tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/compose_scripts/tool_metadata_generator.py

@@ -3,15 +3,16 @@ Tool Metadata Generation Pipeline
 Generates comprehensive metadata for a list of tools by extracting details from their configuration files
 """
 
+
 def compose(arguments, tooluniverse, call_tool):
     """
     Main composition function for Tool Metadata Generation
-    
+
     Args:
         arguments (dict): Input arguments containing a list of tool config JSONs as well as a tool_type_mappings dict for non-API tools (e.g., {'Databases': ['XMLTool']})
         tooluniverse: ToolUniverse instance
         call_tool: Function to call other tools
-        
+
     Returns:
         list: List of tool metadata dictionaries (JSON-compatible)
     """
@@ -26,23 +27,27 @@ def compose(arguments, tooluniverse, call_tool):
             try:
                 return json.loads(output)
             except json.JSONDecodeError:
-                print(f"Failed to parse JSON string from {tool_name}; received: {output[:200]}")
-                return {} # Return empty dict on failure to prevent crash
-        
-        if isinstance(output, dict) and 'success' in output and 'result' in output:
+                print(
+                    f"Failed to parse JSON string from {tool_name}; received: {output[:200]}"
+                )
+                return {}  # Return empty dict on failure to prevent crash
+
+        if isinstance(output, dict) and "success" in output and "result" in output:
             # Handle wrapped output like {'success': True, 'result': '{...}'}
-            inner_result = output.get('result')
+            inner_result = output.get("result")
             if isinstance(inner_result, str) and inner_result.strip():
                 try:
                     return json.loads(inner_result)
                 except json.JSONDecodeError:
-                    print(f"Failed to parse inner result JSON from {tool_name}; using empty metadata.")
+                    print(
+                        f"Failed to parse inner result JSON from {tool_name}; using empty metadata."
+                    )
                     return {}
             elif isinstance(inner_result, dict):
-                return inner_result # Result is already a dict
+                return inner_result  # Result is already a dict
             else:
-                return {} # No valid inner result
-        
+                return {}  # No valid inner result
+
         return {}
 
     DEFAULT_TOOL_TYPE_MAPPINGS = {
@@ -50,26 +55,54 @@ def compose(arguments, tooluniverse, call_tool):
         "Database": ["XMLTool", "DatasetTool"],
         "Scientific Software Package": ["PackageTool"],
         "AI Agent": ["AgenticTool"],
-        "ML Model": ["ADMETAITool","AlphaFoldRESTTool","boltz2_docking","compute_depmap24q2_gene_correlations","run_compass_prediction","run_pinnacle_ppi_retrieval","run_transcriptformer_embedding_retrieval","get_abstract_from_patent_app_number","get_claims_from_patent_app_number","get_full_text_from_patent_app_number"],
-        "Human Expert Feedback": ["mcp_auto_loader_human_expert","consult_human_expert","get_expert_response","get_expert_status","list_pending_expert_requests","submit_expert_response"],
-        "MCP": ["MCPAutoLoaderTool","MCPClientTool","MCPProxyTool"],
+        "ML Model": [
+            "ADMETAITool",
+            "AlphaFoldRESTTool",
+            "boltz2_docking",
+            "compute_depmap24q2_gene_correlations",
+            "run_compass_prediction",
+            "run_pinnacle_ppi_retrieval",
+            "run_transcriptformer_embedding_retrieval",
+            "get_abstract_from_patent_app_number",
+            "get_claims_from_patent_app_number",
+            "get_full_text_from_patent_app_number",
+        ],
+        "Human Expert Feedback": [
+            "mcp_auto_loader_human_expert",
+            "consult_human_expert",
+            "get_expert_response",
+            "get_expert_status",
+            "list_pending_expert_requests",
+            "submit_expert_response",
+        ],
+        "MCP": ["MCPAutoLoaderTool", "MCPClientTool", "MCPProxyTool"],
         "Compositional Tool": ["ComposeTool"],
-        "Tool Finder Tool": ["ToolFinderEmbedding","ToolFinderLLM","ToolFinderKeyword"],
-        "Special Tool": ["Finish","CallAgent"]
+        "Tool Finder Tool": [
+            "ToolFinderEmbedding",
+            "ToolFinderLLM",
+            "ToolFinderKeyword",
+        ],
+        "Special Tool": ["Finish", "CallAgent"],
     }
 
