Fixes for multiple backup runs

app.py

@@ -168,7 +168,7 @@ def format_local_time_filter(utc_dt, format_str='%Y-%m-%d %H:%M'):
 
 def schedule_all_repositories():
     """Schedule all active repositories on startup"""
-    from datetime import datetime  # Import to ensure availability
+    from datetime import datetime, timedelta  # Import to ensure availability
 
     try:
         # Clean up any stuck 'running' jobs from previous sessions
@@ -182,13 +182,47 @@ def schedule_all_repositories():
                 logger.info(f"Marked stuck job as failed: {stuck_job.id} for repository {stuck_job.repository_id}")
             db.session.commit()
 
+        # Auto-cleanup: Remove duplicate backup jobs created within last hour
+        cutoff = datetime.utcnow() - timedelta(hours=1)
+        recent_jobs = BackupJob.query.filter(BackupJob.created_at > cutoff).all()
+
+        # Group by repository and find duplicates
+        repo_jobs = {}
+        for job in recent_jobs:
+            repo_id = job.repository_id
+            if repo_id not in repo_jobs:
+                repo_jobs[repo_id] = []
+            repo_jobs[repo_id].append(job)
+
+        duplicates_cleaned = 0
+        for repo_id, jobs in repo_jobs.items():
+            if len(jobs) > 1:
+                # Sort by creation time, keep the first one, mark others as failed
+                jobs.sort(key=lambda j: j.created_at)
+                for duplicate_job in jobs[1:]:
+                    if duplicate_job.status in ['pending', 'running']:
+                        duplicate_job.status = 'failed'
+                        duplicate_job.error_message = 'Duplicate job automatically cleaned up'
+                        duplicate_job.completed_at = datetime.utcnow()
+                        duplicates_cleaned += 1
+                        logger.info(f"Auto-cleaned duplicate job {duplicate_job.id} for repository {repo_id}")
+
+        if duplicates_cleaned > 0:
+            db.session.commit()
+            logger.info(f"Auto-cleaned {duplicates_cleaned} duplicate backup jobs")
+
         # First, clear any existing jobs to prevent duplicates
         existing_jobs = scheduler.get_jobs()
         for job in existing_jobs:
             if job.id.startswith('backup_'):
                 scheduler.remove_job(job.id)
                 logger.info(f"Removed existing job on startup: {job.id}")
 
+        # Clear our tracking as well
+        with _job_tracking_lock:
+            _scheduled_jobs.clear()
+            logger.info("Cleared job tracking set")
+
         repositories = Repository.query.filter_by(is_active=True).all()
         scheduled_count = 0
         for repository in repositories:
@@ -197,6 +231,65 @@ def schedule_all_repositories():
                 scheduled_count += 1
                 logger.info(f"Scheduled backup job for repository: {repository.name} ({repository.schedule_type})")
         logger.info(f"Scheduled {scheduled_count} backup jobs on startup")
+
+        # Schedule a periodic health check job to monitor for duplicates
+        def scheduler_health_check():
+            from datetime import datetime, timedelta
+            with app.app_context():
+                try:
+                    # Check for duplicate jobs in scheduler
+                    all_jobs = scheduler.get_jobs()
+                    backup_jobs = [job for job in all_jobs if job.id.startswith('backup_')]
+                    job_ids = [job.id for job in backup_jobs]
+
+                    # Check for duplicate job IDs
+                    if len(job_ids) != len(set(job_ids)):
+                        logger.error("Duplicate scheduler job IDs detected! Cleaning up...")
+                        # Remove all backup jobs and reschedule
+                        for job in backup_jobs:
+                            scheduler.remove_job(job.id)
+
+                        # Clear tracking and reschedule
+                        with _job_tracking_lock:
+                            _scheduled_jobs.clear()
+
+                        # Reschedule active repositories
+                        repositories = Repository.query.filter_by(is_active=True).all()
+                        for repo in repositories:
+                            if repo.schedule_type != 'manual':
+                                schedule_backup_job(repo)
+
+                        logger.info("Scheduler health check: cleaned up and rescheduled jobs")
+
+                    # Auto-cleanup old failed jobs (older than 7 days)
+                    old_cutoff = datetime.utcnow() - timedelta(days=7)
+                    old_jobs = BackupJob.query.filter(
+                        BackupJob.status == 'failed',
+                        BackupJob.created_at < old_cutoff
+                    ).all()
+
+                    if old_jobs:
+                        for old_job in old_jobs:
+                            db.session.delete(old_job)
+                        db.session.commit()
+                        logger.info(f"Auto-cleaned {len(old_jobs)} old failed backup jobs")
+
+                except Exception as e:
+                    logger.error(f"Scheduler health check failed: {e}")
+
+        # Schedule health check to run every 6 hours
+        scheduler.add_job(
+            func=scheduler_health_check,
+            trigger=CronTrigger(hour='*/6', timezone=LOCAL_TZ),
+            id='scheduler_health_check',
+            name='Scheduler Health Check',
+            replace_existing=True,
+            misfire_grace_time=300,
+            coalesce=True,
+            max_instances=1
+        )
+        logger.info("Scheduled periodic scheduler health check")
+
     except Exception as e:
         logger.error(f"Error scheduling repositories on startup: {e}")
 
