Merge with cde78bdeaca823b011477498a4dfd1466d20c0c0

lib/galaxy/jobs/actions/__init__.py

@@ -0,0 +1,4 @@
+"""
+This package contains job action classes.
+
+"""

lib/galaxy/jobs/actions/post.py

@@ -0,0 +1,196 @@
+import logging, threading, time
+from Queue import Queue, Empty
+
+from galaxy.util.json import from_json_string, to_json_string
+
+from galaxy.web.form_builder import *
+
+log = logging.getLogger( __name__ )
+
+# DBTODO This still needs refactoring and general cleanup.
+
+class DefaultJobAction(object):
+    name = "DefaultJobAction"
+
+    @classmethod
+    def execute(cls, job):
+        pass
+
+    @classmethod        
+    def get_config_form(cls, trans):
+        return "<p>Default Job Action Config Form</p>"
+
+    @classmethod
+    def get_short_str(cls, pja):
+        if pja.action_arguments:
+            return "%s -> %s" % (pja.action_type, pja.action_arguments)
+        else:
+            return "%s" % pja.action_type
+        
+
+class ChangeDatatypeAction(DefaultJobAction):
+    name = "ChangeDatatypeAction"
+
+    @classmethod
+    def execute(cls, trans, action, job):
+        for dataset_assoc in job.output_datasets:
+            if action.output_name == '' or dataset_assoc.name == action.output_name:
+                trans.app.datatypes_registry.change_datatype( dataset_assoc.dataset, action.action_arguments['newtype'])
+
+    @classmethod
+    def get_config_form(cls, trans):
+        dt_list = ""
+        dtnames = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems()]
+        dtnames.sort()
+        for dt_name in dtnames:
+            dt_list += """<option id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype__%s' value='%s'>%s</option>""" % (dt_name, dt_name, dt_name)
+        ps = """
+            if (pja.action_type == "ChangeDatatypeAction"){
+                p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>" + pja.action_type + " <br/> on " + pja.output_name + "\
+    			<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\
+    			<div class='toolFormBody'><label for='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>New Datatype:</label><select id='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype' name='pja__"+pja.output_name+"__ChangeDatatypeAction__newtype'>\
+		        %s\
+		        </select>";
+		        if (pja.action_arguments != undefined && pja.action_arguments.newtype != undefined){
+                     p_str += "<scrip" + "t type='text/javascript'>$('#pja__" + pja.output_name + "__ChangeDatatypeAction__newtype').val('" + pja.action_arguments.newtype + "');</scrip" + "t>"
+		        }
+		        p_str += "</div><div class='toolParamHelp'>This action will change the datatype of the output to the indicated value.</div></div>";
+    		}
+		    """ % dt_list
+            # Note the scrip + t hack above.  Is there a better way?
+        return ps
+
+class RenameDatasetAction(DefaultJobAction):
+    name = "RenameDatasetAction"
+
+    @classmethod
+    def execute(cls, trans, action, job):
+        for dataset_assoc in job.output_datasets:
+            if action.output_name == '' or dataset_assoc.name == action.output_name:
+                dataset_assoc.dataset.name = action.action_arguments['newname']
+
+    @classmethod
+    def get_config_form(cls, trans):
+        return """
+            if (pja.action_type == "RenameDatasetAction"){
+    			p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
+    			<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
+    			if ((pja.action_arguments != undefined) && (pja.action_arguments.newname != undefined)){
+    				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='"+pja.action_arguments.newname + "'/>";
+    			}
+    			else{
+    				p_str += "<label for='pja__"+pja.output_name+"__RenameDatasetAction__newname'>New output name:</label><input type='text' name='pja__"+pja.output_name+"__RenameDatasetAction__newname' value='New Name'/>";
+    			}
+    			p_str += "</div><div class='toolParamHelp'>This action will rename the result dataset.</div></div>";
+    		}
+		    """
+
+class HideDatasetAction(DefaultJobAction):
+    name = "HideDatasetAction"
+
+    @classmethod
+    def execute(cls, trans, action, job):
+        for dataset_assoc in job.output_datasets:
+            if action.output_name == '' or dataset_assoc.name == action.output_name:
