vfbquery 0.4.1__py3-none-any.whl → 0.5.1__py3-none-any.whl

test/test_query_performance.py

@@ -0,0 +1,739 @@
+#!/usr/bin/env python3
+"""
+Comprehensive performance test for all VFB queries.
+
+Tests the execution time of all implemented queries to ensure they meet performance thresholds.
+Results are formatted for GitHub Actions reporting.
+"""
+
+import unittest
+import time
+import sys
+import os
+
+# Add the src directory to the path
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
+
+from vfbquery.vfb_queries import (
+    get_term_info,
+    get_neurons_with_part_in,
+    get_neurons_with_synapses_in,
+    get_neurons_with_presynaptic_terminals_in,
+    get_neurons_with_postsynaptic_terminals_in,
+    get_components_of,
+    get_parts_of,
+    get_subclasses_of,
+    get_neuron_classes_fasciculating_here,
+    get_tracts_nerves_innervating_here,
+    get_lineage_clones_in,
+    get_images_neurons,
+    get_images_that_develop_from,
+    get_expression_pattern_fragments,
+    get_instances,
+    get_similar_neurons,
+    get_neuron_neuron_connectivity,
+    get_neuron_region_connectivity,
+    get_individual_neuron_inputs,
+    get_expression_overlaps_here,
+    get_anatomy_scrnaseq,
+    get_cluster_expression,
+    get_expression_cluster,
+    get_scrnaseq_dataset_data,
+)
+
+
+class QueryPerformanceTest(unittest.TestCase):
+    """Comprehensive performance tests for all VFB queries"""
+    
+    # Performance thresholds (in seconds)
+    THRESHOLD_FAST = 1.0       # Fast queries (simple SOLR lookups)
+    THRESHOLD_MEDIUM = 3.0     # Medium queries (Owlery + SOLR)
+    THRESHOLD_SLOW = 15.0      # Slow queries (Neo4j + complex processing)
+    THRESHOLD_VERY_SLOW = 31.0  # Very slow queries (complex OWL reasoning - over 30 seconds)
+    
+    @classmethod
+    def setUpClass(cls):
+        """Set up for performance tests"""
+        # SOLR caching is enabled by default
+        print("\n🔥 SOLR caching enabled for performance tests")
+    
+    def setUp(self):
+        """Set up test data"""
+        self.test_terms = {
+            'mushroom_body': 'FBbt_00003748',      # Class - mushroom body
+            'antennal_lobe': 'FBbt_00007401',       # Synaptic neuropil
+            'medulla': 'FBbt_00003982',             # Visual system
+            'broad_root': 'FBbt_00003987',          # Neuron projection bundle (tract)
+            'individual_neuron': 'VFB_00101567',    # Individual anatomy
+            'neuron_with_nblast': 'VFB_00017894',   # Neuron with NBLAST data (alternative)
+            'clone': 'FBbt_00050024',               # Clone
+            'connected_neuron': 'VFB_jrchk00s',     # LPC1 neuron with connectivity AND NBLAST data
+        }
+        
+        self.results = []
+        
+    def _time_query(self, query_name, query_func, *args, **kwargs):
+        """Helper to time a query execution"""
+        start_time = time.time()
+        try:
+            result = query_func(*args, **kwargs)
+            duration = time.time() - start_time
+            success = result is not None
+            error = None
+        except Exception as e:
+            duration = time.time() - start_time
+            success = False
+            result = None
+            error = str(e)
+        
+        self.results.append({
+            'name': query_name,
+            'duration': duration,
+            'success': success,
+            'error': error
+        })
+        
+        return result, duration, success
+    
+    def test_01_term_info_queries(self):
+        """Test term info query performance"""
+        print("\n" + "="*80)
+        print("TERM INFO QUERIES")
+        print("="*80)
+        
+        # Test basic term info retrieval
+        result, duration, success = self._time_query(
+            "get_term_info (mushroom body)",
+            get_term_info,
+            self.test_terms['mushroom_body'],
+            preview=True
+        )
+        print(f"get_term_info (mushroom body): {duration:.4f}s {'✅' if success else '❌'}")
+        # term_info with preview can be very slow due to extensive sub-queries
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "term_info query exceeded threshold")
+        
+        result, duration, success = self._time_query(
+            "get_term_info (individual)",
+            get_term_info,
+            self.test_terms['individual_neuron'],
+            preview=True
+        )
+        print(f"get_term_info (individual): {duration:.4f}s {'✅' if success else '❌'}")
+        # term_info with preview can be very slow due to extensive sub-queries
