import tempfile, os
from __init__ import ToolAction
from galaxy.util.odict import odict
from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper, JobExportHistoryArchiveWrapper
import logging
log = logging.getLogger( __name__ )
[docs]class ImportHistoryToolAction( ToolAction ):
"""Tool action used for importing a history to an archive. """
[docs] def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, **kwargs ):
#
# Create job.
#
job = trans.app.model.Job()
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 )
#
# 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 ).iteritems():
job.add_parameter( name, value )
job.state = start_job_state #job inputs have been configured, restore initial job state
job.set_handler(tool.get_job_handler(None))
trans.sa_session.flush()
# Queue the job for execution
trans.app.job_queue.put( job.id, tool.id )
trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
return job, odict()
[docs]class ExportHistoryToolAction( ToolAction ):
"""Tool action used for exporting a history to an archive. """
[docs] def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, **kwargs ):
#
# Get history to export.
#
history = None
for name, value in incoming.iteritems():
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()
session = trans.get_galaxy_session()
job.session_id = session and session.id
if history:
history_id = history.id
else:
history_id = trans.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 )
# Create dataset that will serve as archive.
archive_dataset = trans.app.model.Dataset()
trans.sa_session.add( archive_dataset )
trans.sa_session.flush() #ensure job.id and archive_dataset.id are available
trans.app.object_store.create( archive_dataset ) # set the object store id, create dataset (if applicable)
#
# Setup job and job wrapper.
#
# Add association for keeping track of job, history, archive relationship.
jeha = trans.app.model.JobExportHistoryArchive( job=job, history=history, \
dataset=archive_dataset, \
compressed=incoming[ 'compress' ] )
trans.sa_session.add( jeha )
job_wrapper = JobExportHistoryArchiveWrapper( job )
cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ], \
include_deleted=incoming[ 'include_deleted' ] )
#
# Add parameters to job_parameter table.
#
# Set additional parameters.
incoming[ '__HISTORY_TO_EXPORT__' ] = history.id
incoming[ '__EXPORT_HISTORY_COMMAND_INPUTS_OPTIONS__' ] = cmd_line
for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
job.add_parameter( name, value )
job.state = start_job_state #job inputs have been configured, restore initial job state
job.set_handler(tool.get_job_handler(None))
trans.sa_session.flush()
# Queue the job for execution
trans.app.job_queue.put( job.id, tool.id )
trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
return job, odict()