aurelian 0.4.1__py3-none-any.whl → 0.4.2__py3-none-any.whl

aurelian/agents/ubergraph/ubergraph_tools.py

@@ -4,9 +4,9 @@ Tools for interacting with the UberGraph SPARQL endpoint.
 import asyncio
 from typing import Any, Dict, List, Optional
 
+import requests
 from pydantic import BaseModel
 from pydantic_ai import RunContext, ModelRetry
-from SPARQLWrapper import JSON, SPARQLWrapper
 
 from .ubergraph_config import Dependencies, get_config
 
@@ -88,13 +88,23 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
     print("##")
     
     try:
-        # Create SPARQL wrapper
-        sw = SPARQLWrapper(endpoint)
-        sw.setQuery(prefixed_query)
-        sw.setReturnFormat(JSON)
+        # Define a function to execute in a thread pool
+        def run_query():
+            response = requests.post(
+                endpoint,
+                data={
+                    'query': prefixed_query,
+                },
+                headers={
+                    'Accept': 'application/sparql-results+json',
+                    'Content-Type': 'application/x-www-form-urlencoded'
+                }
+            )
+            response.raise_for_status()  # Raise an exception for HTTP errors
+            return response.json()
         
         # Execute the query in a thread pool
-        ret = await asyncio.to_thread(sw.queryAndConvert)
+        ret = await asyncio.to_thread(run_query)
         
         # Process the results
         results = simplify_results(ret, prefixes, limit=config.max_results)
@@ -105,6 +115,8 @@ async def query_ubergraph(ctx: RunContext[Dependencies], query: str) -> QueryRes
             raise ModelRetry(f"No results found for SPARQL query. Try refining your query.")
             
         return QueryResults(results=results)
+    except requests.RequestException as e:
+        raise ModelRetry(f"Error connecting to SPARQL endpoint: {str(e)}")
     except Exception as e:
         if "ModelRetry" in str(type(e)):
             raise e

{aurelian-0.4.1.dist-info → aurelian-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: aurelian
-Version: 0.4.1
+Version: 0.4.2
 Summary: aurelian
 License: MIT
 Author: Author 1

{aurelian-0.4.1.dist-info → aurelian-0.4.2.dist-info}/RECORD

@@ -215,7 +215,7 @@ aurelian/agents/ubergraph/ubergraph_agent.py,sha256=dW1IG35w7OgNgC5SDgNFB6K2RJCs
 aurelian/agents/ubergraph/ubergraph_config.py,sha256=Fi2hFVu92v55IinNYFlLjdvt9THXtRFPkSEcXtTrC10,2774
 aurelian/agents/ubergraph/ubergraph_gradio.py,sha256=Gig_3AK0B4AkfvjlNklHkr87z2vcphll2I9DLgfdmdU,1372
 aurelian/agents/ubergraph/ubergraph_mcp.py,sha256=p_YbEkSF4yN0T5OJ8FKIkuOtutOYvFL3TJDtJydSnws,2475
-aurelian/agents/ubergraph/ubergraph_tools.py,sha256=9LLlOWXWu8crXCADpvzEJ0gQVNi9fuFYx8SkrDS175s,3428
+aurelian/agents/ubergraph/ubergraph_tools.py,sha256=OtyqOyRviuBInCuMwK5dn1jaFJRJIZq6QFImqK3uFWk,3909
 aurelian/agents/uniprot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aurelian/agents/uniprot/uniprot_agent.py,sha256=KMTRKGVpRpSchz7YEShh9ZSSGHzmeaGEUaNFKJPDWSI,1648
 aurelian/agents/uniprot/uniprot_config.py,sha256=YhL265Z0GnTeXINHawe5iMcpR2ETLmdY3XhNXcYIc8w,1404
@@ -259,8 +259,8 @@ aurelian/utils/pubmed_utils.py,sha256=Gk00lu1Lv0GRSNeF5M4zplp3UMSpe5byCaVKCJimUH
 aurelian/utils/pytest_report_to_markdown.py,sha256=WH1NlkVYj0UfUqpXjRD1KMpkMgEW3qev3fDdPvZG9Yw,1406
 aurelian/utils/robot_ontology_utils.py,sha256=aaRe9eyLgJCtj1EfV13v4Q7khFTWzUoFFEE_lizGuGg,3591
 aurelian/utils/search_utils.py,sha256=9MloT3SzOE4JsElsYlCznp9N6fv_OQK7YWOU8MIy1WU,2818
-aurelian-0.4.1.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
-aurelian-0.4.1.dist-info/METADATA,sha256=jQhaYsfYEvlpDSotKJrxSYgXLxprb_Ictzd33LVqbco,3557
-aurelian-0.4.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-aurelian-0.4.1.dist-info/entry_points.txt,sha256=EnGehbtRm0YmhdfwfcoGJjVG3Man-zgKvob20fTIBik,102
-aurelian-0.4.1.dist-info/RECORD,,
+aurelian-0.4.2.dist-info/LICENSE,sha256=FB6RpUUfbUeKS4goWrvpp1QmOtyywrMiNBsYPMlLT3A,1086
+aurelian-0.4.2.dist-info/METADATA,sha256=Wtded6_NxBHSXTCFxjUcXUrbLz00vOQgoy7xsHPM8YM,3557
+aurelian-0.4.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+aurelian-0.4.2.dist-info/entry_points.txt,sha256=EnGehbtRm0YmhdfwfcoGJjVG3Man-zgKvob20fTIBik,102
+aurelian-0.4.2.dist-info/RECORD,,