@@ -205,6 +298,10 @@ def schedule_all_repositories():
 _scheduler_lock = threading.Lock()
 _scheduler_initialized = False
 
+# Global tracking of scheduled jobs to prevent duplicates
+_scheduled_jobs = set()
+_job_tracking_lock = threading.Lock()
+
 def ensure_scheduler_initialized():
     """Ensure scheduler is initialized with existing repositories (thread-safe)"""
     global _scheduler_initialized
@@ -622,11 +719,23 @@ def favicon():
 
 def schedule_backup_job(repository):
     """Schedule a backup job for a repository"""
+    global _scheduled_jobs
+
     if not repository.is_active:
         logger.info(f"Repository {repository.name} is inactive, not scheduling")
         return
 
     job_id = f'backup_{repository.id}'
+
+    # Thread-safe check to prevent duplicate scheduling
+    with _job_tracking_lock:
+        if job_id in _scheduled_jobs:
+            logger.warning(f"Job {job_id} already being scheduled, skipping duplicate")
+            return
+
+        # Mark this job as being scheduled
+        _scheduled_jobs.add(job_id)
+
     logger.info(f"Attempting to schedule job {job_id} for repository {repository.name}")
 
     # Remove existing job if it exists - try multiple ways to ensure it's gone
@@ -635,6 +744,9 @@ def schedule_backup_job(repository):
         if existing_job:
             scheduler.remove_job(job_id)
             logger.info(f"Removed existing scheduled job: {job_id}")
+            # Also remove from our tracking
+            with _job_tracking_lock:
+                _scheduled_jobs.discard(job_id)
         else:
             logger.info(f"No existing job found for {job_id}")
     except Exception as e:
@@ -643,6 +755,8 @@ def schedule_backup_job(repository):
     # Double-check that job is really gone
     if scheduler.get_job(job_id):
         logger.error(f"Job {job_id} still exists after removal attempt, aborting schedule")
+        with _job_tracking_lock:
+            _scheduled_jobs.discard(job_id)
         return
 
     # Create a wrapper function that includes Flask app context
@@ -657,7 +771,26 @@ def backup_with_context():
                     logger.warning(f"Repository {repository.id} not found or inactive, skipping backup")
                     return
 
