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Bug Fixes: Error Handling and Stability Improvements #108 #117

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86aae73
Enhance GitHub RAG application: Introduced retry mechanism for error …
chojuninengu Apr 29, 2025
bec6a16
Refactor session state management and repository loading in GitHub RA…
chojuninengu Apr 29, 2025
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332 changes: 207 additions & 125 deletions github-rag/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
import pandas as pd
from typing import Optional, Dict, Any
import logging
from functools import wraps
import time

from gitingest import ingest
from llama_index.core import Settings, PromptTemplate, VectorStoreIndex, SimpleDirectoryReader
Expand All @@ -13,51 +15,117 @@
from dotenv import load_dotenv

# Configure logging
logging.basicConfig(level=logging.INFO)
logging.basicConfig(
level=logging.INFO,
format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
)
logger = logging.getLogger(__name__)

Comment on lines +18 to 23
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🛠️ Refactor suggestion

Avoid duplicating log handlers on every Streamlit rerun

logging.basicConfig() gets executed on every Streamlit script rerun, which may attach multiple handlers and cause duplicated log lines.
Guard the configuration or add handlers only once:

-logging.basicConfig(
-    level=logging.INFO,
-    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
-)
-if not logger.handlers:
-    logger = logging.getLogger(__name__)
+logger = logging.getLogger(__name__)
+if not logger.handlers:
+    logging.basicConfig(
+        level=logging.INFO,
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+    )

Committable suggestion skipped: line range outside the PR's diff.

load_dotenv()

# Constants
MAX_REPO_SIZE = 100 * 1024 * 1024 # 100MB
SUPPORTED_REPO_TYPES = ['.py', '.md', '.ipynb', '.js', '.ts', '.json']
MAX_RETRIES = 3
RETRY_DELAY = 1 # seconds

class GitHubRAGError(Exception):
"""Custom exception for GitHub RAG application errors"""
"""Base exception for GitHub RAG application errors"""
pass

class ValidationError(GitHubRAGError):
"""Raised when input validation fails"""
pass

class ProcessingError(GitHubRAGError):
"""Raised when repository processing fails"""
pass

class QueryEngineError(GitHubRAGError):
"""Raised when query engine creation or operation fails"""
pass

class SessionError(GitHubRAGError):
"""Raised when session management fails"""
pass

def retry_on_error(max_retries=MAX_RETRIES, delay=RETRY_DELAY):
"""Decorator for retrying operations on failure"""
def decorator(func):
@wraps(func)
def wrapper(*args, **kwargs):
last_exception = None
for attempt in range(max_retries):
try:
return func(*args, **kwargs)
except Exception as e:
last_exception = e
if attempt < max_retries - 1:
logger.warning(f"Attempt {attempt + 1} failed: {str(e)}. Retrying...")
time.sleep(delay)
raise last_exception
return wrapper
return decorator

def validate_github_url(url: str) -> bool:
"""Validate GitHub repository URL"""
return url.startswith(('https://github.com/', 'http://github.com/'))
if not url:
raise ValidationError("Repository URL cannot be empty")
if not url.startswith(('https://github.com/', 'http://github.com/')):
raise ValidationError("Invalid GitHub URL format. URL must start with 'https://github.com/' or 'http://github.com/'")
return True

def get_repo_name(url: str) -> str:
"""Extract repository name from URL"""
try:
return url.split('/')[-1].replace('.git', '')
parts = url.split('/')
if len(parts) < 5:
raise ValidationError("Invalid repository URL format")
repo_name = parts[-1].replace('.git', '')
if not repo_name:
raise ValidationError("Could not extract repository name from URL")
return repo_name
except Exception as e:
raise ValidationError(f"Failed to extract repository name: {str(e)}")

Comment on lines 78 to +90
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⚠️ Potential issue

