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History export - now works for a guest user.

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Dannon Baker
2012-02-02 10:51:13 -05:00
parent 219cf0c74f
commit 5a2dffdf85
1 changed files with 26 additions and 24 deletions
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lib/galaxy/tools/actions/history_imp_exp.py
+26 -24
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@@ -9,7 +9,7 @@ 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 ):
def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ):
#
# Create job.
#
@@ -20,43 +20,43 @@ class ImportHistoryToolAction( ToolAction ):
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.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,
# 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( job )
#
# 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
trans.sa_session.flush()
# Queue the job for execution
trans.app.job_queue.put( job.id, tool )
trans.log_event( "Added import history job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )
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 ):
#
# Get history to export.
@@ -68,10 +68,10 @@ class ExportHistoryToolAction( ToolAction ):
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
#
@@ -79,22 +79,24 @@ class ExportHistoryToolAction( ToolAction ):
job.session_id = trans.get_galaxy_session().id
job.history_id = trans.history.id
job.tool_id = tool.id
job.user_id = trans.user.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, \
@@ -104,23 +106,23 @@ class ExportHistoryToolAction( ToolAction ):
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()