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Cleanup in history_imp_exp.py while looking for hid bug.

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dannon
2015-03-11 15:32:38 -04:00
parent d4e37db5d9
commit bc07d3adfd
1 changed files with 22 additions and 19 deletions
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lib/galaxy/tools/actions/history_imp_exp.py
+22 -19
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@@ -1,15 +1,18 @@
import tempfile, os
from __init__ import ToolAction
import os
import tempfile
from galaxy.tools.actions import ToolAction
from galaxy.tools.imp_exp import JobExportHistoryArchiveWrapper, JobImportHistoryArchiveWrapper
from galaxy.util.odict import odict
from galaxy.tools.imp_exp import JobImportHistoryArchiveWrapper, JobExportHistoryArchiveWrapper
import logging
log = logging.getLogger( __name__ )
class ImportHistoryToolAction( ToolAction ):
"""Tool action used for importing a history to an archive. """
def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, **kwargs ):
def execute( self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, **kwargs ):
#
# Create job.
#
@@ -25,10 +28,10 @@ class ImportHistoryToolAction( ToolAction ):
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
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
trans.sa_session.flush() # ensure job.id are available
#
# Setup job and job wrapper.
@@ -51,7 +54,7 @@ class ImportHistoryToolAction( ToolAction ):
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.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()
@@ -61,10 +64,11 @@ class ImportHistoryToolAction( ToolAction ):
return job, odict()
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, history=None, **kwargs ):
def execute( self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, **kwargs ):
#
# Get history to export.
#
@@ -94,30 +98,30 @@ class ExportHistoryToolAction( ToolAction ):
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
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)
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, \
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' ] )
cmd_line = job_wrapper.setup_job( trans, jeha, include_hidden=incoming[ 'include_hidden' ],
include_deleted=incoming[ 'include_deleted' ] )
#
# Add parameters to job_parameter table.
@@ -129,11 +133,10 @@ class ExportHistoryToolAction( ToolAction ):
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.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 )