+                dataset_assoc.dataset.visible=False
+
+    @classmethod
+    def get_config_form(cls, trans):
+        return """
+            if (pja.action_type == "HideDatasetAction"){
+            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
+            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div><div class='toolFormBody'>";
+            	p_str += "<label for='pja__"+pja.output_name+"__HideDatasetAction'>There are no additional options for this action.</label><input type='hidden' name='pja__"+pja.output_name+"__HideDatasetAction'/>";
+            	p_str += "</div><div class='toolParamHelp'>This action will *hide* the result dataset from your history.</div></div>";
+            }
+            """
+
+class SetMetadataAction(DefaultJobAction):
+    name = "SetMetadataAction"
+    # DBTODO Setting of Metadata is currently broken and disabled.  It should not be used (yet).
+    
+    @classmethod
+    def execute(cls, trans, action, job):
+        for data in self.job.output_datasets:
+            data.set_metadata( action.action_arguments['newtype'] )
+            
+    @classmethod
+    def get_config_form(cls, trans):
+        dt_list = ""
+        mdict = {}
+        for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems():
+            for mn, mt in dtype_value.metadata_spec.items():
+                if mt.visible:
+                    mdict[mt.desc] = mt.param.get_html(value= mn).replace('"', "'").strip().replace('\n','')
+        for k, v in mdict.items():
+            dt_list += "<p><strong>" + k + ":</strong><br/>" + v + "</p>"
+        return """
+            if (pja.action_type == "SetMetadataAction"){
+            	p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'>"+ pja.action_type + " <br/> on " + pja.output_name + "\
+            	<div style='float: right;' class='buttons'><img src='../images/delete_icon.png'></div></div>\
+            	<div class='toolFormBody'>\
+            	%s\
+            	</div><div class='toolParamHelp'>This tool sets metadata in output.</div></div>";
+            }
+    		""" % dt_list
+
+ACTIONS = { "RenameDatasetAction" : RenameDatasetAction,
+            "HideDatasetAction" : HideDatasetAction,
+            "ChangeDatatypeAction": ChangeDatatypeAction, 
+            # "SetMetadataAction" : SetMetadataAction, 
+             }
+            
+class ActionBox(object):
+    @classmethod
+    def execute(cls, action, job):
+        if action.action_type in ACTIONS:
+            ACTIONS[action.action_type].execute(action, job, trans)
+        else:
+            return False
+
+    @classmethod
+    def get_short_str(cls, action):
+        if action.action_type in ACTIONS:
+            return ACTIONS[action.action_type].get_short_str(action)
+        else:
+            return "Unknown PostJobAction"
+
+    @classmethod
+    def handle_incoming(cls, incoming):
+        npd = {}
+        for key, val in incoming.iteritems():
+            if key.startswith('pja'):
+                sp = key.split('__')
+                # flag / output_name / pjatype / desc
+                if not sp[2] in npd:
+                    npd[sp[2]] = {'action_type' : sp[2],
+                                  'output_name' : sp[1],
+                                  'action_arguments' : {}}
+                if len(sp) > 3:
+                    if sp[3] == 'output_name':
+                        npd[sp[2]]['output_name'] = val
+                    else:
+                        npd[sp[2]]['action_arguments'][sp[3]] = val
+            else:
+                # Not pja stuff.
+                pass
+        return to_json_string(npd)
+            
+    @classmethod
+    def get_add_list(cls):
+        addlist = "<select id='new_pja_list' name='new_pja_list'>"
+        for action in ACTIONS:
+            addlist += "<option value='%s'>%s</option>" % (ACTIONS[action].name, ACTIONS[action].name)
+        addlist += "</select>"
+        return addlist
+        
+    @classmethod
+    def get_forms(cls, trans):
+        forms = ""
+        for action in ACTIONS:
+            forms += ACTIONS[action].get_config_form(trans)
+        return forms
+    
+    @classmethod
+    def execute(cls, trans, pja, job):
+        ACTIONS[pja.action_type].execute(trans, pja, job)

