details: http://www.bx.psu.edu/hg/galaxy/rev/6741f6000e03 changeset: 3228:6741f6000e03 user: Greg Von Kuster greg@bx.psu.edu date: Tue Jan 12 14:08:17 2010 -0500 description: Preserve teh order of a tool's output datasets by storing them in an odict rather than a dict - loosely based on the "patch" contributed by Alexander Rose.
diffstat:
lib/galaxy/tools/__init__.py | 6 +++--- lib/galaxy/tools/actions/__init__.py | 3 ++- lib/galaxy/tools/actions/metadata.py | 3 ++- lib/galaxy/tools/actions/upload_common.py | 6 +++++- test/base/twilltestcase.py | 3 +-- 5 files changed, 13 insertions(+), 8 deletions(-)
diffs (95 lines):
diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Jan 12 14:08:17 2010 -0500 @@ -372,7 +372,7 @@ # Parse tool help self.parse_help( root ) # Description of outputs produced by an invocation of the tool - self.outputs = {} + self.outputs = odict() out_elem = root.find("outputs") if out_elem: for data_elem in out_elem.findall("data"): @@ -790,10 +790,10 @@ elif state.page == self.last_page: out_data = self.execute( trans, incoming=params ) try: - assert type( out_data ) is types.DictType + assert isinstance( out_data, odict ) return 'tool_executed.mako', dict( out_data=out_data ) except: - return 'message.mako', dict( message_type='error', message=out_data, refresh_frames=[] ) + return 'message.mako', dict( message_type='error', message='odict not returned from tool execution', refresh_frames=[] ) # Otherwise move on to the next page else: state.page += 1 diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,4 +1,5 @@ from galaxy.util.bunch import Bunch +from galaxy.util.odict import odict from galaxy.tools.parameters import * from galaxy.tools.parameters.grouping import * from galaxy.util.template import fill_template @@ -107,7 +108,7 @@ input_values[ input.name ] = galaxy.tools.SelectToolParameterWrapper( input, input_values[ input.name ], tool.app, other_values = incoming ) else: input_values[ input.name ] = galaxy.tools.InputValueWrapper( input, input_values[ input.name ], incoming ) - out_data = {} + out_data = odict() # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans )
diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,5 +1,6 @@ from __init__ import ToolAction from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper +from galaxy.util.odict import odict
import logging log = logging.getLogger( __name__ ) @@ -59,4 +60,4 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return [] + return odict() diff -r 892199a8078e -r 6741f6000e03 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Jan 12 11:42:22 2010 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Jan 12 14:08:17 2010 -0500 @@ -1,6 +1,7 @@ import os, tempfile, StringIO from cgi import FieldStorage from galaxy import datatypes, util +from galaxy.util.odict import odict from galaxy.datatypes import sniff from galaxy.util.json import to_json_string from galaxy.model.orm import eagerload_all @@ -321,7 +322,10 @@ # Queue the job for execution trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) - return dict( [ ( 'output%i' % i, v ) for i, v in enumerate( data_list ) ] ) + output = odict() + for i, v in enumerate( data_list ): + output[ 'output%i' % i ] = v + return output def active_folders( trans, folder ): # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). # Much faster way of retrieving all active sub-folders within a given folder than the diff -r 892199a8078e -r 6741f6000e03 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Jan 12 11:42:22 2010 -0500 +++ b/test/base/twilltestcase.py Tue Jan 12 14:08:17 2010 -0500 @@ -81,8 +81,7 @@ def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)' ): """Uploads a file""" filename = self.get_filename(filename) - self.home() - self.visit_page( "tool_runner/index?tool_id=upload1" ) + self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: tc.fv("1","file_type", ftype) tc.fv("1","dbkey", dbkey)