     # Step 0: Parse inputs and set up variables
-    tool_configs = arguments.get('tool_configs', [])
-    tool_type_mappings = arguments.get('tool_type_mappings', {})
-    add_existing_tooluniverse_labels = arguments.get('add_existing_tooluniverse_labels', True)
-    max_new_tooluniverse_labels = arguments.get('max_new_tooluniverse_labels', 0)
+    tool_configs = arguments.get("tool_configs", [])
+    tool_type_mappings = arguments.get("tool_type_mappings", {})
+    add_existing_tooluniverse_labels = arguments.get(
+        "add_existing_tooluniverse_labels", True
+    )
+    max_new_tooluniverse_labels = arguments.get("max_new_tooluniverse_labels", 0)
 
     # Merge tool type mappings with defaults, prioritizing user-provided mappings
     for key, value in DEFAULT_TOOL_TYPE_MAPPINGS.items():
         if key not in tool_type_mappings:
             tool_type_mappings[key] = value
-    warnings.warn("Warning: Augmenting your provided tool_type_mappings with default tool_type_mappings to ensure compatibility with existing ToolUniverse tools. The default tool_type_mappings are:\n" + json.dumps(DEFAULT_TOOL_TYPE_MAPPINGS, indent=4))
-    
+    warnings.warn(
+        "Warning: Augmenting your provided tool_type_mappings with default tool_type_mappings to ensure compatibility with existing ToolUniverse tools. The default tool_type_mappings are:\n"
+        + json.dumps(DEFAULT_TOOL_TYPE_MAPPINGS, indent=4),
+        stacklevel=2,
+    )
+
     # Add existing ToolUniverse labels if specified
     tool_labels_set = set()
     if add_existing_tooluniverse_labels:
@@ -82,23 +115,27 @@ def compose(arguments, tooluniverse, call_tool):
                 import importlib_resources  # type: ignore
 
             # Access the JSON file inside the package (tooluniverse/website_data/v3_standardized_tags.json)
-            json_path = importlib_resources.files('tooluniverse.website_data').joinpath('v3_standardized_tags.json')
-            with json_path.open('r', encoding='utf-8') as f:
+            json_path = importlib_resources.files("tooluniverse.website_data").joinpath(
+                "v3_standardized_tags.json"
+            )
+            with json_path.open("r", encoding="utf-8") as f:
                 existing_metadata_list = json.load(f)
 
             if isinstance(existing_metadata_list, list):
                 for item in existing_metadata_list:
                     if isinstance(item, dict):
-                        tags = item.get('tags', [])
+                        tags = item.get("tags", [])
                         if isinstance(tags, list):
                             for tag in tags:
                                 if isinstance(tag, str) and tag.strip():
                                     tool_labels_set.add(tag.strip())
-        except Exception as e:  # Fail gracefully; downstream logic will just proceed without enrichment
+        except (
+            Exception
+        ) as e:  # Fail gracefully; downstream logic will just proceed without enrichment
             print(f"Failed to load existing ToolUniverse labels: {e}")
 
     if not tool_configs:
-        return [] 
+        return []
 