Handle trailing slashes and preserve exception context in get_repo_name

  1. URLs ending with a trailing slash (…/repo/) trigger a false “invalid format” error because parts[-1] is empty.
  2. except Exception as e: re-raises without from e, losing the stack.
-        repo_name = parts[-1].replace('.git', '')
+        repo_segment = parts[-1] or parts[-2]          # supports trailing “/”
+        repo_name = repo_segment.replace('.git', '')
@@
-    except Exception as e:
-        raise ValidationError(f"Failed to extract repository name: {str(e)}")
+    except Exception as e:
+        raise ValidationError(
+            f"Failed to extract repository name: {e}"
+        ) from e
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def get_repo_name(url: str) -> str:
"""Extract repository name from URL"""
try:
return url.split('/')[-1].replace('.git', '')
parts = url.split('/')
if len(parts) < 5:
raise ValidationError("Invalid repository URL format")
repo_name = parts[-1].replace('.git', '')
if not repo_name:
raise ValidationError("Could not extract repository name from URL")
return repo_name
except Exception as e:
raise ValidationError(f"Failed to extract repository name: {str(e)}")
def get_repo_name(url: str) -> str:
"""Extract repository name from URL"""
try:
parts = url.split('/')
if len(parts) < 5:
raise ValidationError("Invalid repository URL format")
- repo_name = parts[-1].replace('.git', '')
+ repo_segment = parts[-1] or parts[-2] # supports trailing “/”
+ repo_name = repo_segment.replace('.git', '')
if not repo_name:
raise ValidationError("Could not extract repository name from URL")
return repo_name
- except Exception as e:
- raise ValidationError(f"Failed to extract repository name: {str(e)}")
+ except Exception as e:
+ raise ValidationError(
+ f"Failed to extract repository name: {e}"
+ ) from e
🧰 Tools
🪛 Ruff (0.8.2)

89-89: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

def cleanup_session():
"""Clean up session resources"""
try:
if hasattr(st.session_state, 'file_cache'):
for key, value in st.session_state.file_cache.items():
try:
del value
except Exception as e:
logger.warning(f"Failed to cleanup cache entry {key}: {str(e)}")
st.session_state.file_cache.clear()
gc.collect()
logger.info("Session cleanup completed successfully")
except Exception as e:
raise GitHubRAGError(f"Invalid repository URL: {str(e)}")
logger.error(f"Error during session cleanup: {str(e)}")
raise SessionError(f"Failed to cleanup session: {str(e)}")

Comment on lines +91 to 106
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🛠️ Refactor suggestion

cleanup_session does not actually remove cached objects

del value only deletes the local reference, not the entry stored in st.session_state.file_cache.
Also adopt from e per Ruff B904.

-        if hasattr(st.session_state, 'file_cache'):
-            for key, value in st.session_state.file_cache.items():
-                try:
-                    del value
-                except Exception as e:
-                    logger.warning(f"Failed to cleanup cache entry {key}: {str(e)}")
-            st.session_state.file_cache.clear()
+        cache = getattr(st.session_state, "file_cache", {})
+        for key in list(cache.keys()):
+            try:
+                del cache[key]
+            except Exception as e:
+                logger.warning("Failed to cleanup cache entry %s: %s", key, e)
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def cleanup_session():
"""Clean up session resources"""
try:
if hasattr(st.session_state, 'file_cache'):
for key, value in st.session_state.file_cache.items():
try:
del value
except Exception as e:
logger.warning(f"Failed to cleanup cache entry {key}: {str(e)}")
st.session_state.file_cache.clear()
gc.collect()
logger.info("Session cleanup completed successfully")
except Exception as e:
raise GitHubRAGError(f"Invalid repository URL: {str(e)}")
logger.error(f"Error during session cleanup: {str(e)}")
raise SessionError(f"Failed to cleanup session: {str(e)}")
def cleanup_session():
"""Clean up session resources"""
try:
- if hasattr(st.session_state, 'file_cache'):
- for key, value in st.session_state.file_cache.items():
- try:
- del value
- except Exception as e:
- logger.warning(f"Failed to cleanup cache entry {key}: {str(e)}")
- st.session_state.file_cache.clear()
+ cache = getattr(st.session_state, "file_cache", {})
+ for key in list(cache.keys()):
+ try:
+ del cache[key]
+ except Exception as e:
+ logger.warning("Failed to cleanup cache entry %s: %s", key, e)
gc.collect()
logger.info("Session cleanup completed successfully")
except Exception as e:
- logger.error(f"Error during session cleanup: {str(e)}")
- raise SessionError(f"Failed to cleanup session: {str(e)}")
+ logger.error(f"Error during session cleanup: {str(e)}")
+ raise SessionError(f"Failed to cleanup session: {str(e)}") from e
🧰 Tools
🪛 Ruff (0.8.2)

