From b11002bef32d83b058e3495f96695c8dc12cb91b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 15:34:15 +0000
Subject: [PATCH 01/12] Don't iterate over unused key.

Thanks to @bgruening.
---
 test/api/workflows_format_2/converter.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/api/workflows_format_2/converter.py b/test/api/workflows_format_2/converter.py
index e4a5bb9cc24..cf123de7998 100644
--- a/test/api/workflows_format_2/converter.py
+++ b/test/api/workflows_format_2/converter.py
@@ -91,7 +91,7 @@ def _python_to_workflow(as_python, conversion_context):
         as_python["steps"] = steps_as_dict
         steps = steps_as_dict
 
-    for i, step in steps.iteritems():
+    for step in steps.itervalues():
         step_type = step.get("type", None)
         if "run" in step:
             if step_type is not None:
@@ -113,7 +113,7 @@ def _python_to_workflow(as_python, conversion_context):
             run_to_step_function(conversion_context, step, run_action)
             del step["run"]
 
-    for i, step in steps.iteritems():
+    for step in steps.itervalues():
         step_type = step.get("type", "tool")
         step_type = STEP_TYPE_ALIASES.get(step_type, step_type)
         if step_type not in STEP_TYPES:

From 2aa7f04364e10e46c655de636925883a43698694 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 15:43:20 +0000
Subject: [PATCH 02/12] Replace __rip_value with dict.pop.

Thanks @bgruening.
---
 test/api/workflows_format_2/converter.py | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/test/api/workflows_format_2/converter.py b/test/api/workflows_format_2/converter.py
index cf123de7998..7ab6b2d6ff3 100644
--- a/test/api/workflows_format_2/converter.py
+++ b/test/api/workflows_format_2/converter.py
@@ -148,14 +148,14 @@ def convert_inputs_to_steps(inputs, steps):
         if "label" not in input_def and "id" not in input_def:
             raise Exception("Input must define a label.")
 
-        raw_label = __rip_value(input_def, "label")
-        raw_id = __rip_value(input_def, "id")
+        raw_label = input_def.pop("label", None)
+        raw_id = input_def.pop("id", None)
         label = raw_label or raw_id
 
         if not label:
             raise Exception("Input label must not be empty.")
 
-        input_type = __rip_value(input_def, "type", "data")
+        input_type = input_def.pop("type", "data")
         if input_type in ["File", "data", "data_input"]:
             step_type = "data_input"
         elif input_type in ["collection", "data_collection", "data_collection_input"]:
@@ -380,15 +380,6 @@ def __join_prefix(prefix, key):
     return new_key
 
 
-def __rip_value(input_def, key, default=None):
-    if key in input_def:
-        value = input_def[key]
-        del input_def[key]
-    else:
-        value = default
-    return value
-
-
 def __init_connect_dict(step):
     if "connect" not in step:
         step["connect"] = {}

From 98249058e85d8133748519ac59ebed96a28a77ac Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 15:47:13 +0000
Subject: [PATCH 03/12] Cleanup error message.

Thanks @bgruening.
---
 lib/galaxy/workflow/run.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
index f9efbd6056b..b06b770e830 100644
--- a/lib/galaxy/workflow/run.py
+++ b/lib/galaxy/workflow/run.py
@@ -235,8 +235,8 @@ class WorkflowProgress( object ):
             if not hasattr( step, 'module' ):
                 self.module_injector.inject( step )
                 if step_id not in step_states:
-                    template = "Workflow invocation [%s] has no step state for step id [%s]. States are [%s]."
-                    message = template % (self.workflow_invocation.id, step_id, step_states)
+                    template = "Workflow invocation [%s] has no step state for step id [%s]. States ids are %s."
+                    message = template % (self.workflow_invocation.id, step_id, step_states.keys())
                     raise Exception(message)
                 runtime_state = step_states[ step_id ].value
                 step.state = step.module.recover_runtime_state( runtime_state )

From f17a6c996a060f68bc8a250effa23f60b96b44a7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 4 Dec 2015 21:21:33 +0000
Subject: [PATCH 04/12] Synchronize decoding ids across base controller and
 manager base.

To ensure we have the same kind of exception thrown in both cases.
---
 lib/galaxy/managers/base.py       | 16 +++++++++++-----
 lib/galaxy/web/base/controller.py |  9 +--------
 2 files changed, 12 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/managers/base.py b/lib/galaxy/managers/base.py
index c12ae7a513c..13820752c79 100644
--- a/lib/galaxy/managers/base.py
+++ b/lib/galaxy/managers/base.py
@@ -112,6 +112,16 @@ def get_class( class_name ):
     return item_class
 
 
+def decode_id(app, id):
+    try:
+        # note: use str - occasionally a fully numeric id will be placed in post body and parsed as int via JSON
+        #   resulting in error for valid id
+        return app.security.decode_id( str( id ) )
+    except ( ValueError, TypeError ):
+        msg = "Malformed id ( %s ) specified, unable to decode" % ( str( id ) )
+        raise exceptions.MalformedId( msg, id=str( id ) )
+
+
 def get_object( trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ):
     """
     Convenience method to get a model object with the specified checks. This is
@@ -119,11 +129,7 @@ def get_object( trans, id, class_name, check_ownership=False, check_accessible=F
     controller mixin code - however whenever possible the managers for a
     particular model should be used to load objects.
     """
-    try:
-        decoded_id = trans.security.decode_id( id )
-    except:
-        raise exceptions.MessageException( "Malformed %s id ( %s ) specified, unable to decode"
-                                           % ( class_name, str( id ) ), type='error' )
+    decoded_id = decode_id(trans.app, id)
     try:
         item_class = get_class( class_name )
         assert item_class is not None
diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py
index dba14dc3ece..3c46652783c 100644
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -11,7 +11,6 @@ from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
 from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable
 from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException
 from galaxy.exceptions import MessageException
-from galaxy import exceptions
 
 from galaxy import web
 from galaxy import model
@@ -94,13 +93,7 @@ class BaseController( object ):
 
     # ---- parsing query params
     def decode_id( self, id ):
-        try:
-            # note: use str - occasionally a fully numeric id will be placed in post body and parsed as int via JSON
-            #   resulting in error for valid id
-            return self.app.security.decode_id( str( id ) )
-        except ( ValueError, TypeError ):
-            msg = "Malformed id ( %s ) specified, unable to decode" % ( str( id ) )
-            raise exceptions.MalformedId( msg, id=str( id ) )
+        return managers_base.decode_id( self.app, id )
 
     def encode_all_ids( self, trans, rval, recursive=False ):
         """

From f6d26c9ee6f148fd033d1b070c2dbe8c69b08fa8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 4 Dec 2015 18:08:07 +0000
Subject: [PATCH 05/12] Small refactor making workflow views and modules tad
 more generic.

 - Reduce duplication between initializing generic modules and tool modules.
 - Switch tool_id to content_id as variable names throughout the client.
 - Rename get_tool_id to get_content_id on workflow modules.
 - Add some minimal documentation to the workflow module about get_content_id.

Downstream in the subworkflow commit I switch the over-the-wire communication to use content_id instead of tool_id also and use content_ids to refer to workflow ids in subworkflow moduls.
---
 .../scripts/mvc/workflow/workflow-manager.js  |  6 +--
 .../scripts/mvc/workflow/workflow-view.js     | 40 ++++++++-----------
 lib/galaxy/managers/workflows.py              |  4 +-
 .../webapps/galaxy/controllers/workflow.py    |  2 +-
 lib/galaxy/workflow/modules.py                | 21 +++++-----
 test/unit/workflows/test_modules.py           |  4 +-
 6 files changed, 37 insertions(+), 40 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 08c247672b9..42de4396f43 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -9,8 +9,8 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         this.active_form_has_changes = false;
     }
     $.extend( Workflow.prototype, {
-        create_node: function ( type, title_text, tool_id ) {
-            var node = this.app.prebuildNode( type, title_text, tool_id );
+        create_node: function ( type, title_text, content_id ) {
+            var node = this.app.prebuildNode( type, title_text, content_id );
             this.add_node( node );
             this.fit_canvas_to_nodes();
             this.app.canvas_manager.draw_overview();
@@ -131,7 +131,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                 var node_data = {
                     id : node.id,
                     type : node.type,
-                    tool_id : node.tool_id,
+                    tool_id : node.content_id,
                     tool_state : node.tool_state,
                     tool_errors : node.tool_errors,
                     input_connections : input_connections,
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index fe712da025e..a15ec495aa8 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -525,12 +525,10 @@ EditorFormView = Backbone.View.extend({
             cc.css( { left: left, top: top } );
         },
 
-        // Add a new step to the workflow by tool id
-        add_node_for_tool: function ( id, title ) {
-            node = this.workflow.create_node( 'tool', title, id );
+        _moduleInitAjax: function(node, request_data) {
             $.ajax( {
                 url: this.urls.get_new_module_info,
-                data: { type: "tool", tool_id: id, "_": "true" },
+                data: request_data,
                 global: false,
                 dataType: "json",
                 success: function( data ) {
@@ -546,23 +544,21 @@ EditorFormView = Backbone.View.extend({
             });
         },
 
+        // Add a new step to the workflow by tool id
+        add_node_for_tool: function ( id, title ) {
+            node = this.workflow.create_node( 'tool', title, id );
+            this._moduleInitAjax(node, { type: "tool", content_id: id, "_": "true" });
+        },
+
+        // Add a new step to the workflow by tool id
+        add_node_for_subworkflow: function ( id, title ) {
+            node = this.workflow.create_node( 'subworkflow', title, id );
+            this._moduleInitAjax(node, { type: "subworkflow", subworkflow_id: id, "_": "true" });
+        },
+
         add_node_for_module: function ( type, title ) {
             node = this.workflow.create_node( type, title );
-            $.ajax( {
-                url: this.urls.get_new_module_info,
-                data: { type: type, "_": "true" },
-                dataType: "json",
-                success: function( data ) {
-                    node.init_field_data( data );
-                },
-                error: function( x, e ) {
-                    var m = "error loading field data"
-                    if ( x.status == 0 ) {
-                        m += ", server unavailable"
-                    }
-                    node.error( m );
-                }
-            });
+            this._moduleInitAjax(node, { type: type, "_": "true" });
         },
 
         // This function preloads how to display known pja's.
@@ -704,14 +700,12 @@ EditorFormView = Backbone.View.extend({
             return ( this.type_to_type[child] ) && ( parent in this.type_to_type[child] );
         },
 
-        prebuildNode: function ( type, title_text, tool_id ) {
+        prebuildNode: function ( type, title_text, content_id ) {
             var self = this;
             var f = $("<div class='toolForm toolFormInCanvas'></div>");
             var node = new Node( this, { element: f } );
             node.type = type;
-            if ( type == 'tool' ) {
-                node.tool_id = tool_id;
-            }
+            node.content_id = content_id;
             var title = $("<div class='toolFormTitle unselectable'>" + title_text + "</div>" );
             f.append( title );
             f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index c43dbf69983..a5b259de134 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -348,7 +348,7 @@ class WorkflowContentsManager(UsesAnnotations):
             step_dict = {
                 'id': step.order_index,
                 'type': module.type,
-                'tool_id': module.get_tool_id(),
+                'tool_id': module.get_content_id(),
                 'name': module.get_name(),
                 'tool_state': module.get_state(),
                 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
@@ -449,7 +449,7 @@ class WorkflowContentsManager(UsesAnnotations):
             step_dict = {
                 'id': step.order_index,
                 'type': module.type,
-                'tool_id': module.get_tool_id(),
+                'tool_id': module.get_content_id(),
                 'tool_version': step.tool_version,
                 'name': module.get_name(),
                 'tool_state': module.get_state( secure=False ),
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index 8ab9bbc8638..e7a63f0cdac 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -664,7 +664,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         return {
             'type': module.type,
             'name': module.get_name(),
-            'tool_id': module.get_tool_id(),
+            'tool_id': module.get_content_id(),
             'tool_state': module.get_state(),
             'tool_model': tool_model,
             'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ),
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 4383038def2..0e93e984652 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -42,7 +42,7 @@ class WorkflowModule( object ):
     # ---- Creating modules from various representations ---------------------
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
+    def new( Class, trans, content_id=None ):
         """
         Create a new instance of the module with default state
         """
@@ -73,7 +73,10 @@ class WorkflowModule( object ):
     def get_name( self ):
         return self.name
 
-    def get_tool_id( self ):
+    def get_content_id( self ):
+        """ If this component has an identifier external to the step (such
+        as a tool or another workflow) return the identifier for that content.
+        """
         return None
 
     def get_tooltip( self, static_path='' ):
@@ -194,7 +197,7 @@ class WorkflowModule( object ):
 class SimpleWorkflowModule( WorkflowModule ):
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
+    def new( Class, trans, content_id=None ):
         module = Class( trans )
         module.state = Class.default_state()
         return module
@@ -502,10 +505,10 @@ class ToolModule( WorkflowModule ):
             self.errors[ tool_id ] = 'Tool unavailable'
 
     @classmethod
-    def new( Class, trans, tool_id=None ):
-        module = Class( trans, tool_id )
+    def new( Class, trans, content_id=None ):
+        module = Class( trans, content_id )
         if module.tool is None:
-            error_message = "Attempted to create new workflow module for invalid tool_id, no tool with id - %s." % tool_id
+            error_message = "Attempted to create new workflow module for invalid tool_id, no tool with id - %s." % content_id
             raise Exception( error_message )
         module.state = module.tool.new_state( trans )
         return module
@@ -615,7 +618,7 @@ class ToolModule( WorkflowModule ):
             return self.tool.name
         return 'unavailable'
 
-    def get_tool_id( self ):
+    def get_content_id( self ):
         return self.tool_id
 
     def get_tool_version( self ):
@@ -943,13 +946,13 @@ class WorkflowModuleFactory( object ):
     def __init__( self, module_types ):
         self.module_types = module_types
 
-    def new( self, trans, type, tool_id=None ):
+    def new( self, trans, type, content_id=None ):
         """
         Return module for type and (optional) tool_id intialized with
         new / default state.
         """
         assert type in self.module_types
-        return self.module_types[type].new( trans, tool_id )
+        return self.module_types[type].new( trans, content_id )
 
     def from_dict( self, trans, d, **kwargs ):
         """
diff --git a/test/unit/workflows/test_modules.py b/test/unit/workflows/test_modules.py
index 4a92b716d23..d0910ea77af 100644
--- a/test/unit/workflows/test_modules.py
+++ b/test/unit/workflows/test_modules.py
@@ -19,7 +19,7 @@ def test_valid_new_tool_has_no_errors():
     trans = MockTrans()
     mock_tool = mock.Mock()
     trans.app.toolbox.tools[ "cat1" ] = mock_tool
-    tool_module = modules.module_factory.new( trans, "tool", tool_id="cat1" )
+    tool_module = modules.module_factory.new( trans, "tool", content_id="cat1" )
     assert not tool_module.get_errors()
 
 
@@ -194,7 +194,7 @@ def test_cannot_create_tool_modules_for_missing_tools():
     trans = MockTrans()
     exception = False
     try:
-        modules.module_factory.new( trans, "tool", tool_id="cat1" )
+        modules.module_factory.new( trans, "tool", content_id="cat1" )
     except Exception:
         exception = True
     assert exception

From 73bfbf016347f764a0747ad7c6d138c74b6f519d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 4 Dec 2015 19:35:04 +0000
Subject: [PATCH 06/12] Refactor some workflow API code into workflows manager.

