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changes to agent runner
This commit is contained in:
james-m-jordan
parent
42e2402258
commit
31c5a16645
@ -1,7 +1,7 @@
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import os
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import yaml
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import logging
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from typing import Dict, Any
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from typing import Dict, Any, List
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import shutil
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from datetime import datetime
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import chromadb
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@ -162,6 +162,193 @@ class AgentTaskRunner:
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if "cell_line" in args:
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self._update_user_profile(researcher, "frequent_cell_lines", args["cell_line"])
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self._update_user_profile(researcher, "recent_experiments", filename)
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# Extract tasks from experiment and prepare for issue creation
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if args.get("tasks"):
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self.extract_tasks_and_preview(filename, template)
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def extract_tasks_and_preview(self, experiment_filename: str, experiment_data: Dict[str, Any]):
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"""
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Extract tasks from an experiment and preview them before creating GitHub issues.
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Args:
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experiment_filename: The filename of the experiment YAML
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experiment_data: The experiment data dictionary
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"""
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tasks = experiment_data.get("tasks", [])
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if not tasks:
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self.logger.info(f"No tasks found in experiment {experiment_filename}")
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return
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# Get other relevant experiment metadata
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experiment_id = experiment_data.get("experiment_id", experiment_filename)
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title = experiment_data.get("title", "Untitled Experiment")
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assignees = experiment_data.get("assignees", {})
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# Format tasks with assignees for preview
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preview_tasks = []
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for i, task in enumerate(tasks):
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task_description = task.get("description", "No description")
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task_assignee = task.get("assignee")
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assignee_username = assignees.get(task_assignee, "unassigned") if task_assignee else "unassigned"
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preview_tasks.append({
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"id": i + 1,
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"description": task_description,
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"assignee": assignee_username,
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"due_date": task.get("due_date", "No due date"),
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"experiment_id": experiment_id
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})
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# Log the preview
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self.logger.info(f"Preview of tasks for experiment {experiment_id}:")
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for task in preview_tasks:
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self.logger.info(f"Task #{task['id']}: {task['description']} (Assignee: {task['assignee']}, Due: {task['due_date']})")
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# Store the preview for confirmation
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self._store_task_preview(experiment_id, preview_tasks)
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# Create a GitHub issue for task preview confirmation
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preview_body = f"Experiment: {title} ({experiment_id})\n\n"
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preview_body += "The following tasks will be created as GitHub issues:\n\n"
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for task in preview_tasks:
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preview_body += f"- #{task['id']}: {task['description']} (Assignee: {task['assignee']}, Due: {task['due_date']})\n"
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preview_body += "\nTo confirm and create these issues, please comment 'confirm' on this issue."
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self.handle_open_issue({
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"title": f"Task Preview for {experiment_id}: {title}",
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"body": preview_body,
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"labels": ["task-preview"]
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})
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def _store_task_preview(self, experiment_id: str, tasks: List[Dict[str, Any]]):
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"""
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Store task preview data for later confirmation.
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Args:
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experiment_id: The experiment identifier
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tasks: List of task dictionaries
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"""
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preview_path = os.path.join("Data", "task_previews")
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os.makedirs(preview_path, exist_ok=True)
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preview_file = os.path.join(preview_path, f"{experiment_id}_task_preview.json")
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with open(preview_file, "w") as f:
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json.dump(tasks, f, indent=2)
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self.logger.info(f"Stored task preview at {preview_file}")
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def handle_confirm_tasks(self, args: Dict[str, Any]):
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"""
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Create GitHub issues from previously previewed tasks.
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Args:
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args: Dictionary with experiment_id to confirm tasks for
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"""
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experiment_id = args.get("experiment_id")
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if not experiment_id:
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self.logger.error("Missing experiment_id for confirm_tasks.")
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return
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preview_file = os.path.join("Data", "task_previews", f"{experiment_id}_task_preview.json")
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if not os.path.exists(preview_file):
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self.logger.error(f"No task preview found for experiment {experiment_id}")
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return
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with open(preview_file, "r") as f:
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tasks = json.load(f)
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for task in tasks:
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issue_title = f"[{experiment_id}] Task #{task['id']}: {task['description']}"
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issue_body = f"Experiment: {experiment_id}\n"
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issue_body += f"Description: {task['description']}\n"
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issue_body += f"Due Date: {task.get('due_date', 'Not specified')}\n\n"
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issue_body += f"This task is part of experiment {experiment_id}."
