diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 5e55e665157..2716e1ceea3 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/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 diff --git a/lib/galaxy/web/legacy_framework/grids.py b/lib/galaxy/web/legacy_framework/grids.py index 169074aa4b0..2b2507d06d6 100644 --- a/lib/galaxy/web/legacy_framework/grids.py +++ b/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 diff --git a/templates/webapps/galaxy/visualization/display_in_frame.mako b/templates/webapps/galaxy/visualization/display_in_frame.mako index f4fc1aec632..ec7d787c50e 100644 --- a/templates/webapps/galaxy/visualization/display_in_frame.mako +++ b/templates/webapps/galaxy/visualization/display_in_frame.mako @@ -49,7 +49,7 @@ <%def name="render_item( visualization, config )">