Merge branch 'dev' of git://github.com/galaxyproject/galaxy into run_…

…workflow_form_004

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -82,7 +82,7 @@ define(['utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view',
                     self._buildForm(new_model['tool_model'] || new_model);
                     !hide_message && self.message.update({
                         status      : 'success',
-                        message     : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + '.',
+                        message     : 'Now you are using \'' + self.options.name + '\' version ' + self.options.version + ', id \'' + self.options.id + '\'.',
                         persistent  : false
                     });
                     Galaxy.emit.debug('tool-form-base::initialize()', 'Initial tool model ready.', new_model);

lib/galaxy/managers/histories.py

@@ -294,7 +294,8 @@ def serialize_history_state( self, history, key, **context ):
                     hda_state_counts[states.UPLOAD] > 0):
                 state = states.RUNNING
             # TODO: this method may be more useful if we *also* polled the histories jobs here too
-            elif hda_state_counts[ states.QUEUED ] > 0:
+            elif (hda_state_counts[ states.QUEUED ] > 0 or
+                    hda_state_counts[states.NEW] > 0):
                 state = states.QUEUED
             elif (hda_state_counts[states.ERROR] > 0 or
                     hda_state_counts[states.FAILED_METADATA] > 0):

lib/galaxy/managers/workflows.py

@@ -334,6 +334,10 @@ def _workflow_to_dict_editor(self, trans, stored):
                 # FIXME: Frontend should be able to handle workflow messages
                 #        as a dictionary not just the values
                 data['upgrade_messages'][step.order_index] = upgrade_message.values()
+                # Dispay version/tool_id changes
+                data['upgrade_messages'] = [step.order_index][module.tool.name] = "\n".join( module.version_changes )
+            elif (hasattr(module, "version_changes")) and (module.version_changes):
+                data['upgrade_messages'] = {step.order_index: {module.tool.name: "\n".join( module.version_changes )}}
             # Get user annotation.
             step_annotation = self.get_item_annotation_obj( trans.sa_session, trans.user, step )
             annotation_str = ""

lib/galaxy/model/__init__.py

@@ -14,7 +14,7 @@
 import socket
 import time
 from datetime import datetime, timedelta
-from itertools import ifilter
+from itertools import ifilter, imap
 from string import Template
 from uuid import UUID, uuid4
 
@@ -1078,6 +1078,10 @@ def __init__( self, user, group ):
         self.group = group
 
 
+def is_hda(d):
+    return isinstance( d, HistoryDatasetAssociation )
+
+
 class History( object, Dictifiable, UsesAnnotations, HasName ):
 
     dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' )
@@ -1151,7 +1155,7 @@ def add_datasets( self, sa_session, datasets, parent_id=None, genome_build=None,
         """ Optimized version of add_dataset above that minimizes database
         interactions when adding many datasets to history at once.
         """
-        all_hdas = all( map( lambda d: isinstance( d, HistoryDatasetAssociation ), datasets ) )
+        all_hdas = all( imap( is_hda, datasets ) )
         optimize = len( datasets) > 1 and parent_id is None and all_hdas and set_hid and not quota
         if optimize:
             self.__add_datasets_optimized( datasets, genome_build=genome_build )
@@ -1173,11 +1177,11 @@ def __add_datasets_optimized( self, datasets, genome_build=None ):
         n = len( datasets )
 
         base_hid = self._next_hid( n=n )
-
+        set_genome = genome_build not in [None, '?']
         for i, dataset in enumerate( datasets ):
             dataset.hid = base_hid + i
             dataset.history = self
-            if genome_build not in [None, '?']:
+            if set_genome:
                 self.genome_build = genome_build
         self.datasets.extend( datasets )
         return datasets

lib/galaxy/tools/__init__.py

@@ -1342,14 +1342,14 @@ def handle_input( self, trans, incoming, history=None, source='html' ):
             else:
                 raise exceptions.MessageException( execution_tracker.execution_errors[ 0 ] )
 
-    def handle_single_execution( self, trans, rerun_remap_job_id, params, history, mapping_over_collection ):
+    def handle_single_execution( self, trans, rerun_remap_job_id, params, history, mapping_over_collection, execution_cache=None ):
         """
         Return a pair with whether execution is successful as well as either
         resulting output data or an error message indicating the problem.
         """
         try:
             params = self.__remove_meta_properties( params )
-            job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id, mapping_over_collection=mapping_over_collection )
+            job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id, mapping_over_collection=mapping_over_collection, execution_cache=execution_cache )
         except httpexceptions.HTTPFound, e:
             # if it's a paste redirect exception, pass it up the stack
             raise e
@@ -2576,18 +2576,17 @@ def _compare_tool_version( self, trans, job ):
                         # for some reason jobs don't always keep track of the tool version.
                         message = ''
                     else:
-                        message = 'This job was initially run with tool version "%s", which is currently not available.  ' % tool_version
+                        message = 'This job was run with tool version "%s", which is not available.  ' % tool_version
                         if len( tools ) > 1:
-                            message += 'You can re-run the job with the selected tool or choose another derivation of the tool.'
+                            message += 'You can re-run the job with the selected tool or choose another version of the tool.'
                         else:
-                            message += 'You can re-run the job with this tool version, which is a derivation of the original tool.'
+                            message += 'You can re-run the job with this tool version, which is a different version of the original tool.'
                 else:
+                    message = 'This job was run with tool id "%s", version "%s", which is not available.  ' % ( tool_id, tool_version )
                     if len( tools ) > 1:
-                        message = 'This job was initially run with tool version "%s", which is currently not available.  ' % tool_version
-                        message += 'You can re-run the job with the selected tool or choose another derivation of the tool.'
+                        message += 'You can re-run the job with the selected tool id "%s" or choose another derivation of the tool.' % self.id
                     else:
-                        message = 'This job was initially run with tool id "%s", version "%s", which is ' % ( tool_id, tool_version )
-                        message += 'currently not available.  You can re-run the job with this tool, which is a derivation of the original tool.'
+                        message += 'You can re-run the job with tool id "%s", which is a derivation of the original tool.' % self.id
         except Exception, e:
             raise exceptions.MessageException( str( e ) )
         return message