105-105: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

def reset_chat():
"""Reset chat session and clean up resources"""
try:
st.session_state.messages = []
st.session_state.context = None
gc.collect()
cleanup_session()
logger.info("Chat session reset successfully")
except Exception as e:
logger.error(f"Error resetting chat: {str(e)}")
raise GitHubRAGError("Failed to reset chat session")
raise SessionError("Failed to reset chat session")

Comment on lines 107 to 117
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⚠️ Potential issue

reset_chat should also reset the loaded engine

After a reset the previous query_engine lingers in memory, allowing questions against a supposedly “cleared” session.

-        st.session_state.context = None
+        st.session_state.context = None
+        st.session_state.query_engine = None
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def reset_chat():
"""Reset chat session and clean up resources"""
try:
st.session_state.messages = []
st.session_state.context = None
gc.collect()
cleanup_session()
logger.info("Chat session reset successfully")
except Exception as e:
logger.error(f"Error resetting chat: {str(e)}")
raise GitHubRAGError("Failed to reset chat session")
raise SessionError("Failed to reset chat session")
def reset_chat():
"""Reset chat session and clean up resources"""
try:
st.session_state.messages = []
st.session_state.context = None
st.session_state.query_engine = None
cleanup_session()
logger.info("Chat session reset successfully")
except Exception as e:
logger.error(f"Error resetting chat: {str(e)}")
raise SessionError("Failed to reset chat session")
🧰 Tools
🪛 Ruff (0.8.2)

116-116: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling

(B904)

@retry_on_error()
def process_with_gitingets(github_url: str) -> tuple:
"""Process GitHub repository using gitingest"""
try:
summary, tree, content = ingest(github_url)
if not all([summary, tree, content]):
raise GitHubRAGError("Failed to process repository: Missing data")
raise ProcessingError("Failed to process repository: Missing data")
return summary, tree, content
except Exception as e:
logger.error(f"Error processing repository: {str(e)}")
raise GitHubRAGError(f"Failed to process repository: {str(e)}")
raise ProcessingError(f"Failed to process repository: {str(e)}")

def create_query_engine(content_path: str, repo_name: str) -> Any:
"""Create and configure query engine"""
Expand Down Expand Up @@ -97,130 +165,144 @@ def create_query_engine(content_path: str, repo_name: str) -> Any:
return query_engine
except Exception as e:
logger.error(f"Error creating query engine: {str(e)}")
raise GitHubRAGError(f"Failed to create query engine: {str(e)}")

# Initialize session state
if "id" not in st.session_state:
st.session_state.id = uuid.uuid4()
st.session_state.file_cache = {}
st.session_state.messages = []

session_id = st.session_state.id

# Sidebar
with st.sidebar:
st.header("Add your GitHub repository!")

github_url = st.text_input(
"Enter GitHub repository URL",
placeholder="https://github.com/username/repo",
help="Enter a valid GitHub repository URL"
)

load_repo = st.button("Load Repository", type="primary")

if github_url and load_repo:
try:
# Validate URL
if not validate_github_url(github_url):
st.error("Please enter a valid GitHub repository URL")
st.stop()

repo_name = get_repo_name(github_url)
file_key = f"{session_id}-{repo_name}"

if file_key not in st.session_state.file_cache:
with st.spinner("Processing your repository..."):
with tempfile.TemporaryDirectory() as temp_dir:
try:
summary, tree, content = process_with_gitingets(github_url)

