Source code for

import getpass
import logging
import os
import shutil
from typing import Optional

from sqlalchemy import select

from galaxy import model
from galaxy.model import store
from galaxy.model.base import transaction
from galaxy.schema.tasks import SetupHistoryExportJob
from galaxy.util.path import external_chown

log = logging.getLogger(__name__)

[docs]class JobImportHistoryArchiveWrapper: """ Class provides support for performing jobs that import a history from an archive. """
[docs] def __init__(self, app, job_id): = app self.job_id = job_id self.sa_session =
[docs] def setup_job(self, jiha, archive_source, archive_type): if if archive_type != "url": external_chown( archive_source, jiha.job.user.system_user_pwent(,, "history import archive", ) external_chown( jiha.archive_dir, jiha.job.user.system_user_pwent(,, "history import archive directory", )
[docs] def cleanup_after_job(self): """Set history, datasets, collections and jobs' attributes and clean up archive directory. """ # # Import history. # stmt = select(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).limit(1) jiha = self.sa_session.scalars(stmt).first() if not jiha: return None user = jiha.job.user new_history = None try: archive_dir = jiha.archive_dir if external_chown( archive_dir, jiha.job.user.system_user_pwent(getpass.getuser()),, "history import archive directory", ) model_store = store.get_import_model_store_for_directory( archive_dir,, user=user,, ) job = jiha.job with model_store.target_history(default_history=job.history) as new_history: jiha.history = new_history with transaction(self.sa_session): self.sa_session.commit() model_store.perform_import(new_history, job=job, new_history=True) # Cleanup. if os.path.exists(archive_dir): shutil.rmtree(archive_dir) except Exception as e: jiha.job.tool_stderr += f"Error cleaning up history import job: {e}" with transaction(self.sa_session): self.sa_session.commit() raise return new_history
[docs]class JobExportHistoryArchiveWrapper: """ Class provides support for performing jobs that export a history to an archive. """
[docs] def __init__(self, app, job_id): = app self.job_id = job_id self.sa_session =
[docs] def setup_job( self, history, store_directory, include_hidden=False, include_deleted=False, compressed=True, user: Optional[model.User] = None, ): """ Perform setup for job to export a history into an archive. """ # TODO: prevent circular import here... from galaxy.celery.tasks import export_history app = # TODO: parameterize API on include_files here... request = SetupHistoryExportJob(, job_id=self.job_id, store_directory=store_directory, include_files=True, include_hidden=include_hidden, include_deleted=include_deleted, ) if app.config.enable_celery_tasks: # symlink files on export, on worker files will tarred up in a dereferenced manner. export_history.delay(request=request, task_user_id=getattr(user, "id", None)) else: export_history(request=request)