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Source code for galaxy.tools.actions.history_imp_exp

import datetime
import logging
import os
import tempfile
from collections import OrderedDict

from galaxy.job_execution.setup import create_working_directory_for_job
from galaxy.tools.actions import ToolAction
from galaxy.tools.imp_exp import (
    JobExportHistoryArchiveWrapper,
    JobImportHistoryArchiveWrapper
)
from galaxy.util import ready_name_for_url

log = logging.getLogger(__name__)


[docs]class ImportHistoryToolAction(ToolAction): """Tool action used for importing a history to an archive. """ produces_real_jobs = True
[docs] def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs): # # Create job. # incoming = incoming or {} trans.check_user_activation() job = trans.app.model.Job() job.galaxy_version = trans.app.config.version_major session = trans.get_galaxy_session() job.session_id = session and session.id if history: history_id = history.id elif trans.history: history_id = trans.history.id else: history_id = None job.history_id = history_id job.tool_id = tool.id job.user_id = trans.user.id start_job_state = job.state # should be job.states.NEW job.state = job.states.WAITING # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add(job) trans.sa_session.flush() # ensure job.id are available # # Setup job and job wrapper. # # Add association for keeping track of job, history relationship. # Use abspath because mkdtemp() does not, contrary to the documentation, # always return an absolute path. archive_dir = os.path.abspath(tempfile.mkdtemp()) jiha = trans.app.model.JobImportHistoryArchive(job=job, archive_dir=archive_dir) trans.sa_session.add(jiha) job_wrapper = JobImportHistoryArchiveWrapper(trans.app, job) job_wrapper.setup_job(jiha, incoming['__ARCHIVE_SOURCE__'], incoming["__ARCHIVE_TYPE__"]) # # Add parameters to job_parameter table. # # Set additional parameters. incoming['__DEST_DIR__'] = jiha.archive_dir for name, value in tool.params_to_strings(incoming, trans.app).items(): job.add_parameter(name, value) job.state = start_job_state # job inputs have been configured, restore initial job state # Queue the job for execution trans.app.job_manager.enqueue(job, tool=tool) trans.log_event("Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id) return job, OrderedDict()
[docs]class ExportHistoryToolAction(ToolAction): """Tool action used for exporting a history to an archive. """ produces_real_jobs = True
[docs] def execute(self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, **kwargs): trans.check_user_activation() # # Get history to export. # incoming = incoming or {} history = None for name, value in incoming.items(): if isinstance(value, trans.app.model.History): history_param_name = name history = value del incoming[history_param_name] break if not history: raise Exception('There is no history to export.') # # Create the job and output dataset objects # job = trans.app.model.Job() job.galaxy_version = trans.app.config.version_major session = trans.get_galaxy_session() job.session_id = session and session.id history_id = history.id job.history_id = history_id job.tool_id = tool.id if trans.user: # If this is an actual user, run the job as that individual. Otherwise we're running as guest. job.user_id = trans.user.id start_job_state = job.state # should be job.states.NEW job.state = job.states.WAITING # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters trans.sa_session.add(job) compressed = incoming['compress'] exporting_to_uri = "directory_uri" in incoming if not exporting_to_uri: # see comment below about how this should be transitioned to occuring in a # job handler or detached MQ-driven thread jeha = trans.app.model.JobExportHistoryArchive.create_for_history( history, job, trans.sa_session, trans.app.object_store, compressed ) store_directory = jeha.temp_directory else: # creating a job directory in the web thread is bad (it is slow, bypasses # dynamic objectstore assignment, etc..) but it is arguably less bad than # creating a dataset (like above for dataset export case). # ensure job.id is available trans.sa_session.flush() job_directory = create_working_directory_for_job(trans.app.object_store, job) store_directory = os.path.join(job_directory, "working", "_object_export") os.makedirs(store_directory) # # Setup job and job wrapper. # job_wrapper = JobExportHistoryArchiveWrapper(trans.app, job) cmd_line = job_wrapper.setup_job(history, store_directory, include_hidden=incoming['include_hidden'], include_deleted=incoming['include_deleted'], compressed=compressed) # # Add parameters to job_parameter table. # # Set additional parameters. incoming['__HISTORY_TO_EXPORT__'] = history.id incoming['__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__'] = cmd_line if exporting_to_uri: directory_uri = incoming["directory_uri"] file_name = incoming.get("file_name") if file_name is None: hname = ready_name_for_url(history.name) human_timestamp = datetime.datetime.now().strftime("%Y%m%d%H%M%S") if compressed: extension = ".tar.gz" else: extension = ".tar" file_name = f"Galaxy-History-{hname}-{human_timestamp}.{extension}" file_name = os.path.basename(os.path.abspath(file_name)) sep = "" if directory_uri.endswith("/") else "/" incoming['__EXPORT_TO_URI__'] = f"{directory_uri}{sep}{file_name}" for name, value in tool.params_to_strings(incoming, trans.app).items(): job.add_parameter(name, value) job.state = start_job_state # job inputs have been configured, restore initial job state # Queue the job for execution trans.app.job_manager.enqueue(job, tool=tool) trans.log_event("Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id) return job, OrderedDict()