     # Step 1: Generate detailed metadata for each tool
     all_tool_metadata = []
@@ -106,66 +143,90 @@ def compose(arguments, tooluniverse, call_tool):
         tool_config_str = json.dumps(tool_config)
         try:
             metadata_params = {
-                'tool_config': tool_config_str,
-                'tool_type_mappings': tool_type_mappings
+                "tool_config": tool_config_str,
+                "tool_type_mappings": tool_type_mappings,
             }
             generated_metadata = {}
             for _ in range(5):  # Retry up to 5 times
-                raw_output = call_tool('ToolMetadataGenerator', metadata_params)
-                generated_metadata = _parse_agent_output(raw_output, 'ToolMetadataGenerator')
+                raw_output = call_tool("ToolMetadataGenerator", metadata_params)
+                generated_metadata = _parse_agent_output(
+                    raw_output, "ToolMetadataGenerator"
+                )
                 if generated_metadata:  # If the result is not empty, break
                     break
             # Attempt to enrich tags using LabelGenerator if tags are empty or default
             try:
                 # Prepare inputs for LabelGenerator
-                tool_name = tool_config.get('name') or generated_metadata.get('name') or ''
-                tool_description = tool_config.get('description') or generated_metadata.get('description') or ''
+                tool_name = (
+                    tool_config.get("name") or generated_metadata.get("name") or ""
+                )
+                tool_description = (
+                    tool_config.get("description")
+                    or generated_metadata.get("description")
+                    or ""
+                )
                 # The parameter schema may be nested under parameter->properties
-                param_properties = tool_config.get('parameter', {}).get('properties', {})
+                param_properties = tool_config.get("parameter", {}).get(
+                    "properties", {}
+                )
+
                 # Convert parameters to a JSON-like string representation (without importing json to keep dependencies minimal)
                 # Safe string construction
                 def _stringify_params(props):
                     parts = []
                     for k, v in props.items():
                         if isinstance(v, dict):
-                            type_val = v.get('type', 'unknown')
-                            desc_val = v.get('description', '')
-                            parts.append(f"\"{k}\": {{ 'type': '{type_val}', 'description': '{desc_val}' }}")
+                            type_val = v.get("type", "unknown")
+                            desc_val = v.get("description", "")
+                            parts.append(
+                                f"\"{k}\": {{ 'type': '{type_val}', 'description': '{desc_val}' }}"
+                            )
                         else:
-                            parts.append(f"\"{k}\": " + repr(v))
-                    return '{' + ', '.join(parts) + '}'
+                            parts.append(f'"{k}": ' + repr(v))
+                    return "{" + ", ".join(parts) + "}"
 
                 tool_parameters_str = _stringify_params(param_properties)
-                category = tool_config.get('category') or tool_config.get('type') or generated_metadata.get('category') or ''
+                category = (
+                    tool_config.get("category")
+                    or tool_config.get("type")
+                    or generated_metadata.get("category")
+                    or ""
+                )
 
                 label_params = {
-                    'tool_name': tool_name,
-                    'tool_description': tool_description,
-                    'tool_parameters': tool_parameters_str,
-                    'category': category,
-                    'existing_labels': json.dumps(list(tool_labels_set))
+                    "tool_name": tool_name,
+                    "tool_description": tool_description,
+                    "tool_parameters": tool_parameters_str,
+                    "category": category,
+                    "existing_labels": json.dumps(list(tool_labels_set)),
                 }
-                label_result = call_tool('LabelGenerator', label_params)
-                label_result = _parse_agent_output(label_result, 'LabelGenerator')
+                label_result = call_tool("LabelGenerator", label_params)
+                label_result = _parse_agent_output(label_result, "LabelGenerator")
 
                 # Parse label_result which may be dict or JSON string
                 labels = []
                 if isinstance(label_result, dict):
-                    labels = label_result.get('labels', [])
+                    labels = label_result.get("labels", [])
                 # Replace tags
                 if labels:
-                    generated_metadata['tags'] = labels
+                    generated_metadata["tags"] = labels
             except Exception as tag_exc:
-                print(f"Label generation failed for tool {tool_config.get('name', 'N/A')}: {tag_exc}")
+                print(
+                    f"Label generation failed for tool {tool_config.get('name', 'N/A')}: {tag_exc}"
+                )
 
