache_term_id=VFB_jrchk00s, should_cache=True
 DEBUG: Attempting cache lookup for neuron_neuron_connectivity_query(VFB_jrchk00s) with full results
 DEBUG: Cache lookup result: True
-NeuronNeuronConnectivity: 1.4230s ✅
+NeuronNeuronConnectivity: 1.8654s ✅
 
 ================================================================================
 ANATOMICAL HIERARCHY QUERIES
 ================================================================================
 DEBUG: Checking cache for components_of, term_id=FBbt_00003748, cache_term_id=FBbt_00003748, should_cache=True
 DEBUG: Attempting cache lookup for components_of(FBbt_00003748) with full results
 DEBUG: Cache lookup result: True
-ComponentsOf: 1.4422s ✅
+ComponentsOf: 1.9131s ✅
 DEBUG: Checking cache for parts_of, term_id=FBbt_00003748, cache_term_id=FBbt_00003748, should_cache=True
 DEBUG: Attempting cache lookup for parts_of(FBbt_00003748) with full results
 DEBUG: Cache lookup result: True
-PartsOf: 1.4995s ✅
+PartsOf: 1.8686s ✅
 DEBUG: Checking cache for subclasses_of, term_id=FBbt_00003748, cache_term_id=FBbt_00003748, should_cache=True
 DEBUG: Attempting cache lookup for subclasses_of(FBbt_00003748) with full results
 DEBUG: Cache lookup result: True
-SubclassesOf: 1.4281s ✅
+SubclassesOf: 1.9097s ✅
 
 ================================================================================
 TRACT/NERVE AND LINEAGE QUERIES
 ================================================================================
 DEBUG: Checking cache for neuron_classes_fasciculating_here, term_id=FBbt_00003987, cache_term_id=FBbt_00003987, should_cache=True
 DEBUG: Attempting cache lookup for neuron_classes_fasciculating_here(FBbt_00003987) with full results
 DEBUG: Cache lookup result: True
-NeuronClassesFasciculatingHere: 1.3040s ✅
+NeuronClassesFasciculatingHere: 1.8420s ✅
 DEBUG: Checking cache for tracts_nerves_innervating_here, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for tracts_nerves_innervating_here(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-TractsNervesInnervatingHere: 1.4423s ✅
+TractsNervesInnervatingHere: 1.9248s ✅
 DEBUG: Checking cache for lineage_clones_in, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for lineage_clones_in(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-LineageClonesIn: 1.6949s ✅
+LineageClonesIn: 1.8395s ✅
 
 ================================================================================
 IMAGE AND DEVELOPMENTAL QUERIES
 ================================================================================
 DEBUG: Checking cache for images_neurons, term_id=FBbt_00007401, cache_term_id=FBbt_00007401, should_cache=True
 DEBUG: Attempting cache lookup for images_neurons(FBbt_00007401) with full results
 DEBUG: Cache lookup result: True
-ImagesNeurons: 1.2312s ✅
+ImagesNeurons: 1.8432s ✅
 DEBUG: Checking cache for images_that_develop_from, term_id=FBbt_00001419, cache_term_id=FBbt_00001419, should_cache=True
 DEBUG: Attempting cache lookup for images_that_develop_from(FBbt_00001419) with full results
 DEBUG: Cache lookup result: True
-ImagesThatDevelopFrom: 1.2507s ✅
+ImagesThatDevelopFrom: 1.8482s ✅
 DEBUG: Checking cache for expression_pattern_fragments, term_id=FBtp0000001, cache_term_id=FBtp0000001, should_cache=True
 DEBUG: Attempting cache lookup for expression_pattern_fragments(FBtp0000001) with full results
 DEBUG: Cache lookup result: True
-epFrag: 1.2327s ✅
+epFrag: 1.9066s ✅
 