This allows for reuse outside of the API controller, such as loading subworkflows downstream.
---
 lib/galaxy/managers/workflows.py           | 38 ++++++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/workflows.py | 30 ++---------------
 2 files changed, 41 insertions(+), 27 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index a5b259de134..a3d312dfdb0 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -2,12 +2,18 @@ from __future__ import absolute_import
 
 from collections import namedtuple
 import json
+import uuid
+
+from sqlalchemy import and_
 
 from galaxy import model
+from galaxy import util
 from galaxy import exceptions
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.workflow import modules
 
+from .base import decode_id
+
 # For WorkflowContentManager
 from galaxy.util.sanitize_html import sanitize_html
 from galaxy.workflow.steps import attach_ordered_steps
@@ -26,6 +32,38 @@ class WorkflowsManager( object ):
     def __init__( self, app ):
         self.app = app
 
+    def get_stored_workflow( self, trans, workflow_id ):
+        """ Use a supplied ID (UUID or encoded stored workflow ID) to find
+        a workflow.
+        """
+        if util.is_uuid(workflow_id):
+            # see if they have passed in the UUID for a workflow that is attached to a stored workflow
+            workflow_uuid = uuid.UUID(workflow_id)
+            stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
+                trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
+                trans.app.model.Workflow.uuid == workflow_uuid
+            )).first()
+            if stored_workflow is None:
+                raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
+        else:
+            workflow_id = decode_id( self.app, workflow_id )
+            query = trans.sa_session.query( trans.app.model.StoredWorkflow )
+            stored_workflow = query.get( workflow_id )
+        if stored_workflow is None:
+            raise exceptions.ObjectNotFound( "No such workflow found." )
+        return stored_workflow
+
+    def get_stored_accessible_workflow( self, trans, workflow_id ):
+        stored_workflow = self.get_stored_workflow( trans, workflow_id )
+
+        # check to see if user has permissions to selected workflow
+        if stored_workflow.user != trans.user and not trans.user_is_admin():
+            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
+                message = "Workflow is not owned by or shared with current user"
+                raise exceptions.ItemAccessibilityException( message )
+
+        return stored_workflow
+
     def check_security( self, trans, has_workflow, check_ownership=True, check_accessible=True):
         """ check accessibility or ownership of workflows, storedworkflows, and
         workflowinvocations. Throw an exception or returns True if user has
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index 4e7107d44c3..be1ff669617 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -4,11 +4,10 @@ API operations for Workflows
 
 from __future__ import absolute_import
 
-import uuid
 import logging
 import copy
 import urllib
-from sqlalchemy import and_, desc, false, or_, true
+from sqlalchemy import desc, false, or_, true
 from galaxy import exceptions, util
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.managers import histories
@@ -570,33 +569,10 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
         )
 
     def __get_stored_accessible_workflow( self, trans, workflow_id ):
-        stored_workflow = self.__get_stored_workflow( trans, workflow_id )
-
-        # check to see if user has permissions to selected workflow
-        if stored_workflow.user != trans.user and not trans.user_is_admin():
-            if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0:
-                message = "Workflow is not owned by or shared with current user"
-                raise exceptions.ItemAccessibilityException( message )
-
-        return stored_workflow
+        return self.workflow_manager.get_stored_accessible_workflow( trans, workflow_id )
 
     def __get_stored_workflow( self, trans, workflow_id ):
-        if util.is_uuid(workflow_id):
-            # see if they have passed in the UUID for a workflow that is attached to a stored workflow
-            workflow_uuid = uuid.UUID(workflow_id)
-            stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).filter( and_(
-                trans.app.model.StoredWorkflow.latest_workflow_id == trans.app.model.Workflow.id,
-                trans.app.model.Workflow.uuid == workflow_uuid
-            )).first()
-            if stored_workflow is None:
-                raise exceptions.ObjectNotFound( "Workflow not found: %s" % workflow_id )
-        else:
-            workflow_id = self.decode_id( workflow_id )
-            query = trans.sa_session.query( trans.app.model.StoredWorkflow )
-            stored_workflow = query.get( workflow_id )
-        if stored_workflow is None:
-            raise exceptions.ObjectNotFound( "No such workflow found." )
-        return stored_workflow
+        return self.workflow_manager.get_stored_workflow( trans, workflow_id )
 
     def __encode_invocation( self, trans, invocation, view="element", step_details=False ):
         return self.encode_all_ids(

From f92220a74f216d937dc5b147472261d154779512 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 13:11:09 +0000
Subject: [PATCH 07/12] Allow workflow outputs on non-tool steps.

---
 lib/galaxy/managers/workflows.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index a3d312dfdb0..11f93623eff 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -429,11 +429,13 @@ class WorkflowContentsManager(UsesAnnotations):
                         action_arguments=pja.action_arguments
                     )
                 step_dict['post_job_actions'] = pja_dict
-                # workflow outputs
-                outputs = []
-                for output in step.workflow_outputs:
-                    outputs.append({"output_name": output.output_name})
-                step_dict['workflow_outputs'] = outputs
+
+            # workflow outputs
+            outputs = []
+            for output in step.workflow_outputs:
+                outputs.append({"output_name": output.output_name})
+            step_dict['workflow_outputs'] = outputs
+
             # Encode input connections as dictionary
             input_conn_dict = {}
             for conn in input_connections:

From d18c75ceb875632f9e68a74ebeb88389262d6fa8 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 17:08:13 +0000
Subject: [PATCH 08/12] Bring gneric and tool module styles into alignment in
 workflow editor.

---
 .../scripts/mvc/workflow/workflow-view.js     |  2 +-
 .../galaxy/workflow/editor_generic_form.mako  | 57 +++++++++++--------
 2 files changed, 34 insertions(+), 25 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index a15ec495aa8..c8d6a9bd4d5 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -61,7 +61,7 @@ EditorFormView = Backbone.View.extend({
         this.setElement($el);
 
         if (node && node.id != 'no-node') {
-            $el.find('.toolForm:first').after(this._genericStepAttributesTemplate( node ));
+            $el.find('table:first').after(this._genericStepAttributesTemplate( node ));
             ($el.find( 'form' ).length > 0) && $el.find( 'form' ).ajaxForm( {
                 type: 'POST',
                 dataType: 'json',
diff --git a/templates/webapps/galaxy/workflow/editor_generic_form.mako b/templates/webapps/galaxy/workflow/editor_generic_form.mako
index 5f744fdf4bf..f12073948b8 100644
--- a/templates/webapps/galaxy/workflow/editor_generic_form.mako
+++ b/templates/webapps/galaxy/workflow/editor_generic_form.mako
@@ -1,12 +1,22 @@
 <form name="${form.name}" action="${h.url_for( controller='workflow', action='editor_form_post' )}" method="post">
-    <div class="toolForm">
-        <div class="toolFormTitle">${form.title}</div>
-        <div class="toolFormBody">
+    <div class="ui-portlet-narrow">
+        <div class="portlet-header">
+          <div class="portlet-title">
+            <span class="portlet-title-text"><b>${form.title}</b></span>
+          </div>
+        </div>
+        <div class="portlet-content">
+          <div class="content">
+            <div class="ui-margin-top"></div>
+            <div>
             <input type="hidden" name="type" value="${module.type}" />
+            <table class="ui-table-plain">
+              <thead></thead>
+              <tbody>
             %if form.inputs:
               %for input in form.inputs:
                   <%
-                  cls = "form-row"
+                  cls = "section-row"
                   if input.error:
                       cls += " form-row-error"
                   extra_attributes = ""
@@ -16,38 +26,37 @@
                   if input.type:
                     type_attribute = "type=\"input.type\""
                   %>
-                  <div class="${cls}">
-                    <label>
+                  <tr class="${cls}"><td><div class="ui-table-form-element">
+                    <div class="ui-table-form-title">
                         ${input.label}:
-                    </label>
-                    <div style="float: left; width: 250px; margin-right: 10px;">
-
+                    </div>
+                    <div class="ui-table-form-field" style="display: block;">
                         <input ${type_attribute} name="${input.name | h}" value="${input.value | h}" size="30" ${extra_attributes}>
                         %if hasattr( input, "body_html" ):
                               ${input.body_html()}
                             </input>
                         %endif
-                    </div>
-                    %if input.error:
-                    <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
-                        <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${input.error}</span></div>
-                    </div>
-                    %endif
+                      %if input.error:
+                      <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;">
+                          <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}">&nbsp;<span style="vertical-align: middle;">${input.error}</span></div>
+                      </div>
+                      %endif
   
-                    %if input.help:
-                    <div class="toolParamHelp" style="clear: both;">
-                        ${input.help}
-                    </div>
-                    %endif
+                      %if input.help:
+                      <div class="ui-table-form-info">
+                          ${input.help}
+                      </div>
+                      %endif
+                    </div><!-- ui-table-form-field -->
   
-                    <div style="clear: both"></div>
-  
-                  </div>
+                  </div></td></tr>
               %endfor
             %else:
               <div class="form-row"><i>No options</i></div>
             %endif
+              </tbody>
             </table>
-        </div>
+          </div> <!-- content -->
+        </div><!-- portlet-content -->
     </div>
 </form>

From d7ac52f6bb61fe360198f91310a3e22076183d7b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 17:49:33 +0000
Subject: [PATCH 09/12] Add icons to existing workflow steps in workflow
 editor.

Tools have an icon there.
---
 .../scripts/mvc/workflow/workflow-view.js       | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index c8d6a9bd4d5..cd799467ab4 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -44,6 +44,21 @@ function reset_tool_search( initValue ) {
     }
 }
 
+NODE_ICONS = {
+    'tool': 'fa-wrench',
+    'data_input': 'fa-file-o',
+    'data_collection_input': 'fa-folder-o',
+    'pause': 'fa-pause'
+}
+
+add_node_icon = function($to_el, nodeType) {
+    var iconStyle = NODE_ICONS[nodeType];
+    if(iconStyle) {
+        var $icon = $('<i class="icon fa">&nbsp;</i>').addClass(iconStyle);
+        $to_el.before($icon);
+    }
+}
+
 
 // Really a shell of a real backbone view, but refactoring in the right
 // direction I think.
@@ -62,6 +77,8 @@ EditorFormView = Backbone.View.extend({
 
         if (node && node.id != 'no-node') {
             $el.find('table:first').after(this._genericStepAttributesTemplate( node ));
+            var nodeType = node.type;
+            add_node_icon($el.find('.portlet-title-text'), nodeType);
             ($el.find( 'form' ).length > 0) && $el.find( 'form' ).ajaxForm( {
                 type: 'POST',
                 dataType: 'json',

From e3161b4671e9fb19a47c7f341e3fb46617111a9e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 5 Dec 2015 18:49:11 +0000
Subject: [PATCH 10/12] Add support for workflow step labels in editor.

 - If a step has a label, display it in the step editor side panel title.
 - Allow clicking the title to change the label.
 - Display the label (if set) as the workflow node box title.
 - Add icon to workflow node since the title might not be related to type anymore.
 - Enforce unique labels accross the workflow in the editor.
 - Qunit test cases for some of this behavior and other recent changes.
---
 .../scripts/mvc/workflow/workflow-manager.js  | 39 +++++++++++++
 .../scripts/mvc/workflow/workflow-node.js     |  9 ++-
 .../mvc/workflow/workflow-view-node.js        |  4 ++
 .../scripts/mvc/workflow/workflow-view.js     | 58 ++++++++++++++-----
 .../webapps/galaxy/controllers/workflow.py    |  7 ++-
 lib/galaxy/workflow/modules.py                |  7 +++
 .../maps/mvc/workflow/workflow-manager.js.map |  2 +-
 static/maps/mvc/workflow/workflow-node.js.map |  2 +-
 .../mvc/workflow/workflow-view-node.js.map    |  2 +-
 static/maps/mvc/workflow/workflow-view.js.map |  2 +-
 .../scripts/mvc/workflow/workflow-manager.js  |  2 +-
 static/scripts/mvc/workflow/workflow-node.js  |  2 +-
 .../mvc/workflow/workflow-view-node.js        |  2 +-
 static/scripts/mvc/workflow/workflow-view.js  |  2 +-
 .../galaxy/workflow/editor_generic_form.mako  | 10 +++-
 test/qunit/tests/workflow_editor_tests.js     | 39 ++++++++++---
 16 files changed, 154 insertions(+), 35 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 42de4396f43..7fea600a132 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -7,8 +7,47 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         this.name = null;
         this.has_changes = false;
         this.active_form_has_changes = false;
+        this.nodeLabels = {}; // TODO: track and enforce output labels also
     }
     $.extend( Workflow.prototype, {
+        canLabelNodeWith: function( label ) {
+            if( label ) {
+                return ! (label in this.nodeLabels);
+            } else {
+                // empty labels are non-exclusive, so allow this one.
+                return true;
+            }
+        },
+        registerNodeLabel: function( label ) {
+            if( label ) {
+                this.nodeLabels[label] = true;
+            }
+        },
+        unregisterNodeLabel: function( label ) {
+            if( label ) {
+                delete this.nodeLabels[label];
+            }
+        },
+        updateNodeLabel: function( fromLabel, toLabel ) {
+            if( fromLabel ) {
+                this.unregisterNodeLabel( fromLabel );
+            }
+            if( ! this.canLabelNodeWith( toLabel ) ) {
+                // TODO: Improve display of this error.
+                alert("Workflow contains duplicate node labels " + toLabel + ". This must be fixed before it can be saved.");
+            }
+            if( toLabel ) {
+                this.registerNodeLabel( toLabel );
+            }
+        },
+        attemptUpdateNodeLabel: function( node, label ) {
+            if( this.canLabelNodeWith( label ) ) {
+                node.setLabel( label );
+                return true;
+            } else {
+                return false;
+            }
+        },
         create_node: function ( type, title_text, content_id ) {
             var node = this.app.prebuildNode( type, title_text, content_id );
             this.add_node( node );
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index fb4feb69844..7395f22a8ff 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -124,6 +124,10 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             // Remove active class
             $(element).removeClass( "toolForm-active" );
         },
+        setLabel: function(label) {
+            this.app.workflow.updateNodeLabel(this.label, label);
+            this.label = label || null;
+        },
         init_field_data : function ( data ) {
             if ( data.type ) {
                 this.type = data.type;
@@ -135,7 +139,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             this.tooltip = data.tooltip ? data.tooltip : "";
             this.annotation = data.annotation;
             this.post_job_actions = data.post_job_actions ? data.post_job_actions : {};
-            this.label = data.label;
+            this.setLabel(data.label);
             this.uuid = data.uuid;
             this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];
 
@@ -165,6 +169,8 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
             this.form_html = data.form_html;
             this.tool_errors = data.tool_errors;
             this.annotation = data['annotation'];
+            this.setLabel(data.label);
+
             if( "post_job_actions" in data ) {
                 // Won't be present in response for data inputs
                 var pja_in = $.parseJSON(data.post_job_actions);
@@ -184,6 +190,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) {
                 unusedView.el.terminal.destroy();
             } );
             nodeView.terminalViews = newTerminalViews;
+            node.nodeView.render();
             // In general workflow editor assumes tool outputs don't change in # or
             // type (not really valid right?) but adding special logic here for
             // data collection input parameters that can have their collection
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index d702d17e7b3..9fb01bb4980 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -11,6 +11,10 @@ define(['mvc/workflow/workflow-view-terminals', 'mvc/workflow/workflow-view-data
         },
 
         render: function() {
+            var label = this.node.label;
+            if(label) {
+                this.$el.find(".nodeTitle").text(label);
+            }
             this.renderToolErrors();
             this.$el.css( "width", Math.min(250, Math.max( this.$el.width(), this.output_width )));
         },
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index cd799467ab4..f694825ce78 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -7,6 +7,7 @@ define([
     'mvc/workflow/workflow-node',
     'mvc/tool/tools-form-workflow',
     'utils/async-save-text',
+    'ui/editable-text',
 ], function( Utils, Globals, Workflow, WorkflowCanvas, Node, ToolsForm, async_save_text ){
 
