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 05:34:18 UTC
-**Git Commit:** 79b56375c1d2ee9c3a834eec161afe6bc9e8c3cc
+**Test Date:** 2025-11-18 05:43:28 UTC
+**Git Commit:** 1ddf8f61f4b96f0f67f327dd38ed718db221ddc9
 **Branch:** dev
-**Workflow Run:** [19455345018](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19455345018)
+**Workflow Run:** [19455519320](https://github.com/VirtualFlyBrain/VFBquery/actions/runs/19455519320)
 
 ## Test Overview
 
@@ -119,135 +119,135 @@ 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): 2.6784s ✅
+get_term_info (mushroom body): 2.9183s ✅
 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): 2.0806s ✅
+get_term_info (individual): 2.8792s ✅
 
 ================================================================================
 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: 2.1887s ✅
+NeuronsPartHere: 2.1206s ✅
 
 ================================================================================
 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: 2.0091s ✅
+NeuronsSynaptic: 2.5344s ✅
 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: 1.6482s ✅
+NeuronsPresynapticHere: 2.2726s ✅
 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: 1.6713s ✅
+NeuronsPostsynapticHere: 2.4168s ✅
 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: 1.6746s ✅
+NeuronNeuronConnectivity: 2.2787s ✅
 
 ================================================================================
 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: 1.7128s ✅
+ComponentsOf: 2.0133s ✅
 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: 1.6442s ✅
+PartsOf: 1.9823s ✅
 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: 1.6578s ✅
+SubclassesOf: 1.9607s ✅
 
 ================================================================================
 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: 1.6767s ✅
+NeuronClassesFasciculatingHere: 1.9888s ✅
 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: 1.6851s ✅
+TractsNervesInnervatingHere: 1.9912s ✅
 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: 1.6409s ✅
+LineageClonesIn: 2.0070s ✅
 
 ================================================================================
 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: 1.6546s ✅
+ImagesNeurons: 1.9815s ✅
 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: 1.7211s ✅
+ImagesThatDevelopFrom: 2.0005s ✅
 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: 1.6588s ✅
+epFrag: 1.9962s ✅
 
 ================================================================================
 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: 1.6514s ✅
+ListAllAvailableImages: 1.9818s ✅
 
 ================================================================================
 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: 1.6855s ✅
+NeuronNeuronConnectivityQuery: 1.9807s ✅
 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: 1.6768s ✅
+NeuronRegionConnectivityQuery: 2.0210s ✅
 
 ================================================================================
 SIMILARITY QUERIES (Neo4j NBLAST)
 ================================================================================
 ✅ Neo4j connection established
-SimilarMorphologyTo: 10.4635s ✅
+SimilarMorphologyTo: 10.6665s ✅
 
 ================================================================================
 NEURON INPUT QUERIES (Neo4j)
 ================================================================================
-NeuronInputsTo: 2.7887s ✅
+NeuronInputsTo: 3.0466s ✅
 
 ================================================================================
 EXPRESSION PATTERN QUERIES (Neo4j)
 ================================================================================
-ExpressionOverlapsHere: 0.9829s ✅
+ExpressionOverlapsHere: 1.1556s ✅
   └─ Found 3922 total expression patterns, returned 10
 
 ================================================================================
 TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)
 ================================================================================
-anatScRNAseqQuery: 0.6916s ✅
+anatScRNAseqQuery: 0.9381s ✅
   └─ Found 0 total clusters
-clusterExpression: 0.7119s ✅
+clusterExpression: 0.9403s ✅
   └─ Found 0 genes expressed
-expressionCluster: 0.6544s ✅
+expressionCluster: 0.8181s ✅
   └─ Found 0 clusters expressing gene
-scRNAdatasetData: 0.6564s ✅
+scRNAdatasetData: 0.7578s ✅
 ok
 test_12_nblast_queries (src.test.test_query_performance.QueryPerformanceTest)
 Test NBLAST similarity queries ... ok
@@ -257,47 +257,47 @@ test_14_publication_transgene_queries (src.test.test_query_performance.QueryPerf
 Test publication and transgene queries ... ok
 
 ----------------------------------------------------------------------
-Ran 15 tests in 60.843s
+Ran 15 tests in 69.911s
 