 ================================================================================
 INSTANCE QUERIES
 ================================================================================
 DEBUG: Checking cache for instances, term_id=FBbt_00003982, cache_term_id=FBbt_00003982, should_cache=True
 DEBUG: Attempting cache lookup for instances(FBbt_00003982) with full results
 DEBUG: Cache lookup result: True
-ListAllAvailableImages: 1.6223s ✅
+ListAllAvailableImages: 1.8490s ✅
 
 ================================================================================
 CONNECTIVITY QUERIES
 ================================================================================
 DEBUG: Checking cache for neuron_neuron_connectivity_query, term_id=VFB_jrchk00s, cache_term_id=VFB_jrchk00s, should_cache=True
 DEBUG: Attempting cache lookup for neuron_neuron_connectivity_query(VFB_jrchk00s) with full results
 DEBUG: Cache lookup result: True
-NeuronNeuronConnectivityQuery: 1.2764s ✅
+NeuronNeuronConnectivityQuery: 1.8815s ✅
 DEBUG: Checking cache for neuron_region_connectivity_query, term_id=VFB_jrchk00s, cache_term_id=VFB_jrchk00s, should_cache=True
 DEBUG: Attempting cache lookup for neuron_region_connectivity_query(VFB_jrchk00s) with full results
 DEBUG: Cache lookup result: True
-NeuronRegionConnectivityQuery: 1.4228s ✅
+NeuronRegionConnectivityQuery: 1.9162s ✅
 
 ================================================================================
 SIMILARITY QUERIES (Neo4j NBLAST)
 ================================================================================
 DEBUG: Checking cache for similar_neurons, term_id=VFB_jrchk00s, cache_term_id=VFB_jrchk00s_score_NBLAST_score, should_cache=False
 DEBUG: Attempting cache lookup for similar_neurons(VFB_jrchk00s_score_NBLAST_score) with full results
-DEBUG: Cache lookup result: True
-DEBUG: Cannot slice cached result of type <class 'dict'>, returning full result
-SimilarMorphologyTo: 0.6367s ✅
+DEBUG: Cache lookup result: False
+✅ Neo4j connection established
+SimilarMorphologyTo: 11.5191s ✅
 
 ================================================================================
 NEURON INPUT QUERIES (Neo4j)
 ================================================================================
-✅ Neo4j connection established
-NeuronInputsTo: 3.1173s ✅
+NeuronInputsTo: 2.9445s ✅
 
 ================================================================================
 EXPRESSION PATTERN QUERIES (Neo4j)
 ================================================================================
-ExpressionOverlapsHere: 0.8056s ✅
+ExpressionOverlapsHere: 0.8948s ✅
   └─ Found 3922 total expression patterns, returned 10
 
 ================================================================================
@@ -253,55 +252,55 @@ test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerf
 Test publication and transgene queries ... ok
 
 ----------------------------------------------------------------------
-Ran 15 tests in 42.424s
+Ran 15 tests in 66.210s
 
 OK
 ================================================================================
-anatScRNAseqQuery: 0.7638s ✅
+anatScRNAseqQuery: 0.8003s ✅
   └─ Found 0 total clusters
-clusterExpression: 0.5019s ✅
+clusterExpression: 1.0486s ✅
   └─ Found 0 genes expressed
-expressionCluster: 0.6482s ✅
+expressionCluster: 0.7234s ✅
   └─ Found 0 clusters expressing gene
-scRNAdatasetData: 0.7309s ✅
+scRNAdatasetData: 0.8565s ✅
   └─ Found 0 clusters in dataset
 
 ================================================================================
 NBLAST SIMILARITY QUERIES
 ================================================================================
-SimilarMorphologyTo: 0.8105s ✅
+SimilarMorphologyTo: 1.1879s ✅
   └─ Found 227 NBLAST matches, returned 10
-SimilarMorphologyToPartOf: 0.5331s ✅
+SimilarMorphologyToPartOf: 0.7253s ✅
   └─ Found 0 NBLASTexp matches
-SimilarMorphologyToPartOfexp: 0.5064s ✅
+SimilarMorphologyToPartOfexp: 0.7637s ✅
   └─ Found 0 reverse NBLASTexp matches
-SimilarMorphologyToNB: 0.5924s ✅
+SimilarMorphologyToNB: 0.7215s ✅
   └─ Found 15 NeuronBridge matches, returned 10
-SimilarMorphologyToNBexp: 0.5750s ✅
+SimilarMorphologyToNBexp: 0.7202s ✅
   └─ Found 15 NeuronBridge expression matches, returned 10
 ✅ All NBLAST similarity queries completed
 