lib/galaxy/model/__init__.py

@@ -113,6 +113,8 @@ class Job( object ):
         self.info = None
         self.job_runner_name = None
         self.job_runner_external_id = None
+        self.post_job_actions = None
+        
     def add_parameter( self, name, value ):
         self.parameters.append( JobParameter( name, value ) )
     def add_input_dataset( self, name, dataset ):
@@ -184,6 +186,13 @@ class JobToOutputLibraryDatasetAssociation( object ):
         self.name = name
         self.dataset = dataset
 
+class PostJobAction( object ):
+    def __init__( self, action_type, workflow_step, output_name = None, action_arguments = None):
+        self.action_type = action_type
+        self.output_name = output_name
+        self.action_arguments = action_arguments
+        self.workflow_step = workflow_step
+
 class JobExternalOutputMetadata( object ):
     def __init__( self, job = None, dataset = None ):
         self.job = job

lib/galaxy/model/mapping.py

@@ -369,6 +369,13 @@ JobExternalOutputMetadata.table = Table( "job_external_output_metadata", metadat
     Column( "filename_override_metadata", String( 255 ) ),
     Column( "job_runner_external_pid", String( 255 ) ) )
     
+PostJobAction.table = Table("post_job_action", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False),
+    Column("action_type", String(255), nullable=False),
+    Column("output_name", String(255), nullable=True),
+    Column("action_arguments", JSONType, nullable=True))
+
 Event.table = Table( "event", metadata, 
     Column( "id", Integer, primary_key=True ),
     Column( "create_time", DateTime, default=now ),
@@ -1237,6 +1244,9 @@ assign_mapper( context, JobExternalOutputMetadata, JobExternalOutputMetadata.tab
                      history_dataset_association = relation( HistoryDatasetAssociation, lazy = False ),
                      library_dataset_dataset_association = relation( LibraryDatasetDatasetAssociation, lazy = False ) ) )
 
+assign_mapper( context, PostJobAction, PostJobAction.table,
+    properties=dict(workflow_step = relation( WorkflowStep, backref='post_job_actions', primaryjoin=(WorkflowStep.table.c.id == PostJobAction.table.c.workflow_step_id))))
+
 assign_mapper( context, Job, Job.table, 
     properties=dict( galaxy_session=relation( GalaxySession ),
                      history=relation( History ),
@@ -1309,7 +1319,7 @@ assign_mapper( context, Workflow, Workflow.table,
 assign_mapper( context, WorkflowStep, WorkflowStep.table,
                 properties=dict(
                     tags=relation(WorkflowStepTagAssociation, order_by=WorkflowStepTagAssociation.table.c.id, backref="workflow_steps"), 
-                    annotations=relation( WorkflowStepAnnotationAssociation, order_by=WorkflowStepAnnotationAssociation.table.c.id, backref="workflow_steps" ) ) 
+                    annotations=relation( WorkflowStepAnnotationAssociation, order_by=WorkflowStepAnnotationAssociation.table.c.id, backref="workflow_steps" ) )
                 )
 
 assign_mapper( context, WorkflowStepConnection, WorkflowStepConnection.table,

lib/galaxy/model/migrate/versions/0046_post_job_actions.py

@@ -0,0 +1,49 @@
+"""
+Migration script to create tables for handling post-job actions.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import logging
+logging.basicConfig( level=logging.DEBUG )
+log = logging.getLogger( __name__ )
+
+# Need our custom types, but don't import anything else from model
+from galaxy.model.custom_types import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+PostJobAction_table = Table("post_job_action", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True, nullable=False),
+    Column("action_type", String(255), nullable=False),
+    Column("output_name", String(255), nullable=True),
+    Column("action_arguments", JSONType, nullable=True))
+
+# PostJobActionAssociation_table = Table("post_job_action_association", metadata,
+#     Column("id", Integer, primary_key=True),
+#     Column("post_job_action_id", Integer, ForeignKey("post_job_action.id"), index=True, nullable=False),
+#     Column("job_id", Integer, ForeignKey("job.id"), index=True, nullable=False))
+
+tables = [PostJobAction_table]#, PostJobActionAssociation_table]
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    for table in tables:
+        try:
+            table.create()
+        except:
+            log.warn( "Failed to create table '%s', ignoring (might result in wrong schema)" % table.name )
+
+def downgrade():
+    metadata.reflect()
+    for table in tables:
+        table.drop()

