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https://github.com/galaxyproject/galaxy.git
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Remove unused legacy grid column types
This commit is contained in:
guerler
@@ -129,13 +129,6 @@ class GridColumn:
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return query
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class ReverseSortColumn(GridColumn):
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"""Column that reverses sorting; this is useful when the natural sort is descending."""
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def sort(self, trans, query, ascending, column_name=None):
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return GridColumn.sort(self, trans, query, (not ascending), column_name=column_name)
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class TextColumn(GridColumn):
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"""Generic column that employs freetext and, hence, supports freetext, case-independent filtering."""
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@@ -182,495 +175,6 @@ class TextColumn(GridColumn):
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return query
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class DateTimeColumn(TextColumn):
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def sort(self, trans, query, ascending, column_name=None):
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"""Sort query using this column."""
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return GridColumn.sort(self, trans, query, ascending, column_name=column_name)
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class BooleanColumn(TextColumn):
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def sort(self, trans, query, ascending, column_name=None):
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"""Sort query using this column."""
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return GridColumn.sort(self, trans, query, ascending, column_name=column_name)
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def get_single_filter(self, user, a_filter):
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if self.key.find(".") > -1:
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a_key = self.key.split(".")[1]
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else:
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a_key = self.key
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model_class_key_field = getattr(self.model_class, a_key)
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return model_class_key_field == a_filter
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class IntegerColumn(TextColumn):
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"""
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Integer column that employs freetext, but checks that the text is an integer,
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so support filtering on integer values.
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IMPORTANT NOTE: grids that use this column type should not include the column
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in the cols_to_filter list of MulticolFilterColumn ( i.e., searching on this
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column type should not be performed in the grid's standard search - it won't
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throw exceptions, but it also will not find what you're looking for ). Grids
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that search on this column should use 'filterable="advanced"' so that searching
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is only performed in the advanced search component, restricting the search to
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the specific column.
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This is useful for searching on object ids or other integer columns. See the
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JobIdColumn column in the SpecifiedDateListGrid class in the jobs controller of
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the reports webapp for an example.
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"""
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def get_single_filter(self, user, a_filter):
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model_class_key_field = getattr(self.model_class, self.key)
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assert int(a_filter), "The search entry must be an integer"
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return model_class_key_field == int(a_filter)
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def sort(self, trans, query, ascending, column_name=None):
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"""Sort query using this column."""
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return GridColumn.sort(self, trans, query, ascending, column_name=column_name)
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class CommunityRatingColumn(GridColumn, UsesItemRatings):
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"""Column that displays community ratings for an item."""
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def get_value(self, trans, grid, item):
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if not hasattr(item, "average_rating"):
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# No prefetched column property, generate it on the fly.
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ave_item_rating, num_ratings = self.get_ave_item_rating_data(
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trans.sa_session, item, webapp_model=trans.model
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)
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else:
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ave_item_rating = item.average_rating
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num_ratings = 2 # just used for pluralization
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if not ave_item_rating:
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ave_item_rating = 0
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return trans.fill_template(
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"tool_shed_rating.mako",
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ave_item_rating=ave_item_rating,
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num_ratings=num_ratings,
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item_id=trans.security.encode_id(item.id),
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)
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def sort(self, trans, query, ascending, column_name=None):
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# Get the columns that connect item's table and item's rating association table.
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item_rating_assoc_class = getattr(trans.model, f"{self.model_class.__name__}RatingAssociation")
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foreign_key = get_foreign_key(item_rating_assoc_class, self.model_class)
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fk_col = foreign_key.parent
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referent_col = foreign_key.get_referent(self.model_class.table)
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# Do sorting using a subquery.
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# Subquery to get average rating for each item.
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ave_rating_subquery = (
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trans.sa_session.query(fk_col, func.avg(item_rating_assoc_class.table.c.rating).label("avg_rating"))
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.group_by(fk_col)
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.subquery()
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)
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# Integrate subquery into main query.
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query = query.outerjoin((ave_rating_subquery, referent_col == ave_rating_subquery.columns[fk_col.name]))
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# Sort using subquery results; use coalesce to avoid null values.
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if (
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not ascending
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): # TODO: for now, reverse sorting b/c first sort is ascending, and that should be the natural sort.
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query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).asc())
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else:
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query = query.order_by(func.coalesce(ave_rating_subquery.c.avg_rating, 0).desc())
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return query
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class OwnerAnnotationColumn(TextColumn, UsesAnnotations):
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"""Column that displays and filters item owner's annotations."""
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def __init__(self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None):
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GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
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self.sortable = False
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self.model_annotation_association_class = model_annotation_association_class
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def get_value(self, trans, grid, item):
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"""Returns first 150 characters of annotation."""
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annotation = self.get_item_annotation_str(trans.sa_session, item.user, item)
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if annotation:
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ann_snippet = annotation[:155]
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if len(annotation) > 155:
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ann_snippet = ann_snippet[: ann_snippet.rfind(" ")]
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ann_snippet += "..."