# Write content to temporary file
content_path = os.path.join(temp_dir, f"{repo_name}_content.md")
with open(content_path, "w", encoding="utf-8") as f:
f.write(content)

# Create and cache query engine
query_engine = create_query_engine(temp_dir, repo_name)
st.session_state.file_cache[file_key] = query_engine

st.success("Repository loaded successfully! Ready to chat.")
logger.info(f"Successfully processed repository: {repo_name}")

except GitHubRAGError as e:
st.error(str(e))
logger.error(f"Error processing repository {repo_name}: {str(e)}")
st.stop()
except Exception as e:
st.error("An unexpected error occurred while processing the repository")
logger.error(f"Unexpected error: {str(e)}")
st.stop()
else:
st.info("Repository already loaded. Ready to chat!")

except Exception as e:
st.error(f"An error occurred: {str(e)}")
logger.error(f"Error in repository loading process: {str(e)}")
st.stop()

# Main content
col1, col2 = st.columns([6, 1])

with col1:
st.header("Chat with GitHub using RAG </>")

with col2:
st.button("Clear Chat ↺", on_click=reset_chat, help="Clear chat history and reset session")
raise QueryEngineError(f"Failed to create query engine: {str(e)}")

# Display chat history
for message in st.session_state.messages:
with st.chat_message(message["role"]):
st.markdown(message["content"])
def initialize_session_state():
"""Initialize or reset session state variables"""
try:
if 'messages' not in st.session_state:
st.session_state.messages = []
if 'context' not in st.session_state:
st.session_state.context = None
if 'file_cache' not in st.session_state:
st.session_state.file_cache = {}
if 'current_repo' not in st.session_state:
st.session_state.current_repo = None
if 'query_engine' not in st.session_state:
st.session_state.query_engine = None
logger.info("Session state initialized successfully")
except Exception as e:
logger.error(f"Error initializing session state: {str(e)}")
raise SessionError("Failed to initialize session state")

# Chat input
if prompt := st.chat_input("What's up?"):
def handle_repository_loading(github_url: str) -> None:
"""Handle repository loading process with proper error handling"""
try:
# Add user message to chat history
st.session_state.messages.append({"role": "user", "content": prompt})
validate_github_url(github_url)
repo_name = get_repo_name(github_url)

# Display user message
with st.chat_message("user"):
st.markdown(prompt)

# Process and display assistant response
with st.chat_message("assistant"):
message_placeholder = st.empty()
full_response = ""
with st.spinner(f"Processing repository {repo_name}..."):
summary, tree, content = process_with_gitingets(github_url)

try:
repo_name = get_repo_name(github_url)
file_key = f"{session_id}-{repo_name}"
query_engine = st.session_state.file_cache.get(file_key)
# Create temporary directory for repository content
with tempfile.TemporaryDirectory() as temp_dir:
content_path = os.path.join(temp_dir, repo_name)
os.makedirs(content_path, exist_ok=True)

if query_engine is None:
raise GitHubRAGError("Please load a repository first!")
# Save repository content
for file_path, file_content in content.items():
file_dir = os.path.dirname(os.path.join(content_path, file_path))
os.makedirs(file_dir, exist_ok=True)
with open(os.path.join(content_path, file_path), 'w', encoding='utf-8') as f:
f.write(file_content)

response = query_engine.query(prompt)
# Create query engine
query_engine = create_query_engine(content_path, repo_name)

if hasattr(response, 'response_gen'):
for chunk in response.response_gen:
if isinstance(chunk, str):
full_response += chunk
message_placeholder.markdown(full_response + "▌")
else:
full_response = str(response)
message_placeholder.markdown(full_response)

message_placeholder.markdown(full_response)
st.session_state.messages.append({"role": "assistant", "content": full_response})
# Update session state
st.session_state.query_engine = query_engine
st.session_state.current_repo = repo_name
st.session_state.context = {
'summary': summary,
'tree': tree,
'content': content
}