             all_tool_metadata.append(generated_metadata)
         except Exception as e:
-            print(f"Failed to generate metadata for tool {tool_config.get('name', 'N/A')}: {e}")
+            print(
+                f"Failed to generate metadata for tool {tool_config.get('name', 'N/A')}: {e}"
+            )
             # Optionally, append an error object or skip the tool
-            all_tool_metadata.append({
-                'error': f"Metadata generation failed for {tool_config.get('name', 'N/A')}",
-                'details': str(e)
-            })
+            all_tool_metadata.append(
+                {
+                    "error": f"Metadata generation failed for {tool_config.get('name', 'N/A')}",
+                    "details": str(e),
+                }
+            )
 
     # Step 2: Validate schema
     validated_metadata = []
@@ -188,11 +249,11 @@ def compose(arguments, tooluniverse, call_tool):
         "parameters": {},
         "inputSchema": {},
         "exampleInput": {},
-        "apiEndpoints": []
+        "apiEndpoints": [],
     }
 
     for metadata in all_tool_metadata:
-        if 'error' in metadata:
+        if "error" in metadata:
             validated_metadata.append(metadata)
             continue
 
@@ -210,23 +271,27 @@ def compose(arguments, tooluniverse, call_tool):
                 elif isinstance(default_value, bool) and not isinstance(value, bool):
                     value = bool(value)
                 else:
-                    value = default_value # Fallback to default if type is complex/unexpected
+                    value = default_value  # Fallback to default if type is complex/unexpected
             validated_item[key] = value
         validated_metadata.append(validated_item)
-    
+
     all_tool_metadata = validated_metadata
 
     # Step 3: Standardize sources and tags using ToolMetadataStandardizer
     try:
         source_list = []
         for tool in all_tool_metadata:
-            if 'error' not in tool and tool.get('source'):
-                source_list.append(tool.get('source'))
+            if "error" not in tool and tool.get("source"):
+                source_list.append(tool.get("source"))
         # Standardize sources
         if source_list:
-            standardizer_params = {'metadata_list': list(set(source_list))}
-            standardized_sources_map = call_tool('ToolMetadataStandardizer', standardizer_params)
-            standardized_sources_map = _parse_agent_output(standardized_sources_map, 'ToolMetadataStandardizer')
+            standardizer_params = {"metadata_list": list(set(source_list))}
+            standardized_sources_map = call_tool(
+                "ToolMetadataStandardizer", standardizer_params
+            )
+            standardized_sources_map = _parse_agent_output(
+                standardized_sources_map, "ToolMetadataStandardizer"
+            )
             print("Standardized sources mapping:", standardized_sources_map)
 
             # Create a reverse map for easy lookup
@@ -234,33 +299,43 @@ def compose(arguments, tooluniverse, call_tool):
             for standard_name, raw_names in standardized_sources_map.items():
                 for raw_name in raw_names:
                     source_to_standard_map[raw_name] = standard_name
-            
+
             # Update the source in each metadata object
             for tool_metadata in all_tool_metadata:
-                if 'error' not in tool_metadata:
-                    original_source = tool_metadata.get('source')
+                if "error" not in tool_metadata:
+                    original_source = tool_metadata.get("source")
                     if original_source in source_to_standard_map:
-                        tool_metadata['source'] = source_to_standard_map[original_source]
+                        tool_metadata["source"] = source_to_standard_map[
+                            original_source
+                        ]
     except Exception as e:
         print(f"An error occurred during source standardization: {e}")
-    
+
     try:
         # Step 4: Standardize tags, with an optional second pass to meet label limits
         all_raw_tags = []
         for tool in all_tool_metadata:
-            if 'error' not in tool and isinstance(tool.get('tags'), list):
-                all_raw_tags.extend(tool.get('tags', []))
-        
+            if "error" not in tool and isinstance(tool.get("tags"), list):
+                all_raw_tags.extend(tool.get("tags", []))
+
         # Filter out existing labels before standardization
-        tags_to_standardize = [tag for tag in set(all_raw_tags) if tag not in tool_labels_set]
+        tags_to_standardize = [
+            tag for tag in set(all_raw_tags) if tag not in tool_labels_set
+        ]
         if max_new_tooluniverse_labels <= 0:
             # If no new labels are allowed, skip standardization and just remove new tags
             for tool_metadata in all_tool_metadata:
-                if 'error' not in tool_metadata and isinstance(tool_metadata.get('tags'), list):
-                    original_tags = tool_metadata.get('tags', [])
-                    filtered_tags = [tag for tag in original_tags if tag in tool_labels_set]
-                    tool_metadata['tags'] = sorted(list(set(filtered_tags)))
-            return all_tool_metadata  # Return early since no further processing is needed
+                if "error" not in tool_metadata and isinstance(
+                    tool_metadata.get("tags"), list
+                ):
+                    original_tags = tool_metadata.get("tags", [])
+                    filtered_tags = [
+                        tag for tag in original_tags if tag in tool_labels_set
+                    ]
+                    tool_metadata["tags"] = sorted(list(set(filtered_tags)))
+            return (
+                all_tool_metadata  # Return early since no further processing is needed
+            )
 
