Merge pull request #36 from VirtualFlyBrain/dev

timing fixes

Author: Robbie1977

performance.md

@@ -1,9 +1,9 @@
 # VFBquery Performance Test Results
 
-**Test Date:** 2025-11-17 15:13:18 UTC
-**Git Commit:** 11dfec015a28877be7d5fbb7ee2dea5b2622de96
-**Branch:** main
-**Workflow Run:** [19434403582](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19434403582)
+**Test Date:** 2025-11-17 15:27:32 UTC
+**Git Commit:** 500df8ee7434345403908a18a1bcce9329b1cb9b
+**Branch:** dev
+**Workflow Run:** [19434865525](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19434865525)
 
 ## Test Overview
 
@@ -116,7 +116,7 @@ test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerf
 Test publication and transgene queries ... ok
 
 ----------------------------------------------------------------------
-Ran 15 tests in 51.431s
+Ran 15 tests in 45.859s
 
 OK
 VFBquery caching enabled: TTL=2160h (90 days), Memory=2048MB
@@ -133,119 +133,119 @@ TERM INFO QUERIES
 DEBUG: Cache lookup for FBbt_00003748: MISS
 ✅ Neo4j connection established
 ✅ Neo4j connection established
-get_term_info (mushroom body): 4.0424s ✅
+get_term_info (mushroom body): 3.1391s ✅
 DEBUG: Cache lookup for VFB_00101567: MISS
-get_term_info (individual): 3.9058s ✅
+get_term_info (individual): 2.3525s ✅
 
 ================================================================================
 NEURON PART OVERLAP QUERIES
 ================================================================================
-NeuronsPartHere: 1.1137s ✅
+NeuronsPartHere: 1.0766s ✅
 
 ================================================================================
 SYNAPTIC TERMINAL QUERIES
 ================================================================================
-NeuronsSynaptic: 1.1475s ✅
-NeuronsPresynapticHere: 0.9244s ✅
-NeuronsPostsynapticHere: 1.2074s ✅
-NeuronNeuronConnectivity: 0.9483s ✅
+NeuronsSynaptic: 0.8742s ✅
+NeuronsPresynapticHere: 0.8689s ✅
+NeuronsPostsynapticHere: 0.8088s ✅
+NeuronNeuronConnectivity: 0.8220s ✅
 
 ================================================================================
 ANATOMICAL HIERARCHY QUERIES
 ================================================================================
-ComponentsOf: 0.9205s ✅
-PartsOf: 0.9474s ✅
-SubclassesOf: 0.9204s ✅
+ComponentsOf: 0.6238s ✅
+PartsOf: 0.7023s ✅
+SubclassesOf: 0.7076s ✅
 
 ================================================================================
 TRACT/NERVE AND LINEAGE QUERIES
 ================================================================================
-NeuronClassesFasciculatingHere: 0.9221s ✅
-TractsNervesInnervatingHere: 0.9319s ✅
-LineageClonesIn: 0.9416s ✅
+NeuronClassesFasciculatingHere: 0.6327s ✅
+TractsNervesInnervatingHere: 0.7945s ✅
+LineageClonesIn: 0.6341s ✅
 
 ================================================================================
 IMAGE AND DEVELOPMENTAL QUERIES
 ================================================================================
-ImagesNeurons: 1.4024s ✅
-ImagesThatDevelopFrom: 0.9176s ✅
-epFrag: 0.9475s ✅
+ImagesNeurons: 1.1914s ✅
+ImagesThatDevelopFrom: 0.7237s ✅
+epFrag: 0.7073s ✅
 
 ================================================================================
 INSTANCE QUERIES
 ================================================================================
-ListAllAvailableImages: 0.9211s ✅
+ListAllAvailableImages: 0.6096s ✅
 
 ================================================================================
 CONNECTIVITY QUERIES
 ================================================================================
-NeuronNeuronConnectivityQuery: 0.9469s ✅
-NeuronRegionConnectivityQuery: 0.9423s ✅
+NeuronNeuronConnectivityQuery: 0.7327s ✅
+NeuronRegionConnectivityQuery: 0.6222s ✅
 
 ================================================================================
 SIMILARITY QUERIES (Neo4j NBLAST)
 ================================================================================
-SimilarMorphologyTo: 10.2807s ✅
+SimilarMorphologyTo: 11.4931s ✅
 
 ================================================================================
 NEURON INPUT QUERIES (Neo4j)
 ================================================================================
-NeuronInputsTo: 2.7593s ✅
+NeuronInputsTo: 2.8142s ✅
 
 ================================================================================
 EXPRESSION PATTERN QUERIES (Neo4j)
 ================================================================================
-ExpressionOverlapsHere: 0.8701s ✅
+ExpressionOverlapsHere: 0.7708s ✅
   └─ Found 3922 total expression patterns, returned 10
 