-                # Check if there's already a running backup for this repository
+                # Multiple layers of duplicate prevention
+
+                # 0. Auto-cleanup: Mark any long-running jobs as failed
+                stuck_cutoff = datetime.utcnow() - timedelta(hours=2)
+                stuck_jobs = BackupJob.query.filter_by(
+                    repository_id=repository.id,
+                    status='running'
+                ).filter(
+                    BackupJob.started_at < stuck_cutoff
+                ).all()
+
+                if stuck_jobs:
+                    logger.warning(f"Found {len(stuck_jobs)} stuck running jobs for repository {repo.name}, cleaning up")
+                    for stuck in stuck_jobs:
+                        stuck.status = 'failed'
+                        stuck.error_message = 'Job stuck for over 2 hours, automatically failed'
+                        stuck.completed_at = datetime.utcnow()
+                    db.session.commit()
+
+                # 1. Check if there's already a running backup for this repository
                 running_job = BackupJob.query.filter_by(
                     repository_id=repository.id, 
                     status='running'
@@ -667,20 +800,45 @@ def backup_with_context():
                     logger.warning(f"Backup already running for repository {repo.name} (job {running_job.id}), skipping")
                     return
 
-                # Additional check: ensure no backup started in the last 30 seconds to prevent rapid duplicates
-                recent_cutoff = datetime.utcnow() - timedelta(seconds=30)
+                # 2. Check for very recent backups (within last 2 minutes) to prevent rapid duplicates
+                recent_cutoff = datetime.utcnow() - timedelta(minutes=2)
                 recent_backup = BackupJob.query.filter_by(
                     repository_id=repository.id
                 ).filter(
                     BackupJob.started_at > recent_cutoff
                 ).first()
 
                 if recent_backup:
-                    logger.warning(f"Recent backup found for repository {repo.name} (started at {recent_backup.started_at}), skipping")
+                    logger.warning(f"Recent backup found for repository {repo.name} (started at {recent_backup.started_at}), skipping to prevent duplicates")
                     return
 
-                logger.info(f"Starting scheduled backup for repository: {repo.name}")
-                backup_service.backup_repository(repo)
+                # 3. Use a file-based lock to prevent concurrent executions
+                import fcntl
+                import tempfile
+                import os
+
+                lock_file_path = os.path.join(tempfile.gettempdir(), f"backup_lock_{repository.id}")
+
+                try:
+                    lock_file = open(lock_file_path, 'w')
+                    fcntl.flock(lock_file.fileno(), fcntl.LOCK_EX | fcntl.LOCK_NB)
+                    logger.info(f"Acquired file lock for repository {repo.name}")
+
+                    try:
+                        logger.info(f"Starting scheduled backup for repository: {repo.name}")
+                        backup_service.backup_repository(repo)
+                        logger.info(f"Completed scheduled backup for repository: {repo.name}")
+                    finally:
+                        fcntl.flock(lock_file.fileno(), fcntl.LOCK_UN)
+                        lock_file.close()
+                        try:
+                            os.unlink(lock_file_path)
+                        except:
+                            pass
+
+                except (IOError, OSError) as lock_error:
+                    logger.warning(f"Could not acquire lock for repository {repo.name}, another backup may be running: {lock_error}")
+                    return
 
             except Exception as e:
                 logger.error(f"Error in scheduled backup for repository {repository.id}: {e}", exc_info=True)
@@ -771,6 +929,9 @@ def backup_with_context():
         logger.info(f"Job {job_id} successfully scheduled, next run: {added_job.next_run_time}")
     else:
         logger.error(f"Failed to schedule job {job_id} - job not found after creation")
+        # Remove from tracking if scheduling failed
+        with _job_tracking_lock:
+            _scheduled_jobs.discard(job_id)
 
 # Initialize scheduler with existing repositories at startup
 # This runs after all functions are defined

backup_service.py

@@ -43,6 +43,12 @@ def backup_repository(self, repository):
             logger.warning(f"Very recent backup found for repository {repository.name} (started at {recent_job.started_at}), skipping to prevent duplicates")
             return
 
+        # Auto-cleanup: Check for and clean up any orphaned temp directories
+        user_backup_dir = self.backup_base_dir / f"user_{repository.user_id}"
+        repo_backup_dir = user_backup_dir / repository.name
+        if repo_backup_dir.exists():
+            self._cleanup_temp_directories(repo_backup_dir)
+
         # Create backup job record
         backup_job = BackupJob(
             user_id=repository.user_id,