 OK
   └─ Found 0 clusters in dataset
 
 ================================================================================
 NBLAST SIMILARITY QUERIES
 ================================================================================
-SimilarMorphologyTo: 0.9599s ✅
+SimilarMorphologyTo: 1.1595s ✅
   └─ Found 227 NBLAST matches, returned 10
-SimilarMorphologyToPartOf: 0.7706s ✅
+SimilarMorphologyToPartOf: 0.7496s ✅
   └─ Found 0 NBLASTexp matches
-SimilarMorphologyToPartOfexp: 0.6529s ✅
+SimilarMorphologyToPartOfexp: 0.7568s ✅
   └─ Found 0 reverse NBLASTexp matches
-SimilarMorphologyToNB: 0.6337s ✅
+SimilarMorphologyToNB: 0.9024s ✅
   └─ Found 15 NeuronBridge matches, returned 10
-SimilarMorphologyToNBexp: 0.6581s ✅
+SimilarMorphologyToNBexp: 0.7271s ✅
   └─ Found 15 NeuronBridge expression matches, returned 10
 ✅ All NBLAST similarity queries completed
 
 ================================================================================
 DATASET/TEMPLATE QUERIES
 ================================================================================
-PaintedDomains: 0.6873s ✅
+PaintedDomains: 0.7915s ✅
   └─ Found 0 painted domains
-DatasetImages: 0.6552s ✅
+DatasetImages: 0.7476s ✅
   └─ Found 0 images in dataset
-AllAlignedImages: 0.6416s ✅
+AllAlignedImages: 0.7569s ✅
   └─ Found 0 aligned images
-AlignedDatasets: 0.8906s ✅
+AlignedDatasets: 1.0724s ✅
   └─ Found 0 aligned datasets
-AllDatasets: 0.9012s ✅
+AllDatasets: 0.9878s ✅
   └─ Found 115 total datasets, returned 20
 ✅ All dataset/template queries completed
 
 ================================================================================
 PUBLICATION/TRANSGENE QUERIES
 ================================================================================
-TermsForPub: 1.7069s ✅
+TermsForPub: 0.7249s ✅
   └─ Found 0 terms for publication
-TransgeneExpressionHere: 0.7152s ✅
+TransgeneExpressionHere: 0.8826s ✅
   └─ Found 2339 transgene expressions, returned 10
 ✅ All publication/transgene queries completed
 
@@ -307,25 +307,12 @@ 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. ... ERROR
+Performance test for specific term info queries. ... ok
 
-======================================================================
-ERROR: 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 536, in test_term_info_performance
-    result_1 = vfb.get_term_info('FBbt_00003748')
-  File "/home/runner/work/VFBquery/VFBquery/src/vfbquery/cached_functions.py", line 100, in get_term_info_cached
-    return _original_get_term_info(short_form=short_form, preview=preview)
-  File "/home/runner/work/VFBquery/VFBquery/src/vfbquery/solr_result_cache.py", line 763, in wrapper
-    full_result = func(*args, **full_kwargs)
-TypeError: get_term_info() got an unexpected keyword argument 'limit'
+Ran 1 test in 3.983s
 
-----------------------------------------------------------------------
-Ran 1 test in 0.807s
-
-FAILED (errors=1)
+OK
 VFBquery functions patched with caching support
 VFBquery: SOLR caching enabled by default (3-month TTL)
          Disable with: export VFBQUERY_CACHE_ENABLED=false
@@ -334,8 +321,20 @@ 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_False, should_cache=True
 DEBUG: Attempting cache lookup for term_info(FBbt_00003748_preview_False) with full results
-DEBUG: Cache lookup result: False
-DEBUG: Executing term_info with limit=-1 for caching
+DEBUG: Cache lookup result: True
+DEBUG: Checking cache for term_info, term_id=VFB_00101567, cache_term_id=VFB_00101567_preview_False, should_cache=True
+DEBUG: Attempting cache lookup for term_info(VFB_00101567_preview_False) with full results
+DEBUG: Cache lookup result: True
+
+==================================================
+Performance Test Results:
+==================================================
+FBbt_00003748 query took: 1.9984 seconds
+VFB_00101567 query took: 1.9844 seconds
+Total time for both queries: 3.9828 seconds
+Performance Level: 🟠 Acceptable (3-6 seconds)
+==================================================
+Performance test completed successfully!
 ```
 
 ## Summary
@@ -351,4 +350,4 @@ Track performance trends across commits:
 - [GitHub Actions History](https://github.com/VirtualFlyBrain/VFBquery/actions/workflows/performance-test.yml)
 
 ---
-*Last updated: 2025-11-18 05:34:18 UTC*
+*Last updated: 2025-11-18 05:43:28 UTC*