except GitHubRAGError as e:
st.error(str(e))
logger.error(f"Error in chat processing: {str(e)}")
except Exception as e:
st.error("An unexpected error occurred while processing your query")
logger.error(f"Unexpected error in chat: {str(e)}")
st.success(f"Successfully loaded repository: {repo_name}")
logger.info(f"Repository {repo_name} loaded successfully")

except ValidationError as e:
st.error(f"Validation error: {str(e)}")
logger.warning(f"Validation error for URL {github_url}: {str(e)}")
except ProcessingError as e:
st.error(f"Processing error: {str(e)}")
logger.error(f"Error processing repository {github_url}: {str(e)}")
except QueryEngineError as e:
st.error(f"Query engine error: {str(e)}")
logger.error(f"Error creating query engine for {github_url}: {str(e)}")
except Exception as e:
st.error(f"Unexpected error: {str(e)}")
logger.error(f"Unexpected error processing {github_url}: {str(e)}")
finally:
cleanup_session()

Comment on lines +194 to +238
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⚠️ Potential issue

Path-traversal & binary-file issues when writing repo content

  1. A malicious repo file path such as ../../etc/passwd escapes temp_dir.
  2. Opening files with 'w' fails on binary blobs.
-                for file_path, file_content in content.items():
-                    file_dir = os.path.dirname(os.path.join(content_path, file_path))
+                for file_path, file_content in content.items():
+                    safe_path = os.path.normpath(os.path.join(content_path, file_path))
+                    if not safe_path.startswith(content_path):
+                        logger.warning("Skipping suspicious path: %s", file_path)
+                        continue
+                    file_dir = os.path.dirname(safe_path)
@@
-                    with open(os.path.join(content_path, file_path), 'w', encoding='utf-8') as f:
-                        f.write(file_content)
+                    mode, kwargs = ('wb', {}) if isinstance(file_content, (bytes, bytearray)) else ('w', {'encoding': 'utf-8'})
+                    with open(safe_path, mode, **kwargs) as f:
+                        f.write(file_content)

This mitigates a critical security flaw and handles binary assets gracefully.

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
with st.spinner(f"Processing repository {repo_name}..."):
summary, tree, content = process_with_gitingets(github_url)
try:
repo_name = get_repo_name(github_url)
file_key = f"{session_id}-{repo_name}"
query_engine = st.session_state.file_cache.get(file_key)
# Create temporary directory for repository content
with tempfile.TemporaryDirectory() as temp_dir:
content_path = os.path.join(temp_dir, repo_name)
os.makedirs(content_path, exist_ok=True)
if query_engine is None:
raise GitHubRAGError("Please load a repository first!")
# Save repository content
for file_path, file_content in content.items():
file_dir = os.path.dirname(os.path.join(content_path, file_path))
os.makedirs(file_dir, exist_ok=True)
with open(os.path.join(content_path, file_path), 'w', encoding='utf-8') as f:
f.write(file_content)
response = query_engine.query(prompt)
# Create query engine
query_engine = create_query_engine(content_path, repo_name)
if hasattr(response, 'response_gen'):
for chunk in response.response_gen:
if isinstance(chunk, str):
full_response += chunk
message_placeholder.markdown(full_response + "▌")
else:
full_response = str(response)
message_placeholder.markdown(full_response)
message_placeholder.markdown(full_response)
st.session_state.messages.append({"role": "assistant", "content": full_response})
# Update session state
st.session_state.query_engine = query_engine
st.session_state.current_repo = repo_name
st.session_state.context = {
'summary': summary,
'tree': tree,
'content': content
}
except GitHubRAGError as e:
st.error(str(e))
logger.error(f"Error in chat processing: {str(e)}")
except Exception as e:
st.error("An unexpected error occurred while processing your query")
logger.error(f"Unexpected error in chat: {str(e)}")
st.success(f"Successfully loaded repository: {repo_name}")
logger.info(f"Repository {repo_name} loaded successfully")
except ValidationError as e:
st.error(f"Validation error: {str(e)}")
logger.warning(f"Validation error for URL {github_url}: {str(e)}")
except ProcessingError as e:
st.error(f"Processing error: {str(e)}")
logger.error(f"Error processing repository {github_url}: {str(e)}")
except QueryEngineError as e:
st.error(f"Query engine error: {str(e)}")
logger.error(f"Error creating query engine for {github_url}: {str(e)}")
except Exception as e:
st.error(f"Unexpected error: {str(e)}")
logger.error(f"Unexpected error processing {github_url}: {str(e)}")
finally:
cleanup_session()
with st.spinner(f"Processing repository {repo_name}..."):
summary, tree, content = process_with_gitingets(github_url)
# Create temporary directory for repository content
with tempfile.TemporaryDirectory() as temp_dir:
content_path = os.path.join(temp_dir, repo_name)
os.makedirs(content_path, exist_ok=True)
# Save repository content
for file_path, file_content in content.items():
safe_path = os.path.normpath(os.path.join(content_path, file_path))
if not safe_path.startswith(content_path):
logger.warning("Skipping suspicious path: %s", file_path)
continue
file_dir = os.path.dirname(safe_path)
os.makedirs(file_dir, exist_ok=True)
mode, kwargs = (
("wb", {})
if isinstance(file_content, (bytes, bytearray))
else ("w", {"encoding": "utf-8"})
)
with open(safe_path, mode, **kwargs) as f:
f.write(file_content)
# Create query engine
query_engine = create_query_engine(content_path, repo_name)
# Update session state
st.session_state.query_engine = query_engine
st.session_state.current_repo = repo_name
st.session_state.context = {
"summary": summary,
"tree": tree,
"content": content,
}
st.success(f"Successfully loaded repository: {repo_name}")
logger.info(f"Repository {repo_name} loaded successfully")
except ValidationError as e:
…
finally:
cleanup_session()