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "term_info query exceeded threshold")
+    
+    def test_02_neuron_part_queries(self):
+        """Test neuron part overlap queries"""
+        print("\n" + "="*80)
+        print("NEURON PART OVERLAP QUERIES")
+        print("="*80)
+        
+        result, duration, success = self._time_query(
+            "NeuronsPartHere (antennal lobe)",
+            get_neurons_with_part_in,
+            self.test_terms['antennal_lobe'],
+            return_dataframe=False,
+            limit=-1  # Changed to -1 to enable caching
+        )
+        print(f"NeuronsPartHere: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "NeuronsPartHere exceeded threshold")
+    
+    def test_03_synaptic_queries(self):
+        """Test synaptic terminal queries"""
+        print("\n" + "="*80)
+        print("SYNAPTIC TERMINAL QUERIES")
+        print("="*80)
+        
+        test_term = self.test_terms['antennal_lobe']
+        
+        result, duration, success = self._time_query(
+            "NeuronsSynaptic",
+            get_neurons_with_synapses_in,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronsSynaptic: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "NeuronsSynaptic exceeded threshold")
+        
+        result, duration, success = self._time_query(
+            "NeuronsPresynapticHere",
+            get_neurons_with_presynaptic_terminals_in,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronsPresynapticHere: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "NeuronsPresynapticHere exceeded threshold")
+        
+        result, duration, success = self._time_query(
+            "NeuronsPostsynapticHere",
+            get_neurons_with_postsynaptic_terminals_in,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronsPostsynapticHere: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "NeuronsPostsynapticHere exceeded threshold")
+        
+        # Test neuron-neuron connectivity query
+        result, duration, success = self._time_query(
+            "NeuronNeuronConnectivity",
+            get_neuron_neuron_connectivity,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronNeuronConnectivity: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronNeuronConnectivity exceeded threshold")
+    
+    def test_04_anatomy_hierarchy_queries(self):
+        """Test anatomical hierarchy queries"""
+        print("\n" + "="*80)
+        print("ANATOMICAL HIERARCHY QUERIES")
+        print("="*80)
+        
+        test_term = self.test_terms['mushroom_body']
+        
+        result, duration, success = self._time_query(
+            "ComponentsOf",
+            get_components_of,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"ComponentsOf: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "ComponentsOf exceeded threshold")
+        
+        result, duration, success = self._time_query(
+            "PartsOf",
+            get_parts_of,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"PartsOf: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "PartsOf exceeded threshold")
+        
+        result, duration, success = self._time_query(
+            "SubclassesOf",
+            get_subclasses_of,
+            test_term,
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"SubclassesOf: {duration:.4f}s {'✅' if success else '❌'}")
+        # SubclassesOf can be very slow for complex terms like mushroom body
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "SubclassesOf exceeded threshold")
+    
+    def test_05_tract_lineage_queries(self):
+        """Test tract/nerve and lineage clone queries"""
+        print("\n" + "="*80)
+        print("TRACT/NERVE AND LINEAGE QUERIES")
+        print("="*80)
+        
+        # NeuronClassesFasciculatingHere
+        result, duration, success = self._time_query(
+            "NeuronClassesFasciculatingHere",
+            get_neuron_classes_fasciculating_here,
+            self.test_terms['broad_root'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronClassesFasciculatingHere: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronClassesFasciculatingHere exceeded threshold")
+        
+        # TractsNervesInnervatingHere
+        result, duration, success = self._time_query(
+            "TractsNervesInnervatingHere",
+            get_tracts_nerves_innervating_here,
+            self.test_terms['antennal_lobe'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"TractsNervesInnervatingHere: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "TractsNervesInnervatingHere exceeded threshold")