 // Reset tool search to start state.
@@ -79,6 +80,26 @@ EditorFormView = Backbone.View.extend({
             $el.find('table:first').after(this._genericStepAttributesTemplate( node ));
             var nodeType = node.type;
             add_node_icon($el.find('.portlet-title-text'), nodeType);
+            var $titleText = $el.find(".portlet-title-text");
+            $titleText.data('last-value', $titleText.text());
+            $titleText.make_text_editable({
+                on_finish: function( newLabel ){
+                    var lastValue = $titleText.data("last-value");
+                    if( newLabel == lastValue ) {
+                        return;
+                    }
+
+                    var workflow = workflowView.workflow;
+                    if( workflow.attemptUpdateNodeLabel( node, newLabel ) ) {
+                        $el.find("input[name='label']").val(newLabel);
+                        $titleText.data("last-value", newLabel);
+                        $el.find('form').submit();
+                    } else {
+                        alert("Step label " + newLabel + " already exists, cannot update label.");
+                        $titleText.text(lastValue);
+                    }
+                }
+            });
             ($el.find( 'form' ).length > 0) && $el.find( 'form' ).ajaxForm( {
                 type: 'POST',
                 dataType: 'json',
@@ -717,20 +738,27 @@ EditorFormView = Backbone.View.extend({
             return ( this.type_to_type[child] ) && ( parent in this.type_to_type[child] );
         },
 
+        $newNodeElement: function(type, title_text) {
+            var $f = $("<div class='toolForm toolFormInCanvas'></div>");
+            var $title = $("<div class='toolFormTitle unselectable'><span class='nodeTitle'>" + title_text + "</div></div>" );
+            add_node_icon($title.find('.nodeTitle'), type);
+            $f.append( $title );
+            $f.css( "left", $(window).scrollLeft() + 20 );
+            $f.css( "top", $(window).scrollTop() + 20 );
+            var $b = $("<div class='toolFormBody'></div>");
+            $f.append($b);
+            return $f
+        },
+
         prebuildNode: function ( type, title_text, content_id ) {
             var self = this;
-            var f = $("<div class='toolForm toolFormInCanvas'></div>");
-            var node = new Node( this, { element: f } );
+            var $f = this.$newNodeElement( type, title_text );
+            var node = new Node( this, { element: $f } );
             node.type = type;
             node.content_id = content_id;
-            var title = $("<div class='toolFormTitle unselectable'>" + title_text + "</div>" );
-            f.append( title );
-            f.css( "left", $(window).scrollLeft() + 20 ); f.css( "top", $(window).scrollTop() + 20 );
-            var b = $("<div class='toolFormBody'></div>");
             var tmp = "<div><img height='16' align='middle' src='" + Galaxy.root + "static/images/loading_small_white_bg.gif'/> loading tool info...</div>";
-            b.append( tmp );
+            $f.find(".toolFormBody").append(tmp);
             node.form_html = tmp;
-            f.append( b );
             // Fix width to computed width
             // Now add floats
             var buttons = $("<div class='buttons' style='float: right;'></div>");
@@ -738,17 +766,17 @@ EditorFormView = Backbone.View.extend({
                 node.destroy();
             }));
             // Place inside container
-            f.appendTo( "#canvas-container" );
+            $f.appendTo( "#canvas-container" );
             // Position in container
             var o = $("#canvas-container").position();
             var p = $("#canvas-container").parent();
-            var width = f.width();
-            var height = f.height();
-            f.css( { left: ( - o.left ) + ( p.width() / 2 ) - ( width / 2 ), top: ( - o.top ) + ( p.height() / 2 ) - ( height / 2 ) } );
-            buttons.prependTo( title );
+            var width = $f.width();
+            var height = $f.height();
+            $f.css( { left: ( - o.left ) + ( p.width() / 2 ) - ( width / 2 ), top: ( - o.top ) + ( p.height() / 2 ) - ( height / 2 ) } );
+            buttons.prependTo( $f.find(".toolFormTitle" ) );
             width += ( buttons.width() + 10 );
-            f.css( "width", width );
-            $(f).bind( "dragstart", function() {
+            $f.css( "width", width );
+            $f.bind( "dragstart", function() {
                 self.workflow.activate_node( node );
             }).bind( "dragend", function() {
                 self.workflow.node_changed( this );
diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py
index e7a63f0cdac..24eb397b893 100644
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -613,7 +613,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         return trans.fill_template( "workflow/editor.mako", stored=stored, annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) )
 
     @web.json
-    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, **incoming ):
+    def editor_form_post( self, trans, type='tool', tool_id=None, annotation=None, label=None, **incoming ):
         """
         Accepts a tool state and incoming values, and generates a new tool
         form and some additional information, packed into a json dictionary.
@@ -625,12 +625,14 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         module = module_factory.from_dict( trans, {
             'type': type,
             'tool_id': tool_id,
-            'tool_state': tool_state
+            'tool_state': tool_state,
+            'label': label or None,
         } )
         # update module state
         module.update_state( incoming )
         if type == 'tool':
             return {
+                'label': module.label,
                 'tool_state': module.get_state(),
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),
@@ -641,6 +643,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             }
         else:
             return {
+                'label': module.label,
                 'tool_state': module.get_state(),
                 'data_inputs': module.get_data_inputs(),
                 'data_outputs': module.get_data_outputs(),
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
index 0e93e984652..30a67c9913f 100644
--- a/lib/galaxy/workflow/modules.py
+++ b/lib/galaxy/workflow/modules.py
@@ -200,6 +200,7 @@ class SimpleWorkflowModule( WorkflowModule ):
     def new( Class, trans, content_id=None ):
         module = Class( trans )
         module.state = Class.default_state()
+        module.label = None
         return module
 
     @classmethod
@@ -207,12 +208,14 @@ class SimpleWorkflowModule( WorkflowModule ):
         module = Class( trans )
         state = loads( d["tool_state"] )
         module.recover_state( state )
+        module.label = d.get("label", None) or None
         return module
 
     @classmethod
     def from_workflow_step( Class, trans, step ):
         module = Class( trans )
         module.recover_state( step.tool_inputs )
+        module.label = step.label
         return module
 
     @classmethod
@@ -511,6 +514,7 @@ class ToolModule( WorkflowModule ):
             error_message = "Attempted to create new workflow module for invalid tool_id, no tool with id - %s." % content_id
             raise Exception( error_message )
         module.state = module.tool.new_state( trans )
+        module.label = None
         return module
 
     @classmethod
@@ -519,6 +523,7 @@ class ToolModule( WorkflowModule ):
         tool_version = str( d.get( 'tool_version', None ) )
         module = Class( trans, tool_id, tool_version=tool_version )
         module.state = galaxy.tools.DefaultToolState()
+        module.label = d.get("label", None) or None
         if module.tool is not None:
             if d.get('tool_version', 'Unspecified') != module.get_tool_version():
                 message = "%s: using version '%s' instead of version '%s' indicated in this workflow." % ( tool_id, d.get( 'tool_version', 'Unspecified' ), module.get_tool_version() )
@@ -555,6 +560,7 @@ class ToolModule( WorkflowModule ):
             module.recover_state( step.tool_inputs )
             module.errors = step.tool_errors
             module.workflow_outputs = step.workflow_outputs
+            module.label = step.label or None
             pjadict = {}
             for pja in step.post_job_actions:
                 pjadict[pja.action_type] = pja
@@ -730,6 +736,7 @@ class ToolModule( WorkflowModule ):
         # set. We also need to make sure all datasets have a dummy value
         # for dependencies to see
 
+        self.label = incoming.get("label", None) or None
         self.post_job_actions = ActionBox.handle_incoming(incoming)
 