def handle_chat_message(prompt: str) -> None:
"""Handle chat message processing with proper error handling"""
try:
if not st.session_state.query_engine:
raise QueryEngineError("Please load a repository first!")

if not prompt.strip():
raise ValidationError("Please enter a non-empty message")

# Add user message to chat
st.session_state.messages.append({"role": "user", "content": prompt})

# Get response from query engine
response = st.session_state.query_engine.query(prompt)

# Format and display response
full_response = f"Repository: {st.session_state.current_repo}\n\n{response}"
st.session_state.messages.append({"role": "assistant", "content": full_response})

logger.info(f"Successfully processed chat message for repository {st.session_state.current_repo}")

except ValidationError as e:
st.error(f"Validation error: {str(e)}")
logger.warning(f"Chat validation error: {str(e)}")
except QueryEngineError as e:
st.error(f"Query engine error: {str(e)}")
logger.error(f"Error in chat processing: {str(e)}")
except Exception as e:
st.error("An error occurred in the chat system")
logger.error(f"Chat system error: {str(e)}")
st.error(f"Unexpected error: {str(e)}")
logger.error(f"Unexpected error in chat: {str(e)}")

def main():
"""Main application function"""
st.title("GitHub Repository RAG")

try:
# Initialize session state
initialize_session_state()

# Sidebar for repository input
with st.sidebar:
st.header("Repository Settings")
github_url = st.text_input("Enter GitHub Repository URL")

if st.button("Load Repository"):
if github_url:
handle_repository_loading(github_url)
else:
st.warning("Please enter a GitHub repository URL")

if st.button("Reset Chat"):
reset_chat()

# Main chat interface
for message in st.session_state.messages:
with st.chat_message(message["role"]):
st.write(message["content"])

if prompt := st.chat_input("Ask a question about the repository"):
handle_chat_message(prompt)

except SessionError as e:
st.error(f"Session error: {str(e)}")
logger.error(f"Session error in main: {str(e)}")
except Exception as e:
st.error(f"Unexpected error: {str(e)}")
logger.error(f"Unexpected error in main: {str(e)}")

if __name__ == "__main__":
main()