+        
+        # LineageClonesIn
+        result, duration, success = self._time_query(
+            "LineageClonesIn",
+            get_lineage_clones_in,
+            self.test_terms['antennal_lobe'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"LineageClonesIn: {duration:.4f}s {'✅' if success else '❌'}")
+        # LineageClonesIn can be very slow due to complex OWL reasoning
+        self.assertLess(duration, self.THRESHOLD_VERY_SLOW, "LineageClonesIn exceeded threshold")
+    
+    def test_05b_image_queries(self):
+        """Test image and developmental lineage queries"""
+        print("\n" + "="*80)
+        print("IMAGE AND DEVELOPMENTAL QUERIES")
+        print("="*80)
+        
+        # ImagesNeurons
+        result, duration, success = self._time_query(
+            "ImagesNeurons",
+            get_images_neurons,
+            self.test_terms['antennal_lobe'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"ImagesNeurons: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "ImagesNeurons exceeded threshold")
+        
+        # ImagesThatDevelopFrom test (neuroblast developmental lineages)
+        result, duration, success = self._time_query(
+            "ImagesThatDevelopFrom",
+            get_images_that_develop_from,
+            "FBbt_00001419",  # neuroblast MNB - has 336 neuron images
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"ImagesThatDevelopFrom: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "ImagesThatDevelopFrom exceeded threshold")
+        
+        # epFrag test (expression pattern fragments)
+        result, duration, success = self._time_query(
+            "epFrag",
+            get_expression_pattern_fragments,
+            "FBtp0000001",  # expression pattern example
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"epFrag: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "epFrag exceeded threshold")
+    
+    def test_06_instance_queries(self):
+        """Test instance retrieval queries"""
+        print("\n" + "="*80)
+        print("INSTANCE QUERIES")
+        print("="*80)
+        
+        result, duration, success = self._time_query(
+            "ListAllAvailableImages",
+            get_instances,
+            self.test_terms['medulla'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"ListAllAvailableImages: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "ListAllAvailableImages exceeded threshold")
+    
+    def test_07_connectivity_queries(self):
+        """Test neuron connectivity queries"""
+        print("\n" + "="*80)
+        print("CONNECTIVITY QUERIES")
+        print("="*80)
+        
+        # NeuronNeuronConnectivity
+        result, duration, success = self._time_query(
+            "NeuronNeuronConnectivityQuery",
+            get_neuron_neuron_connectivity,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronNeuronConnectivityQuery: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronNeuronConnectivityQuery exceeded threshold")
+        
+        # NeuronRegionConnectivity
+        result, duration, success = self._time_query(
+            "NeuronRegionConnectivityQuery",
+            get_neuron_region_connectivity,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=-1  # Enable caching for performance tests
+        )
+        print(f"NeuronRegionConnectivityQuery: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronRegionConnectivityQuery exceeded threshold")
+    
+    def test_08_similarity_queries(self):
+        """Test NBLAST similarity queries"""
+        print("\n" + "="*80)
+        print("SIMILARITY QUERIES (Neo4j NBLAST)")
+        print("="*80)
+        
+        # SimilarMorphologyTo (NBLAST)
+        result, duration, success = self._time_query(
+            "SimilarMorphologyTo",
+            get_similar_neurons,
+            self.test_terms['connected_neuron'],  # VFB_jrchk00s has NBLAST data
+            similarity_score='NBLAST_score',
+            return_dataframe=False,
+            limit=5
+        )
+        print(f"SimilarMorphologyTo: {duration:.4f}s {'✅' if success else '❌'}")
+        # Legacy NBLAST similarity can be slower
+        self.assertLess(duration, self.THRESHOLD_SLOW, "SimilarMorphologyTo exceeded threshold")
+    
+    def test_09_neuron_input_queries(self):
+        """Test neuron input/synapse queries"""
+        print("\n" + "="*80)
+        print("NEURON INPUT QUERIES (Neo4j)")
+        print("="*80)
+        
+        # NeuronInputsTo
+        result, duration, success = self._time_query(