         make_runtime_key = incoming.get( 'make_runtime', None )
diff --git a/static/maps/mvc/workflow/workflow-manager.js.map b/static/maps/mvc/workflow/workflow-manager.js.map
index 6c4348c37c4..047ff3aaf0a 100644
--- a/static/maps/mvc/workflow/workflow-manager.js.map
+++ b/static/maps/mvc/workflow/workflow-manager.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/workflow/workflow-node.js.map b/static/maps/mvc/workflow/workflow-node.js.map
index f07e1b25d75..eff73424320 100644
--- a/static/maps/mvc/workflow/workflow-node.js.map
+++ b/static/maps/mvc/workflow/workflow-node.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/workflow/workflow-view-node.js.map b/static/maps/mvc/workflow/workflow-view-node.js.map
index b248c82942a..3563b9c8659 100644
--- a/static/maps/mvc/workflow/workflow-view-node.js.map
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diff --git a/static/maps/mvc/workflow/workflow-view.js.map b/static/maps/mvc/workflow/workflow-view.js.map
index 29e6d1f76fd..fd3ed8a7d9b 100644
--- a/static/maps/mvc/workflow/workflow-view.js.map
+++ b/static/maps/mvc/workflow/workflow-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-manager.js b/static/scripts/mvc/workflow/workflow-manager.js
index 2bbfa9d4f99..f6bc230e567 100644
--- a/static/scripts/mvc/workflow/workflow-manager.js
+++ b/static/scripts/mvc/workflow/workflow-manager.js
@@ -1,2 +1,2 @@
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a=!1,b=!1;if($.each(this.nodes,function(c,d){d.workflow_outputs&&d.workflow_outputs.length>0&&(a=!0),$.each(d.post_job_actions,function(a,c){"HideDatasetAction"===c.action_type&&(b=!0)})}),a!==!1||b!==!1){var c=this;$.each(this.nodes,function(b,d){if("tool"===d.type){var e=!1;null==d.post_job_actions&&(d.post_job_actions={},e=!0);var f=[];$.each(d.post_job_actions,function(a,b){"HideDatasetAction"==b.action_type&&f.push(a)}),f.length>0&&$.each(f,function(a,b){e=!0,delete d.post_job_actions[b]}),a&&$.each(d.output_terminals,function(a,b){var c=!d.isWorkflowOutput(b.name);if(c===!0){e=!0;var f={action_type:"HideDatasetAction",output_name:b.name,action_arguments:{}};d.post_job_actions["HideDatasetAction"+b.name]=null,d.post_job_actions["HideDatasetAction"+b.name]=f}}),c.active_node==d&&e===!0&&c.reload_active_node()}})}},to_simple:function(){var a={};return $.each(this.nodes,function(b,c){var d={};$.each(c.input_terminals,function(a,b){d[b.name]=null;var c=[];$.each(b.connectors,function(a,e){c[a]={id:e.handle1.node.id,output_name:e.handle1.name},d[b.name]=c})});var e={};c.post_job_actions&&$.each(c.post_job_actions,function(a,b){var c={action_type:b.action_type,output_name:b.output_name,action_arguments:b.action_arguments};e[b.action_type+b.output_name]=null,e[b.action_type+b.output_name]=c}),c.workflow_outputs||(c.workflow_outputs=[]);var f={id:c.id,type:c.type,tool_id:c.tool_id,tool_state:c.tool_state,tool_errors:c.tool_errors,input_connections:d,position:$(c.element).position(),annotation:c.annotation,post_job_actions:c.post_job_actions,uuid:c.uuid,label:c.label,workflow_outputs:c.workflow_outputs};a[c.id]=f}),{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var d=!1;$.each(b.steps,function(a,b){var e=wf.app.prebuildNode(b.type,b.name,b.tool_id);e.init_field_data(b),b.position&&e.element.css({top:b.position.top,left:b.position.left}),e.id=b.id,wf.nodes[e.id]=e,c=Math.max(c,parseInt(a)),d||"tool"!==e.type||(e.workflow_outputs.length>0?d=!0:$.each(e.post_job_actions,function(a,b){"HideDatasetAction"===b.action_type&&(d=!0)}))}),wf.id_counter=c+1,$.each(b.steps,function(b,c){var e=wf.nodes[b];$.each(c.input_connections,function(b,c){c&&($.isArray(c)||(c=[c]),$.each(c,function(c,d){var f=wf.nodes[d.id],g=new a;g.connect(f.output_terminals[d.output_name],e.input_terminals[b]),g.redraw()}))}),d&&"tool"===e.type&&$.each(e.output_terminals,function(a,b){void 0===e.post_job_actions["HideDatasetAction"+b.name]&&(e.addWorkflowOutput(b.name),callout=$(e.element).find(".callout."+b.name),callout.find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),wf.has_changes=!0)})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,$("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node(),this.activate_node(a)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showToolForm("<div>No node selected</div>",{id:"no-node"})},activate_node:function(a){this.active_node!=a&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showToolForm(a.form_html,a),a.make_active(),this.active_node=a)},node_changed:function(a,b){this.has_changes=!0,this.active_node==a&&b&&(this.check_changes_in_active_form(),this.app.showToolForm(a.form_html,a))},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var a={},b={};for($.each(this.nodes,function(c){void 0===a[c]&&(a[c]=0),void 0===b[c]&&(b[c]=[])}),$.each(this.nodes,function(c,d){$.each(d.input_terminals,function(c,e){$.each(e.connectors,function(c,e){var f=e.handle1.node;a[d.id]+=1,b[f.id].push(d.id)})})}),node_ids_by_level=[];;){level_parents=[];for(var c in a)0==a[c]&&level_parents.push(c);if(0==level_parents.length)break;node_ids_by_level.push(level_parents);for(var d in level_parents){var e=level_parents[d];delete a[e];for(var f in b[e])a[b[e][f]]-=1}}if(!a.length){var g=this.nodes,h=80;v_pad=30;var i=h;$.each(node_ids_by_level,function(a,b){b.sort(function(a,b){return $(g[a].element).position().top-$(g[b].element).position().top});var c=0,d=v_pad;$.each(b,function(a,b){var e=g[b],f=$(e.element);$(f).css({top:d,left:i}),c=Math.max(c,$(f).width()),d+=$(f).height()+v_pad}),i+=c+h}),$.each(g,function(a,b){b.redraw()})}},bounds_for_all_nodes:function(){var a,b=1/0,c=-(1/0),d=1/0,f=-(1/0);return $.each(this.nodes,function(g,h){e=$(h.element),a=e.position(),b=Math.min(b,a.left),c=Math.max(c,a.left+e.width()),d=Math.min(d,a.top),f=Math.max(f,a.top+e.width())}),{xmin:b,xmax:c,ymin:d,ymax:f}},fit_canvas_to_nodes:function(){function a(a,b){return Math.ceil(a/b)*b}function b(a,b){return b>a||a>3*b?(new_pos=(Math.ceil(a%b/b)+1)*b,-(a-new_pos)):0}var c=this.bounds_for_all_nodes(),d=this.canvas_container.position(),e=this.canvas_container.parent(),f=b(c.xmin,100),g=b(c.ymin,100);f=Math.max(f,d.left),g=Math.max(g,d.top);var h=d.left-f,i=d.top-g,j=a(c.xmax+100,100)+f,k=a(c.ymax+100,100)+g;j=Math.max(j,-h+e.width()),k=Math.max(k,-i+e.height()),this.canvas_container.css({left:h,top:i,width:j,height:k}),this.canvas_container.children().each(function(){var a=$(this).position();$(this).css("left",a.left+f),$(this).css("top",a.top+g)})}}),b});
+define(["mvc/workflow/workflow-connector"],function(a){function b(a,b){this.app=a,this.canvas_container=b,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.nodeLabels={}}return $.extend(b.prototype,{canLabelNodeWith:function(a){return a?!(a in this.nodeLabels):!0},registerNodeLabel:function(a){a&&(this.nodeLabels[a]=!0)},unregisterNodeLabel:function(a){a&&delete this.nodeLabels[a]},updateNodeLabel:function(a,b){a&&this.unregisterNodeLabel(a),this.canLabelNodeWith(b)||alert("Workflow contains duplicate node labels "+b+". This must be fixed before it can be saved."),b&&this.registerNodeLabel(b)},attemptUpdateNodeLabel:function(a,b){return this.canLabelNodeWith(b)?(a.setLabel(b),!0):!1},create_node:function(a,b,c){var d=this.app.prebuildNode(a,b,c);return this.add_node(d),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(d),d},add_node:function(a){a.id=this.id_counter,a.element.attr("id","wf-node-step-"+a.id),this.id_counter++,this.nodes[a.id]=a,this.has_changes=!0,a.workflow=this},remove_node:function(a){this.active_node==a&&this.clear_active_node(),delete this.nodes[a.id],this.has_changes=!0},remove_all:function(){wf=this,$.each(this.nodes,function(a,b){b.destroy(),wf.remove_node(b)})},rectify_workflow_outputs:function(){var a=!1,b=!1;if($.each(this.nodes,function(c,d){d.workflow_outputs&&d.workflow_outputs.length>0&&(a=!0),$.each(d.post_job_actions,function(a,c){"HideDatasetAction"===c.action_type&&(b=!0)})}),a!==!1||b!==!1){var c=this;$.each(this.nodes,function(b,d){if("tool"===d.type){var e=!1;null==d.post_job_actions&&(d.post_job_actions={},e=!0);var f=[];$.each(d.post_job_actions,function(a,b){"HideDatasetAction"==b.action_type&&f.push(a)}),f.length>0&&$.each(f,function(a,b){e=!0,delete d.post_job_actions[b]}),a&&$.each(d.output_terminals,function(a,b){var c=!d.isWorkflowOutput(b.name);if(c===!0){e=!0;var f={action_type:"HideDatasetAction",output_name:b.name,action_arguments:{}};d.post_job_actions["HideDatasetAction"+b.name]=null,d.post_job_actions["HideDatasetAction"+b.name]=f}}),c.active_node==d&&e===!0&&c.reload_active_node()}})}},to_simple:function(){var a={};return $.each(this.nodes,function(b,c){var d={};$.each(c.input_terminals,function(a,b){d[b.name]=null;var c=[];$.each(b.connectors,function(a,e){c[a]={id:e.handle1.node.id,output_name:e.handle1.name},d[b.name]=c})});var e={};c.post_job_actions&&$.each(c.post_job_actions,function(a,b){var c={action_type:b.action_type,output_name:b.output_name,action_arguments:b.action_arguments};e[b.action_type+b.output_name]=null,e[b.action_type+b.output_name]=c}),c.workflow_outputs||(c.workflow_outputs=[]);var f={id:c.id,type:c.type,tool_id:c.content_id,tool_state:c.tool_state,tool_errors:c.tool_errors,input_connections:d,position:$(c.element).position(),annotation:c.annotation,post_job_actions:c.post_job_actions,uuid:c.uuid,label:c.label,workflow_outputs:c.workflow_outputs};a[c.id]=f}),{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var d=!1;$.each(b.steps,function(a,b){var e=wf.app.prebuildNode(b.type,b.name,b.tool_id);e.init_field_data(b),b.position&&e.element.css({top:b.position.top,left:b.position.left}),e.id=b.id,wf.nodes[e.id]=e,c=Math.max(c,parseInt(a)),d||"tool"!==e.type||(e.workflow_outputs.length>0?d=!0:$.each(e.post_job_actions,function(a,b){"HideDatasetAction"===b.action_type&&(d=!0)}))}),wf.id_counter=c+1,$.each(b.steps,function(b,c){var e=wf.nodes[b];$.each(c.input_connections,function(b,c){c&&($.isArray(c)||(c=[c]),$.each(c,function(c,d){var f=wf.nodes[d.id],g=new a;g.connect(f.output_terminals[d.output_name],e.input_terminals[b]),g.redraw()}))}),d&&"tool"===e.type&&$.each(e.output_terminals,function(a,b){void 0===e.post_job_actions["HideDatasetAction"+b.name]&&(e.addWorkflowOutput(b.name),callout=$(e.element).find(".callout."+b.name),callout.find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),wf.has_changes=!0)})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,$("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node(),this.activate_node(a)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showToolForm("<div>No node selected</div>",{id:"no-node"})},activate_node:function(a){this.active_node!=a&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showToolForm(a.form_html,a),a.make_active(),this.active_node=a)},node_changed:function(a,b){this.has_changes=!0,this.active_node==a&&b&&(this.check_changes_in_active_form(),this.app.showToolForm(a.form_html,a))},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var a={},b={};for($.each(this.nodes,function(c){void 0===a[c]&&(a[c]=0),void 0===b[c]&&(b[c]=[])}),$.each(this.nodes,function(c,d){$.each(d.input_terminals,function(c,e){$.each(e.connectors,function(c,e){var f=e.handle1.node;a[d.id]+=1,b[f.id].push(d.id)})})}),node_ids_by_level=[];;){level_parents=[];for(var c in a)0==a[c]&&level_parents.push(c);if(0==level_parents.length)break;node_ids_by_level.push(level_parents);for(var d in level_parents){var e=level_parents[d];delete a[e];for(var f in b[e])a[b[e][f]]-=1}}if(!a.length){var g=this.nodes,h=80;v_pad=30;var i=h;$.each(node_ids_by_level,function(a,b){b.sort(function(a,b){return $(g[a].element).position().top-$(g[b].element).position().top});var c=0,d=v_pad;$.each(b,function(a,b){var e=g[b],f=$(e.element);$(f).css({top:d,left:i}),c=Math.max(c,$(f).width()),d+=$(f).height()+v_pad}),i+=c+h}),$.each(g,function(a,b){b.redraw()})}},bounds_for_all_nodes:function(){var a,b=1/0,c=-(1/0),d=1/0,f=-(1/0);return $.each(this.nodes,function(g,h){e=$(h.element),a=e.position(),b=Math.min(b,a.left),c=Math.max(c,a.left+e.width()),d=Math.min(d,a.top),f=Math.max(f,a.top+e.width())}),{xmin:b,xmax:c,ymin:d,ymax:f}},fit_canvas_to_nodes:function(){function a(a,b){return Math.ceil(a/b)*b}function b(a,b){return b>a||a>3*b?(new_pos=(Math.ceil(a%b/b)+1)*b,-(a-new_pos)):0}var c=this.bounds_for_all_nodes(),d=this.canvas_container.position(),e=this.canvas_container.parent(),f=b(c.xmin,100),g=b(c.ymin,100);f=Math.max(f,d.left),g=Math.max(g,d.top);var h=d.left-f,i=d.top-g,j=a(c.xmax+100,100)+f,k=a(c.ymax+100,100)+g;j=Math.max(j,-h+e.width()),k=Math.max(k,-i+e.height()),this.canvas_container.css({left:h,top:i,width:j,height:k}),this.canvas_container.children().each(function(){var a=$(this).position();$(this).css("left",a.left+f),$(this).css("top",a.top+g)})}}),b});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-manager.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-node.js b/static/scripts/mvc/workflow/workflow-node.js
index c91dbe18b4d..046aff233e0 100644
--- a/static/scripts/mvc/workflow/workflow-node.js
+++ b/static/scripts/mvc/workflow/workflow-node.js
@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.tool_errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a){this.isWorkflowOutput(a)||this.workflow_outputs.push({output_name:a})},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.form_html=b.form_html,this.tool_state=b.tool_state,this.tool_errors=b.tool_errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.label=b.label,this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.form_html=a.form_html,this.tool_errors=a.tool_errors,this.annotation=a.annotation,"post_job_actions"in a){var c=$.parseJSON(a.post_job_actions);this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+a+"</div>";this.form_html=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b});
+define(["mvc/workflow/workflow-view-node"],function(a){var b=Backbone.Model.extend({initialize:function(a,b){this.app=a,this.element=b.element,this.input_terminals={},this.output_terminals={},this.tool_errors={},this.workflow_outputs=[]},getWorkflowOutput:function(a){return _.findWhere(this.workflow_outputs,{output_name:a})},isWorkflowOutput:function(a){return void 0!=this.getWorkflowOutput(a)},removeWorkflowOutput:function(a){for(;this.isWorkflowOutput(a);)this.workflow_outputs.splice(this.getWorkflowOutput(a),1)},addWorkflowOutput:function(a){this.isWorkflowOutput(a)||this.workflow_outputs.push({output_name:a})},connectedOutputTerminals:function(){return this._connectedTerminals(this.output_terminals)},_connectedTerminals:function(a){var b=[];return $.each(a,function(a,c){c.connectors.length>0&&b.push(c)}),b},hasConnectedOutputTerminals:function(){var a=this.output_terminals;for(var b in a)if(a[b].connectors.length>0)return!0;return!1},connectedMappedInputTerminals:function(){return this._connectedMappedTerminals(this.input_terminals)},hasConnectedMappedInputTerminals:function(){var a=this.input_terminals;for(var b in a){var c=a[b];if(c.connectors.length>0&&c.isMappedOver())return!0}return!1},_connectedMappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&c.connectors.length>0&&b.push(c)}),b},mappedInputTerminals:function(){return this._mappedTerminals(this.input_terminals)},_mappedTerminals:function(a){var b=[];return $.each(a,function(a,c){var d=c.mapOver();d.isCollection&&b.push(c)}),b},hasMappedOverInputTerminals:function(){var a=!1;return _.each(this.input_terminals,function(b){var c=b.mapOver();c.isCollection&&(a=!0)}),a},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()}),$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()}),$.each(this.output_terminals,function(a,b){b.destroy()}),this.app.workflow.remove_node(this),$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);!function(b){b.removeChild(a),b.appendChild(a)}(a.parentNode),$(a).removeClass("toolForm-active")},setLabel:function(a){this.app.workflow.updateNodeLabel(this.label,a),this.label=a||null},init_field_data:function(b){b.type&&(this.type=b.type),this.name=b.name,this.form_html=b.form_html,this.tool_state=b.tool_state,this.tool_errors=b.tool_errors,this.tooltip=b.tooltip?b.tooltip:"",this.annotation=b.annotation,this.post_job_actions=b.post_job_actions?b.post_job_actions:{},this.setLabel(b.label),this.uuid=b.uuid,this.workflow_outputs=b.workflow_outputs?b.workflow_outputs:[];var c=this,d=new a({el:this.element[0],node:c});c.nodeView=d,$.each(b.data_inputs,function(a,b){d.addDataInput(b)}),b.data_inputs.length>0&&b.data_outputs.length>0&&d.addRule(),$.each(b.data_outputs,function(a,b){d.addDataOutput(b)}),d.render(),this.app.workflow.node_changed(this,!0)},update_field_data:function(a){var b=this;if(nodeView=b.nodeView,this.tool_state=a.tool_state,this.form_html=a.form_html,this.tool_errors=a.tool_errors,this.annotation=a.annotation,this.setLabel(a.label),"post_job_actions"in a){var c=$.parseJSON(a.post_job_actions);this.post_job_actions=c?c:{}}b.nodeView.renderToolErrors();var d=nodeView.$("div.inputs"),e=nodeView.newInputsDiv(),f={};_.each(a.data_inputs,function(a){var c=b.nodeView.addDataInput(a,e);f[a.name]=c}),_.each(_.difference(_.values(nodeView.terminalViews),_.values(f)),function(a){a.el.terminal.destroy()}),nodeView.terminalViews=f,b.nodeView.render(),1==a.data_outputs.length&&"collection_type"in a.data_outputs[0]&&nodeView.updateDataOutput(a.data_outputs[0]),d.replaceWith(e),this.markChanged(),this.redraw()},error:function(a){var b=$(this.element).find(".toolFormBody");b.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+a+"</div>";this.form_html=c,b.html(c),this.app.workflow.node_changed(this)},markChanged:function(){this.app.workflow.node_changed(this)}});return b});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-node.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-view-node.js b/static/scripts/mvc/workflow/workflow-view-node.js
index 14b00a490da..95c4063adb2 100644
--- a/static/scripts/mvc/workflow/workflow-view-node.js
+++ b/static/scripts/mvc/workflow/workflow-view-node.js
@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
+define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){var a=this.node.label;a&&this.$el.find(".nodeTitle").text(a),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view-node.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-view.js b/static/scripts/mvc/workflow/workflow-view.js
index 514217500e9..1a17fa9ffc4 100644
--- a/static/scripts/mvc/workflow/workflow-view.js
+++ b/static/scripts/mvc/workflow/workflow-view.js
@@ -1,2 +1,2 @@
-define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text"],function(a,b,c,d,e,f,g){function h(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id&&(c.find(".toolForm:first").after(this._genericStepAttributesTemplate(e)),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})}))},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function i(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)h(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?i():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?i():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),$.ajax({url:this.urls.get_new_module_info,data:{type:"tool",tool_id:a,_:"true"},global:!1,dataType:"json",success:function(a){node.init_field_data(a)},error:function(a){var b="error loading field data";0===a.status&&(b+=", server unavailable"),node.error(b)}})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),$.ajax({url:this.urls.get_new_module_info,data:{type:a,_:"true"},dataType:"json",success:function(a){node.init_field_data(a)},error:function(a){var b="error loading field data";0==a.status&&(b+=", server unavailable"),node.error(b)}})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},prebuildNode:function(a,b,c){var d=this,f=$("<div class='toolForm toolFormInCanvas'></div>"),g=new e(this,{element:f});g.type=a,"tool"==a&&(g.tool_id=c);var h=$("<div class='toolFormTitle unselectable'>"+b+"</div>");f.append(h),f.css("left",$(window).scrollLeft()+20),f.css("top",$(window).scrollTop()+20);var i=$("<div class='toolFormBody'></div>"),j="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";i.append(j),g.form_html=j,f.append(i);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var l=$("#canvas-container").position(),m=$("#canvas-container").parent(),n=f.width(),o=f.height();return f.css({left:-l.left+m.width()/2-n/2,top:-l.top+m.height()/2-o/2}),k.prependTo(h),n+=k.width()+10,f.css("width",n),$(f).bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
+define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text","ui/editable-text"],function(a,b,c,d,e,f,g){function h(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$('<i class="icon fa">&nbsp;</i>').addClass(c);a.before(d)}},EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;if(b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id){c.find("table:first").after(this._genericStepAttributesTemplate(e));var f=e.type;add_node_icon(c.find(".portlet-title-text"),f);var g=c.find(".portlet-title-text");g.data("last-value",g.text()),g.make_text_editable({on_finish:function(a){var b=g.data("last-value");if(a!=b){var f=d.workflow;f.attemptUpdateNodeLabel(e,a)?(c.find("input[name='label']").val(a),g.data("last-value",a),c.find("form").submit()):(alert("Step label "+a+" already exists, cannot update label."),g.text(b))}}}),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})})}},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function i(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)h(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?i():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?i():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},_moduleInitAjax:function(a,b){$.ajax({url:this.urls.get_new_module_info,data:b,global:!1,dataType:"json",success:function(b){a.init_field_data(b)},error:function(b){var c="error loading field data";0===b.status&&(c+=", server unavailable"),a.error(c)}})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),this._moduleInitAjax(node,{type:"tool",content_id:a,_:"true"})},add_node_for_subworkflow:function(a,b){node=this.workflow.create_node("subworkflow",b,a),this._moduleInitAjax(node,{type:"subworkflow",subworkflow_id:a,_:"true"})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),this._moduleInitAjax(node,{type:a,_:"true"})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},$newNodeElement:function(a,b){var c=$("<div class='toolForm toolFormInCanvas'></div>"),d=$("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+b+"</div></div>");add_node_icon(d.find(".nodeTitle"),a),c.append(d),c.css("left",$(window).scrollLeft()+20),c.css("top",$(window).scrollTop()+20);var e=$("<div class='toolFormBody'></div>");return c.append(e),c},prebuildNode:function(a,b,c){var d=this,f=this.$newNodeElement(a,b),g=new e(this,{element:f});g.type=a,g.content_id=c;var h="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";f.find(".toolFormBody").append(h),g.form_html=h;var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var j=$("#canvas-container").position(),k=$("#canvas-container").parent(),l=f.width(),m=f.height();return f.css({left:-j.left+k.width()/2-l/2,top:-j.top+k.height()/2-m/2}),i.prependTo(f.find(".toolFormTitle")),l+=i.width()+10,f.css("width",l),f.bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/workflow/editor_generic_form.mako b/templates/webapps/galaxy/workflow/editor_generic_form.mako
index f12073948b8..7c9add037b9 100644
--- a/templates/webapps/galaxy/workflow/editor_generic_form.mako
+++ b/templates/webapps/galaxy/workflow/editor_generic_form.mako
@@ -1,8 +1,15 @@
 <form name="${form.name}" action="${h.url_for( controller='workflow', action='editor_form_post' )}" method="post">
+    <%
+    label = module.label
+    if label is not None:
+        title = label
+    else:
+        title = form.title
+    %>
     <div class="ui-portlet-narrow">
         <div class="portlet-header">
           <div class="portlet-title">
-            <span class="portlet-title-text"><b>${form.title}</b></span>
+            <span class="portlet-title-text"><b>${title}</b></span>
           </div>
         </div>
         <div class="portlet-content">
@@ -10,6 +17,7 @@
             <div class="ui-margin-top"></div>
             <div>
             <input type="hidden" name="type" value="${module.type}" />
+            <input type="hidden" name="label" value="${label or ''}" />
             <table class="ui-table-plain">
               <thead></thead>
               <tbody>
diff --git a/test/qunit/tests/workflow_editor_tests.js b/test/qunit/tests/workflow_editor_tests.js
index 28954ee6029..46d9bdd671d 100644
--- a/test/qunit/tests/workflow_editor_tests.js
+++ b/test/qunit/tests/workflow_editor_tests.js
@@ -2,6 +2,7 @@
 define([
     "sinon-qunit",
     "test-app",
+    'utils/utils',
     "mvc/workflow/workflow-view",
     "mvc/workflow/workflow-node",
     "mvc/workflow/workflow-view-node",
@@ -11,6 +12,7 @@ define([
 ], function(
     sinon,
     testApp,
+    Utils,
     App,
     Node,
     NodeView,
@@ -296,8 +298,8 @@ define([
         setup: function() {
             this.input_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
             this.output_terminal = { destroy: sinon.spy(), redraw: sinon.spy() };
-            this.element = $("<div><div class='toolFormBody'></div></div>");
             this.app = create_app();
+            this.element = this.app.$newNodeElement( "tool", "newnode" );
             this.node = new Node( this.app, { element: this.element } );
             this.node.input_terminals.i1 = this.input_terminal;
             this.node.output_terminals.o1 = this.output_terminal;
@@ -311,22 +313,24 @@ define([
             f();
             ok( node_changed_spy.calledWith( node ) );
         },
-        init_field_data_simple: function() {
-            var data = {
+        init_field_data_simple: function(option_overrides) {
+            var data = Utils.merge(option_overrides, {
                 data_inputs: [ {name: "input1", extensions: [ "data" ] } ],
                 data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
-            };
+                label: null,
+            });
             this.node.init_field_data( data );
         },
-        update_field_data_with_new_input: function() {
-            var new_data = {
+        update_field_data_with_new_input: function(option_overrides) {
+            var new_data = Utils.merge(option_overrides, {
                 data_inputs: [
                     { name: "input1", extensions: [ "data" ] },
                     { name: "extra_0|input1", extensions: [ "data" ] },
                 ],
                 data_outputs: [ {name: "output1", extensions: [ "data" ] } ],
-                post_job_actions: "{}"
-            };
+                post_job_actions: "{}",
+                label: "New Label"
+            });
             this.node.update_field_data( new_data );
         }
     } );
@@ -368,6 +372,7 @@ define([
                 tooltip: "tool tooltip",
                 annotation: "tool annotation",
                 workflow_outputs: [ {"output_name": "out1"} ],
+                label: "Cat that data.",
             };
             node.init_field_data( data );
             equal( node.type, "tool" );
@@ -376,6 +381,7 @@ define([
             equal( node.tool_state, "ok" );
             equal( node.tooltip, "tool tooltip" );
             equal( node.annotation, "tool annotation" );
+            equal( node.label, "Cat that data." );
             deepEqual( node.post_job_actions, {} );
             deepEqual( node.workflow_outputs, [  {"output_name": "out1"} ] );
         } );
@@ -394,9 +400,26 @@ define([
             equal( test.$( ".input-terminal" ).length, 1 );
             equal( test.$( ".rule" ).length, 1 );
             equal( test.$( ".toolFormBody" ).children().length, 3 );
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            ok( test.$( ".toolFormTitle" ).find("i").hasClass("fa-wrench") );
         } );
     } );
 