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else:
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ann_snippet = ""
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return escape(ann_snippet)
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def get_single_filter(self, user, a_filter):
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"""Filter by annotation and annotation owner."""
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return self.model_class.annotations.any(
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and_(
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func.lower(self.model_annotation_association_class.annotation).like(f"%{a_filter.lower()}%"),
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# TODO: not sure why, to filter by owner's annotations, we have to do this rather than
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# 'self.model_class.user==self.model_annotation_association_class.user'
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self.model_annotation_association_class.table.c.user_id == self.model_class.table.c.user_id,
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)
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)
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class CommunityTagsColumn(TextColumn):
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"""Column that supports community tags."""
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def __init__(
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self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None
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):
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GridColumn.__init__(
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self, col_name, key=key, model_class=model_class, nowrap=True, filterable=filterable, sortable=False
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)
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self.model_tag_association_class = model_tag_association_class
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# Column-specific attributes.
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self.grid_name = grid_name
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def get_value(self, trans, grid, item):
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return trans.fill_template(
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"/tagging_common.mako",
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tag_type="community",
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trans=trans,
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user=trans.get_user(),
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tagged_item=item,
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elt_context=self.grid_name,
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tag_click_fn="add_tag_to_grid_filter",
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use_toggle_link=True,
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)
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter model_class by tag. Multiple filters are ANDed."""
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if column_filter == "All":
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pass
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elif column_filter:
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query = query.filter(self.get_filter(trans, user, column_filter))
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return query
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def get_filter(self, trans, user, column_filter):
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# Parse filter to extract multiple tags.
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if isinstance(column_filter, list):
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# Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
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column_filter = ",".join(column_filter)
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raw_tags = trans.app.tag_handler.parse_tags(column_filter)
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clause_list = []
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for name, value in raw_tags:
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if name:
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# Filter by all tags.
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clause_list.append(
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self.model_class.tags.any(
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func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%")
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)
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)
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if value:
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# Filter by all values.
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clause_list.append(
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self.model_class.tags.any(
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func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%")
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)
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)
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return and_(*clause_list)
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class IndividualTagsColumn(CommunityTagsColumn):
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"""Column that supports individual tags."""
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def get_value(self, trans, grid, item):
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return trans.fill_template(
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"/tagging_common.mako",
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tag_type="individual",
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user=trans.user,
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tagged_item=item,
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elt_context=self.grid_name,
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tag_click_fn="add_tag_to_grid_filter",
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use_toggle_link=True,
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)
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def get_filter(self, trans, user, column_filter):
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# Parse filter to extract multiple tags.
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if isinstance(column_filter, list):
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# Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags.
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column_filter = ",".join(column_filter)
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raw_tags = trans.app.tag_handler.parse_tags(column_filter)
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clause_list = []
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for name, value in raw_tags:
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if name:
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# Filter by individual's tag names.
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clause_list.append(
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self.model_class.tags.any(
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and_(
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func.lower(self.model_tag_association_class.user_tname).like(f"%{name.lower()}%"),
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self.model_tag_association_class.user == user,
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)
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)
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)
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if value:
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# Filter by individual's tag values.
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clause_list.append(
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self.model_class.tags.any(
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and_(
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func.lower(self.model_tag_association_class.user_value).like(f"%{value.lower()}%"),
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self.model_tag_association_class.user == user,
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)
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)
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)
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return and_(*clause_list)
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class MulticolFilterColumn(TextColumn):
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"""Column that performs multicolumn filtering."""
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def __init__(self, col_name, cols_to_filter, key, visible, filterable="default"):
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GridColumn.__init__(self, col_name, key=key, visible=visible, filterable=filterable)
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self.cols_to_filter = cols_to_filter
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter model_class by tag. Multiple filters are ANDed."""
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if column_filter == "All":
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return query
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if isinstance(column_filter, list):
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clause_list = []
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for filter in column_filter:
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part_clause_list = []
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for column in self.cols_to_filter:
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part_clause_list.append(column.get_filter(trans, user, filter))
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clause_list.append(or_(*part_clause_list))
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complete_filter = and_(*clause_list)
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else:
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clause_list = []
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for column in self.cols_to_filter:
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clause_list.append(column.get_filter(trans, user, column_filter))
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complete_filter = or_(*clause_list)
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return query.filter(complete_filter)
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class OwnerColumn(TextColumn):
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"""Column that lists item's owner."""
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def get_value(self, trans, grid, item):
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return item.user.username
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def sort(self, trans, query, ascending, column_name=None):
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"""Sort column using case-insensitive alphabetical sorting on item's username."""
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if ascending:
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query = query.order_by(func.lower(self.model_class.username).asc())
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else:
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query = query.order_by(func.lower(self.model_class.username).desc())
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return query
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class PublicURLColumn(TextColumn):
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"""Column displays item's public URL based on username and slug."""
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def get_link(self, trans, grid, item):
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if item.user.username and item.slug:
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return dict(action="display_by_username_and_slug", username=item.user.username, slug=item.slug)
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elif not item.user.username:
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# TODO: provide link to set username.
