1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/57c80f54cd51/ changeset: 57c80f54cd51 user: dannon date: 2013-03-08 18:29:52 summary: Remove import * from tool_runner, fixes rerun (missing visit_input_values function) after recent import refactoring. affected #: 1 file
diff -r 3317f0d7f848445cff6b384bf5a1915db677d139 -r 57c80f54cd51a5b427692df6d29513c88554a112 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -2,15 +2,20 @@ Upload class """
-from galaxy.web.base.controller import * +import logging +import galaxy.util + +from galaxy import web +from galaxy.tools import DefaultToolState +from galaxy.tools.actions import upload_common +from galaxy.tools.parameters import params_to_incoming, visit_input_values +from galaxy.tools.parameters.basic import DataToolParameter, UnvalidatedValue from galaxy.util.bunch import Bunch from galaxy.util.hash_util import is_hashable -from galaxy.tools import DefaultToolState -from galaxy.tools.parameters.basic import UnvalidatedValue -from galaxy.tools.parameters import params_to_incoming -from galaxy.tools.actions import upload_common +from galaxy.web import error, url_for +from galaxy.web.base.controller import BaseUIController +from galaxy.web.form_builder import SelectField
-import logging log = logging.getLogger( __name__ )
class AddFrameData: @@ -47,7 +52,7 @@ tools = [] tool = None # Backwards compatibility for datasource tools that have default tool_id configured, but which are now using only GALAXY_URL. - tool_ids = util.listify( tool_id ) + tool_ids = galaxy.util.listify( tool_id ) for tool_id in tool_ids: if get_loaded_tools_by_lineage: tools = toolbox.get_loaded_tools_by_lineage( tool_id ) @@ -83,7 +88,7 @@ message=message, status=status, redirect=redirect ) ) - params = util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers + params = galaxy.util.Params( kwd, sanitize = False ) #Sanitize parameters when substituting into command line via input wrappers #do param translation here, used by datasource tools if tool.input_translator: tool.input_translator.translate( params ) @@ -103,7 +108,7 @@ toolbox=self.get_toolbox(), tool_version_select_field=tool_version_select_field, tool=tool, - util=util, + util=galaxy.util, add_frame=add_frame, **vars )
@@ -215,7 +220,7 @@ #create an incoming object from the original job's dataset-modified param objects incoming = {} params_to_incoming( incoming, tool.inputs, params_objects, trans.app ) - incoming[ "tool_state" ] = util.object_to_string( state.encode( tool, trans.app ) ) + incoming[ "tool_state" ] = galaxy.util.object_to_string( state.encode( tool, trans.app ) ) template, vars = tool.handle_input( trans, incoming, old_errors=upgrade_messages ) #update new state with old parameters # Is the "add frame" stuff neccesary here? add_frame = AddFrameData() @@ -228,7 +233,7 @@ toolbox=self.get_toolbox(), tool_version_select_field=tool_version_select_field, tool=tool, - util=util, + util=galaxy.util, add_frame=add_frame, tool_id_version_message=tool_id_version_message, **vars ) @@ -288,9 +293,9 @@ tool = self.get_toolbox().get_tool( tool_id ) if not tool: return False # bad tool_id - nonfile_params = util.Params( kwd, sanitize=False ) + nonfile_params = galaxy.util.Params( kwd, sanitize=False ) if kwd.get( 'tool_state', None ) not in ( None, 'None' ): - encoded_state = util.string_to_object( kwd["tool_state"] ) + encoded_state = galaxy.util.string_to_object( kwd["tool_state"] ) tool_state = DefaultToolState() tool_state.decode( encoded_state, tool, trans.app ) else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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