+            "NeuronInputsTo",
+            get_individual_neuron_inputs,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=5
+        )
+        print(f"NeuronInputsTo: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronInputsTo exceeded threshold")
+    
+    def test_10_expression_queries(self):
+        """Test expression pattern queries"""
+        print("\n" + "="*80)
+        print("EXPRESSION PATTERN QUERIES (Neo4j)")
+        print("="*80)
+        
+        # ExpressionOverlapsHere - test with adult brain which has many expression patterns
+        result, duration, success = self._time_query(
+            "ExpressionOverlapsHere (adult brain)",
+            get_expression_overlaps_here,
+            self.test_terms['medulla'],  # FBbt_00003982 (adult brain/medulla)
+            return_dataframe=False,
+            limit=10  # Limit to 10 for performance test
+        )
+        print(f"ExpressionOverlapsHere: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            print(f"  └─ Found {result.get('count', 0)} total expression patterns, returned 10")
+        self.assertLess(duration, self.THRESHOLD_SLOW, "ExpressionOverlapsHere exceeded threshold")
+    
+    def test_11_transcriptomics_queries(self):
+        """Test scRNAseq transcriptomics queries"""
+        print("\n" + "="*80)
+        print("TRANSCRIPTOMICS QUERIES (Neo4j scRNAseq)")
+        print("="*80)
+        
+        # Note: These tests use example IDs that may need to be updated based on actual database content
+        # The queries are designed to work even if no data is found (will return empty results)
+        
+        # anatScRNAseqQuery - test with adult brain
+        result, duration, success = self._time_query(
+            "anatScRNAseqQuery (adult brain)",
+            get_anatomy_scrnaseq,
+            self.test_terms['medulla'],  # FBbt_00003982 (adult brain/medulla)
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"anatScRNAseqQuery: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} total clusters" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_SLOW, "anatScRNAseqQuery exceeded threshold")
+        
+        # clusterExpression - test with a cluster ID (may return empty if cluster doesn't exist)
+        # Using a dummy ID - test will pass even with empty results
+        try:
+            result, duration, success = self._time_query(
+                "clusterExpression (example cluster)",
+                get_cluster_expression,
+                "VFBc_00101567",  # Example cluster ID
+                return_dataframe=False,
+                limit=10
+            )
+            print(f"clusterExpression: {duration:.4f}s {'✅' if success else '❌'}")
+            if success and result:
+                count = result.get('count', 0)
+                print(f"  └─ Found {count} genes expressed" + (", returned 10" if count > 10 else ""))
+            self.assertLess(duration, self.THRESHOLD_SLOW, "clusterExpression exceeded threshold")
+        except Exception as e:
+            print(f"clusterExpression: Skipped (test data may not exist): {e}")
+        
+        # expressionCluster - test with a gene ID (may return empty if no scRNAseq data)
+        try:
+            result, duration, success = self._time_query(
+                "expressionCluster (example gene)",
+                get_expression_cluster,
+                "FBgn_00000024",  # Example gene ID
+                return_dataframe=False,
+                limit=10
+            )
+            print(f"expressionCluster: {duration:.4f}s {'✅' if success else '❌'}")
+            if success and result:
+                count = result.get('count', 0)
+                print(f"  └─ Found {count} clusters expressing gene" + (", returned 10" if count > 10 else ""))
+            self.assertLess(duration, self.THRESHOLD_SLOW, "expressionCluster exceeded threshold")
+        except Exception as e:
+            print(f"expressionCluster: Skipped (test data may not exist): {e}")
+        
+        # scRNAdatasetData - test with a dataset ID (may return empty if dataset doesn't exist)
+        try:
+            result, duration, success = self._time_query(
+                "scRNAdatasetData (example dataset)",
+                get_scrnaseq_dataset_data,
+                "VFBds_00001234",  # Example dataset ID
+                return_dataframe=False,
+                limit=10
+            )
+            print(f"scRNAdatasetData: {duration:.4f}s {'✅' if success else '❌'}")
+            if success and result:
+                count = result.get('count', 0)
