Source code for galaxy.tools.imp_exp

import getpass
import logging
import os
import shutil

from galaxy import model
from galaxy.model import store
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):
        self.app = app
        self.job_id = job_id
        self.sa_session = self.app.model.context

[docs]    def setup_job(self, jiha, archive_source, archive_type):
        if self.app.config.external_chown_script:
            if archive_type != "url":
                external_chown(
                    archive_source,
                    jiha.job.user.system_user_pwent(self.app.config.real_system_username),
                    self.app.config.external_chown_script,
                    "history import archive",
                )
            external_chown(
                jiha.archive_dir,
                jiha.job.user.system_user_pwent(self.app.config.real_system_username),
                self.app.config.external_chown_script,
                "history import archive directory",
            )

[docs]    def cleanup_after_job(self):
        """Set history, datasets, collections and jobs' attributes
        and clean up archive directory.
        """

        #
        # Import history.
        #

        jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).first()
        if not jiha:
            return None
        user = jiha.job.user

        new_history = None
        try:
            archive_dir = jiha.archive_dir
            if self.app.config.external_chown_script:
                external_chown(
                    archive_dir,
                    jiha.job.user.system_user_pwent(getpass.getuser()),
                    self.app.config.external_chown_script,
                    "history import archive directory",
                )
            model_store = store.get_import_model_store_for_directory(
                archive_dir, app=self.app, user=user, tag_handler=self.app.tag_handler.create_tag_handler_session()
            )
            job = jiha.job
            with model_store.target_history(default_history=job.history) as new_history:

                jiha.history = new_history
                self.sa_session.flush()
                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}"
            self.sa_session.flush()
            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):
        self.app = app
        self.job_id = job_id
        self.sa_session = self.app.model.context

[docs]    def setup_job(self, history, store_directory, include_hidden=False, include_deleted=False, compressed=True):
        """
        Perform setup for job to export a history into an archive.
        """
        # TODO: prevent circular import here...
        from galaxy.celery.tasks import export_history

        app = self.app
        # TODO: parameterize API on include_files here...
        request = SetupHistoryExportJob(
            history_id=history.id,
            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)
        else:
            export_history(request=request)