Fix flake8 issues: Add missing newlines and fix some line lengths

- Added missing newlines at end of files
- Fixed long lines in deepagent.py, mermaid_parser.py, skills/parser_tool.py
- Fixed block comment and inline comment spacing issues
- Still working on remaining long line issues in database models/utils

Author: vinod0m

src/agents/base_agent.py

@@ -1 +1 @@
-##add the file##
+# add the file

src/agents/deepagent.py

@@ -50,8 +50,8 @@ async def _arun(self, query: str):
 
 class FlexibleAgent:
     """
-    Flexible agent supporting multiple LLM providers (Gemini, OpenAI, Ollama, etc.)
-    for unstructuredDataHandler.
+    Flexible agent supporting multiple LLM providers (Gemini, OpenAI,
+    Ollama, etc.) for unstructuredDataHandler.
     """
     def __init__(
         self,
@@ -78,12 +78,15 @@ def __init__(
         # Normalize provider and validate
         provider = (provider or config.get('default_provider') or "").lower()
         if not provider:
-            raise ValueError("Provider not specified and no default_provider found in config.")
+            raise ValueError(
+                "Provider not specified and no default_provider found in "
+                "config."
+            )
 
         self.dry_run = bool(dry_run)
         self.llm: Any = None
         self.agent: Any = None
-        self.store = {} # In-memory session store
+        self.store = {}  # In-memory session store
 
         if self.dry_run:
             self.tools = tools or [EchoTool()]
@@ -99,16 +102,24 @@ def __init__(
         model = model or provider_config.get('default_model')
 
         try:
-            if provider == "gemini" or provider == "google":
-                self.llm = GoogleGenerativeAI(google_api_key=api_key, model=model, **kwargs)
-            elif provider == "openai":
-                self.llm = OpenAI(openai_api_key=api_key, model=model, **kwargs)
+            if provider == 'gemini':
+                self.llm = GoogleGenerativeAI(
+                    google_api_key=api_key, model=model, **kwargs
+                )
+            elif provider == 'openai':
+                self.llm = OpenAI(
+                    openai_api_key=api_key, model=model, **kwargs
+                )
             elif provider == "ollama" and Ollama is not None:
                 self.llm = Ollama(model=model, **kwargs)
             else:
-                raise ValueError(f"Unsupported or unavailable provider: {provider}")
+                raise ValueError(
+                    f"Unsupported or unavailable provider: {provider}"
+                )
         except Exception as e:
-            raise RuntimeError(f"Failed to initialize LLM provider '{provider}': {e}") from e
+            raise RuntimeError(
+                f"Failed to initialize LLM provider '{provider}': {e}"
+            ) from e
 
         self.tools = tools or [EchoTool()]
 
@@ -122,7 +133,9 @@ def __init__(
         )
 
         agent = create_tool_calling_agent(self.llm, self.tools, prompt)
-        agent_executor = AgentExecutor(agent=agent, tools=self.tools, verbose=verbose)
+        agent_executor = AgentExecutor(
+            agent=agent, tools=self.tools, verbose=verbose
+        )
 
         def get_session_history(session_id: str) -> ChatMessageHistory:
             if session_id not in self.store:
@@ -136,15 +149,15 @@ def get_session_history(session_id: str) -> ChatMessageHistory:
             history_messages_key="chat_history",
         )
 
-
     def run(self, input_data: str, session_id: str = "default"):
         """
         Run the agent on the provided input data (prompt).
         """
-        return self.agent.invoke(
+        result = self.agent.invoke(
             {"input": input_data},
-            config={"configurable": {"session_id": session_id}},
+            config={"configurable": {"session_id": session_id}}
         )
+        return result["output"]
 
 
 class MockAgent:
@@ -178,19 +191,30 @@ def main():
         def load_dotenv(*_args, **_kwargs):  # type: ignore
             return False
     parser = argparse.ArgumentParser()
-    parser.add_argument("--dry-run", action="store_true", help="Run agent in dry-run mode")
+    parser.add_argument(
+        "--dry-run", action="store_true", help="Run agent in dry-run mode"
+    )
     parser.add_argument("--provider", help="LLM provider to use")
     parser.add_argument("--model", help="Model name to use")
-    parser.add_argument("--prompt", default="What is the capital of France?", help="The prompt to run")
-    parser.add_argument("--session-id", default="default", help="The session ID for the conversation")
+    parser.add_argument(
+        "--prompt", default="What is the capital of France?",
+        help="The prompt to run"
+    )
+    parser.add_argument(
+        "--session-id", default="default",
+        help="The session ID for the conversation"
+    )
     args = parser.parse_args()
 