+    test( "node title behavior", function() {
+        var test = this;
+        this.expect_workflow_node_changed( function( ) {
+            // Node created with name newnode
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            // init_field_data_simple doesn't change label, so it should
+            // remain original name.
+            test.init_field_data_simple();
+            equal( test.$( ".nodeTitle" ).text(), "newnode" );
+            // Despite awkward name, update does change the label...
+            test.update_field_data_with_new_input();
+            equal( test.$( ".nodeTitle" ).text(), "New Label" );
+        });
+    });
+
     test( "update_field_data updated data inputs and outputs", function() {
         var test = this;
         this.expect_workflow_node_changed( function( ) {

From ef0b6cc459a40227db2e63ee709e9dd5d8fd37c6 Mon Sep 17 00:00:00 2001
From: Martin Cech <cech.marten@gmail.com>
Date: Mon, 7 Dec 2015 15:07:14 -0500
Subject: [PATCH 11/12] show notifications as Toasts and not like JS alerts
 (bleh)

---
 .../galaxy/scripts/mvc/workflow/workflow-manager.js  | 12 ++++++++----
 client/galaxy/scripts/mvc/workflow/workflow-view.js  |  7 ++++---
 static/maps/mvc/workflow/workflow-manager.js.map     |  2 +-
 static/maps/mvc/workflow/workflow-view.js.map        |  2 +-
 static/scripts/mvc/workflow/workflow-manager.js      |  2 +-
 static/scripts/mvc/workflow/workflow-view.js         |  2 +-
 6 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 7fea600a132..070c3aa15f8 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -1,4 +1,8 @@
-define(['mvc/workflow/workflow-connector'], function( Connector ) {
+define([
+    'mvc/workflow/workflow-connector',
+    'libs/toastr'
+    ],
+function( Connector, Toastr ) {
     function Workflow( app, canvas_container ) {
         this.app = app;
         this.canvas_container = canvas_container;
@@ -8,6 +12,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         this.has_changes = false;
         this.active_form_has_changes = false;
         this.nodeLabels = {}; // TODO: track and enforce output labels also
+
     }
     $.extend( Workflow.prototype, {
         canLabelNodeWith: function( label ) {
@@ -33,8 +38,7 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
                 this.unregisterNodeLabel( fromLabel );
             }
             if( ! this.canLabelNodeWith( toLabel ) ) {
-                // TODO: Improve display of this error.
-                alert("Workflow contains duplicate node labels " + toLabel + ". This must be fixed before it can be saved.");
+                Toastr.warning("Workflow contains duplicate node labels " + toLabel + ". This must be fixed before it can be saved.");
             }
             if( toLabel ) {
                 this.registerNodeLabel( toLabel );
@@ -422,4 +426,4 @@ define(['mvc/workflow/workflow-connector'], function( Connector ) {
         }
     });
     return Workflow;
-});
\ No newline at end of file
+});
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index f694825ce78..d2cb0035ceb 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -7,8 +7,9 @@ define([
     'mvc/workflow/workflow-node',
     'mvc/tool/tools-form-workflow',
     'utils/async-save-text',
-    'ui/editable-text',
-], function( Utils, Globals, Workflow, WorkflowCanvas, Node, ToolsForm, async_save_text ){
+    'libs/toastr',
+    'ui/editable-text'
+], function( Utils, Globals, Workflow, WorkflowCanvas, Node, ToolsForm, async_save_text, Toastr ){
 
