Fix linting broken in #3080

Also fix import order and Python3 compatibility.

.ci/flake8_lint_include_list.txt

@@ -341,6 +341,7 @@ lib/galaxy/webapps/galaxy/api/roles.py
 lib/galaxy/webapps/galaxy/api/samples.py
 lib/galaxy/webapps/galaxy/api/tools.py
 lib/galaxy/webapps/galaxy/api/tours.py
+lib/galaxy/webapps/galaxy/api/workflows.py
 lib/galaxy/webapps/galaxy/controllers/async.py
 lib/galaxy/webapps/galaxy/controllers/data_manager.py
 lib/galaxy/webapps/galaxy/controllers/error.py

.ci/py3_sources.txt

@@ -64,6 +64,7 @@ lib/galaxy/web/framework/middleware/error.py
 lib/galaxy/web/framework/middleware/static.py
 lib/galaxy/web/__init__.py
 lib/galaxy/webapps/galaxy/api/tours.py
+lib/galaxy/webapps/galaxy/api/workflows.py
 lib/galaxy/webapps/galaxy/controllers/userskeys.py
 lib/galaxy/webapps/reports/__init__.py
 lib/galaxy/webapps/tool_shed/controllers/user.py

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -1,25 +1,35 @@
 """
 API operations for Workflows
 """
-
 from __future__ import absolute_import
 
 import logging
-import urllib
+from six.moves.urllib.parse import unquote_plus
+
 from sqlalchemy import desc, false, or_, true
-from galaxy import exceptions, util
+
+from galaxy import (
+    exceptions,
+    model,
+    util
+)
+from galaxy.managers import (
+    histories,
+    workflows
+)
 from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.managers import histories
-from galaxy.managers import workflows
+from galaxy.util.sanitize_html import sanitize_html
 from galaxy.web import _future_expose_api as expose_api
-from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin
-from galaxy.web.base.controller import SharableMixin
+from galaxy.web.base.controller import (
+    BaseAPIController,
+    SharableMixin,
+    url_for,
+    UsesStoredWorkflowMixin
+)
 from galaxy.workflow.extract import extract_workflow
+from galaxy.workflow.modules import module_factory
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
-from galaxy.workflow.modules import module_factory
-from galaxy import model
-from galaxy.util.sanitize_html import sanitize_html
 
 log = logging.getLogger(__name__)
 
@@ -161,7 +171,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             from_history_id = self.decode_id( from_history_id )
             history = self.history_manager.get_accessible( from_history_id, trans.user, current_history=trans.history )
 
-            job_ids = map( self.decode_id, payload.get( 'job_ids', [] ) )
+            job_ids = [ self.decode_id(_) for _ in payload.get( 'job_ids', [] ) ]
             dataset_ids = payload.get( 'dataset_ids', [] )
             dataset_collection_ids = payload.get( 'dataset_collection_ids', [] )
             workflow_name = payload[ 'workflow_name' ]
@@ -216,7 +226,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         rval['outputs'] = []
         for step in workflow.steps:
             if step.type == 'tool' or step.type is None:
-                for v in outputs[ step.id ].itervalues():
+                for v in outputs[ step.id ].values():
                     rval[ 'outputs' ].append( trans.security.encode_id( v.id ) )
 
         # Newer version of this API just returns the invocation as a dict, to
@@ -306,8 +316,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
                          name defaults to existing name
             * annotation optional string annotation for the workflow, if not present in payload,
                          annotation defaults to existing annotation
-            * menu_entry optional boolean marking if the workflow should appear in the user's menu, 
-                         if not present, workflow menu entries are not modified   
+            * menu_entry optional boolean marking if the workflow should appear in the user's menu,
+                         if not present, workflow menu entries are not modified
 
         :rtype:     dict
         :returns:   serialized version of the workflow
@@ -315,18 +325,18 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         stored_workflow = self.__get_stored_workflow( trans, id )
         if 'workflow' in payload:
             stored_workflow.name = sanitize_html(payload['name']) if ('name' in payload) else stored_workflow.name
-            
+
             if 'annotation' in payload:
                 newAnnotation = sanitize_html(payload['annotation'])
                 self.add_item_annotation(trans.sa_session, trans.get_user(), stored_workflow, newAnnotation)
-            
+
             if 'menu_entry' in payload:
                 if payload['menu_entry']:
                     menuEntry = model.StoredWorkflowMenuEntry()
                     menuEntry.stored_workflow = stored_workflow
                     trans.get_user().stored_workflow_menu_entries.append(menuEntry)
                 else:
-                    #remove if in list
+                    # remove if in list
                     entries = {x.stored_workflow_id: x for x in trans.get_user().stored_workflow_menu_entries}
                     if (trans.security.decode_id(id) in entries):
                         trans.get_user().stored_workflow_menu_entries.remove(entries[trans.security.decode_id(id)])
@@ -380,7 +390,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
     # -- Helper methods --
     #
     def _get_tool( self, id, tool_version=None, user=None ):
-        id = urllib.unquote_plus( id )
+        id = unquote_plus( id )
         tool = self.app.toolbox.get_tool( id, tool_version )
         if not tool or not tool.allow_user_access( user ):
             raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id)