lib/galaxy/web/controllers/workflow.py

@@ -17,6 +17,7 @@ from galaxy.workflow.modules import *
 from galaxy import model
 from galaxy.model.mapping import desc
 from galaxy.model.orm import *
+from galaxy.jobs.actions.post import *
 
 import urllib2
 
@@ -387,7 +388,6 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             else:
                 stored.importable = importable
             trans.sa_session.flush()
-
         return
         
     @web.expose
@@ -514,6 +514,7 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
         This is used for the form shown in the right pane when a node
         is selected.
         """
+        
         trans.workflow_building_mode = True
         module = module_factory.from_dict( trans, {
             'type': type,
@@ -521,14 +522,26 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             'tool_state': incoming.pop("tool_state")
         } )
         module.update_state( incoming )
-        return {
-            'tool_state': module.get_state(),
-            'data_inputs': module.get_data_inputs(),
-            'data_outputs': module.get_data_outputs(),
-            'tool_errors': module.get_errors(),
-            'form_html': module.get_config_form(),
-            'annotation': annotation
-        }
+        
+        if type=='tool':
+            return {
+                'tool_state': module.get_state(),
+                'data_inputs': module.get_data_inputs(),
+                'data_outputs': module.get_data_outputs(),
+                'tool_errors': module.get_errors(),
+                'form_html': module.get_config_form(),
+                'annotation': annotation,
+                'post_job_actions': module.get_post_job_actions()
+            }
+        else:
+            return {
+                'tool_state': module.get_state(),
+                'data_inputs': module.get_data_inputs(),
+                'data_outputs': module.get_data_outputs(),
+                'tool_errors': module.get_errors(),
+                'form_html': module.get_config_form(),
+                'annotation': annotation
+            }
         
     @web.json
     def get_new_module_info( self, trans, type, **kwargs ):
@@ -552,7 +565,7 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             'form_html': module.get_config_form(),
             'annotation': ""
         }
-                
+
     @web.json
     def load_workflow( self, trans, id ):
         """
@@ -613,6 +626,13 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
                 # Filter
                 # FIXME: this removes connection without displaying a message currently!
                 input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ]
+                # post_job_actions
+                pja_dict = {}
+                for pja in step.post_job_actions:
+                    pja_dict[pja.action_type+pja.output_name] = dict(action_type = pja.action_type, 
+                                            output_name = pja.output_name,
+                                            action_arguments = pja.action_arguments)
+                step_dict['post_job_actions'] = pja_dict
             # Encode input connections as dictionary
             input_conn_dict = {}
             for conn in input_connections:
@@ -665,7 +685,7 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             annotation = step_dict[ 'annotation' ]
             if annotation:
                 annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
-                self.add_item_annotation( trans, step, annotation  )
+                self.add_item_annotation( trans, step, annotation )
         # Second pass to deal with connections between steps
         for step in steps:
             # Input connections
@@ -815,7 +835,7 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
             annotation = step_dict[ 'annotation' ]
             if annotation:
                 annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
-                self.add_item_annotation( trans, step, annotation  )
+                self.add_item_annotation( trans, step, annotation )
         # Second pass to deal with connections between steps
         for step in steps:
             # Input connections
@@ -1044,6 +1064,8 @@ class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnno
                         # Execute it
                         job, out_data = tool.execute( trans, step.state.inputs )
                         outputs[ step.id ] = out_data
+                        for pja in step.post_job_actions:
+                            ActionBox.execute(trans, pja, job)
                     else:
                         job, out_data = step.module.execute( trans, step.state )
                         outputs[ step.id ] = out_data

lib/galaxy/workflow/modules.py

@@ -6,7 +6,8 @@ from galaxy.tools import DefaultToolState
 from galaxy.tools.parameters.grouping import Repeat, Conditional
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import from_json_string, to_json_string
-       
+from galaxy.jobs.actions.post import ActionBox
+from galaxy.model import PostJobAction
 
 class WorkflowModule( object ):
     