 // Reset tool search to start state.
 function reset_tool_search( initValue ) {
@@ -95,7 +96,7 @@ EditorFormView = Backbone.View.extend({
                         $titleText.data("last-value", newLabel);
                         $el.find('form').submit();
                     } else {
-                        alert("Step label " + newLabel + " already exists, cannot update label.");
+                        Toastr.warning("Step label " + newLabel + " already exists, cannot update label.");
                         $titleText.text(lastValue);
                     }
                 }
diff --git a/static/maps/mvc/workflow/workflow-manager.js.map b/static/maps/mvc/workflow/workflow-manager.js.map
index 047ff3aaf0a..27171ddefe9 100644
--- a/static/maps/mvc/workflow/workflow-manager.js.map
+++ b/static/maps/mvc/workflow/workflow-manager.js.map
@@ -1 +1 @@
-{"version":3,"file":"workflow-manager.js","sources":["../../../src/mvc/workflow/workflow-manager.js"],"names":["define","Connector","Workflow","app","canvas_container","this","id_counter","nodes","name","has_changes","active_form_has_changes","nodeLabels","$","extend","prototype","canLabelNodeWith","label","registerNodeLabel","unregisterNodeLabel","updateNodeLabel","fromLabel","toLabel","alert","attemptUpdateNodeLabel","node","setLabel","create_node","type","title_text","content_id","prebuildNode","add_node","fit_canvas_to_nodes","canvas_manager","draw_overview","activate_node","id","element","attr","workflow","remove_node","active_node","clear_active_node","remove_all","wf","each","k","v","destroy","rectify_workflow_outputs","using_workflow_outputs","has_existing_pjas","workflow_outputs","length","post_job_actions","pja_id","pja","action_type","self","node_changed","pjas_to_rem","push","i","pja_name","output_terminals","ot_id","ot","create_pja","isWorkflowOutput","output_name","action_arguments","reload_active_node","to_simple","input_connections","input_terminals","t","cons","connectors","c","handle1","act","node_data","tool_id","tool_state","tool_errors","position","annotation","uuid","steps","from_simple","data","max_id","step","init_field_data","css","top","left","Math","max","parseInt","isArray","l","x","other_node","connect","redraw","undefined","addWorkflowOutput","callout","find","Galaxy","root","check_changes_in_active_form","submit","make_inactive","showToolForm","form_html","make_active","force","layout","n_pred","successors","j","other","node_ids_by_level","level_parents","pred_k","sk","all_nodes","h_pad","v_pad","ids","sort","a","b","max_width","width","height","_","bounds_for_all_nodes","p","xmin","xmax","ymin","ymax","e","min","round_up","n","ceil","fix_delta","new_pos","bounds","parent","xmin_delta","ymin_delta","children"],"mappings":"AAAAA,QAAQ,mCAAoC,SAAUC,GAClD,QAASC,GAAUC,EAAKC,GACpBC,KAAKF,IAAMA,EACXE,KAAKD,iBAAmBA,EACxBC,KAAKC,WAAa,EAClBD,KAAKE,SACLF,KAAKG,KAAO,KACZH,KAAKI,aAAc,EACnBJ,KAAKK,yBAA0B,EAC/BL,KAAKM,cA8ZT,MA5ZAC,GAAEC,OAAQX,EAASY,WACfC,iBAAkB,SAAUC,GACxB,MAAIA,KACUA,IAASX,MAAKM,aAGjB,GAGfM,kBAAmB,SAAUD,GACrBA,IACAX,KAAKM,WAAWK,IAAS,IAGjCE,oBAAqB,SAAUF,GACvBA,SACOX,MAAKM,WAAWK,IAG/BG,gBAAiB,SAAUC,EAAWC,GAC9BD,GACAf,KAAKa,oBAAqBE,GAExBf,KAAKU,iBAAkBM,IAEzBC,MAAM,2CAA6CD,EAAU,gDAE7DA,GACAhB,KAAKY,kBAAmBI,IAGhCE,uBAAwB,SAAUC,EAAMR,GACpC,MAAIX,MAAKU,iBAAkBC,IACvBQ,EAAKC,SAAUT,IACR,IAEA,GAGfU,YAAa,SAAWC,EAAMC,EAAYC,GACtC,GAAIL,GAAOnB,KAAKF,IAAI2B,aAAcH,EAAMC,EAAYC,EAKpD,OAJAxB,MAAK0B,SAAUP,GACfnB,KAAK2B,sBACL3B,KAAKF,IAAI8B,eAAeC,gBACxB7B,KAAK8B,cAAeX,GACbA,GAEXO,SAAW,SAAUP,GACjBA,EAAKY,GAAK/B,KAAKC,WACfkB,EAAKa,QAAQC,KAAM,KAAM,gBAAkBd,EAAKY,IAChD/B,KAAKC,aACLD,KAAKE,MAAOiB,EAAKY,IAAOZ,EACxBnB,KAAKI,aAAc,EACnBe,EAAKe,SAAWlC,MAEpBmC,YAAc,SAAUhB,GACfnB,KAAKoC,aAAejB,GACrBnB,KAAKqC,0BAEFrC,MAAKE,MAAOiB,EAAKY,IACxB/B,KAAKI,aAAc,GAEvBkC,WAAa,WACTC,GAAKvC,KACLO,EAAEiC,KAAMxC,KAAKE,MAAO,SAAWuC,EAAGC,GAC9BA,EAAEC,UACFJ,GAAGJ,YAAaO,MAGxBE,yBAA2B,WAEvB,GAAIC,IAAyB,EACzBC,GAAoB,CAWxB,IAVAvC,EAAEiC,KAAMxC,KAAKE,MAAO,SAAWuC,EAAGtB,GAC1BA,EAAK4B,kBAAoB5B,EAAK4B,iBAAiBC,OAAS,IACxDH,GAAyB,GAE7BtC,EAAEiC,KAAKrB,EAAK8B,iBAAkB,SAASC,EAAQC,GACnB,sBAApBA,EAAIC,cACJN,GAAoB,OAI5BD,KAA2B,GAASC,KAAsB,EAAM,CAEhE,GAAIO,GAAOrD,IACXO,GAAEiC,KAAKxC,KAAKE,MAAO,SAAUuC,EAAGtB,GAC5B,GAAkB,SAAdA,EAAKG,KAAgB,CACrB,GAAIgC,IAAe,CACU,OAAzBnC,EAAK8B,mBACL9B,EAAK8B,oBACLK,GAAe,EAEnB,IAAIC,KACJhD,GAAEiC,KAAKrB,EAAK8B,iBAAkB,SAASC,EAAQC,GACpB,qBAAnBA,EAAIC,aACJG,EAAYC,KAAKN,KAGrBK,EAAYP,OAAS,GACrBzC,EAAEiC,KAAKe,EAAa,SAASE,EAAGC,GAC5BJ,GAAe,QACRnC,GAAK8B,iBAAiBS,KAGjCb,GACAtC,EAAEiC,KAAKrB,EAAKwC,iBAAkB,SAASC,EAAOC,GAC1C,GAAIC,IAAc3C,EAAK4C,iBAAiBF,EAAG1D,KAC3C,IAAI2D,KAAe,EAAK,CACpBR,GAAe,CACf,IAAIH,IACAC,YAAc,oBACdY,YAAcH,EAAG1D,KACjB8D,oBAEJ9C,GAAK8B,iBAAiB,oBAAoBY,EAAG1D,MAAQ,KACrDgB,EAAK8B,iBAAiB,oBAAoBY,EAAG1D,MAAQgD,KAK7DE,EAAKjB,aAAejB,GAAQmC,KAAiB,GAC7CD,EAAKa,0BAMzBC,UAAY,WACR,GAAIjE,KA6CJ,OA5CAK,GAAEiC,KAAMxC,KAAKE,MAAO,SAAWuD,EAAGtC,GAC9B,GAAIiD,KACJ7D,GAAEiC,KAAMrB,EAAKkD,gBAAiB,SAAW5B,EAAG6B,GACxCF,EAAmBE,EAAEnE,MAAS,IAG9B,IAAIoE,KACJhE,GAAEiC,KAAM8B,EAAEE,WAAY,SAAWf,EAAGgB,GAChCF,EAAKd,IAAO1B,GAAI0C,EAAEC,QAAQvD,KAAKY,GAAIiC,YAAaS,EAAEC,QAAQvE,MAC1DiE,EAAmBE,EAAEnE,MAASoE,KAGtC,IAAItB,KACA9B,GAAK8B,kBACL1C,EAAEiC,KAAMrB,EAAK8B,iBAAkB,SAAWQ,EAAGkB,GACzC,GAAIxB,IACAC,YAAcuB,EAAIvB,YAClBY,YAAcW,EAAIX,YAClBC,iBAAmBU,EAAIV,iBAE3BhB,GAAkB0B,EAAIvB,YAAcuB,EAAIX,aAAgB,KACxDf,EAAkB0B,EAAIvB,YAAcuB,EAAIX,aAAgBb,IAG3DhC,EAAK4B,mBACN5B,EAAK4B,oBAGT,IAAI6B,IACA7C,GAAKZ,EAAKY,GACVT,KAAOH,EAAKG,KACZuD,QAAU1D,EAAKK,WACfsD,WAAa3D,EAAK2D,WAClBC,YAAc5D,EAAK4D,YACnBX,kBAAoBA,EACpBY,SAAWzE,EAAEY,EAAKa,SAASgD,WAC3BC,WAAY9D,EAAK8D,WACjBhC,iBAAkB9B,EAAK8B,iBACvBiC,KAAM/D,EAAK+D,KACXvE,MAAOQ,EAAKR,MACZoC,iBAAkB5B,EAAK4B,iBAE3B7C,GAAOiB,EAAKY,IAAO6C,KAEdO,MAAOjF,IAEpBkF,YAAc,SAAWC,GACrB9C,GAAKvC,IACL,IAAIsF,GAAS,CACb/C,IAAGpC,KAAOkF,EAAKlF,IAEf,IAAI0C,IAAyB,CAC7BtC,GAAEiC,KAAM6C,EAAKF,MAAO,SAAUpD,EAAIwD,GAC9B,GAAIpE,GAAOoB,GAAGzC,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diff --git a/static/maps/mvc/workflow/workflow-view.js.map b/static/maps/mvc/workflow/workflow-view.js.map
index fd3ed8a7d9b..607e9d3c2b9 100644
--- a/static/maps/mvc/workflow/workflow-view.js.map
+++ b/static/maps/mvc/workflow/workflow-view.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-manager.js b/static/scripts/mvc/workflow/workflow-manager.js
index f6bc230e567..b648ac54704 100644
--- a/static/scripts/mvc/workflow/workflow-manager.js
+++ b/static/scripts/mvc/workflow/workflow-manager.js
@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-connector"],function(a){function b(a,b){this.app=a,this.canvas_container=b,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.nodeLabels={}}return $.extend(b.prototype,{canLabelNodeWith:function(a){return a?!(a in this.nodeLabels):!0},registerNodeLabel:function(a){a&&(this.nodeLabels[a]=!0)},unregisterNodeLabel:function(a){a&&delete this.nodeLabels[a]},updateNodeLabel:function(a,b){a&&this.unregisterNodeLabel(a),this.canLabelNodeWith(b)||alert("Workflow contains duplicate node labels "+b+". This must be fixed before it can be saved."),b&&this.registerNodeLabel(b)},attemptUpdateNodeLabel:function(a,b){return this.canLabelNodeWith(b)?(a.setLabel(b),!0):!1},create_node:function(a,b,c){var d=this.app.prebuildNode(a,b,c);return this.add_node(d),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(d),d},add_node:function(a){a.id=this.id_counter,a.element.attr("id","wf-node-step-"+a.id),this.id_counter++,this.nodes[a.id]=a,this.has_changes=!0,a.workflow=this},remove_node:function(a){this.active_node==a&&this.clear_active_node(),delete this.nodes[a.id],this.has_changes=!0},remove_all:function(){wf=this,$.each(this.nodes,function(a,b){b.destroy(),wf.remove_node(b)})},rectify_workflow_outputs:function(){var a=!1,b=!1;if($.each(this.nodes,function(c,d){d.workflow_outputs&&d.workflow_outputs.length>0&&(a=!0),$.each(d.post_job_actions,function(a,c){"HideDatasetAction"===c.action_type&&(b=!0)})}),a!==!1||b!==!1){var c=this;$.each(this.nodes,function(b,d){if("tool"===d.type){var e=!1;null==d.post_job_actions&&(d.post_job_actions={},e=!0);var f=[];$.each(d.post_job_actions,function(a,b){"HideDatasetAction"==b.action_type&&f.push(a)}),f.length>0&&$.each(f,function(a,b){e=!0,delete d.post_job_actions[b]}),a&&$.each(d.output_terminals,function(a,b){var c=!d.isWorkflowOutput(b.name);if(c===!0){e=!0;var f={action_type:"HideDatasetAction",output_name:b.name,action_arguments:{}};d.post_job_actions["HideDatasetAction"+b.name]=null,d.post_job_actions["HideDatasetAction"+b.name]=f}}),c.active_node==d&&e===!0&&c.reload_active_node()}})}},to_simple:function(){var a={};return $.each(this.nodes,function(b,c){var d={};$.each(c.input_terminals,function(a,b){d[b.name]=null;var c=[];$.each(b.connectors,function(a,e){c[a]={id:e.handle1.node.id,output_name:e.handle1.name},d[b.name]=c})});var e={};c.post_job_actions&&$.each(c.post_job_actions,function(a,b){var c={action_type:b.action_type,output_name:b.output_name,action_arguments:b.action_arguments};e[b.action_type+b.output_name]=null,e[b.action_type+b.output_name]=c}),c.workflow_outputs||(c.workflow_outputs=[]);var f={id:c.id,type:c.type,tool_id:c.content_id,tool_state:c.tool_state,tool_errors:c.tool_errors,input_connections:d,position:$(c.element).position(),annotation:c.annotation,post_job_actions:c.post_job_actions,uuid:c.uuid,label:c.label,workflow_outputs:c.workflow_outputs};a[c.id]=f}),{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var d=!1;$.each(b.steps,function(a,b){var e=wf.app.prebuildNode(b.type,b.name,b.tool_id);e.init_field_data(b),b.position&&e.element.css({top:b.position.top,left:b.position.left}),e.id=b.id,wf.nodes[e.id]=e,c=Math.max(c,parseInt(a)),d||"tool"!==e.type||(e.workflow_outputs.length>0?d=!0:$.each(e.post_job_actions,function(a,b){"HideDatasetAction"===b.action_type&&(d=!0)}))}),wf.id_counter=c+1,$.each(b.steps,function(b,c){var e=wf.nodes[b];$.each(c.input_connections,function(b,c){c&&($.isArray(c)||(c=[c]),$.each(c,function(c,d){var f=wf.nodes[d.id],g=new a;g.connect(f.output_terminals[d.output_name],e.input_terminals[b]),g.redraw()}))}),d&&"tool"===e.type&&$.each(e.output_terminals,function(a,b){void 0===e.post_job_actions["HideDatasetAction"+b.name]&&(e.addWorkflowOutput(b.name),callout=$(e.element).find(".callout."+b.name),callout.find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),wf.has_changes=!0)})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,$("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node(),this.activate_node(a)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showToolForm("<div>No node selected</div>",{id:"no-node"})},activate_node:function(a){this.active_node!=a&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showToolForm(a.form_html,a),a.make_active(),this.active_node=a)},node_changed:function(a,b){this.has_changes=!0,this.active_node==a&&b&&(this.check_changes_in_active_form(),this.app.showToolForm(a.form_html,a))},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var a={},b={};for($.each(this.nodes,function(c){void 0===a[c]&&(a[c]=0),void 0===b[c]&&(b[c]=[])}),$.each(this.nodes,function(c,d){$.each(d.input_terminals,function(c,e){$.each(e.connectors,function(c,e){var f=e.handle1.node;a[d.id]+=1,b[f.id].push(d.id)})})}),node_ids_by_level=[];;){level_parents=[];for(var c in a)0==a[c]&&level_parents.push(c);if(0==level_parents.length)break;node_ids_by_level.push(level_parents);for(var d in level_parents){var e=level_parents[d];delete a[e];for(var f in b[e])a[b[e][f]]-=1}}if(!a.length){var g=this.nodes,h=80;v_pad=30;var i=h;$.each(node_ids_by_level,function(a,b){b.sort(function(a,b){return $(g[a].element).position().top-$(g[b].element).position().top});var c=0,d=v_pad;$.each(b,function(a,b){var e=g[b],f=$(e.element);$(f).css({top:d,left:i}),c=Math.max(c,$(f).width()),d+=$(f).height()+v_pad}),i+=c+h}),$.each(g,function(a,b){b.redraw()})}},bounds_for_all_nodes:function(){var a,b=1/0,c=-(1/0),d=1/0,f=-(1/0);return $.each(this.nodes,function(g,h){e=$(h.element),a=e.position(),b=Math.min(b,a.left),c=Math.max(c,a.left+e.width()),d=Math.min(d,a.top),f=Math.max(f,a.top+e.width())}),{xmin:b,xmax:c,ymin:d,ymax:f}},fit_canvas_to_nodes:function(){function a(a,b){return Math.ceil(a/b)*b}function b(a,b){return b>a||a>3*b?(new_pos=(Math.ceil(a%b/b)+1)*b,-(a-new_pos)):0}var c=this.bounds_for_all_nodes(),d=this.canvas_container.position(),e=this.canvas_container.parent(),f=b(c.xmin,100),g=b(c.ymin,100);f=Math.max(f,d.left),g=Math.max(g,d.top);var h=d.left-f,i=d.top-g,j=a(c.xmax+100,100)+f,k=a(c.ymax+100,100)+g;j=Math.max(j,-h+e.width()),k=Math.max(k,-i+e.height()),this.canvas_container.css({left:h,top:i,width:j,height:k}),this.canvas_container.children().each(function(){var a=$(this).position();$(this).css("left",a.left+f),$(this).css("top",a.top+g)})}}),b});
