Merge pull request #33 from VirtualFlyBrain/dev

Robbie1977 · web-flow · commit 87f09e6395d9 · 2025-10-21T21:50:59.000+01:00
Fix for testing and encoding
diff --git a/README.md b/README.md
@@ -97,34 +97,34 @@ vfb.get_term_info('FBbt_00003748')
                   "id": "VFB_00102107",
                   "label": "[ME on JRC2018Unisex adult brain](VFB_00102107)",
                   "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
-                  "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018Unisex](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018Unisex')](VFB_00101567,VFB_00102107)"
+                  "thumbnail": "[![ME on JRC2018Unisex adult brain aligned to JRC2018U](http://www.virtualflybrain.org/data/VFB/i/0010/2107/VFB_00101567/thumbnail.png 'ME on JRC2018Unisex adult brain aligned to JRC2018U')](VFB_00101567,VFB_00102107)"
                },
                {
                   "id": "VFB_00101385",
-                  "label": "[ME%28R%29 on JRC_FlyEM_Hemibrain](VFB_00101385)",
+                  "label": "[ME(R) on JRC_FlyEM_Hemibrain](VFB_00101385)",
                   "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
-                  "thumbnail": "[![ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRC_FlyEM_Hemibrain')](VFB_00101384,VFB_00101385)"
+                  "thumbnail": "[![ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum')](VFB_00101384,VFB_00101385)"
                },
                {
                   "id": "VFB_00030810",
                   "label": "[medulla on adult brain template Ito2014](VFB_00030810)",
-                  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
+                  "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
                   "thumbnail": "[![medulla on adult brain template Ito2014 aligned to adult brain template Ito2014](http://www.virtualflybrain.org/data/VFB/i/0003/0810/VFB_00030786/thumbnail.png 'medulla on adult brain template Ito2014 aligned to adult brain template Ito2014')](VFB_00030786,VFB_00030810)"
                },
                {
                   "id": "VFB_00030624",
                   "label": "[medulla on adult brain template JFRC2](VFB_00030624)",
-                  "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
-                  "thumbnail": "[![medulla on adult brain template JFRC2 aligned to adult brain template JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to adult brain template JFRC2')](VFB_00017894,VFB_00030624)"
+                  "tags": "Nervous_system|Visual_system|Adult|Synaptic_neuropil_domain",
+                  "thumbnail": "[![medulla on adult brain template JFRC2 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to JFRC2')](VFB_00017894,VFB_00030624)"
                }
             ]
          },
          "output_format": "table",
          "count": 4
       }
    ],
-   "IsIndividual": false,
-   "IsClass": true,
+   "IsIndividual": False,
+   "IsClass": True,
    "Examples": {
       "VFB_00101384": [
          {
