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Robbie1977Robbie1977
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Merge pull request #34 from VirtualFlyBrain/dev
Expanding queries
2 parents faabc5d + 1999824 commit 3b3e1f4

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‎.github/workflows/performance-test.yml‎

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- name: Run Performance Test
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run: |
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export PYTHONPATH=$PYTHONPATH:$PWD/
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echo "Running performance test for term info queries..."
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python -m unittest -v src.test.term_info_queries_test.TermInfoQueriesTest.test_term_info_performance 2>&1 | tee performance_test_output.log
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continue-on-error: true # Continue even if performance thresholds are exceeded
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python -m unittest src.test.test_query_performance -v 2>&1 | tee performance_test_output.log
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- name: Run Legacy Performance Test
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run: |
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python -m unittest -v src.test.term_info_queries_test.TermInfoQueriesTest.test_term_info_performance 2>&1 | tee -a performance_test_output.log
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- name: Create Performance Report
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if: always() # Always run this step, even if the test fails
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**Test Date:** $(date -u '+%Y-%m-%d %H:%M:%S UTC')
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**Git Commit:** ${{ github.sha }}
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**Branch:** ${{ github.ref_name }}
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**Workflow Run:** ${{ github.run_id }}
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**Workflow Run:** [${{ github.run_id }}](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }})
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## Test Overview
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This performance test measures the execution time of VFB term info queries for specific terms:
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This performance test measures the execution time of all implemented VFB queries including:
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### Core Queries
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- **Term Info Queries**: Basic term information retrieval
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- **Neuron Part Queries**: Neurons with parts overlapping regions
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- **Synaptic Terminal Queries**: Pre/post synaptic terminals
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- **Anatomical Hierarchy**: Components, parts, subclasses
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- **Instance Queries**: Available images and instances
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- **FBbt_00003748**: mushroom body (anatomical class)
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- **VFB_00101567**: individual anatomy data
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### New Queries (2025)
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- **NeuronClassesFasciculatingHere**: Neurons fasciculating with tracts
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- **TractsNervesInnervatingHere**: Tracts/nerves innervating neuropils
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- **LineageClonesIn**: Lineage clones in neuropils
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## Performance Thresholds
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- Maximum single query time: 2 seconds
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- Maximum total time for both queries: 4 seconds
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- **Fast queries**: < 1 second (SOLR lookups)
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- **Medium queries**: < 3 seconds (Owlery + SOLR)
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- **Slow queries**: < 10 seconds (Neo4j + complex processing)
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## Test Results
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```
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\`\`\`
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$(cat performance_test_output.log)
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```
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\`\`\`
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## Summary
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EOF
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# Extract timing information from the test output
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if grep -q "Performance Test Results:" performance_test_output.log; then
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echo "✅ **Test Status**: Performance test completed" >> performance.md
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# Check overall test status
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if grep -q "OK" performance_test_output.log || grep -q "Ran.*test" performance_test_output.log; then
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echo "✅ **Test Status**: Performance tests completed" >> performance.md
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echo "" >> performance.md
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# Extract timing data
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if grep -q "FBbt_00003748 query took:" performance_test_output.log; then
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TIMING1=$(grep "FBbt_00003748 query took:" performance_test_output.log | sed 's/.*took: \([0-9.]*\) seconds.*/\1/')
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echo "- **FBbt_00003748 Query Time**: ${TIMING1} seconds" >> performance.md
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fi
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# Count successes and failures
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TOTAL_TESTS=$(grep -c "^test_" performance_test_output.log || echo "0")
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FAILED_TESTS=$(grep -c "FAIL:" performance_test_output.log || echo "0")
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ERROR_TESTS=$(grep -c "ERROR:" performance_test_output.log || echo "0")
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PASSED_TESTS=$((TOTAL_TESTS - FAILED_TESTS - ERROR_TESTS))