+define(["mvc/workflow/workflow-connector","libs/toastr"],function(a,b){function c(a,b){this.app=a,this.canvas_container=b,this.id_counter=0,this.nodes={},this.name=null,this.has_changes=!1,this.active_form_has_changes=!1,this.nodeLabels={}}return $.extend(c.prototype,{canLabelNodeWith:function(a){return a?!(a in this.nodeLabels):!0},registerNodeLabel:function(a){a&&(this.nodeLabels[a]=!0)},unregisterNodeLabel:function(a){a&&delete this.nodeLabels[a]},updateNodeLabel:function(a,c){a&&this.unregisterNodeLabel(a),this.canLabelNodeWith(c)||b.warning("Workflow contains duplicate node labels "+c+". This must be fixed before it can be saved."),c&&this.registerNodeLabel(c)},attemptUpdateNodeLabel:function(a,b){return this.canLabelNodeWith(b)?(a.setLabel(b),!0):!1},create_node:function(a,b,c){var d=this.app.prebuildNode(a,b,c);return this.add_node(d),this.fit_canvas_to_nodes(),this.app.canvas_manager.draw_overview(),this.activate_node(d),d},add_node:function(a){a.id=this.id_counter,a.element.attr("id","wf-node-step-"+a.id),this.id_counter++,this.nodes[a.id]=a,this.has_changes=!0,a.workflow=this},remove_node:function(a){this.active_node==a&&this.clear_active_node(),delete this.nodes[a.id],this.has_changes=!0},remove_all:function(){wf=this,$.each(this.nodes,function(a,b){b.destroy(),wf.remove_node(b)})},rectify_workflow_outputs:function(){var a=!1,b=!1;if($.each(this.nodes,function(c,d){d.workflow_outputs&&d.workflow_outputs.length>0&&(a=!0),$.each(d.post_job_actions,function(a,c){"HideDatasetAction"===c.action_type&&(b=!0)})}),a!==!1||b!==!1){var c=this;$.each(this.nodes,function(b,d){if("tool"===d.type){var e=!1;null==d.post_job_actions&&(d.post_job_actions={},e=!0);var f=[];$.each(d.post_job_actions,function(a,b){"HideDatasetAction"==b.action_type&&f.push(a)}),f.length>0&&$.each(f,function(a,b){e=!0,delete d.post_job_actions[b]}),a&&$.each(d.output_terminals,function(a,b){var c=!d.isWorkflowOutput(b.name);if(c===!0){e=!0;var f={action_type:"HideDatasetAction",output_name:b.name,action_arguments:{}};d.post_job_actions["HideDatasetAction"+b.name]=null,d.post_job_actions["HideDatasetAction"+b.name]=f}}),c.active_node==d&&e===!0&&c.reload_active_node()}})}},to_simple:function(){var a={};return $.each(this.nodes,function(b,c){var d={};$.each(c.input_terminals,function(a,b){d[b.name]=null;var c=[];$.each(b.connectors,function(a,e){c[a]={id:e.handle1.node.id,output_name:e.handle1.name},d[b.name]=c})});var e={};c.post_job_actions&&$.each(c.post_job_actions,function(a,b){var c={action_type:b.action_type,output_name:b.output_name,action_arguments:b.action_arguments};e[b.action_type+b.output_name]=null,e[b.action_type+b.output_name]=c}),c.workflow_outputs||(c.workflow_outputs=[]);var f={id:c.id,type:c.type,tool_id:c.content_id,tool_state:c.tool_state,tool_errors:c.tool_errors,input_connections:d,position:$(c.element).position(),annotation:c.annotation,post_job_actions:c.post_job_actions,uuid:c.uuid,label:c.label,workflow_outputs:c.workflow_outputs};a[c.id]=f}),{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var d=!1;$.each(b.steps,function(a,b){var e=wf.app.prebuildNode(b.type,b.name,b.tool_id);e.init_field_data(b),b.position&&e.element.css({top:b.position.top,left:b.position.left}),e.id=b.id,wf.nodes[e.id]=e,c=Math.max(c,parseInt(a)),d||"tool"!==e.type||(e.workflow_outputs.length>0?d=!0:$.each(e.post_job_actions,function(a,b){"HideDatasetAction"===b.action_type&&(d=!0)}))}),wf.id_counter=c+1,$.each(b.steps,function(b,c){var e=wf.nodes[b];$.each(c.input_connections,function(b,c){c&&($.isArray(c)||(c=[c]),$.each(c,function(c,d){var f=wf.nodes[d.id],g=new a;g.connect(f.output_terminals[d.output_name],e.input_terminals[b]),g.redraw()}))}),d&&"tool"===e.type&&$.each(e.output_terminals,function(a,b){void 0===e.post_job_actions["HideDatasetAction"+b.name]&&(e.addWorkflowOutput(b.name),callout=$(e.element).find(".callout."+b.name),callout.find("img").attr("src",Galaxy.root+"static/images/fugue/asterisk-small.png"),wf.has_changes=!0)})})},check_changes_in_active_form:function(){this.active_form_has_changes&&(this.has_changes=!0,$("#right-content").find("form").submit(),this.active_form_has_changes=!1)},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node(),this.activate_node(a)}},clear_active_node:function(){this.active_node&&(this.active_node.make_inactive(),this.active_node=null),this.app.showToolForm("<div>No node selected</div>",{id:"no-node"})},activate_node:function(a){this.active_node!=a&&(this.check_changes_in_active_form(),this.clear_active_node(),this.app.showToolForm(a.form_html,a),a.make_active(),this.active_node=a)},node_changed:function(a,b){this.has_changes=!0,this.active_node==a&&b&&(this.check_changes_in_active_form(),this.app.showToolForm(a.form_html,a))},layout:function(){this.check_changes_in_active_form(),this.has_changes=!0;var a={},b={};for($.each(this.nodes,function(c){void 0===a[c]&&(a[c]=0),void 0===b[c]&&(b[c]=[])}),$.each(this.nodes,function(c,d){$.each(d.input_terminals,function(c,e){$.each(e.connectors,function(c,e){var f=e.handle1.node;a[d.id]+=1,b[f.id].push(d.id)})})}),node_ids_by_level=[];;){level_parents=[];for(var c in a)0==a[c]&&level_parents.push(c);if(0==level_parents.length)break;node_ids_by_level.push(level_parents);for(var d in level_parents){var e=level_parents[d];delete a[e];for(var f in b[e])a[b[e][f]]-=1}}if(!a.length){var g=this.nodes,h=80;v_pad=30;var i=h;$.each(node_ids_by_level,function(a,b){b.sort(function(a,b){return $(g[a].element).position().top-$(g[b].element).position().top});var c=0,d=v_pad;$.each(b,function(a,b){var e=g[b],f=$(e.element);$(f).css({top:d,left:i}),c=Math.max(c,$(f).width()),d+=$(f).height()+v_pad}),i+=c+h}),$.each(g,function(a,b){b.redraw()})}},bounds_for_all_nodes:function(){var a,b=1/0,c=-(1/0),d=1/0,f=-(1/0);return $.each(this.nodes,function(g,h){e=$(h.element),a=e.position(),b=Math.min(b,a.left),c=Math.max(c,a.left+e.width()),d=Math.min(d,a.top),f=Math.max(f,a.top+e.width())}),{xmin:b,xmax:c,ymin:d,ymax:f}},fit_canvas_to_nodes:function(){function a(a,b){return Math.ceil(a/b)*b}function b(a,b){return b>a||a>3*b?(new_pos=(Math.ceil(a%b/b)+1)*b,-(a-new_pos)):0}var c=this.bounds_for_all_nodes(),d=this.canvas_container.position(),e=this.canvas_container.parent(),f=b(c.xmin,100),g=b(c.ymin,100);f=Math.max(f,d.left),g=Math.max(g,d.top);var h=d.left-f,i=d.top-g,j=a(c.xmax+100,100)+f,k=a(c.ymax+100,100)+g;j=Math.max(j,-h+e.width()),k=Math.max(k,-i+e.height()),this.canvas_container.css({left:h,top:i,width:j,height:k}),this.canvas_container.children().each(function(){var a=$(this).position();$(this).css("left",a.left+f),$(this).css("top",a.top+g)})}}),c});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-manager.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-view.js b/static/scripts/mvc/workflow/workflow-view.js
index 1a17fa9ffc4..7733fb65178 100644
--- a/static/scripts/mvc/workflow/workflow-view.js
+++ b/static/scripts/mvc/workflow/workflow-view.js
@@ -1,2 +1,2 @@
-define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text","ui/editable-text"],function(a,b,c,d,e,f,g){function h(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$('<i class="icon fa">&nbsp;</i>').addClass(c);a.before(d)}},EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;if(b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id){c.find("table:first").after(this._genericStepAttributesTemplate(e));var f=e.type;add_node_icon(c.find(".portlet-title-text"),f);var g=c.find(".portlet-title-text");g.data("last-value",g.text()),g.make_text_editable({on_finish:function(a){var b=g.data("last-value");if(a!=b){var f=d.workflow;f.attemptUpdateNodeLabel(e,a)?(c.find("input[name='label']").val(a),g.data("last-value",a),c.find("form").submit()):(alert("Step label "+a+" already exists, cannot update label."),g.text(b))}}}),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})})}},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function i(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)h(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?i():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?i():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},_moduleInitAjax:function(a,b){$.ajax({url:this.urls.get_new_module_info,data:b,global:!1,dataType:"json",success:function(b){a.init_field_data(b)},error:function(b){var c="error loading field data";0===b.status&&(c+=", server unavailable"),a.error(c)}})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),this._moduleInitAjax(node,{type:"tool",content_id:a,_:"true"})},add_node_for_subworkflow:function(a,b){node=this.workflow.create_node("subworkflow",b,a),this._moduleInitAjax(node,{type:"subworkflow",subworkflow_id:a,_:"true"})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),this._moduleInitAjax(node,{type:a,_:"true"})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},$newNodeElement:function(a,b){var c=$("<div class='toolForm toolFormInCanvas'></div>"),d=$("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+b+"</div></div>");add_node_icon(d.find(".nodeTitle"),a),c.append(d),c.css("left",$(window).scrollLeft()+20),c.css("top",$(window).scrollTop()+20);var e=$("<div class='toolFormBody'></div>");return c.append(e),c},prebuildNode:function(a,b,c){var d=this,f=this.$newNodeElement(a,b),g=new e(this,{element:f});g.type=a,g.content_id=c;var h="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";f.find(".toolFormBody").append(h),g.form_html=h;var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var j=$("#canvas-container").position(),k=$("#canvas-container").parent(),l=f.width(),m=f.height();return f.css({left:-j.left+k.width()/2-l/2,top:-j.top+k.height()/2-m/2}),i.prependTo(f.find(".toolFormTitle")),l+=i.width()+10,f.css("width",l),f.bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
+define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text","libs/toastr","ui/editable-text"],function(a,b,c,d,e,f,g,h){function i(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$('<i class="icon fa">&nbsp;</i>').addClass(c);a.before(d)}},EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;if(b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id){c.find("table:first").after(this._genericStepAttributesTemplate(e));var f=e.type;add_node_icon(c.find(".portlet-title-text"),f);var g=c.find(".portlet-title-text");g.data("last-value",g.text()),g.make_text_editable({on_finish:function(a){var b=g.data("last-value");if(a!=b){var f=d.workflow;f.attemptUpdateNodeLabel(e,a)?(c.find("input[name='label']").val(a),g.data("last-value",a),c.find("form").submit()):(h.warning("Step label "+a+" already exists, cannot update label."),g.text(b))}}}),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})})}},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function h(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)i(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?h():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?h():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},_moduleInitAjax:function(a,b){$.ajax({url:this.urls.get_new_module_info,data:b,global:!1,dataType:"json",success:function(b){a.init_field_data(b)},error:function(b){var c="error loading field data";0===b.status&&(c+=", server unavailable"),a.error(c)}})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),this._moduleInitAjax(node,{type:"tool",content_id:a,_:"true"})},add_node_for_subworkflow:function(a,b){node=this.workflow.create_node("subworkflow",b,a),this._moduleInitAjax(node,{type:"subworkflow",subworkflow_id:a,_:"true"})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),this._moduleInitAjax(node,{type:a,_:"true"})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},$newNodeElement:function(a,b){var c=$("<div class='toolForm toolFormInCanvas'></div>"),d=$("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+b+"</div></div>");add_node_icon(d.find(".nodeTitle"),a),c.append(d),c.css("left",$(window).scrollLeft()+20),c.css("top",$(window).scrollTop()+20);var e=$("<div class='toolFormBody'></div>");return c.append(e),c},prebuildNode:function(a,b,c){var d=this,f=this.$newNodeElement(a,b),g=new e(this,{element:f});g.type=a,g.content_id=c;var h="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";f.find(".toolFormBody").append(h),g.form_html=h;var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var j=$("#canvas-container").position(),k=$("#canvas-container").parent(),l=f.width(),m=f.height();return f.css({left:-j.left+k.width()/2-l/2,top:-j.top+k.height()/2-m/2}),i.prependTo(f.find(".toolFormTitle")),l+=i.width()+10,f.css("width",l),f.bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view.js.map
\ No newline at end of file

