add to performance tests

Author: Clare72

.github/workflows/performance-test.yml

@@ -41,15 +41,30 @@ jobs:
         run: |
           python -m unittest src.test.test_query_performance -v 2>&1 | tee performance_test_output.log
         
-      - name: Run Legacy Performance Test  
+      - name: Run Legacy Performance Test
         env:
           VFBQUERY_CACHE_ENABLED: 'true'
           MPLBACKEND: 'Agg'
           VISPY_GL_LIB: 'osmesa'
           VISPY_USE_EGL: '0'
         run: |
           python -m unittest -v src.test.term_info_queries_test.TermInfoQueriesTest.test_term_info_performance 2>&1 | tee -a performance_test_output.log
-        
+
+      - name: Run Connectivity Tests
+        env:
+          VFBQUERY_CACHE_ENABLED: 'true'
+          MPLBACKEND: 'Agg'
+          VISPY_GL_LIB: 'osmesa'
+          VISPY_USE_EGL: '0'
+        run: |
+          python -m unittest -v \
+            src.test.test_neuron_neuron_connectivity \
+            src.test.test_neuron_region_connectivity \
+            src.test.test_upstream_class_connectivity \
+            src.test.test_downstream_class_connectivity \
+            src.test.test_vfb_connectivity \
+            2>&1 | tee -a performance_test_output.log
+
       - name: Create Performance Report
         if: always()  # Always run this step, even if the test fails
         run: |
@@ -177,7 +192,7 @@ jobs:
               echo "|-------|----------|--------|" >> performance.md
               
               # Parse timing information
-              grep -E "^(get_term_info|NeuronsPartHere|NeuronsSynaptic|NeuronsPresynapticHere|NeuronsPostsynapticHere|ComponentsOf|PartsOf|SubclassesOf|NeuronClassesFasciculatingHere|TractsNervesInnervatingHere|LineageClonesIn|ListAllAvailableImages):" performance_test_output.log | while read line; do
+              grep -E "^(get_term_info|NeuronsPartHere|NeuronsSynaptic|NeuronsPresynapticHere|NeuronsPostsynapticHere|ComponentsOf|PartsOf|SubclassesOf|NeuronClassesFasciculatingHere|TractsNervesInnervatingHere|LineageClonesIn|ListAllAvailableImages|NeuronNeuronConnectivityQuery|NeuronRegionConnectivityQuery|NeuronInputsTo|DownstreamClassConnectivity|UpstreamClassConnectivity|QueryConnectivity):" performance_test_output.log | while read line; do
                 QUERY=$(echo "$line" | sed 's/:.*//') 
                 DURATION=$(echo "$line" | sed 's/.*: \([0-9.]*\)s.*/\1/')
                 if echo "$line" | grep -q "✅"; then

src/test/test_query_performance.py

@@ -34,12 +34,15 @@
     get_neuron_neuron_connectivity,
     get_neuron_region_connectivity,
     get_individual_neuron_inputs,
+    get_downstream_class_connectivity,
+    get_upstream_class_connectivity,
     get_expression_overlaps_here,
     get_anatomy_scrnaseq,
     get_cluster_expression,
     get_expression_cluster,
     get_scrnaseq_dataset_data,
 )
+from vfbquery.vfb_connectivity import query_connectivity
 
 
 class QueryPerformanceTest(unittest.TestCase):
@@ -348,7 +351,57 @@ def test_07_connectivity_queries(self):
         )
         print(f"NeuronRegionConnectivityQuery: {duration:.4f}s {'✅' if success else '❌'}")
         self.assertLess(duration, self.THRESHOLD_SLOW, "NeuronRegionConnectivityQuery exceeded threshold")
-    
+
+    def test_07b_class_connectivity_queries(self):
+        """Test class-level connectivity queries (pre-indexed Solr)"""
+        print("\n" + "="*80)
+        print("CLASS CONNECTIVITY QUERIES (Solr pre-indexed)")
+        print("="*80)
+
+        # FBbt_00001482 = lineage NB3-2 primary interneuron — known to have
+        # downstream/upstream connectivity data in the vfb_json Solr core.
+        test_class = "FBbt_00001482"
+
+        # DownstreamClassConnectivity
+        result, duration, success = self._time_query(
+            "DownstreamClassConnectivity",
+            get_downstream_class_connectivity,
+            test_class,
+            return_dataframe=False,
+        )
+        print(f"DownstreamClassConnectivity: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "DownstreamClassConnectivity exceeded threshold")
+
+        # UpstreamClassConnectivity
+        result, duration, success = self._time_query(
+            "UpstreamClassConnectivity",
+            get_upstream_class_connectivity,
+            test_class,
+            return_dataframe=False,
+        )
+        print(f"UpstreamClassConnectivity: {duration:.4f}s {'✅' if success else '❌'}")
+        self.assertLess(duration, self.THRESHOLD_MEDIUM, "UpstreamClassConnectivity exceeded threshold")
+
+    def test_07c_cross_dataset_connectivity(self):
+        """Test cross-dataset query_connectivity (live, both-end filtered)"""
+        print("\n" + "="*80)
+        print("CROSS-DATASET CONNECTIVITY (live, slow)")
+        print("="*80)
+
+        # Both-end + group_by_class is the fastest variant per LLM guidance.
+        # giant fiber neuron → peripherally synapsing interneuron is a
+        # known-good pair with non-zero results.
+        result, duration, success = self._time_query(
+            "QueryConnectivity",
+            query_connectivity,
+            upstream_type="giant fiber neuron",
+            downstream_type="peripherally synapsing interneuron",
+            group_by_class=True,
+        )
+        print(f"QueryConnectivity: {duration:.4f}s {'✅' if success else '❌'}")
+        # Live cross-dataset query — allow up to 5 min per the MCP timeout.
+        self.assertLess(duration, 300.0, "QueryConnectivity exceeded threshold")
+
     def test_08_similarity_queries(self):
         """Test NBLAST similarity queries"""
         print("\n" + "="*80)