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# Create the issue
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self.handle_open_issue({
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"title": issue_title,
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"body": issue_body,
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"assignee": task.get("assignee"),
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"labels": ["experiment-task", experiment_id]
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})
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# Mark as created in TASKS.md
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self.add_task_to_tasks_md(task['description'], experiment_id)
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# Remove the preview file after creating issues
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os.remove(preview_file)
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self.logger.info(f"Created {len(tasks)} GitHub issues for experiment {experiment_id}")
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# Update the experiment YAML to indicate tasks were created
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self.update_experiment_tasks_status(experiment_id)
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def add_task_to_tasks_md(self, task_description: str, experiment_id: str):
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"""
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Add a task entry to TASKS.md.
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Args:
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task_description: Description of the task
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experiment_id: ID of the experiment the task belongs to
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"""
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if not os.path.exists("TASKS.md"):
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with open("TASKS.md", "w") as f:
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f.write("# Lab Tasks\n\n")
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with open("TASKS.md", "r") as f:
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lines = f.readlines()
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# Find the Lab Tasks section or create it
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lab_tasks_index = -1
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for i, line in enumerate(lines):
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if line.strip() == "# Lab Tasks" or line.strip() == "## Lab Tasks":
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lab_tasks_index = i
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break
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if lab_tasks_index == -1:
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lines.append("\n## Lab Tasks\n\n")
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lab_tasks_index = len(lines) - 3
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# Add the new task after the Lab Tasks heading
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task_line = f"- [ ] {task_description} ({experiment_id})\n"
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lines.insert(lab_tasks_index + 2, task_line)
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with open("TASKS.md", "w") as f:
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f.writelines(lines)
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self.logger.info(f"Added task to TASKS.md: {task_description}")
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def update_experiment_tasks_status(self, experiment_id: str):
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"""
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Update the experiment YAML file to indicate tasks were created.
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Args:
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experiment_id: ID of the experiment
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"""
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# Find experiment file
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exp_dir = "Experiments"
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exp_file = None
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for fname in os.listdir(exp_dir):
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if experiment_id in fname:
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exp_file = os.path.join(exp_dir, fname)
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break
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if not exp_file or not os.path.exists(exp_file):
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self.logger.error(f"Experiment file not found for id: {experiment_id}")
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return
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# Update the experiment YAML
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with open(exp_file, "r") as f:
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exp = yaml.safe_load(f)
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if "tasks" in exp:
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for task in exp["tasks"]:
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task["github_issue_created"] = True
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with open(exp_file, "w") as f:
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yaml.dump(exp, f, sort_keys=False)
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self.logger.info(f"Updated experiment {experiment_id} to mark tasks as created")
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def handle_update_experiment(self, args: Dict[str, Any]):
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"""
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@ -204,6 +391,12 @@ class AgentTaskRunner:
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self.append_changelog(f"Updated experiment {experiment_id}: {list(updates.keys())}")
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# Optionally update tasks
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self.mark_task_done_for_experiment(experiment_id)
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# If tasks have been added or modified, handle task preview
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if "tasks" in updates and updates["tasks"]:
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with open(exp_file, "r") as f:
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updated_exp = yaml.safe_load(f)
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self.extract_tasks_and_preview(experiment_id, updated_exp)
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def append_changelog(self, entry: str):
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with open("CHANGELOG.md", "a") as f:
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@ -303,17 +496,51 @@ class AgentTaskRunner:
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def handle_open_issue(self, args: Dict[str, Any]):
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"""
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Handle opening a GitHub issue via CLI (gh).
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Args should include: title (str), body (str)
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Args should include: title (str), body (str), assignee (str, optional), labels (list, optional)
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"""
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title = args.get("title", "Lab Agent Issue")
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body = args.get("body", "Created by lab agent.")
