Merge branch 'master' into dev

config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js

@@ -1,6 +1,7 @@
-
-define(['plugin/charts/nvd3/common/config'], function(nvd3_config) {
-return $.extend(true, {}, nvd3_config, {
+define(['plugin/charts/forms/default'], function(config_default) {
+return $.extend(true, {}, config_default, {
+    library     : 'NVD3',
+    tag         : 'svg',
     title       : 'Histogram',
     category    : 'Data processing (requires \'charts\' tool from Toolshed)',
     execute     : 'histogram',

config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js

@@ -1,6 +1,7 @@
-define(['plugin/charts/nvd3/common/config'], function(nvd3_config) {
-
-return $.extend(true, {}, nvd3_config, {
+define(['plugin/charts/forms/default'], function(config_default) {
+return $.extend(true, {}, config_default, {
+    library     : 'NVD3',
+    tag         : 'svg',
     title       : 'Discrete Histogram',
     category    : 'Data processing (requires \'charts\' tool from Toolshed)',
     execute     : 'histogramdiscrete',

config/plugins/visualizations/charts/static/views/editor.js

@@ -211,7 +211,7 @@ return Backbone.View.extend({
     // add group model
     _addGroupModel: function() {
         var group = new Group({
-            id : Utils.uuid()
+            id : Utils.uid()
         });
         this.chart.groups.add(group);
         return group;
@@ -260,7 +260,7 @@ return Backbone.View.extend({
     // reset
     _resetChart: function() {
         // reset chart details
-        this.chart.set('id', Utils.uuid());
+        this.chart.set('id', Utils.uid());
         this.chart.set('type', 'nvd3_bar');
         this.chart.set('dataset_id', this.app.options.config.dataset_id);
         this.chart.set('title', 'New Chart');

config/plugins/visualizations/charts/static/views/viewport.js

@@ -295,7 +295,7 @@ return Backbone.View.extend({
     _templateContainer: function(tag, width) {
         return  '<div class="charts-viewport-container" style="width:' + width + '%;">' +
                     '<div id="menu"/>' +
-                    '<' + tag + ' id="' + Utils.uuid() + '" class="charts-viewport-canvas">' +
+                    '<' + tag + ' id="' + Utils.uid() + '" class="charts-viewport-canvas">' +
                 '</div>';
     }
     

lib/galaxy/tools/__init__.py

@@ -531,6 +531,16 @@ class Tool( object, Dictifiable ):
 
         return any( map( output_is_dynamic_collection, self.outputs.values() ) )
 
+    @property
+    def produces_collections_with_unknown_structure( self ):
+
+        def output_is_dynamic(output):
+            if not output.collection:
+                return False
+            return output.dynamic_structure
+
+        return any( map( output_is_dynamic, self.outputs.values() ) )
+
     def __get_job_tool_configuration(self, job_params=None):
         """Generalized method for getting this tool's job configuration.
 

lib/galaxy/workflow/run.py

@@ -33,6 +33,12 @@ BASIC_WORKFLOW_STEP_TYPES = [ None, "tool", "data_input", "data_collection_input
 def force_queue( trans, workflow ):
     # Default behavior is still to just schedule workflows completley right
     # away. This can be modified here in various ways.
+
+    # TODO: check for implicit connections - these should also force backgrounding
+    #       this would fix running Dan's data manager workflows via UI.
+    # TODO: ensure state if populated before calling force_queue from old API
+    #       workflow endpoint so the has_module check below is unneeded and these
+    #       interesting workflows will work with the older endpoint.
     config = trans.app.config
     force_for_collection = config.force_beta_workflow_scheduled_for_collections
     force_min_steps = config.force_beta_workflow_scheduled_min_steps
@@ -42,6 +48,10 @@ def force_queue( trans, workflow ):
         log.info("Workflow has many steps %d, backgrounding execution" % step_count)
         return True
     for step in workflow.steps:
+        # State and module haven't been populated if workflow submitted via
+        # the API. API requests for "interesting" workflows should use newer
+        # endpoint that skips this check entirely - POST /api/workflows/<id>/invocations
+        has_module = hasattr(step, "module")
         if step.type not in BASIC_WORKFLOW_STEP_TYPES:
             log.info("Found non-basic workflow step type - backgrounding execution")
             # Force all new beta modules types to be use force queueing of
@@ -50,7 +60,9 @@ def force_queue( trans, workflow ):
         if step.type == "data_collection_input" and force_for_collection:
             log.info("Found collection input step - backgrounding execution")
             return True
-
+        if step.type == "tool" and has_module and step.module.tool.produces_collections_with_unknown_structure:
+            log.info("Found dynamically structured output collection - backgrounding execution")
+            return True
     return False