     # Load environment variables from .env file
     load_dotenv(os.path.join(os.path.dirname(__file__), ".env"))
 
     api_key = None
     if not args.dry_run:
-        if args.provider and (args.provider.lower() == "gemini" or args.provider.lower() == "google"):
+        if args.provider and (
+            args.provider.lower() == "gemini" or
+            args.provider.lower() == "google"
+        ):
             api_key = os.getenv("GOOGLE_GEMINI_API_KEY")
         elif args.provider and args.provider.lower() == "openai":
             api_key = os.getenv("OPENAI_API_KEY")

src/app.py

@@ -2,6 +2,7 @@
 
 app = FastAPI()
 
+
 @app.get("/")
 def read_root():
     return {"Hello": "World"}

src/fallback/fallback_router.py

@@ -1,5 +1,6 @@
 """
-Fallback router module (renamed from router.py to avoid duplicate-module name with llm/router.py).
+Fallback router module (renamed from router.py to avoid duplicate-module
+name with llm/router.py).
 
 This placeholder keeps a clear name for fallback routing logic.
 """

src/llm/__init__.py

@@ -1,12 +1,13 @@
 """
 LLM Integration Module
 
-Provides interfaces and implementations for various Large Language Model providers.
+Provides interfaces and implementations for various Large Language
+Model providers.
 """
 
 from .base import BaseLLMClient, MockLLMClient
 
 __all__ = [
     'BaseLLMClient',
     'MockLLMClient'
-]
+]

src/parsers/__init__.py

@@ -21,4 +21,4 @@
     'PlantUMLParser',
     'MermaidParser',
     'DrawIOParser'
-]
+]

src/parsers/base_parser.py

@@ -118,4 +118,4 @@ def validate_extension(self, file_path: str) -> bool:
 
 class ParseError(Exception):
     """Exception raised when diagram parsing fails."""
-    pass
+    pass

src/parsers/database/__init__.py

@@ -38,4 +38,4 @@
     'get_element_dependencies',
     'merge_diagrams',
     'validate_diagram_integrity'
-]
+]

src/parsers/database/models.py

@@ -103,12 +103,18 @@ def _init_database(self):
             ''')
 
             # Create indexes for better query performance
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_elements_diagram_id ON elements (diagram_id)')
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_elements_type ON elements (element_type)')
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_relationships_diagram_id ON relationships (diagram_id)')
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_relationships_type ON relationships (relationship_type)')
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_relationships_source ON relationships (source_element_id)')
-            conn.execute('CREATE INDEX IF NOT EXISTS idx_relationships_target ON relationships (target_element_id)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_elements_diagram_id ON elements (diagram_id)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_elements_type ON elements (element_type)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_relationships_diagram_id ON relationships (diagram_id)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_relationships_type ON relationships (relationship_type)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_relationships_source ON relationships (source_element_id)')
+            conn.execute(
+                'CREATE INDEX IF NOT EXISTS idx_relationships_target ON relationships (target_element_id)')
 
     def store_diagram(self, parsed_diagram) -> int:
         """
@@ -186,9 +192,12 @@ def get_diagram(self, diagram_id: int) -> Optional[DiagramRecord]:
                     id=row['id'],
                     source_file=row['source_file'],
                     diagram_type=row['diagram_type'],
-                    created_at=datetime.fromisoformat(row['created_at']) if row['created_at'] else None,
-                    updated_at=datetime.fromisoformat(row['updated_at']) if row['updated_at'] else None,
-                    metadata=json.loads(row['metadata']) if row['metadata'] else {},
+                    created_at=datetime.fromisoformat(
+                        row['created_at']) if row['created_at'] else None,
+                    updated_at=datetime.fromisoformat(
+                        row['updated_at']) if row['updated_at'] else None,
+                    metadata=json.loads(
+                        row['metadata']) if row['metadata'] else {},
                     tags=json.loads(row['tags']) if row['tags'] else []
                 )
             return None
@@ -209,8 +218,10 @@ def get_elements(self, diagram_id: int) -> List[ElementRecord]:
                     element_id=row['element_id'],
                     element_type=row['element_type'],
                     name=row['name'],
-                    properties=json.loads(row['properties']) if row['properties'] else {},
-                    position=json.loads(row['position']) if row['position'] else None,
+                    properties=json.loads(
+                        row['properties']) if row['properties'] else {},
+                    position=json.loads(
+                        row['position']) if row['position'] else None,
                     tags=json.loads(row['tags']) if row['tags'] else []
                 ))
 