@@ -171,7 +171,7 @@ vfb.get_term_info('FBbt_00003748')
          }
       ]
    },
-   "IsTemplate": false,
+   "IsTemplate": False,
    "Synonyms": [
       {
          "label": "ME",
@@ -1102,15 +1102,15 @@ vfb.get_instances('FBbt_00003748', return_dataframe=False)
       },
       {
          "id": "VFB_00101385",
-         "label": "[ME%28R%29 on JRC_FlyEM_Hemibrain](VFB_00101385)",
+         "label": "[ME(R) on JRC_FlyEM_Hemibrain](VFB_00101385)",
          "tags": "Nervous_system|Adult|Visual_system|Synaptic_neuropil_domain",
          "parent": "[medulla](FBbt_00003748)",
          "source": "",
          "source_id": "",
          "template": "[JRCFIB2018Fum](VFB_00101384)",
          "dataset": "[JRC_FlyEM_Hemibrain painted domains](Xu2020roi)",
          "license": "",
-         "thumbnail": "[![ME%28R%29 on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum')](VFB_00101384,VFB_00101385)"
+         "thumbnail": "[![ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum](http://www.virtualflybrain.org/data/VFB/i/0010/1385/VFB_00101384/thumbnail.png 'ME(R) on JRC_FlyEM_Hemibrain aligned to JRCFIB2018Fum')](VFB_00101384,VFB_00101385)"
       },
       {
          "id": "VFB_00030810",
@@ -1132,7 +1132,7 @@ vfb.get_instances('FBbt_00003748', return_dataframe=False)
          "source": "",
          "source_id": "",
          "template": "[JFRC2](VFB_00017894)",
-         "dataset": "[BrainName neuropils on adult brain JFRC2 %28Jenett, Shinomya%29](JenettShinomya_BrainName)",
+         "dataset": "[BrainName neuropils on adult brain JFRC2 (Jenett, Shinomya)](JenettShinomya_BrainName)",
          "license": "",
          "thumbnail": "[![medulla on adult brain template JFRC2 aligned to JFRC2](http://www.virtualflybrain.org/data/VFB/i/0003/0624/VFB_00017894/thumbnail.png 'medulla on adult brain template JFRC2 aligned to JFRC2')](VFB_00017894,VFB_00030624)"
       }
@@ -1214,7 +1214,7 @@ vfb.get_templates(return_dataframe=False)
          "name": "[JFRC2](VFB_00017894)",
          "tags": "Nervous_system|Adult",
          "thumbnail": "[![JFRC2](http://www.virtualflybrain.org/data/VFB/i/0001/7894/VFB_00017894/thumbnail.png 'JFRC2')](VFB_00017894)",
-         "dataset": "[FlyLight - GMR GAL4 collection %28Jenett2012%29](Jenett2012)",
+         "dataset": "[FlyLight - GMR GAL4 collection (Jenett2012)](Jenett2012)",
          "license": "[CC-BY-NC-SA](VFBlicense_CC_BY_NC_SA_4_0)"
       },
       {
@@ -1232,7 +1232,7 @@ vfb.get_templates(return_dataframe=False)
          "name": "[L1 larval CNS ssTEM - Cardona/Janelia](VFB_00050000)",
          "tags": "Nervous_system|Larva",
          "thumbnail": "[![L1 larval CNS ssTEM - Cardona/Janelia](http://www.virtualflybrain.org/data/VFB/i/0005/0000/VFB_00050000/thumbnail.png 'L1 larval CNS ssTEM - Cardona/Janelia')](VFB_00050000)",
-         "dataset": "[Neurons involved in larval fast escape response - EM %28Ohyama2016%29](Ohyama2015)",
+         "dataset": "[Neurons involved in larval fast escape response - EM (Ohyama2016)](Ohyama2015)",