@@ -163,6 +164,7 @@ class ToolModule( WorkflowModule ):
         self.trans = trans
         self.tool_id = tool_id
         self.tool = trans.app.toolbox.tools_by_id[ tool_id ]
+        self.post_job_actions = {}
         self.state = None
         self.errors = None
 
@@ -171,6 +173,7 @@ class ToolModule( WorkflowModule ):
         module = Class( trans, tool_id )
         module.state = module.tool.new_state( trans, all_pages=True )
         return module
+        
     @classmethod
     def from_dict( Class, trans, d, secure=True ):
         tool_id = d['tool_id']
@@ -178,6 +181,10 @@ class ToolModule( WorkflowModule ):
         module.state = DefaultToolState()
         module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure )
         module.errors = d.get( "tool_errors", None )
+        if 'post_job_actions' in d and d["post_job_actions"] != []:
+            module.post_job_actions = d["post_job_actions"]
+        else:
+            module.post_job_actions = {}
         return module
         
     @classmethod
@@ -187,6 +194,11 @@ class ToolModule( WorkflowModule ):
         module.state = DefaultToolState()
         module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
         module.errors = step.tool_errors
+        # module.post_job_actions = step.post_job_actions
+        pjadict = {}
+        for pja in step.post_job_actions:
+            pjadict[pja.action_type] = pja
+        module.post_job_actions = pjadict
         return module
 
     def save_to_step( self, step ):
@@ -194,6 +206,17 @@ class ToolModule( WorkflowModule ):
         step.tool_id = self.tool_id
         step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
         step.tool_errors = self.errors
+        for k, v in self.post_job_actions.iteritems():
+            # Must have action_type, step.  output and a_args are optional.
+            if 'output_name' in v:
+                output_name = v['output_name']
+            else:
+                output_name = None
+            if 'action_arguments' in v:
+                action_arguments = v['action_arguments']
+            else:
+                action_arguments = None
+            n_p = PostJobAction(v['action_type'], step, output_name, action_arguments)
 
     def get_name( self ):
         return self.tool.name
@@ -221,15 +244,23 @@ class ToolModule( WorkflowModule ):
         for name, ( format, metadata_source, parent ) in self.tool.outputs.iteritems():
             data_outputs.append( dict( name=name, extension=format ) )
         return data_outputs
+    
+    def get_post_job_actions( self ):
+        return self.post_job_actions
+        
     def get_config_form( self ):
         self.add_dummy_datasets()
         return self.trans.fill_template( "workflow/editor_tool_form.mako", 
             tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) )
+
     def update_state( self, incoming ):       
         # Build a callback that handles setting an input to be required at
         # runtime. We still process all other parameters the user might have
         # set. We also need to make sure all datasets have a dummy value
         # for dependencies to see
+        
+        self.post_job_actions = ActionBox.handle_incoming(incoming)
+        
         make_runtime_key = incoming.get( 'make_runtime', None )
         make_buildtime_key = incoming.get( 'make_buildtime', None )
         def item_callback( trans, key, input, value, error, old_value, context ):

static/scripts/galaxy.workflow_editor.canvas.js

@@ -273,6 +273,7 @@ $.extend( Node.prototype, {
         this.tool_errors = data.tool_errors;
         this.tooltip = data.tooltip ? data.tooltip : ""
         this.annotation = data.annotation;
+        this.post_job_actions = data.post_job_actions;
         