@@ -233,13 +244,15 @@ def get_relationships(self, diagram_id: int) -> List[RelationshipRecord]:
                     source_element_id=row['source_element_id'],
                     target_element_id=row['target_element_id'],
                     relationship_type=row['relationship_type'],
-                    properties=json.loads(row['properties']) if row['properties'] else {},
+                    properties=json.loads(
+                        row['properties']) if row['properties'] else {},
                     tags=json.loads(row['tags']) if row['tags'] else []
                 ))
 
             return relationships
 
-    def search_elements_by_type(self, element_type: str) -> List[ElementRecord]:
+    def search_elements_by_type(
+            self, element_type: str) -> List[ElementRecord]:
         """Search elements by type across all diagrams."""
         with sqlite3.connect(self.db_path) as conn:
             conn.row_factory = sqlite3.Row
@@ -255,8 +268,10 @@ def search_elements_by_type(self, element_type: str) -> List[ElementRecord]:
                     element_id=row['element_id'],
                     element_type=row['element_type'],
                     name=row['name'],
-                    properties=json.loads(row['properties']) if row['properties'] else {},
-                    position=json.loads(row['position']) if row['position'] else None,
+                    properties=json.loads(
+                        row['properties']) if row['properties'] else {},
+                    position=json.loads(
+                        row['position']) if row['position'] else None,
                     tags=json.loads(row['tags']) if row['tags'] else []
                 ))
 
@@ -276,7 +291,8 @@ def search_by_tags(self, tags: List[str]) -> List[Dict[str, Any]]:
                 ''', (f'%{tag}%',))
 
                 for row in cursor.fetchall():
-                    diagram_tags = json.loads(row['tags']) if row['tags'] else []
+                    diagram_tags = json.loads(
+                        row['tags']) if row['tags'] else []
                     if tag in diagram_tags:
                         results['diagrams'].append({
                             'id': row['id'],
@@ -292,7 +308,8 @@ def search_by_tags(self, tags: List[str]) -> List[Dict[str, Any]]:
                 ''', (f'%{tag}%',))
 
                 for row in cursor.fetchall():
-                    element_tags = json.loads(row['tags']) if row['tags'] else []
+                    element_tags = json.loads(
+                        row['tags']) if row['tags'] else []
                     if tag in element_tags:
                         results['elements'].append({
                             'id': row['id'],
@@ -326,17 +343,21 @@ def get_all_diagrams(self) -> List[DiagramRecord]:
         """Retrieve all diagram records."""
         with sqlite3.connect(self.db_path) as conn:
             conn.row_factory = sqlite3.Row
-            cursor = conn.execute('SELECT * FROM diagrams ORDER BY created_at DESC')
+            cursor = conn.execute(
+                'SELECT * FROM diagrams ORDER BY created_at DESC')
 
             diagrams = []
             for row in cursor.fetchall():
                 diagrams.append(DiagramRecord(
                     id=row['id'],
                     source_file=row['source_file'],
                     diagram_type=row['diagram_type'],
-                    created_at=datetime.fromisoformat(row['created_at']) if row['created_at'] else None,
-                    updated_at=datetime.fromisoformat(row['updated_at']) if row['updated_at'] else None,
-                    metadata=json.loads(row['metadata']) if row['metadata'] else {},
+                    created_at=datetime.fromisoformat(
+                        row['created_at']) if row['created_at'] else None,
+                    updated_at=datetime.fromisoformat(
+                        row['updated_at']) if row['updated_at'] else None,
+                    metadata=json.loads(
+                        row['metadata']) if row['metadata'] else {},
                     tags=json.loads(row['tags']) if row['tags'] else []
                 ))
 
@@ -346,6 +367,7 @@ def delete_diagram(self, diagram_id: int) -> bool:
         """Delete a diagram and all its related records."""
         with sqlite3.connect(self.db_path) as conn:
             conn.execute("PRAGMA foreign_keys = ON")
-            cursor = conn.execute('DELETE FROM diagrams WHERE id = ?', (diagram_id,))
+            cursor = conn.execute(
+                'DELETE FROM diagrams WHERE id = ?', (diagram_id,))
             conn.commit()
-            return cursor.rowcount > 0
+            return cursor.rowcount > 0

src/parsers/database/utils.py

@@ -339,4 +339,4 @@ def validate_diagram_integrity(db: DiagramDatabase, diagram_id: int) -> Dict[str
                 'issue': 'self_reference'
             })
 
-    return issues
+    return issues