         tag_to_standard_map = {}
         if tags_to_standardize:
@@ -269,23 +344,32 @@ def compose(arguments, tooluniverse, call_tool):
             # This map will store the final standardized version for each original raw tag.
             tag_to_standard_map = {tag: tag for tag in tags_to_standardize}
 
-            for i in range(5): # Loop for up to 5 standardization passes
+            for i in range(5):  # Loop for up to 5 standardization passes
                 num_tags = len(current_tags_to_standardize)
-                
+
                 # If the number of tags is within the limit, no more standardization is needed.
-                if max_new_tooluniverse_labels > 0 and num_tags <= max_new_tooluniverse_labels:
-                    print(f"Tag count ({num_tags}) is within the limit ({max_new_tooluniverse_labels}). Stopping standardization.")
+                if (
+                    max_new_tooluniverse_labels > 0
+                    and num_tags <= max_new_tooluniverse_labels
+                ):
+                    print(
+                        f"Tag count ({num_tags}) is within the limit ({max_new_tooluniverse_labels}). Stopping standardization."
+                    )
                     break
-                
+
                 print(f"Pass {i+1}: Standardizing {num_tags} tags.")
-                
+
                 # Set the limit for the standardizer tool.
                 # Use a default high limit if max_new_tooluniverse_labels is not set, otherwise use the specified limit.
-                limit = max_new_tooluniverse_labels if max_new_tooluniverse_labels > 0 else 150
+                limit = (
+                    max_new_tooluniverse_labels
+                    if max_new_tooluniverse_labels > 0
+                    else 150
+                )
 
                 standardizer_params = {
-                    'metadata_list': current_tags_to_standardize,
-                    'limit': limit
+                    "metadata_list": current_tags_to_standardize,
+                    "limit": limit,
                 }
 
                 print(f"Pass {i+1} input tags: ", current_tags_to_standardize)
@@ -293,8 +377,12 @@ def compose(arguments, tooluniverse, call_tool):
                 # Call the standardizer tool and parse the output, with retries.
                 pass_output_map = {}
                 for _ in range(5):  # Retry up to 5 times
-                    raw_output = call_tool('ToolMetadataStandardizer', standardizer_params)
-                    pass_output_map = _parse_agent_output(raw_output, 'ToolMetadataStandardizer')
+                    raw_output = call_tool(
+                        "ToolMetadataStandardizer", standardizer_params
+                    )
+                    pass_output_map = _parse_agent_output(
+                        raw_output, "ToolMetadataStandardizer"
+                    )
                     if pass_output_map:  # If the result is not empty, break
                         break
 