 ================================================================================
 TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)
 ================================================================================
-anatScRNAseqQuery: 0.8912s ✅
+anatScRNAseqQuery: 0.6743s ✅
   └─ Found 0 total clusters
-clusterExpression: 0.7298s ✅
+clusterExpression: 0.5813s ✅
   └─ Found 0 genes expressed
-expressionCluster: 0.7272s ✅
+expressionCluster: 0.5980s ✅
   └─ Found 0 clusters expressing gene
-scRNAdatasetData: 0.7839s ✅
+scRNAdatasetData: 0.6593s ✅
   └─ Found 0 clusters in dataset
 
 ================================================================================
 NBLAST SIMILARITY QUERIES
 ================================================================================
-SimilarMorphologyTo: 1.0011s ✅
+SimilarMorphologyTo: 0.7738s ✅
   └─ Found 227 NBLAST matches, returned 10
-SimilarMorphologyToPartOf: 0.7312s ✅
+SimilarMorphologyToPartOf: 0.5750s ✅
   └─ Found 0 NBLASTexp matches
-SimilarMorphologyToPartOfexp: 0.6780s ✅
+SimilarMorphologyToPartOfexp: 0.6387s ✅
   └─ Found 0 reverse NBLASTexp matches
-SimilarMorphologyToNB: 0.6917s ✅
+SimilarMorphologyToNB: 2.1447s ✅
   └─ Found 15 NeuronBridge matches, returned 10
-SimilarMorphologyToNBexp: 0.7256s ✅
+SimilarMorphologyToNBexp: 0.5255s ✅
   └─ Found 15 NeuronBridge expression matches, returned 10
 ✅ All NBLAST similarity queries completed
 
 ================================================================================
 DATASET/TEMPLATE QUERIES
 ================================================================================
-PaintedDomains: 0.7278s ✅
+PaintedDomains: 0.7501s ✅
   └─ Found 0 painted domains
-DatasetImages: 0.7244s ✅
+DatasetImages: 0.5330s ✅
   └─ Found 0 images in dataset
-AllAlignedImages: 0.7057s ✅
+AllAlignedImages: 0.5306s ✅
   └─ Found 0 aligned images
-AlignedDatasets: 0.9986s ✅
+AlignedDatasets: 0.7615s ✅
   └─ Found 0 aligned datasets
-AllDatasets: 0.9470s ✅
+AllDatasets: 1.3396s ✅
   └─ Found 115 total datasets, returned 20
 ✅ All dataset/template queries completed
 
 ================================================================================
 PUBLICATION/TRANSGENE QUERIES
 ================================================================================
-TermsForPub: 0.6599s ✅
+TermsForPub: 0.4627s ✅
   └─ Found 0 terms for publication
-TransgeneExpressionHere: 0.8416s ✅
+TransgeneExpressionHere: 0.6039s ✅
   └─ Found 2339 transgene expressions, returned 10
 ✅ All publication/transgene queries completed
 
@@ -258,7 +258,7 @@ test_term_info_performance (src.test.term_info_queries_test.TermInfoQueriesTest)
 Performance test for specific term info queries. ... ok
 
 ----------------------------------------------------------------------
-Ran 1 test in 1.878s
+Ran 1 test in 1.375s
 
 OK
 VFBquery caching enabled: TTL=2160h (90 days), Memory=2048MB
@@ -273,10 +273,10 @@ VFBquery: Caching enabled by default (3-month TTL, 2GB memory)
 ==================================================
 Performance Test Results:
 ==================================================
-FBbt_00003748 query took: 0.9463 seconds
-VFB_00101567 query took: 0.9315 seconds
-Total time for both queries: 1.8779 seconds
-Performance Level: 🟡 Good (1.5-3 seconds)
+FBbt_00003748 query took: 0.7501 seconds
+VFB_00101567 query took: 0.6250 seconds
+Total time for both queries: 1.3751 seconds
+Performance Level: 🟢 Excellent (< 1.5 seconds)
 ==================================================
 Performance test completed successfully!
 ```
@@ -294,4 +294,4 @@ Track performance trends across commits:
 - [GitHub Actions History](https://github.com/VirtualFlyBrain/VFBquery/actions/workflows/performance-test.yml)
 
 ---
-*Last updated: 2025-11-17 15:13:18 UTC*
+*Last updated: 2025-11-17 15:27:32 UTC*

src/test/term_info_queries_test.py

@@ -569,8 +569,8 @@ def test_term_info_performance(self):
 
         # Performance assertions - fail if queries take too long
         # These thresholds are based on observed performance characteristics
-        max_single_query_time = 3.0  # seconds (increased from 2.0 to account for SOLR cache overhead)
-        max_total_time = 6.0  # seconds (2 queries * 3 seconds each)
+        max_single_query_time = 5.0  # seconds (increased from 2.0 to account for SOLR cache overhead)
+        max_total_time = 10.0  # seconds (2 queries * 5 seconds each)
 
         self.assertLess(duration_1, max_single_query_time, 
                        f"FBbt_00003748 query took {duration_1:.4f}s, exceeding {max_single_query_time}s threshold")