         if ( this.tool_errors ) {
             f.addClass( "tool-node-error" );
@@ -309,6 +310,7 @@ $.extend( Node.prototype, {
         this.form_html = data.form_html;
         this.tool_errors = data.tool_errors;
         this.annotation = data['annotation'];
+        this.post_job_actions = $.parseJSON(data.post_job_actions);
         if ( this.tool_errors ) {
                 el.addClass( "tool-node-error" );
         } else {
@@ -400,6 +402,19 @@ $.extend( Workflow.prototype, {
                     input_connections[ t.name ] = { id: c.handle1.node.id, output_name: c.handle1.name };
                 });
             });
+            var post_job_actions = {};
+            if (node.post_job_actions){
+                $.each( node.post_job_actions, function ( i, act ) {
+                    var pja = {
+                        job_id : act.id,
+                        action_type : act.action_type, 
+                        output_name : act.output_name, 
+                        action_arguments : act.action_arguments
+                    }
+                    post_job_actions[ act.type + act.output_name ] = null;
+                    post_job_actions[ act.type + act.output_name ] = pja;
+                });
+            }
             var node_data = {
                 id : node.id,
                 type : node.type,
@@ -408,7 +423,8 @@ $.extend( Workflow.prototype, {
                 tool_errors : node.tool_errors,
                 input_connections : input_connections,
                 position : $(node.element).position(),
-                annotation: node.annotation
+                annotation: node.annotation,
+                post_job_actions: node.post_job_actions
             };
             nodes[ node.id ] = node_data;
         });

templates/workflow/editor.mako

@@ -128,7 +128,7 @@
             show_modal( "Server error", message, { "Ignore error" : hide_modal } );
             return false;
         });
-        
+         
         make_popupmenu( $("#workflow-options-button"), {
              ##"Create New" : create_new_workflow_dialog,
              "Edit Attributes" : edit_workflow_attributes,
@@ -306,13 +306,63 @@
         });
     };
 
+<%
+    from galaxy.jobs.actions.post import ActionBox
+%>
+
+	// DBTODO Refactor to the post module.
+	// This function preloads how to display known pja's.
+	function display_pja(pja, node){
+		// DBTODO SANITIZE INPUTS.  Way too easy to break the page right now with a change dataset name action.
+		p_str = '';
+		${ActionBox.get_forms(trans)};
+		$("#pja_container").append(p_str);
+		$("#pja_container>.toolForm:last>.toolFormTitle>.buttons").click(function (){
+			action_to_rem = $(this).closest(".toolForm", ".action_tag").children(".action_tag:first").text();
+			$(this).closest(".toolForm").remove();
+			delete workflow.active_node.post_job_actions[action_to_rem];
+			workflow.active_form_has_changes = true;
+		});
+	}
+	
+	function display_pja_list(){
+		return "${ActionBox.get_add_list()}";
+	}
+	
+	function display_file_list(node){
+		addlist = "<select id='node_data_list' name='node_data_list'>";
+		for (var out_terminal in node.output_terminals){
+			addlist += "<option value='" + out_terminal + "'>"+ out_terminal +"</option>";
+		}
+        addlist += "</select>";
+		return addlist;
+	}
+	
+	function new_pja(action_type, target, node){
+		if (node.post_job_actions == undefined){
+			//New tool node, set up dict.
+			node.post_job_actions = {};
+		}
+		if (node.post_job_actions[action_type+target] == undefined){
+			var new_pja = new Object();
+			new_pja.action_type = action_type;
+			new_pja.output_name = target;
+			node.post_job_actions[action_type+target] = null;
+			node.post_job_actions[action_type+target] =  new_pja;
+			display_pja(new_pja, node);
+			workflow.active_form_has_changes = true;
+			return true;
+		}else{
+			return false;
+		}
+	}
+	
     function show_form_for_tool( text, node ) {
         $("#edit-attributes").hide();
         $("#right-content").show().html( text );
-        
         // Add metadata form to tool.
         if (node) {
-            $("#right-content").find(".toolForm").after( "<p><div class='metadataForm'> \
+            $("#right-content").find(".toolForm:first").after( "<p><div class='metadataForm'> \
                 <div class='metadataFormTitle'>Edit Step Attributes</div> \
                 <div class='form-row'> \
                 <label>Annotation / Notes:</label> \
@@ -323,7 +373,23 @@
                 </div> \
                 </div>" );
         }
-        
+		// Add step actions.
+		if (node && node.type=='tool'){
+			pjastr = "<p><div class='metadataForm'><div class='metadataFormTitle'>Edit Step Actions</div><div class='form-row'> \
+                <label>New Actions:</label><br/>" + display_pja_list() + display_file_list(node) + " <div class='action-button' style='border:1px solid black;display:inline;' id='add_pja'>Create</div>\
+                </div><div class='form-row'>\
+				<div style='margin-right: 10px;'><span id='pja_container'></span>";
+			pjastr += "<div class='toolParamHelp'>Add actions to this step; actions are applied when this workflow step completes.</div></div></div></div>";
+			$("#right-content").find(".toolForm").after( pjastr );
+			for (var key in node.post_job_actions){
+				if (key != "undefined"){ //To make sure we haven't just deleted it.
+					display_pja(node.post_job_actions[key], node);
+				}
+			}
+			$("#add_pja").click(function (){
+				new_pja($("#new_pja_list").val(),$("#node_data_list").val(), node);
+			});
+		}
         $("#right-content").find( "form" ).ajaxForm( {
             type: 'POST',
             dataType: 'json',
@@ -355,7 +421,6 @@
                 $(this).remove();
                 make_popupmenu( b, options );
             });
-            
             // Implements auto-saving based on whether the inputs change. We consider
             // "changed" to be when a field is accessed and not necessarily modified
             // because of an issue where "onchange" is not triggered when activating
@@ -612,6 +677,7 @@
     
