Merge remote-tracking branch 'upstream/release_19.01' into dev

client/galaxy/scripts/mvc/form/form-parameters.js

@@ -29,6 +29,7 @@ export default Backbone.Model.extend({
         boolean: "_fieldBoolean",
         drill_down: "_fieldDrilldown",
         color: "_fieldColor",
+        group_tag: "_fieldSelect",
         hidden: "_fieldHidden",
         hidden_data: "_fieldHidden",
         baseurl: "_fieldHidden",
@@ -125,7 +126,7 @@ export default Backbone.Model.extend({
     /** Text input field */
     _fieldText: function(input_def) {
         // field replaces e.g. a select field
-        if (input_def.options && input_def.data) {
+        if (input_def.data_ref || input_def.options && input_def.data) {
             input_def.area = input_def.multiple;
             if (Utils.isEmpty(input_def.value)) {
                 input_def.value = null;

client/webpack.config.js

@@ -113,7 +113,7 @@ let buildconfig = {
                     loader: "file-loader",
                     options: {
                         outputPath: "assets",
-                        publicPath: "/static/scripts/bundled/assets/"
+                        publicPath: "../scripts/bundled/assets/"
                     }
                 }
             },

lib/galaxy/tools/parameters/basic.py

@@ -1080,6 +1080,8 @@ class SelectTagParameter(SelectToolParameter):
         # Get the value of the associated data reference (a dataset)
         history_items = other_values.get(self.data_ref, None)
         # Check if a dataset is selected
+        if is_runtime_value(history_items):
+            return []
         if not history_items:
             return []
         tags = set()
@@ -1110,7 +1112,7 @@ class SelectTagParameter(SelectToolParameter):
         return SelectToolParameter.get_initial_value(self, trans, other_values)
 
     def get_legal_values(self, trans, other_values):
-        if self.data_ref not in other_values:
+        if self.data_ref not in other_values and not trans.workflow_building_mode:
             raise ValueError("Value for associated data reference not found (data_ref).")
         return set(self.get_tag_list(other_values))
 
@@ -1720,7 +1722,7 @@ class DataToolParameter(BaseDataToolParameter):
                 self.conversions.append((name, conv_extension, [conv_type]))
 
     def from_json(self, value, trans, other_values={}):
-        if trans.workflow_building_mode is workflow_building_modes.ENABLED:
+        if trans.workflow_building_mode is workflow_building_modes.ENABLED or is_runtime_value(value):
             return None
         if not value and not self.optional:
             raise ValueError("Specify a dataset of the required format / build for parameter %s." % self.name)

lib/galaxy/web/stack/handlers.py

@@ -287,7 +287,7 @@ class ConfiguresHandlers(object):
         :returns: str -- The assigned handler ID.
         """
         if configured:
-            return self.handler_assignment_method_methods[HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN](
+            return self._handler_assignment_method_methods[HANDLER_ASSIGNMENT_METHODS.DB_PREASSIGN](
                 obj, method, configured, **kwargs
             )
         obj.set_handler(self.app.config.server_name)

templates/webapps/galaxy/galaxy.panels.mako

@@ -42,6 +42,8 @@
             | ${self.galaxy_config['title']}
             %endif
         </title>
+        ## relative href for site root
+        <link rel="index" href="${ h.url_for( '/' ) }"/>
 
         ${self.stylesheets()}
         ${self.javascripts()}