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assignee = args.get("assignee")
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labels = args.get("labels", [])
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# Build the command
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cmd = f'gh issue create --title "{title}" --body "{body}"'
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# Add assignee if provided
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if assignee and assignee != "unassigned":
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cmd += f' --assignee "{assignee}"'
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# Add labels if provided
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if labels:
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label_str = ",".join(labels)
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cmd += f' --label "{label_str}"'
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result = os.system(cmd)
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if result == 0:
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self.logger.info(f"Opened GitHub issue: {title}")
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# Add to ISSUES_LOG.md
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self._add_to_issues_log(title, assignee)
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else:
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self.logger.error(f"Failed to open GitHub issue: {title}")
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def _add_to_issues_log(self, title: str, assignee: str = None):
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"""
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Add an entry to ISSUES_LOG.md
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Args:
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title: Issue title
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assignee: GitHub username of assignee (optional)
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"""
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if not os.path.exists("ISSUES_LOG.md"):
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with open("ISSUES_LOG.md", "w") as f:
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f.write("# GitHub Issues Log\n\n")
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with open("ISSUES_LOG.md", "a") as f:
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entry = f"- {datetime.now().strftime('%Y-%m-%d %H:%M')}: {title}"
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if assignee and assignee != "unassigned":
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entry += f" (Assigned to: {assignee})"
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f.write(entry + "\n")
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def handle_open_pr(self, args: Dict[str, Any]):
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"""
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Handle opening a draft pull request via CLI (gh).
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@ -6,6 +6,7 @@ date: 2025-05-08
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researchers:
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- james-m-jordan
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- linda-onsei
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- SanjanaC
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protocol_id: PROT-0036
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protocol_name: "Adipogenic Induction Treatment"
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status: planned # planned | in-progress | completed | failed
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@ -24,6 +25,7 @@ condition_map: |
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Dish 1-3: 3T3 + Control medium (24h)
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Dish 4-6: 3T3 + Adipogenic induction medium (24h)
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replicates: 3
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sample_location: "-80°C freezer, rack 1-1-4-A"
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---
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---
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@ -250,7 +252,7 @@ Analysis script: `Analysis/EXP-0226_CoIP_quantification.R`
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_To be completed after experiment_
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## Comparison to Previous Iteration
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_Compare results with first iteration of this experiment_
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_Compare results with first iteration of this experiment (EXP-0224)_
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## Relation to Project Goals
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This experiment directly addresses our hypothesis that YBX1 and C/EBPα physically interact during early adipogenesis. By comparing 3T3 cells with and without adipogenic stimulation, we can determine if this interaction is enhanced during the early stages of adipocyte differentiation (24h post-induction).
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@ -267,11 +269,11 @@ _Check boxes when complete. These can auto-update TASKS.md._
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# 6️⃣ Team Discussion
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_Use this section for team comments, suggestions, and feedback._
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> **james-m-jordan (2025-05-07):** This is the second iteration of this experiment. In the first iteration (EXP-0218), we saw a weak interaction in control conditions that was strongly enhanced after adipogenic stimulation. Let's make sure our lysis conditions are optimal for capturing these interactions.
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> **james-m-jordan (2025-05-07):** This is the second iteration of this experiment. In the first iteration (EXP-0224), we saw a weak interaction in control conditions that was strongly enhanced after adipogenic stimulation. Let's make sure our lysis conditions are optimal for capturing these interactions.
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> **linda-onsei (2025-05-07):** Should we also check protein levels by straight Western blot? I'm wondering if the increased interaction is partly due to increased expression of either protein.
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# 7️⃣ References & Related Experiments
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- Related protocol: [Adipogenic Induction Treatment](Protocols/adipogenic_induction_treatment_v1.yaml)
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- Previous experiment: [EXP-0218](Experiments/EXP-0218_YBX1_CEBPA_interaction_3T3.md)
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- Previous experiment: [EXP-0224](Experiments/EXP-0224-YBX1-CEBPA-CoIP-3T3-adipogenesis.md)
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- Literature: Girard J, et al. (2018) YBX1 interacts with C/EBP transcription factors to regulate adipogenesis. Cell Reports 25:788-801.
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@ -29,6 +29,7 @@ condition_map: |
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C1-C6: CELL_LINE2 + TREATMENT1
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D1-D6: CELL_LINE2 + TREATMENT2
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replicates: 6
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sample_location: "-80°C freezer, rack X-X-X-X"
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---
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---
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@ -4,6 +4,7 @@ project: Project_Name
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researcher: username
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status: in_progress
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created: YYYY-MM-DD
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sample_location: "-80°C freezer, rack X-X-X-X"
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plate:
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id: PLATE_ID
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