+                print(f"  └─ Found {count} clusters in dataset" + (", returned 10" if count > 10 else ""))
+            self.assertLess(duration, self.THRESHOLD_SLOW, "scRNAdatasetData exceeded threshold")
+        except Exception as e:
+            print(f"scRNAdatasetData: Skipped (test data may not exist): {e}")
+    
+    def test_12_nblast_queries(self):
+        """Test NBLAST similarity queries"""
+        print("\n" + "="*80)
+        print("NBLAST SIMILARITY QUERIES")
+        print("="*80)
+        
+        # Import the new query functions
+        from vfbquery.vfb_queries import (
+            get_similar_morphology,
+            get_similar_morphology_part_of,
+            get_similar_morphology_part_of_exp,
+            get_similar_morphology_nb,
+            get_similar_morphology_nb_exp,
+            get_similar_morphology_userdata
+        )
+        
+        # SimilarMorphologyTo - NBLAST matches
+        result, duration, success = self._time_query(
+            "SimilarMorphologyTo",
+            get_similar_morphology,
+            self.test_terms['connected_neuron'],  # LPC1 neuron with NBLAST data
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"SimilarMorphologyTo: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} NBLAST matches" + (", returned 10" if count > 10 else ""))
+        # NBLAST queries can be slightly slower due to database complexity
+        self.assertLess(duration, self.THRESHOLD_SLOW, "SimilarMorphologyTo exceeded threshold")
+        
+        # SimilarMorphologyToPartOf - NBLASTexp to expression patterns
+        result, duration, success = self._time_query(
+            "SimilarMorphologyToPartOf",
+            get_similar_morphology_part_of,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"SimilarMorphologyToPartOf: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} NBLASTexp matches" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "SimilarMorphologyToPartOf exceeded threshold")
+        
+        # SimilarMorphologyToPartOfexp - Reverse NBLASTexp
+        result, duration, success = self._time_query(
+            "SimilarMorphologyToPartOfexp",
+            get_similar_morphology_part_of_exp,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"SimilarMorphologyToPartOfexp: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} reverse NBLASTexp matches" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "SimilarMorphologyToPartOfexp exceeded threshold")
+        
+        # SimilarMorphologyToNB - NeuronBridge matches
+        result, duration, success = self._time_query(
+            "SimilarMorphologyToNB",
+            get_similar_morphology_nb,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"SimilarMorphologyToNB: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} NeuronBridge matches" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "SimilarMorphologyToNB exceeded threshold")
+        
+        # SimilarMorphologyToNBexp - NeuronBridge for expression patterns
+        result, duration, success = self._time_query(
+            "SimilarMorphologyToNBexp",
+            get_similar_morphology_nb_exp,
+            self.test_terms['connected_neuron'],
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"SimilarMorphologyToNBexp: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} NeuronBridge expression matches" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "SimilarMorphologyToNBexp exceeded threshold")
+        
+        print(f"✅ All NBLAST similarity queries completed")
+    
+    def test_13_dataset_template_queries(self):
+        """Test dataset and template queries"""
+        print("\n" + "="*80)
+        print("DATASET/TEMPLATE QUERIES")
+        print("="*80)
+        
+        # Import the new query functions
+        from vfbquery.vfb_queries import (
+            get_painted_domains,
+            get_dataset_images,
+            get_all_aligned_images,
+            get_aligned_datasets,
+            get_all_datasets
+        )
+        
+        # Test terms for templates and datasets
+        template_term = 'VFBc_00050000'  # Adult Brain template
+        dataset_term = 'VFBc_00101384'   # Example dataset
+        
+        # PaintedDomains - Template painted anatomy domains
+        result, duration, success = self._time_query(
+            "PaintedDomains",
+            get_painted_domains,
+            template_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"PaintedDomains: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} painted domains" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "PaintedDomains exceeded threshold")
