Remove unused 'prefixes' parameter from get_subclasses and get_instances methods in OwleryClient

Author: Robbie1977

src/vfbquery/owlery_client.py

@@ -66,7 +66,7 @@ def __init__(self, owlery_endpoint: str = "http://owl.virtualflybrain.org/kbs/vf
         self.owlery_endpoint = owlery_endpoint.rstrip('/')
 
     def get_subclasses(self, query: str, query_by_label: bool = True, 
-                      verbose: bool = False, prefixes: bool = False, direct: bool = False) -> List[str]:
+                      verbose: bool = False, direct: bool = False) -> List[str]:
         """
         Query Owlery for subclasses matching an OWL class expression.
         
@@ -77,7 +77,6 @@ def get_subclasses(self, query: str, query_by_label: bool = True,
         :param query_by_label: If True, query uses label syntax (quotes). 
                                If False, uses IRI syntax (angle brackets).
         :param verbose: If True, print debug information
-        :param prefixes: If True, return full IRIs. If False, return short forms.
         :param direct: Return direct subclasses only. Default False.
         :return: List of class IDs (short forms like 'FBbt_00003748')
         """
@@ -187,7 +186,7 @@ def gen_short_form(iri):
             raise
 
     def get_instances(self, query: str, query_by_label: bool = True, 
-                     verbose: bool = False, prefixes: bool = False, direct: bool = False) -> List[str]:
+                     verbose: bool = False, direct: bool = False) -> List[str]:
         """
         Query Owlery for instances matching an OWL class expression.
         
@@ -198,7 +197,6 @@ def get_instances(self, query: str, query_by_label: bool = True,
         :param query_by_label: If True, query uses label syntax (quotes). 
                                If False, uses IRI syntax (angle brackets).
         :param verbose: If True, print debug information
-        :param prefixes: If True, return full IRIs. If False, return short forms.
         :param direct: Return direct instances only. Default False.
         :return: List of instance IDs (short forms like 'VFB_00101567')
         """

src/vfbquery/vfb_queries.py

@@ -3044,13 +3044,7 @@ def _owlery_query_to_results(owl_query_string: str, short_form: str, return_data
         params = {
             'object': owl_query_string,
             'direct': 'true' if query_instances else 'false',  # instances use direct=true, subclasses use direct=false
-            'includeDeprecated': 'false',
-            'prefixes': json.dumps({
-                "FBbt": "http://purl.obolibrary.org/obo/FBbt_",
-                "RO": "http://purl.obolibrary.org/obo/RO_",
-                "BFO": "http://purl.obolibrary.org/obo/BFO_",
-                "VFB": "http://virtualflybrain.org/reports/VFB_"
-            })
+            'includeDeprecated': 'false'
         }
 
         # For subclasses queries, add includeEquivalent parameter