From 3f8950628c3e31d9e2abe0b4f4a360c035133b8e Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 8 Dec 2015 09:18:23 +0000
Subject: [PATCH 12/12] Workflow label UI refinement.

 - Escape workflow labels in mako.
 - Handle unlabelling steps properly (restore original node name to node and editor form titles).
---
 client/galaxy/scripts/mvc/workflow/workflow-view-node.js   | 6 +++++-
 client/galaxy/scripts/mvc/workflow/workflow-view.js        | 4 ++++
 static/maps/mvc/workflow/workflow-view-node.js.map         | 2 +-
 static/maps/mvc/workflow/workflow-view.js.map              | 2 +-
 static/scripts/mvc/workflow/workflow-view-node.js          | 2 +-
 static/scripts/mvc/workflow/workflow-view.js               | 2 +-
 templates/webapps/galaxy/workflow/editor_generic_form.mako | 3 ++-
 7 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index 9fb01bb4980..f08308d6bf7 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -12,9 +12,13 @@ define(['mvc/workflow/workflow-view-terminals', 'mvc/workflow/workflow-view-data
 
         render: function() {
             var label = this.node.label;
+            var title;
             if(label) {
-                this.$el.find(".nodeTitle").text(label);
+                title = label; 
+            } else {
+                title = this.node.name;
             }
+            this.$el.find(".nodeTitle").text(title);
             this.renderToolErrors();
             this.$el.css( "width", Math.min(250, Math.max( this.$el.width(), this.output_width )));
         },
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js
index d2cb0035ceb..6fa56e40d67 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js
@@ -95,6 +95,10 @@ EditorFormView = Backbone.View.extend({
                         $el.find("input[name='label']").val(newLabel);
                         $titleText.data("last-value", newLabel);
                         $el.find('form').submit();
+                        if(newLabel == "") {
+                            // If label unset restore default name as title.
+                            $titleText.text(node.name);
+                        }
                     } else {
                         Toastr.warning("Step label " + newLabel + " already exists, cannot update label.");
                         $titleText.text(lastValue);
diff --git a/static/maps/mvc/workflow/workflow-view-node.js.map b/static/maps/mvc/workflow/workflow-view-node.js.map
index 3563b9c8659..3f658f81891 100644
--- a/static/maps/mvc/workflow/workflow-view-node.js.map
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index 607e9d3c2b9..27284bad95a 100644
--- a/static/maps/mvc/workflow/workflow-view.js.map
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\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-view-node.js b/static/scripts/mvc/workflow/workflow-view-node.js
index 95c4063adb2..86e681d2ab8 100644
--- a/static/scripts/mvc/workflow/workflow-view-node.js
+++ b/static/scripts/mvc/workflow/workflow-view-node.js
@@ -1,2 +1,2 @@
-define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){var a=this.node.label;a&&this.$el.find(".nodeTitle").text(a),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
+define(["mvc/workflow/workflow-view-terminals","mvc/workflow/workflow-view-data"],function(a,b){return Backbone.View.extend({initialize:function(a){this.node=a.node,this.output_width=Math.max(150,this.$el.width()),this.tool_body=this.$el.find(".toolFormBody"),this.tool_body.find("div").remove(),this.newInputsDiv().appendTo(this.tool_body),this.terminalViews={},this.outputTerminlViews={}},render:function(){var a,b=this.node.label;a=b?b:this.node.name,this.$el.find(".nodeTitle").text(a),this.renderToolErrors(),this.$el.css("width",Math.min(250,Math.max(this.$el.width(),this.output_width)))},renderToolErrors:function(){this.node.tool_errors?this.$el.addClass("tool-node-error"):this.$el.removeClass("tool-node-error")},newInputsDiv:function(){return $("<div class='inputs'></div>")},updateMaxWidth:function(a){this.output_width=Math.max(this.output_width,a)},addRule:function(){this.tool_body.append($("<div class='rule'></div>"))},addDataInput:function(c,d){var e=!0;d||(d=this.$(".inputs"),e=!1);var f=this.terminalViews[c.name],g="dataset_collection"==c.input_type?a.InputCollectionTerminalView:a.InputTerminalView;if(!f||f instanceof g||(f.el.terminal.destroy(),f=null),f){var h=f.el.terminal;h.update(c),h.destroyInvalidConnections()}else f=new g({node:this.node,input:c});this.terminalViews[c.name]=f;var i=f.el,j=new b.DataInputView({terminalElement:i,input:c,nodeView:this,skipResize:e}),k=j.$el;return d.append(k.prepend(f.terminalElements())),f},addDataOutput:function(c){var d=c.collection?a.OutputCollectionTerminalView:a.OutputTerminalView,e=new d({node:this.node,output:c}),f=new b.DataOutputView({output:c,terminalElement:e.el,nodeView:this});this.tool_body.append(f.$el.append(e.terminalElements()))},updateDataOutput:function(a){var b=this.node.output_terminals[a.name];b.update(a)}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view-node.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/workflow/workflow-view.js b/static/scripts/mvc/workflow/workflow-view.js
index 7733fb65178..8949e169a71 100644
--- a/static/scripts/mvc/workflow/workflow-view.js
+++ b/static/scripts/mvc/workflow/workflow-view.js
@@ -1,2 +1,2 @@
-define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text","libs/toastr","ui/editable-text"],function(a,b,c,d,e,f,g,h){function i(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$('<i class="icon fa">&nbsp;</i>').addClass(c);a.before(d)}},EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;if(b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id){c.find("table:first").after(this._genericStepAttributesTemplate(e));var f=e.type;add_node_icon(c.find(".portlet-title-text"),f);var g=c.find(".portlet-title-text");g.data("last-value",g.text()),g.make_text_editable({on_finish:function(a){var b=g.data("last-value");if(a!=b){var f=d.workflow;f.attemptUpdateNodeLabel(e,a)?(c.find("input[name='label']").val(a),g.data("last-value",a),c.find("form").submit()):(h.warning("Step label "+a+" already exists, cannot update label."),g.text(b))}}}),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})})}},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function h(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)i(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?h():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?h():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},_moduleInitAjax:function(a,b){$.ajax({url:this.urls.get_new_module_info,data:b,global:!1,dataType:"json",success:function(b){a.init_field_data(b)},error:function(b){var c="error loading field data";0===b.status&&(c+=", server unavailable"),a.error(c)}})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),this._moduleInitAjax(node,{type:"tool",content_id:a,_:"true"})},add_node_for_subworkflow:function(a,b){node=this.workflow.create_node("subworkflow",b,a),this._moduleInitAjax(node,{type:"subworkflow",subworkflow_id:a,_:"true"})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),this._moduleInitAjax(node,{type:a,_:"true"})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},$newNodeElement:function(a,b){var c=$("<div class='toolForm toolFormInCanvas'></div>"),d=$("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+b+"</div></div>");add_node_icon(d.find(".nodeTitle"),a),c.append(d),c.css("left",$(window).scrollLeft()+20),c.css("top",$(window).scrollTop()+20);var e=$("<div class='toolFormBody'></div>");return c.append(e),c},prebuildNode:function(a,b,c){var d=this,f=this.$newNodeElement(a,b),g=new e(this,{element:f});g.type=a,g.content_id=c;var h="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";f.find(".toolFormBody").append(h),g.form_html=h;var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var j=$("#canvas-container").position(),k=$("#canvas-container").parent(),l=f.width(),m=f.height();return f.css({left:-j.left+k.width()/2-l/2,top:-j.top+k.height()/2-m/2}),i.prependTo(f.find(".toolFormTitle")),l+=i.width()+10,f.css("width",l),f.bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
+define("mvc/workflow/workflow-globals",{}),define(["utils/utils","mvc/workflow/workflow-globals","mvc/workflow/workflow-manager","mvc/workflow/workflow-canvas","mvc/workflow/workflow-node","mvc/tool/tools-form-workflow","utils/async-save-text","libs/toastr","ui/editable-text"],function(a,b,c,d,e,f,g,h){function i(a){var b=$("#galaxy_tools").contents();if(0===b.length&&(b=$(document)),$(this).removeClass("search_active"),b.find(".toolTitle").removeClass("search_match"),b.find(".toolSectionBody").hide(),b.find(".toolTitle").show(),b.find(".toolPanelLabel").show(),b.find(".toolSectionWrapper").each(function(){"recently_used_wrapper"!==$(this).attr("id")?$(this).show():$(this).hasClass("user_pref_visible")&&$(this).show()}),b.find("#search-no-results").hide(),b.find("#search-spinner").hide(),a){var c=b.find("#tool-search-query");c.val("search tools")}}return NODE_ICONS={tool:"fa-wrench",data_input:"fa-file-o",data_collection_input:"fa-folder-o",pause:"fa-pause"},add_node_icon=function(a,b){var c=NODE_ICONS[b];if(c){var d=$('<i class="icon fa">&nbsp;</i>').addClass(c);a.before(d)}},EditorFormView=Backbone.View.extend({initialize:function(b){this.options=a.merge(b,{});var c=$("<div/>"),d=b.workflowView,e=b.node;if(b.html&&c.html(b.html),this.setElement(c),e&&"no-node"!=e.id){c.find("table:first").after(this._genericStepAttributesTemplate(e));var f=e.type;add_node_icon(c.find(".portlet-title-text"),f);var g=c.find(".portlet-title-text");g.data("last-value",g.text()),g.make_text_editable({on_finish:function(a){var b=g.data("last-value");if(a!=b){var f=d.workflow;f.attemptUpdateNodeLabel(e,a)?(c.find("input[name='label']").val(a),g.data("last-value",a),c.find("form").submit(),""==a&&g.text(e.name)):(h.warning("Step label "+a+" already exists, cannot update label."),g.text(b))}}}),c.find("form").length>0&&c.find("form").ajaxForm({type:"POST",dataType:"json",success:function(a){d.workflow.active_form_has_changes=!1,e.update_field_data(a),d.showWorkflowParameters()},beforeSubmit:function(a){a.push({name:"tool_state",value:e.tool_state}),a.push({name:"_",value:"true"})}}).each(function(){var a=this;$(this).find('select[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find('input[refresh_on_change="true"]').change(function(){$(a).submit()}),$(this).find("input, textarea, select").each(function(){$(this).bind("focus click",function(){d.workflow.active_form_has_changes=!0})})})}},_genericStepAttributesTemplate:function(a){return'<p><div class="metadataForm"><div class="metadataFormTitle">Edit Step Attributes</div>'+this._annotationTemplate(a)+"</div></p>"},_annotationTemplate:function(a){return'<div class="form-row"><label>Annotation / Notes:</label><div style="margin-right: 10px;"><textarea name="annotation" rows="3" style="width: 100%">'+a.annotation+'</textarea><div class="toolParamHelp">Add an annotation or notes to this step; annotations are available when a workflow is viewed.</div></div></div>'}}),Backbone.View.extend({initialize:function(a){function c(){j.workflow.layout(),j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview()}function e(){j.workflow.clear_active_node(),$(".right-content").hide(),$("#edit-attributes").show()}function f(){$.jStorage.set("overview-off",!1),$("#overview-border").css("right","0px"),$("#close-viewport").css("background-position","0px 0px")}function h(){$.jStorage.set("overview-off",!0),$("#overview-border").css("right","20000px"),$("#close-viewport").css("background-position","12px 0px")}var j=b.app=this;this.options=a,this.urls=a&&a.urls||{},this.active_ajax_call=!1;var k=function(){j.workflow.check_changes_in_active_form(),workflow&&j.workflow.has_changes?(do_close=function(){window.onbeforeunload=void 0,window.document.location=j.urls.workflow_index},window.show_modal("Close workflow editor","There are unsaved changes to your workflow which will be lost.",{Cancel:hide_modal,"Save Changes":function(){l(null,do_close)}},{"Don't Save":do_close})):window.document.location=j.urls.workflow_index},l=function(a,b){if(show_message("Saving workflow","progress"),j.workflow.check_changes_in_active_form(),!j.workflow.has_changes)return hide_modal(),void(b&&b());j.workflow.rectify_workflow_outputs();var c=function(a){$.ajax({url:j.urls.save_workflow,type:"POST",data:{id:j.options.id,workflow_data:function(){return JSON.stringify(j.workflow.to_simple())},_:"true"},dataType:"json",success:function(b){var c=$("<div></div>").text(b.message);if(b.errors){c.addClass("warningmark");var d=$("<ul/>");$.each(b.errors,function(a,b){$("<li></li>").text(b).appendTo(d)}),c.append(d)}else c.addClass("donemark");j.workflow.name=b.name,j.workflow.has_changes=!1,j.workflow.stored=!0,j.showWorkflowParameters(),b.errors?window.show_modal("Saving workflow",c,{Ok:hide_modal}):(a&&a(),hide_modal())}})};j.active_ajax_call?$(document).bind("ajaxStop.save_workflow",function(){$(document).unbind("ajaxStop.save_workflow"),c(),$(document).unbind("ajaxStop.save_workflow"),j.active_ajax_call=!1}):c(b)};$("#tool-search-query").click(function(){$(this).focus(),$(this).select()}).keyup(function(){if($(this).css("font-style","normal"),this.value.length<3)i(!1);else if(this.value!=this.lastValue){$(this).addClass("search_active");var a=this.value;this.timer&&clearTimeout(this.timer),$("#search-spinner").show(),this.timer=setTimeout(function(){$.get(j.urls.tool_search,{q:a},function(a){if($("#search-no-results").hide(),$(".toolSectionWrapper").hide(),$(".toolSectionWrapper").find(".toolTitle").hide(),0!=a.length){var b=$.map(a,function(a){return"link-"+a});$(b).each(function(a,b){$("[id='"+b+"']").parent().addClass("search_match"),$("[id='"+b+"']").parent().show().parent().parent().show().parent().show()}),$(".toolPanelLabel").each(function(){for(var a=$(this),b=a.next(),c=!0;0!==b.length&&b.hasClass("toolTitle");){if(b.is(":visible")){c=!1;break}b=b.next()}c&&a.hide()})}else $("#search-no-results").show();$("#search-spinner").hide()},"json")},400)}this.lastValue=this.value}),this.canvas_manager=b.canvas_manager=new d(this,$("#canvas-viewport"),$("#overview")),this.reset(),this.datatypes=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes",async:!1}).responseText),this.datatypes_mapping=JSON.parse($.ajax({url:Galaxy.root+"api/datatypes/mapping",async:!1}).responseText),this.ext_to_type=this.datatypes_mapping.ext_to_class_name,this.type_to_type=this.datatypes_mapping.class_to_classes,$.ajax({url:j.urls.load_workflow,data:{id:j.options.id,_:"true"},dataType:"json",cache:!1,success:function(a){j.reset(),j.workflow.from_simple(a),j.workflow.has_changes=!1,j.workflow.fit_canvas_to_nodes(),j.scroll_to_nodes(),j.canvas_manager.draw_overview(),upgrade_message="",$.each(a.upgrade_messages,function(a,b){upgrade_message+="<li>Step "+(parseInt(a,10)+1)+": "+j.workflow.nodes[a].name+"<ul>",$.each(b,function(a,b){upgrade_message+="<li>"+b+"</li>"}),upgrade_message+="</ul></li>"}),upgrade_message?window.show_modal("Workflow loaded with changes","Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>"+upgrade_message+"</ul>",{Continue:hide_modal}):hide_modal(),j.showWorkflowParameters()},beforeSubmit:function(){show_message("Loading workflow","progress")}}),$(document).ajaxStart(function(){j.active_ajax_call=!0,$(document).bind("ajaxStop.global",function(){j.active_ajax_call=!1})}),$(document).ajaxError(function(a,b){var c=b.responseText||b.statusText||"Could not connect to server";return window.show_modal("Server error",c,{"Ignore error":hide_modal}),!1}),window.make_popupmenu&&make_popupmenu($("#workflow-options-button"),{Save:l,Run:function(){window.location=j.urls.run_workflow},"Edit Attributes":e,"Auto Re-layout":c,Close:k}),overview_size=$.jStorage.get("overview-size"),void 0!==overview_size&&$("#overview-border").css({width:overview_size,height:overview_size}),$.jStorage.get("overview-off")?h():f(),$("#overview-border").bind("dragend",function(a,b){var c=$(this).offsetParent(),d=c.offset(),e=Math.max(c.width()-(b.offsetX-d.left),c.height()-(b.offsetY-d.top));$.jStorage.set("overview-size",e+"px")}),$("#close-viewport").click(function(){"0px"===$("#overview-border").css("right")?h():f()}),window.onbeforeunload=function(){return workflow&&j.workflow.has_changes?"There are unsaved changes to your workflow which will be lost.":void 0},$("div.toolSectionBody").hide(),$("div.toolSectionTitle > span").wrap("<a href='#'></a>");var m=null;$("div.toolSectionTitle").each(function(){var a=$(this).next("div.toolSectionBody");$(this).click(function(){a.is(":hidden")?(m&&m.slideUp("fast"),m=a,a.slideDown("fast")):(a.slideUp("fast"),m=null)})}),g("workflow-name","workflow-name",j.urls.rename_async,"new_name"),$("#workflow-tag").click(function(){return $(".tag-area").click(),!1}),g("workflow-annotation","workflow-annotation",j.urls.annotate_async,"new_annotation",25,!0,4)},reset:function(){this.workflow&&this.workflow.remove_all(),this.workflow=b.workflow=new c(this,$("#canvas-container"))},scroll_to_nodes:function(){var a,b,c=$("#canvas-viewport"),d=$("#canvas-container");b=d.width()<c.width()?(c.width()-d.width())/2:0,a=d.height()<c.height()?(c.height()-d.height())/2:0,d.css({left:b,top:a})},_moduleInitAjax:function(a,b){$.ajax({url:this.urls.get_new_module_info,data:b,global:!1,dataType:"json",success:function(b){a.init_field_data(b)},error:function(b){var c="error loading field data";0===b.status&&(c+=", server unavailable"),a.error(c)}})},add_node_for_tool:function(a,b){node=this.workflow.create_node("tool",b,a),this._moduleInitAjax(node,{type:"tool",content_id:a,_:"true"})},add_node_for_subworkflow:function(a,b){node=this.workflow.create_node("subworkflow",b,a),this._moduleInitAjax(node,{type:"subworkflow",subworkflow_id:a,_:"true"})},add_node_for_module:function(a,b){node=this.workflow.create_node(a,b),this._moduleInitAjax(node,{type:a,_:"true"})},display_pja:function(a,b){var c=this;$("#pja_container").append(get_pja_form(a,b)),$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function(){action_to_rem=$(this).closest(".toolForm",".action_tag").children(".action_tag:first").text(),$(this).closest(".toolForm").remove(),delete c.workflow.active_node.post_job_actions[action_to_rem],c.workflow.active_form_has_changes=!0})},display_pja_list:function(){return pja_list},display_file_list:function(a){addlist="<select id='node_data_list' name='node_data_list'>";for(var b in a.output_terminals)addlist+="<option value='"+b+"'>"+b+"</option>";return addlist+="</select>",addlist},new_pja:function(a,b,c){if(void 0===c.post_job_actions&&(c.post_job_actions={}),void 0===c.post_job_actions[a+b]){var d={};return d.action_type=a,d.output_name=b,c.post_job_actions[a+b]=null,c.post_job_actions[a+b]=d,display_pja(d,c),this.workflow.active_form_has_changes=!0,!0}return!1},showWorkflowParameters:function(){var a=/\$\{.+?\}/g,b=[],c=$("#workflow-parameters-container"),d=$("#workflow-parameters-box"),e="",f=[];$.each(this.workflow.nodes,function(c,d){var e=d.form_html.match(a);e&&(f=f.concat(e)),d.post_job_actions&&($.each(d.post_job_actions,function(b,c){c.action_arguments&&$.each(c.action_arguments,function(b,c){var d=c.match(a);d&&(f=f.concat(d))})}),f&&$.each(f,function(a,c){-1===$.inArray(c,b)&&b.push(c)}))}),b&&0!==b.length?($.each(b,function(a,b){e+="<div>"+b.substring(2,b.length-1)+"</div>"}),c.html(e),d.show()):(c.html(e),d.hide())},showToolForm:function(b,c){var d="right-content",e=d+"-"+c.id,g=$("#"+d),h=g.find("#"+e);if(h.length>0&&0==h.find(".section-row").length&&h.remove(),0==g.find("#"+e).length){var i=$('<div id="'+e+'" class="'+d+'"/>'),j=null;if("tool"==c.type&&a.isJSON(b)){var k=JSON.parse(b);k.node=c,k.datatypes=this.datatypes,j=new f.View(k)}else{var k={html:b,node:c,workflowView:this};j=new EditorFormView(k)}i.append(j.$el),g.append(i)}$("."+d).hide(),g.find("#"+e).show(),g.show(),g.scrollTop()},isSubType:function(a,b){return a=this.ext_to_type[a],b=this.ext_to_type[b],this.type_to_type[a]&&b in this.type_to_type[a]},$newNodeElement:function(a,b){var c=$("<div class='toolForm toolFormInCanvas'></div>"),d=$("<div class='toolFormTitle unselectable'><span class='nodeTitle'>"+b+"</div></div>");add_node_icon(d.find(".nodeTitle"),a),c.append(d),c.css("left",$(window).scrollLeft()+20),c.css("top",$(window).scrollTop()+20);var e=$("<div class='toolFormBody'></div>");return c.append(e),c},prebuildNode:function(a,b,c){var d=this,f=this.$newNodeElement(a,b),g=new e(this,{element:f});g.type=a,g.content_id=c;var h="<div><img height='16' align='middle' src='"+Galaxy.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";f.find(".toolFormBody").append(h),g.form_html=h;var i=$("<div class='buttons' style='float: right;'></div>");i.append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){g.destroy()})),f.appendTo("#canvas-container");var j=$("#canvas-container").position(),k=$("#canvas-container").parent(),l=f.width(),m=f.height();return f.css({left:-j.left+k.width()/2-l/2,top:-j.top+k.height()/2-m/2}),i.prependTo(f.find(".toolFormTitle")),l+=i.width()+10,f.css("width",l),f.bind("dragstart",function(){d.workflow.activate_node(g)}).bind("dragend",function(){d.workflow.node_changed(this),d.workflow.fit_canvas_to_nodes(),d.canvas_manager.draw_overview()}).bind("dragclickonly",function(){d.workflow.activate_node(g)}).bind("drag",function(a,b){var c=$(this).offsetParent().offset(),d=b.offsetX-c.left,e=b.offsetY-c.top;$(this).css({left:d,top:e}),$(this).find(".terminal").each(function(){this.terminal.redraw()})}),g}})});
 //# sourceMappingURL=../../../maps/mvc/workflow/workflow-view.js.map
\ No newline at end of file
diff --git a/templates/webapps/galaxy/workflow/editor_generic_form.mako b/templates/webapps/galaxy/workflow/editor_generic_form.mako
index 7c9add037b9..32ad4600af2 100644
--- a/templates/webapps/galaxy/workflow/editor_generic_form.mako
+++ b/templates/webapps/galaxy/workflow/editor_generic_form.mako
@@ -1,5 +1,6 @@
 <form name="${form.name}" action="${h.url_for( controller='workflow', action='editor_form_post' )}" method="post">
     <%
+    from xml.sax.saxutils import escape
     label = module.label
     if label is not None:
         title = label
@@ -17,7 +18,7 @@
             <div class="ui-margin-top"></div>
             <div>
             <input type="hidden" name="type" value="${module.type}" />
-            <input type="hidden" name="label" value="${label or ''}" />
+            <input type="hidden" name="label" value="${escape(label or '')}" />
             <table class="ui-table-plain">
               <thead></thead>
               <tbody>