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if grep -q "VFB_00101567 query took:" performance_test_output.log; then
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TIMING2=$(grep "VFB_00101567 query took:" performance_test_output.log | sed 's/.*took: \([0-9.]*\) seconds.*/\1/')
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echo "- **VFB_00101567 Query Time**: ${TIMING2} seconds" >> performance.md
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fi
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echo "### Test Statistics" >> performance.md
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echo "" >> performance.md
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echo "- **Total Tests**: ${TOTAL_TESTS}" >> performance.md
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echo "- **Passed**: ${PASSED_TESTS} ✅" >> performance.md
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echo "- **Failed**: ${FAILED_TESTS} ❌" >> performance.md
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echo "- **Errors**: ${ERROR_TESTS} ⚠️" >> performance.md
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echo "" >> performance.md
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# Extract timing information for key queries
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echo "### Query Performance Details" >> performance.md
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echo "" >> performance.md
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if grep -q "Total time for both queries:" performance_test_output.log; then
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TOTAL_TIME=$(grep "Total time for both queries:" performance_test_output.log | sed 's/.*queries: \([0-9.]*\) seconds.*/\1/')
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echo "- **Total Query Time**: ${TOTAL_TIME} seconds" >> performance.md
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# Extract all timing lines
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if grep -q "seconds" performance_test_output.log; then
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echo "| Query | Duration | Status |" >> performance.md
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echo "|-------|----------|--------|" >> performance.md
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# Parse timing information
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grep -E "^(get_term_info|NeuronsPartHere|NeuronsSynaptic|NeuronsPresynapticHere|NeuronsPostsynapticHere|ComponentsOf|PartsOf|SubclassesOf|NeuronClassesFasciculatingHere|TractsNervesInnervatingHere|LineageClonesIn|ListAllAvailableImages):" performance_test_output.log | while read line; do
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QUERY=$(echo "$line" | sed 's/:.*//')
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DURATION=$(echo "$line" | sed 's/.*: \([0-9.]*\)s.*/\1/')
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if echo "$line" | grep -q "✅"; then
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STATUS="✅ Pass"
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else
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STATUS="❌ Fail"
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fi
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echo "| $QUERY | ${DURATION}s | $STATUS |" >> performance.md
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done
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fi
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# Check if test passed or failed
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if grep -q "OK" performance_test_output.log; then
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echo "" >> performance.md
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echo "" >> performance.md
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# Overall result
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if [ "$FAILED_TESTS" -eq "0" ] && [ "$ERROR_TESTS" -eq "0" ]; then
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echo "🎉 **Result**: All performance thresholds met!" >> performance.md
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elif grep -q "FAILED" performance_test_output.log; then
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else
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echo "⚠️ **Result**: Some performance thresholds exceeded or tests failed" >> performance.md
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echo "" >> performance.md
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echo "⚠️ **Result**: Some performance thresholds exceeded or test failed" >> performance.md
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echo "Please review the failed tests above. Common causes:" >> performance.md
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echo "- Network latency to VFB services" >> performance.md
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echo "- SOLR/Neo4j/Owlery server load" >> performance.md
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echo "- First-time cache population (expected to be slower)" >> performance.md
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fi
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else
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echo "❌ **Test Status**: Performance test failed to run properly" >> performance.md
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echo "❌ **Test Status**: Performance tests failed to run properly" >> performance.md
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echo "" >> performance.md
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echo "Please check the test output above for errors." >> performance.md
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fi
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echo "" >> performance.md
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echo "---" >> performance.md
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echo "" >> performance.md
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echo "## Historical Performance" >> performance.md
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echo "" >> performance.md
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echo "Track performance trends across commits:" >> performance.md
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echo "- [GitHub Actions History](https://github.com/${{ github.repository }}/actions/workflows/performance-test.yml)" >> performance.md
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echo "" >> performance.md
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echo "---" >> performance.md
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echo "*Last updated: $(date -u '+%Y-%m-%d %H:%M:%S UTC')*" >> performance.md

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