Merge branch 'release_21.01' into dev

lib/galaxy/datatypes/tabular.py

@@ -827,7 +827,7 @@ class VcfGz(BaseVcf, binary.Binary):
             index_file = dataset.metadata.spec['tabix_index'].param.new_file(dataset=dataset)
 
         try:
-            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', force=True)
+            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf', keep_original=True, force=True)
         except Exception as e:
             raise Exception('Error setting VCF.gz metadata: %s' % (util.unicodify(e)))
         dataset.metadata.tabix_index = index_file

lib/galaxy/web/legacy_framework/grids.py

@@ -390,9 +390,6 @@ class DeletedColumn(GridColumn):
 class StateColumn(GridColumn):
     """
     Column that tracks and filters for items with state attribute.
-
-    IMPORTANT NOTE: self.model_class must have a states Bunch or dict if
-    this column type is used in the grid.
     """
 
     def get_value(self, trans, grid, item):
@@ -402,7 +399,7 @@ class StateColumn(GridColumn):
         """Modify query to filter self.model_class by state."""
         if column_filter == "All":
             pass
-        elif column_filter in [v for k, v in self.model_class.states.items()]:
+        elif column_filter in list(self.model_class.states):
             query = query.filter(self.model_class.state == column_filter)
         return query
 
@@ -410,9 +407,9 @@ class StateColumn(GridColumn):
         """Returns a list of accepted filters for this column."""
         all = GridColumnFilter('all', {self.key: 'All'})
         accepted_filters = [all]
-        for v in self.model_class.states.values():
-            args = {self.key: v}
-            accepted_filters.append(GridColumnFilter(v, args))
+        for state in self.model_class.states:
+            args = {self.key: state.value}
+            accepted_filters.append(GridColumnFilter(state.value, args))
         return accepted_filters
 
 

templates/webapps/galaxy/visualization/display_in_frame.mako

@@ -49,7 +49,7 @@
 <%def name="render_item( visualization, config )">
     <div id="${trans.security.encode_id( visualization.id )}" class="unified-panel-body" style="overflow:none;top:0px;">
         <iframe frameborder="0" width="100%" height="100%" sandbox="allow-forms allow-same-origin allow-scripts"
-                src="/visualization/saved?id=${encoded_visualization_id}&embedded=True">
+                src="/visualization/saved?id=${encoded_visualization_id}">
         </iframe>
     </div>
 </%def>