root/galaxy-central/lib/galaxy/tools/actions/history_imp_exp.py

from __init__ import ToolAction
from galaxy.util.odict import odict
from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper

import logging
log = logging.getLogger( __name__ )

class ExportHistoryToolAction( ToolAction ):
    """Tool action used for exporting a history to an archive. """
    
    def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True ):
        #
        # 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()
        job.session_id = trans.get_galaxy_session().id
        job.history_id = trans.history.id
        job.tool_id = tool.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
        
        #
        # 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
        trans.sa_session.flush()
        
        
        # Queue the job for execution
        trans.app.job_queue.put( job.id, tool )
        trans.log_event( "Added export history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
                
        return job, odict()