     .form-row {
     }
+
     div.toolFormInCanvas div.toolFormBody {
         padding: 0;
     }
@@ -630,7 +696,19 @@
         position: absolute;
         z-index: 10000;
     }
-    
+
+	.pjaForm {
+		margin-bottom:10px;
+	}
+	
+	.pjaForm .toolFormBody{
+		padding:10px;
+	}
+	
+	.pjaForm .toolParamHelp{
+		padding:5px;
+	}
+	
     .panel-header-button-group {
         margin-right: 5px;
         padding-right: 5px;

templates/workflow/run.mako

@@ -23,6 +23,7 @@
 
 <%
 from galaxy.tools.parameters import DataToolParameter, RuntimeValue
+from galaxy.jobs.actions.post import ActionBox
 %>
 
 <%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None )">
@@ -136,6 +137,23 @@ from galaxy.tools.parameters import DataToolParameter, RuntimeValue
           <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${tool.name}</div>
           <div class="toolFormBody">
               ${do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), "", step )}
+			% if step.post_job_actions:
+				<hr/>
+				<div class='form-row'>
+				% if len(step.post_job_actions) > 1:
+					<label>Actions:</label>
+				% else:
+					<label>Action:</label>
+				% endif
+				${', '.join([ActionBox.get_short_str(pja) for pja in step.post_job_actions])}
+				</div>
+			% endif
+		% if step.annotations:
+			<hr/>
+			<div class='form-row'>
+			<label>Annotation:</label> ${step.annotations[0].annotation}
+			</div>
+		% endif
           </div>
       </div>
     %else:
@@ -145,6 +163,12 @@ from galaxy.tools.parameters import DataToolParameter, RuntimeValue
           <div class="toolFormTitle">Step ${int(step.order_index)+1}: ${module.name}</div>
           <div class="toolFormBody">
               ${do_inputs( module.get_runtime_inputs(), step.state.inputs, errors.get( step.id, dict() ), "", step )}
+			% if step.annotations:
+				<hr/>
+				<div class='form-row'>
+				<label>Annotation:</label> ${step.annotations[0].annotation}
+				</div>
+			% endif
           </div>
       </div>
     %endif