Fix markdown link encoding by decoding URL-encoded strings from SOLR and updating README examples

Author: Robbie1977

README.md

@@ -101,9 +101,9 @@ vfb.get_term_info('FBbt_00003748')
                },
                {
                   "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",

src/vfbquery/vfb_queries.py

@@ -9,6 +9,7 @@
 from marshmallow import ValidationError
 import json
 import numpy as np
+from urllib.parse import unquote
 from .solr_result_cache import with_solr_cache
 
 # Custom JSON encoder to handle NumPy and pandas types
@@ -311,14 +312,13 @@ def __str__(self):
 
 def encode_brackets(text):
     """
-    Encodes brackets in the given text.
+    Encodes square brackets in the given text to prevent breaking markdown link syntax.
+    Parentheses are NOT encoded as they don't break markdown syntax.
 
     :param text: The text to encode.
-    :return: The text with brackets encoded.
+    :return: The text with square brackets encoded.
     """
-    return (text.replace('(', '%28')
-                .replace(')', '%29')
-                .replace('[', '%5B')
+    return (text.replace('[', '%5B')
                 .replace(']', '%5D'))
 
 def encode_markdown_links(df, columns):
@@ -1055,12 +1055,16 @@ def _get_instances_from_solr(short_form: str, return_dataframe=True, limit: int
                 template_label = template_anatomy.get('label', '')
                 if template_anatomy.get('symbol') and len(template_anatomy.get('symbol', '')) > 0:
                     template_label = template_anatomy.get('symbol')
+                # Decode URL-encoded strings from SOLR (e.g., ME%28R%29 -> ME(R))
+                template_label = unquote(template_label)
                 template_short_form = template_anatomy.get('short_form', '')
 
                 # Prefer symbol over label for anatomy (matching Neo4j behavior)
                 anatomy_label = anatomy.get('label', '')
                 if anatomy.get('symbol') and len(anatomy.get('symbol', '')) > 0:
                     anatomy_label = anatomy.get('symbol')
+                # Decode URL-encoded strings from SOLR (e.g., ME%28R%29 -> ME(R))
+                anatomy_label = unquote(anatomy_label)
                 anatomy_short_form = anatomy.get('short_form', '')
 
                 if template_label and anatomy_label:
@@ -1077,6 +1081,8 @@ def _get_instances_from_solr(short_form: str, return_dataframe=True, limit: int
                 template_label = template_anatomy.get('label', '')
                 if template_anatomy.get('symbol') and len(template_anatomy.get('symbol', '')) > 0:
                     template_label = template_anatomy.get('symbol')
+                # Decode URL-encoded strings from SOLR (e.g., ME%28R%29 -> ME(R))
+                template_label = unquote(template_label)
                 template_short_form = template_anatomy.get('short_form', '')
                 if template_label and template_short_form:
                     template_formatted = f"[{template_label}]({template_short_form})"
@@ -1085,6 +1091,8 @@ def _get_instances_from_solr(short_form: str, return_dataframe=True, limit: int
             anatomy_label = anatomy.get('label', 'Unknown')
             if anatomy.get('symbol') and len(anatomy.get('symbol', '')) > 0:
                 anatomy_label = anatomy.get('symbol')
+            # Decode URL-encoded strings from SOLR (e.g., ME%28R%29 -> ME(R))
+            anatomy_label = unquote(anatomy_label)
             anatomy_short_form = anatomy.get('short_form', '')
 
             row = {