Merge, rebuild.

client/galaxy/scripts/viz/trackster/tracks.js

@@ -2507,7 +2507,7 @@ extend(Track.prototype, Drawable.prototype, {
             var data = result.data;
 
             // Tracks may not have stat data either because there is no data or data is not yet ready.
-            if (data !== undefined && data.min !== undefined && data.max !== undefined) {
+            if (data && data.min !== undefined && data.max !== undefined) {
                 // Compute default minimum and maximum values
                 var min_value = data.min,
                     max_value = data.max;

lib/galaxy/model/__init__.py

@@ -961,8 +961,13 @@ class PostJobAction( object ):
 
 
 class PostJobActionAssociation( object ):
-    def __init__(self, pja, job):
-        self.job = job
+    def __init__(self, pja, job=None, job_id=None ):
+        if job is not None:
+            self.job = job
+        elif job_id is not None:
+            self.job_id = job_id
+        else:
+            raise Exception("PostJobActionAssociation must be created with a job or a job_id.")
         self.post_job_action = pja
 
 

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -156,7 +156,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
         if msg:
             return msg
 
-        # Get datasources and check for essages.
+        # Get datasources and check for messages.
         data_sources = dataset.get_datasources( trans )
         messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ]
         return_message = self._get_highest_priority_msg( messages_list )
@@ -251,7 +251,7 @@ class DatasetsController( BaseAPIController, UsesVisualizationMixin ):
 
         registry = trans.app.data_provider_registry
 
-        # allow the caller to specifiy which provider is used
+        # allow the caller to specify which provider is used
         #   pulling from the original providers if possible, then the new providers
         if provider:
             if provider in registry.dataset_type_name_to_data_provider:

lib/galaxy/workflow/modules.py

@@ -1118,6 +1118,7 @@ class ToolModule( WorkflowModule ):
 
         # Combine workflow and runtime post job actions into the effective post
         # job actions for this execution.
+        flush_required = False
         effective_post_job_actions = step.post_job_actions[:]
         for key, value in self.runtime_post_job_actions.iteritems():
             effective_post_job_actions.append( self.__to_pja( key, value, None ) )
@@ -1125,7 +1126,11 @@ class ToolModule( WorkflowModule ):
             if pja.action_type in ActionBox.immediate_actions:
                 ActionBox.execute( self.trans.app, self.trans.sa_session, pja, job, replacement_dict )
             else:
-                job.add_post_job_action( pja )
+                pjaa = model.PostJobActionAssociation( pja, job_id=job.id )
+                self.trans.sa_session.add(pjaa)
+                flush_required = True
+        if flush_required:
+            self.trans.sa_session.flush()
 
     def add_dummy_datasets( self, connections=None):
         if connections:

test/unit/test_lazy_process.py

@@ -1,3 +1,4 @@
+"""Unit module for LazyProcess object in galaxy.util.lazy_process."""
 import os
 import tempfile
 import time
@@ -6,6 +7,7 @@ from galaxy.util.lazy_process import LazyProcess
 
 
 def test_lazy_process():
+    """Create process, ensure start_process starts it and shutdown kills it."""
     t = tempfile.NamedTemporaryFile()
     os.remove(t.name)
     lazy_process = LazyProcess(["bash", "-c", "touch %s; sleep 100" % t.name])
@@ -15,4 +17,10 @@ def test_lazy_process():
         time.sleep(.01)
     assert lazy_process.process.poll() is None
     lazy_process.shutdown()
-    assert lazy_process.process.poll()
+    ret_val = None
+    for i in range(10):
+        ret_val = lazy_process.process.poll()
+        if ret_val is not None:
+            break
+        time.sleep(.01)
+    assert ret_val is not None