          "license": "[CC_BY_SA](VFBlicense_CC_BY_SA_4_0)"
       },
       {
@@ -1241,7 +1241,7 @@ vfb.get_templates(return_dataframe=False)
          "name": "[L1 larval CNS ssTEM - Cardona/Janelia](VFB_00050000)",
          "tags": "Nervous_system|Larva",
          "thumbnail": "[![L1 larval CNS ssTEM - Cardona/Janelia](http://www.virtualflybrain.org/data/VFB/i/0005/0000/VFB_00050000/thumbnail.png 'L1 larval CNS ssTEM - Cardona/Janelia')](VFB_00050000)",
-         "dataset": "[larval hugin neurons - EM %28Schlegel2016%29](Schlegel2016)",
+         "dataset": "[larval hugin neurons - EM (Schlegel2016)](Schlegel2016)",
          "license": "[CC_BY](VFBlicense_CC_BY_4_0)"
       },
       {
@@ -1250,7 +1250,7 @@ vfb.get_templates(return_dataframe=False)
          "name": "[L3 CNS template - Wood2018](VFB_00049000)",
          "tags": "Nervous_system|Larva",
          "thumbnail": "[![L3 CNS template - Wood2018](http://www.virtualflybrain.org/data/VFB/i/0004/9000/VFB_00049000/thumbnail.png 'L3 CNS template - Wood2018')](VFB_00049000)",
-         "dataset": "[L3 Larval CNS Template %28Truman2016%29](Truman2016)",
+         "dataset": "[L3 Larval CNS Template (Truman2016)](Truman2016)",
          "license": "[CC_BY_SA](VFBlicense_CC_BY_SA_4_0)"
       },
       {
@@ -1259,7 +1259,7 @@ vfb.get_templates(return_dataframe=False)
          "name": "[COURT2018VNS](VFB_00100000)",
          "tags": "Nervous_system|Adult|Ganglion",
          "thumbnail": "[![COURT2018VNS](http://www.virtualflybrain.org/data/VFB/i/0010/0000/VFB_00100000/thumbnail.png 'COURT2018VNS')](VFB_00100000)",
-         "dataset": "[Adult VNS neuropils %28Court2017%29](Court2017)",
+         "dataset": "[Adult VNS neuropils (Court2017)](Court2017)",
          "license": "[CC_BY_SA](VFBlicense_CC_BY_SA_4_0)"
       },
       {
@@ -1274,7 +1274,7 @@ vfb.get_templates(return_dataframe=False)
       {
          "id": "VFB_00110000",
          "order": 9,
-         "name": "[Adult Head %28McKellar2020%29](VFB_00110000)",
+         "name": "[Adult Head (McKellar2020)](VFB_00110000)",
          "tags": "Adult|Anatomy",
          "thumbnail": "[![Adult Head (McKellar2020)](http://www.virtualflybrain.org/data/VFB/i/0011/0000/VFB_00110000/thumbnail.png 'Adult Head (McKellar2020)')](VFB_00110000)",
          "dataset": "[GAL4 lines from McKellar et al., 2020](McKellar2020)",
@@ -1283,7 +1283,7 @@ vfb.get_templates(return_dataframe=False)
       {
          "id": "VFB_00120000",
          "order": 10,
-         "name": "[Adult T1 Leg %28Kuan2020%29](VFB_00120000)",
+         "name": "[Adult T1 Leg (Kuan2020)](VFB_00120000)",
          "tags": "Adult|Anatomy",
          "thumbnail": "[![Adult T1 Leg (Kuan2020)](http://www.virtualflybrain.org/data/VFB/i/0012/0000/VFB_00120000/thumbnail.png 'Adult T1 Leg (Kuan2020)')](VFB_00120000)",
          "dataset": "[Millimeter-scale imaging of a Drosophila leg at single-neuron resolution](Kuan2020)",
diff --git a/performance.md b/performance.md
@@ -1,9 +1,9 @@
 # VFBquery Performance Test Results
 