 ================================================================================
 DATASET/TEMPLATE QUERIES
 ================================================================================
-PaintedDomains: 0.5370s ✅
+PaintedDomains: 0.7501s ✅
   └─ Found 0 painted domains
-DatasetImages: 0.6039s ✅
+DatasetImages: 0.7328s ✅
   └─ Found 0 images in dataset
-AllAlignedImages: 0.5049s ✅
+AllAlignedImages: 0.7303s ✅
   └─ Found 0 aligned images
-AlignedDatasets: 0.7918s ✅
+AlignedDatasets: 0.9075s ✅
   └─ Found 0 aligned datasets
-AllDatasets: 0.8552s ✅
+AllDatasets: 0.9532s ✅
   └─ Found 115 total datasets, returned 20
 ✅ All dataset/template queries completed
 
 ================================================================================
 PUBLICATION/TRANSGENE QUERIES
 ================================================================================
-TermsForPub: 0.5697s ✅
+TermsForPub: 0.7036s ✅
   └─ Found 0 terms for publication
-TransgeneExpressionHere: 0.5828s ✅
+TransgeneExpressionHere: 0.7814s ✅
   └─ Found 2339 transgene expressions, returned 10
 ✅ All publication/transgene queries completed
 
@@ -314,7 +313,7 @@ test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
 Performance test for specific term info queries. ... ok
 
 ----------------------------------------------------------------------
-Ran 1 test in 4.055s
+Ran 1 test in 3.791s
 
 OK
 VFBquery functions patched with caching support
@@ -325,10 +324,6 @@ VFBquery: SOLR caching enabled by default (3-month TTL)
          Disable with: export VFBQUERY_CACHE_ENABLED=false
 DEBUG: Checking cache for term_info, term_id=FBbt_00003748, cache_term_id=FBbt_00003748_preview_True, should_cache=True
 DEBUG: Attempting cache lookup for term_info(FBbt_00003748_preview_True) with full results
-DEBUG: Cache lookup result: False
-DEBUG: Executing term_info with full results for caching
-DEBUG: Checking cache for term_info, term_id=FBbt_00003748, cache_term_id=FBbt_00003748_preview_True, should_cache=True
-DEBUG: Attempting cache lookup for term_info(FBbt_00003748_preview_True) with full results
 DEBUG: Cache lookup result: True
 DEBUG: Checking cache for term_info, term_id=VFB_00101567, cache_term_id=VFB_00101567_preview_True, should_cache=True
 DEBUG: Attempting cache lookup for term_info(VFB_00101567_preview_True) with full results
@@ -337,9 +332,9 @@ DEBUG: Cache lookup result: True
 ==================================================
 Performance Test Results:
 ==================================================
-FBbt_00003748 query took: 2.8087 seconds
-VFB_00101567 query took: 1.2458 seconds
-Total time for both queries: 4.0545 seconds
+FBbt_00003748 query took: 1.9029 seconds
+VFB_00101567 query took: 1.8880 seconds
+Total time for both queries: 3.7908 seconds
 Performance Level: 🟠 Acceptable (3-6 seconds)
 ==================================================
 Performance test completed successfully!
@@ -358,4 +353,4 @@ Track performance trends across commits:
 - [GitHub Actions History](https://github.com/VirtualFlyBrain/VFBquery/actions/workflows/performance-test.yml)
 
 ---
-*Last updated: 2025-11-18 06:01:43 UTC*
+*Last updated: 2025-11-18 06:08:22 UTC*