+        
+        # DatasetImages - Images in a dataset
+        result, duration, success = self._time_query(
+            "DatasetImages",
+            get_dataset_images,
+            dataset_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"DatasetImages: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} images in dataset" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "DatasetImages exceeded threshold")
+        
+        # AllAlignedImages - All images aligned to template
+        result, duration, success = self._time_query(
+            "AllAlignedImages",
+            get_all_aligned_images,
+            template_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"AllAlignedImages: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} aligned images" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "AllAlignedImages exceeded threshold")
+        
+        # AlignedDatasets - All datasets aligned to template
+        result, duration, success = self._time_query(
+            "AlignedDatasets",
+            get_aligned_datasets,
+            template_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"AlignedDatasets: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} aligned datasets" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "AlignedDatasets exceeded threshold")
+        
+        # AllDatasets - All available datasets
+        result, duration, success = self._time_query(
+            "AllDatasets",
+            get_all_datasets,
+            return_dataframe=False,
+            limit=20
+        )
+        print(f"AllDatasets: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} total datasets" + (", returned 20" if count > 20 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "AllDatasets exceeded threshold")
+        
+        print(f"✅ All dataset/template queries completed")
+    
+    def test_14_publication_transgene_queries(self):
+        """Test publication and transgene queries"""
+        print("\n" + "="*80)
+        print("PUBLICATION/TRANSGENE QUERIES")
+        print("="*80)
+        
+        # Import the new query functions
+        from vfbquery.vfb_queries import (
+            get_terms_for_pub,
+            get_transgene_expression_here
+        )
+        
+        # Test terms
+        pub_term = 'DOI_10_7554_eLife_04577'  # Example publication
+        anatomy_term = self.test_terms['mushroom_body']  # mushroom body
+        
+        # TermsForPub - Terms referencing a publication
+        result, duration, success = self._time_query(
+            "TermsForPub",
+            get_terms_for_pub,
+            pub_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"TermsForPub: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} terms for publication" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "TermsForPub exceeded threshold")
+        
+        # TransgeneExpressionHere - Complex transgene expression query
+        result, duration, success = self._time_query(
+            "TransgeneExpressionHere",
+            get_transgene_expression_here,
+            anatomy_term,
+            return_dataframe=False,
+            limit=10
+        )
+        print(f"TransgeneExpressionHere: {duration:.4f}s {'✅' if success else '❌'}")
+        if success and result:
+            count = result.get('count', 0)
+            print(f"  └─ Found {count} transgene expressions" + (", returned 10" if count > 10 else ""))
+        self.assertLess(duration, self.THRESHOLD_SLOW, "TransgeneExpressionHere exceeded threshold")
+        
+        print(f"✅ All publication/transgene queries completed")
+    
+    def tearDown(self):
+        """Generate performance summary"""
+        pass
+    
+    @classmethod
+    def tearDownClass(cls):
+        """Generate final performance report"""
+        print("\n" + "="*80)
+        print("PERFORMANCE TEST SUMMARY")
+        print("="*80)
+        
+        # This will be populated by the test instance
+        # For now, just print a summary message
+        print("All performance tests completed!")
+        print("="*80)
+
+
+def run_tests():
+    """Run the performance test suite"""
+    # Create test suite
+    loader = unittest.TestLoader()
+    suite = loader.loadTestsFromTestCase(QueryPerformanceTest)
+    
+    # Run tests with detailed output
+    runner = unittest.TextTestRunner(verbosity=2)
+    result = runner.run(suite)
+    
+    return result.wasSuccessful()
+
+
+if __name__ == '__main__':
+    success = run_tests()
+    sys.exit(0 if success else 1)