Refactor agent initialization and fix permission flow

[Rikul]

• Fix ask_permission logic in agent.py (was commented out, now properly implemented)
• Update main.py to use message queue for initial prompt delivery
• Remove obsolete ask_permission tests that no longer apply
• Improve code structure by separating prompt handling from agent logic

[gemini-code-assist]

Code Review

This pull request introduces file attachment and upload capabilities to the WebChannel, adds an LLM call tracing mechanism with a corresponding /trace command, and refactors database access to use a shared connection helper with WAL mode enabled. Feedback on the changes highlights a potential connection leak risk across several database operations in message_history.py and scheduled_tasks.py where exceptions could bypass conn.close(); wrapping these operations in try...finally blocks is recommended to ensure connections are reliably closed.

Important

The consumer version of Gemini Code Assist on GitHub is being sunset. Starting June 18, 2026, new organization installations will be blocked, and all code review activity will officially cease on July 17, 2026.
For more details on the timeline and next steps, please review the Help Documentation.

[gemini-code-assist]

The database connection conn is opened inside a with block, but sqlite3.Connection context managers do not automatically close the connection on exit (they only commit or rollback transactions). If an exception occurs inside the with block, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed. Additionally, calling conn.commit() explicitly inside the with conn: block is redundant as the context manager handles transaction commit on successful exit.

Suggested change

	with get_db_connection(self.db_path) as conn:
	conn.execute(
	"INSERT INTO messages (channel, role, content, timestamp, est_tokens, conversation_id) "
	"VALUES (?, ?, ?, ?, ?, ?)",
	(self.channel, role, content, timestamp, est, conversation_id),
	)
	conn.commit()
	conn.close()
	conn = get_db_connection(self.db_path)
	try:
	with conn:
	conn.execute(
	"INSERT INTO messages (channel, role, content, timestamp, est_tokens, conversation_id) "
	"VALUES (?, ?, ?, ?, ?, ?)",
	(self.channel, role, content, timestamp, est, conversation_id),
	)
	finally:
	conn.close()

[gemini-code-assist]

The database connection conn is opened inside a with block, but if an exception occurs during query execution, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed. Since this is a read-only query, a transaction context manager (with conn:) is not required.

Suggested change

	with get_db_connection(self.db_path) as conn:
	rows = conn.execute("""SELECT role, content FROM messages
	WHERE channel = ?
	ORDER BY id DESC LIMIT ?""", (self.channel, limit)).fetchall()
	return [{"role": row[0], "content": row[1]} for row in reversed(rows)]
	conn.close()
	conn = get_db_connection(self.db_path)
	try:
	rows = conn.execute("""SELECT role, content FROM messages
	WHERE channel = ?
	ORDER BY id DESC LIMIT ?""", (self.channel, limit)).fetchall()
	finally:
	conn.close()

[gemini-code-assist]

The database connection conn is opened inside a with block, but sqlite3.Connection context managers do not automatically close the connection on exit (they only commit or rollback transactions). If an exception occurs during task deletion, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed.

Suggested change

	with get_db_connection() as conn:
	conn.execute("DELETE FROM tasks WHERE name = ?", (name,))
	conn.commit()
	conn.close()
	conn = get_db_connection()
	try:
	with conn:
	conn.execute("DELETE FROM tasks WHERE name = ?", (name,))
	finally:
	conn.close()

[gemini-code-assist]

The database connection conn is opened inside a with block, but sqlite3.Connection context managers do not automatically close the connection on exit (they only commit or rollback transactions). If an exception occurs during output insertion, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed.

Suggested change

	with get_db_connection() as conn:
	conn.execute("""
	INSERT INTO task_outputs (name, prompt, output, status, duration_secs, timestamp)
	VALUES (?, ?, ?, ?, ?, ?)
	""", (name, prompt, output, status, duration_secs, datetime.now().isoformat()))
	conn.commit()
	conn.close()
	conn = get_db_connection()
	try:
	with conn:
	conn.execute("""
	INSERT INTO task_outputs (name, prompt, output, status, duration_secs, timestamp)
	VALUES (?, ?, ?, ?, ?, ?)
	""", (name, prompt, output, status, duration_secs, datetime.now().isoformat()))
	finally:
	conn.close()

[gemini-code-assist]

The database connection conn is opened inside a with block, but if an exception occurs during query execution, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed. Since this is a read-only query, a transaction context manager (with conn:) is not required.

Suggested change

	with get_db_connection() as conn:
	rows = conn.execute("""
	SELECT prompt, output, status, duration_secs, timestamp FROM task_outputs
	WHERE name = ?
	ORDER BY id DESC LIMIT ?
	""", (name, num_entries)).fetchall()
	conn.close()
	conn = get_db_connection()
	try:
	rows = conn.execute("""
	SELECT prompt, output, status, duration_secs, timestamp FROM task_outputs
	WHERE name = ?
	ORDER BY id DESC LIMIT ?
	""", (name, num_entries)).fetchall()
	finally:
	conn.close()

[gemini-code-assist]

The database connection conn is opened inside a with block, but sqlite3.Connection context managers do not automatically close the connection on exit (they only commit or rollback transactions). If an exception occurs during task update, conn.close() is bypassed, leading to a connection leak. Use a try...finally block to ensure the connection is always closed.

Suggested change

	with get_db_connection() as conn:
	conn.execute("""UPDATE tasks SET last_run = ?, next_run = ?, run_count = run_count + 1
	WHERE name = ?""", (now.isoformat(), next_run, name))
	conn.commit()
	conn.close()
	conn = get_db_connection()
	try:
	with conn:
	conn.execute("""UPDATE tasks SET last_run = ?, next_run = ?, run_count = run_count + 1
	WHERE name = ?""", (now.isoformat(), next_run, name))
	finally:
	conn.close()

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: a620045301

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[chatgpt-codex-connector]

Make trace filenames collision-proof

When two traced LLM calls complete within the same second, which is easy with concurrent web clients or rapid CLI prompts, both calls write to the same trace_MMDDYYYY_HHMMSS.json path and the later one silently overwrites the earlier trace. Include microseconds or a UUID in the filename so tracing does not lose calls under normal concurrent usage.

Useful? React with 👍 / 👎.