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"""
BOINC Client Integration
Handles distributed computing task submission and monitoring
"""
import os
import json
import time
import requests
from typing import Dict, List, Optional
from pathlib import Path
from dataclasses import dataclass, asdict
from datetime import datetime
import yaml
@dataclass
class WorkUnit:
"""Represents a BOINC work unit"""
id: str
name: str
workunit_type: str
input_file: str
status: str
created_at: str
completed_at: Optional[str] = None
result_file: Optional[str] = None
error: Optional[str] = None
class BOINCClient:
"""BOINC client for distributed computing integration"""
def __init__(self, config_path: str = "config.yml"):
with open(config_path, 'r') as f:
self.config = yaml.safe_load(f)['boinc']
self.project_url = self.config['project_url']
self.work_dir = Path(self.config['work_dir'])
self.work_dir.mkdir(parents=True, exist_ok=True)
self.tasks_file = self.work_dir / "tasks.json"
self.tasks = self._load_tasks()
def _load_tasks(self) -> Dict[str, WorkUnit]:
"""Load existing tasks from disk"""
if self.tasks_file.exists():
with open(self.tasks_file, 'r') as f:
data = json.load(f)
return {k: WorkUnit(**v) for k, v in data.items()}
return {}
def _save_tasks(self):
"""Save tasks to disk"""
with open(self.tasks_file, 'w') as f:
data = {k: asdict(v) for k, v in self.tasks.items()}
json.dump(data, f, indent=2)
def submit_task(
self,
workunit_type: str,
input_file: str,
name: Optional[str] = None
) -> str:
"""
Submit a new work unit to BOINC
Args:
workunit_type: Type of analysis (variant_calling, blast_search, etc.)
input_file: Path to input data file
name: Optional custom name for the work unit
Returns:
Work unit ID
"""
task_id = f"wu_{int(time.time() * 1000)}"
if name is None:
name = f"{workunit_type}_{task_id}"
# Create work unit
work_unit = WorkUnit(
id=task_id,
name=name,
workunit_type=workunit_type,
input_file=input_file,
status="pending",
created_at=datetime.now().isoformat()
)
# In a real implementation, this would submit to actual BOINC server
# For now, we simulate the submission
self._simulate_submission(work_unit)
self.tasks[task_id] = work_unit
self._save_tasks()
return task_id
def _simulate_submission(self, work_unit: WorkUnit):
"""
Simulate BOINC submission (for development/demo purposes)
In production, replace with actual BOINC API calls
"""
# Create a work directory for this task
task_dir = self.work_dir / work_unit.id
task_dir.mkdir(exist_ok=True)
# Copy input file
input_path = Path(work_unit.input_file)
if input_path.exists():
import shutil
shutil.copy(input_path, task_dir / input_path.name)
# Create task metadata
metadata = {
"task_id": work_unit.id,
"type": work_unit.workunit_type,
"input": work_unit.input_file,
"submitted": work_unit.created_at
}
with open(task_dir / "metadata.json", 'w') as f:
json.dump(metadata, f, indent=2)
def get_task_status(self, task_id: str) -> Optional[WorkUnit]:
"""Get status of a specific task"""
return self.tasks.get(task_id)
def list_tasks(
self,
status: Optional[str] = None,
workunit_type: Optional[str] = None
) -> List[WorkUnit]:
"""
List all tasks with optional filtering
Args:
status: Filter by status (pending, running, completed, failed)
workunit_type: Filter by work unit type
"""
tasks = list(self.tasks.values())
if status:
tasks = [t for t in tasks if t.status == status]
if workunit_type:
tasks = [t for t in tasks if t.workunit_type == workunit_type]
return sorted(tasks, key=lambda t: t.created_at, reverse=True)
def update_task_status(self, task_id: str, status: str, **kwargs):
"""Update task status and additional fields"""
if task_id in self.tasks:
self.tasks[task_id].status = status
for key, value in kwargs.items():
if hasattr(self.tasks[task_id], key):
setattr(self.tasks[task_id], key, value)
if status == "completed":
self.tasks[task_id].completed_at = datetime.now().isoformat()
self._save_tasks()
def cancel_task(self, task_id: str) -> bool:
"""Cancel a pending or running task"""
if task_id in self.tasks:
task = self.tasks[task_id]
if task.status in ["pending", "running"]:
task.status = "cancelled"
self._save_tasks()
return True
return False
def get_results(self, task_id: str) -> Optional[Path]:
"""Get results file for a completed task"""
if task_id in self.tasks:
task = self.tasks[task_id]
if task.status == "completed" and task.result_file:
result_path = Path(task.result_file)
if result_path.exists():
return result_path
return None
def get_statistics(self) -> Dict:
"""Get overall statistics about BOINC tasks"""
total = len(self.tasks)
by_status = {}
by_type = {}
for task in self.tasks.values():
by_status[task.status] = by_status.get(task.status, 0) + 1
by_type[task.workunit_type] = by_type.get(task.workunit_type, 0) + 1
completed = [t for t in self.tasks.values() if t.completed_at]
if completed:
avg_time = sum([
(datetime.fromisoformat(t.completed_at) -
datetime.fromisoformat(t.created_at)).total_seconds()
for t in completed
]) / len(completed)
else:
avg_time = 0
return {
"total_tasks": total,
"by_status": by_status,
"by_type": by_type,
"completed_tasks": len(completed),
"average_completion_time_seconds": avg_time
}
class BOINCTaskManager:
"""High-level task manager for common workflows"""
def __init__(self):
self.client = BOINCClient()
def submit_variant_calling(self, fastq_file: str) -> str:
"""Submit variant calling task"""
return self.client.submit_task(
workunit_type="variant_calling",
input_file=fastq_file,
name=f"variant_calling_{Path(fastq_file).stem}"
)
def submit_blast_search(self, sequence_file: str) -> str:
"""Submit BLAST search task"""
return self.client.submit_task(
workunit_type="blast_search",
input_file=sequence_file,
name=f"blast_{Path(sequence_file).stem}"
)
def submit_alignment(self, fastq_file: str) -> str:
"""Submit sequence alignment task"""
return self.client.submit_task(
workunit_type="alignment",
input_file=fastq_file,
name=f"alignment_{Path(fastq_file).stem}"
)
def submit_annotation(self, vcf_file: str) -> str:
"""Submit variant annotation task"""
return self.client.submit_task(
workunit_type="annotation",
input_file=vcf_file,
name=f"annotation_{Path(vcf_file).stem}"
)
def batch_submit(
self,
workunit_type: str,
input_files: List[str]
) -> List[str]:
"""Submit multiple tasks at once"""
task_ids = []
for input_file in input_files:
task_id = self.client.submit_task(workunit_type, input_file)
task_ids.append(task_id)
return task_ids
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