@@ -312,7 +400,9 @@ def compose(arguments, tooluniverse, call_tool):
                 for original_tag, current_standard_tag in tag_to_standard_map.items():
                     # If the current standard tag was part of this pass's input and got re-mapped, update it.
                     if current_standard_tag in pass_reverse_map:
-                        tag_to_standard_map[original_tag] = pass_reverse_map[current_standard_tag]
+                        tag_to_standard_map[original_tag] = pass_reverse_map[
+                            current_standard_tag
+                        ]
 
                 # The new set of tags for the next pass are the keys of the current pass's output.
                 current_tags_to_standardize = sorted(list(pass_output_map.keys()))
@@ -324,16 +414,20 @@ def compose(arguments, tooluniverse, call_tool):
 
             # Update tags in each metadata object using the final mapping
             for tool_metadata in all_tool_metadata:
-                if 'error' not in tool_metadata and isinstance(tool_metadata.get('tags'), list):
-                    original_tags = tool_metadata.get('tags', [])
+                if "error" not in tool_metadata and isinstance(
+                    tool_metadata.get("tags"), list
+                ):
+                    original_tags = tool_metadata.get("tags", [])
                     # For each original tag, use its standardized version if available, otherwise keep the original.
                     # This correctly handles tags that were already in tool_labels_set and thus not standardized.
-                    standardized_tags = {tag_to_standard_map.get(tag, tag) for tag in original_tags}
-                    tool_metadata['tags'] = sorted(list(standardized_tags))
+                    standardized_tags = {
+                        tag_to_standard_map.get(tag, tag) for tag in original_tags
+                    }
+                    tool_metadata["tags"] = sorted(list(standardized_tags))
 
     except Exception as e:
         print(f"An error occurred during tag standardization: {e}")
-    
+
     # Step 5: Remove tags that occur only once across the entire dataset,
     # but only for tags that are new (not pre-existing in tooluniverse)
     try:
@@ -341,8 +435,9 @@ def compose(arguments, tooluniverse, call_tool):
         all_new_tags_flat = [
             tag
             for tool_metadata in all_tool_metadata
-            if 'error' not in tool_metadata and isinstance(tool_metadata.get('tags'), list)
-            for tag in tool_metadata.get('tags', [])
+            if "error" not in tool_metadata
+            and isinstance(tool_metadata.get("tags"), list)
+            for tag in tool_metadata.get("tags", [])
             if tag not in tool_labels_set
         ]
 
@@ -351,25 +446,30 @@ def compose(arguments, tooluniverse, call_tool):
             new_tag_counts = Counter(all_new_tags_flat)
 
             # Identify new tags that appear more than once
-            new_tags_to_keep = {tag for tag, count in new_tag_counts.items() if count > 1}
+            new_tags_to_keep = {
+                tag for tag, count in new_tag_counts.items() if count > 1
+            }
 
             # Filter the tags in each tool's metadata
             for tool_metadata in all_tool_metadata:
-                if 'error' not in tool_metadata and isinstance(tool_metadata.get('tags'), list):
-                    original_tags = tool_metadata.get('tags', [])
+                if "error" not in tool_metadata and isinstance(
+                    tool_metadata.get("tags"), list
+                ):
+                    original_tags = tool_metadata.get("tags", [])
                     # Keep all pre-existing tags, and only new tags that appear more than once
                     filtered_tags = [
-                        tag for tag in original_tags
+                        tag
+                        for tag in original_tags
                         if tag in tool_labels_set or tag in new_tags_to_keep
                     ]
-                    tool_metadata['tags'] = sorted(list(set(filtered_tags)))
+                    tool_metadata["tags"] = sorted(list(set(filtered_tags)))
 
     except Exception as e:
         print(f"An error occurred during single-occurrence tag removal: {e}")
-    
+
     # Step 6: Manually set the UUID 'id' field to ensure true randomness
     for tool_metadata in all_tool_metadata:
-        if 'error' not in tool_metadata:
-            tool_metadata['id'] = str(uuid.uuid4())
+        if "error" not in tool_metadata:
+            tool_metadata["id"] = str(uuid.uuid4())
 
     return all_tool_metadata