-**Test Date:** 2025-10-21 18:57:26 UTC
-**Git Commit:** 164cbe98e3ae2151937e3c73a0d12d751e91ec8c
-**Branch:** main
-**Workflow Run:** 18694523268
+**Test Date:** 2025-10-21 20:47:06 UTC
+**Git Commit:** e46b76948e36c2eb4fdebcd64af12bef03300382
+**Branch:** dev
+**Workflow Run:** 18697165949
 
 ## Test Overview
 
@@ -25,11 +25,11 @@ This performance test measures the execution time of VFB term info queries for s
 
 ✅ **Test Status**: Performance test completed
 
-- **FBbt_00003748 Query Time**: 0.8842 seconds
-- **VFB_00101567 Query Time**: 0.7123 seconds
-- **Total Query Time**: 1.5965 seconds
+- **FBbt_00003748 Query Time**: 1.5526 seconds
+- **VFB_00101567 Query Time**: 1.1230 seconds
+- **Total Query Time**: 2.6756 seconds
 
 🎉 **Result**: All performance thresholds met!
 
 ---
-*Last updated: 2025-10-21 18:57:26 UTC*
+*Last updated: 2025-10-21 20:47:06 UTC*
diff --git a/src/test/readme_parser.py b/src/test/readme_parser.py
@@ -27,7 +27,35 @@ def extract_code_blocks(readme_path):
         # Look for vfb.* calls and extract them
         vfb_calls = re.findall(r'(vfb\.[^)]*\))', block)
         if vfb_calls:
-            processed_python_blocks.extend(vfb_calls)
+            # Add force_refresh=True to each call to ensure fresh data in tests
+            # Exceptions:
+            # - get_templates() doesn't support force_refresh (no SOLR cache)
+            # - Performance test terms (FBbt_00003748, VFB_00101567) should use cache
+            for call in vfb_calls:
+                # Check if this is get_templates() - if so, don't add force_refresh
+                if 'get_templates' in call:
+                    processed_python_blocks.append(call)
+                    continue
+                
+                # Check if this call uses performance test terms - skip force_refresh for those
+                if 'FBbt_00003748' in call or 'VFB_00101567' in call:
+                    processed_python_blocks.append(call)
+                    continue
+                
+                # Check if the call already has parameters
+                if '(' in call and ')' in call:
+                    # Insert force_refresh=True before the closing parenthesis
+                    # Handle both cases: with and without existing parameters
+                    if call.rstrip(')').endswith('('):
+                        # No parameters: vfb.function()
+                        modified_call = call[:-1] + 'force_refresh=True)'
+                    else:
+                        # Has parameters: vfb.function(param1, param2)
+                        modified_call = call[:-1] + ', force_refresh=True)'
+                    processed_python_blocks.append(modified_call)
+                else:
+                    # Shouldn't happen, but include original call if no parentheses
+                    processed_python_blocks.append(call)
     
     # Process JSON blocks
     processed_json_blocks = []
diff --git a/src/test/term_info_queries_test.py b/src/test/term_info_queries_test.py
@@ -551,14 +551,14 @@ def test_term_info_performance(self):
         
         # Performance categories
         total_time = duration_1 + duration_2
-        if total_time < 1.0:
-            performance_level = "🟢 Excellent (< 1 second)"
-        elif total_time < 2.0:
-            performance_level = "🟡 Good (1-2 seconds)"  
-        elif total_time < 4.0:
-            performance_level = "🟠 Acceptable (2-4 seconds)"
+        if total_time < 1.5:
+            performance_level = "🟢 Excellent (< 1.5 seconds)"
+        elif total_time < 3.0:
+            performance_level = "🟡 Good (1.5-3 seconds)"  
+        elif total_time < 6.0:
+            performance_level = "🟠 Acceptable (3-6 seconds)"
         else:
-            performance_level = "🔴 Slow (> 4 seconds)"
+            performance_level = "🔴 Slow (> 6 seconds)"
             
         print(f"Performance Level: {performance_level}")
         print(f"="*50)
@@ -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 = 2.0  # seconds
-        max_total_time = 4.0  # seconds (2 queries * 2 seconds each)
+        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)
         
         self.assertLess(duration_1, max_single_query_time, 
                        f"FBbt_00003748 query took {duration_1:.4f}s, exceeding {max_single_query_time}s threshold")
diff --git a/src/vfbquery/__init__.py b/src/vfbquery/__init__.py
@@ -1,4 +1,5 @@
 from .vfb_queries import *
+from .solr_result_cache import get_solr_cache
 
 # Caching enhancements (optional import - don't break if dependencies missing)
 try:
@@ -48,6 +49,26 @@
     __caching_available__ = False
     print("VFBquery: Caching not available (dependencies missing)")
 
+# Convenience function for clearing SOLR cache entries
+def clear_solr_cache(query_type: str, term_id: str) -> bool:
+    """
+    Clear a specific SOLR cache entry to force refresh
+    
+    Args:
+        query_type: Type of query ('term_info', 'instances', etc.)
+        term_id: Term identifier (e.g., 'FBbt_00003748')
+    
+    Returns:
+        True if successfully cleared, False otherwise
+    
+    Example:
+        >>> import vfbquery as vfb
+        >>> vfb.clear_solr_cache('term_info', 'FBbt_00003748')
+        >>> result = vfb.get_term_info('FBbt_00003748')  # Will fetch fresh data
+    """
+    cache = get_solr_cache()
+    return cache.clear_cache_entry(query_type, term_id)
+
 # SOLR-based result caching (experimental - for cold start optimization)
 try:
     from .solr_cache_integration import (
diff --git a/src/vfbquery/solr_result_cache.py b/src/vfbquery/solr_result_cache.py
diff --git a/src/vfbquery/vfb_queries.py b/src/vfbquery/vfb_queries.py