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return None
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elif not item.user.slug:
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# TODO: provide link to set slug.
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return None
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class DeletedColumn(GridColumn):
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"""Column that tracks and filters for items with deleted attribute."""
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def get_accepted_filters(self):
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"""Returns a list of accepted filters for this column."""
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accepted_filter_labels_and_vals = {"active": "False", "deleted": "True", "all": "All"}
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accepted_filters = []
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for label, val in accepted_filter_labels_and_vals.items():
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args = {self.key: val}
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accepted_filters.append(GridColumnFilter(label, args))
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return accepted_filters
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter self.model_class by state."""
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if column_filter == "All":
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pass
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elif column_filter in ["True", "False"]:
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query = query.filter(self.model_class.deleted == (column_filter == "True"))
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return query
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class PurgedColumn(GridColumn):
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"""Column that tracks and filters for items with purged attribute."""
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def get_accepted_filters(self):
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"""Returns a list of accepted filters for this column."""
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accepted_filter_labels_and_vals = {"nonpurged": "False", "purged": "True", "all": "All"}
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accepted_filters = []
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for label, val in accepted_filter_labels_and_vals.items():
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args = {self.key: val}
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accepted_filters.append(GridColumnFilter(label, args))
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return accepted_filters
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter self.model_class by state."""
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if column_filter == "All":
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pass
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elif column_filter in ["True", "False"]:
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query = query.filter(self.model_class.purged == (column_filter == "True"))
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return query
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class StateColumn(GridColumn):
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"""
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Column that tracks and filters for items with state attribute.
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IMPORTANT NOTE: self.model_class must have a states Bunch or dict if
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this column type is used in the grid.
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"""
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def get_value(self, trans, grid, item):
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return item.state
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter self.model_class by state."""
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if column_filter == "All":
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pass
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elif column_filter in [v for k, v in self.model_class.states.items()]:
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query = query.filter(self.model_class.state == column_filter)
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return query
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def get_accepted_filters(self):
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"""Returns a list of accepted filters for this column."""
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all = GridColumnFilter("all", {self.key: "All"})
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accepted_filters = [all]
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for v in self.model_class.states.values():
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args = {self.key: v}
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accepted_filters.append(GridColumnFilter(v, args))
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return accepted_filters
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class SharingStatusColumn(GridColumn):
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"""Grid column to indicate sharing status."""
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def __init__(self, *args, **kwargs):
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self.use_shared_with_count = kwargs.pop("use_shared_with_count", False)
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super().__init__(*args, **kwargs)
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def get_value(self, trans, grid, item):
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# Delete items cannot be shared.
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if item.deleted:
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return ""
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# Build a list of sharing for this item.
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sharing_statuses = []
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if self._is_shared(item):
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sharing_statuses.append("Shared")
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if item.importable:
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sharing_statuses.append("Accessible")
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if item.published:
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sharing_statuses.append("Published")
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return ", ".join(sharing_statuses)
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def _is_shared(self, item):
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if self.use_shared_with_count:
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# optimization to skip join for users_shared_with and loading in that data.
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return item.users_shared_with_count > 0
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return item.users_shared_with
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def filter(self, trans, user, query, column_filter):
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"""Modify query to filter histories by sharing status."""
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if column_filter == "All":
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pass
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elif column_filter:
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if column_filter == "private":
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query = query.filter(self.model_class.users_shared_with == null())
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query = query.filter(self.model_class.importable == false())
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elif column_filter == "shared":
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query = query.filter(self.model_class.users_shared_with != null())
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elif column_filter == "accessible":
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query = query.filter(self.model_class.importable == true())
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elif column_filter == "published":
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query = query.filter(self.model_class.published == true())
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return query
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def get_accepted_filters(self):
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"""Returns a list of accepted filters for this column."""
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accepted_filter_labels_and_vals = {}
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accepted_filter_labels_and_vals["private"] = "private"
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accepted_filter_labels_and_vals["shared"] = "shared"
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accepted_filter_labels_and_vals["accessible"] = "accessible"
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accepted_filter_labels_and_vals["published"] = "published"
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accepted_filter_labels_and_vals["all"] = "All"
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accepted_filters = []
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for label, val in accepted_filter_labels_and_vals.items():
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args = {self.key: val}
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accepted_filters.append(GridColumnFilter(label, args))
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return accepted_filters
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class GridOperation:
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def __init__(
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self,
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label,
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key=None,
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condition=None,
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allow_multiple=True,
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allow_popup=True,
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target=None,
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url_args=None,
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async_compatible=False,
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confirm=None,
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global_operation=None,
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):
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self.label = label
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self.key = key
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self.allow_multiple = allow_multiple
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self.allow_popup = allow_popup
|
||||
self.condition = condition
|
||||
self.target = target
|
||||
self.url_args = url_args
|
||||
self.async_compatible = async_compatible
|
||||
# if 'confirm' is set, then ask before completing the operation
|
||||
self.confirm = confirm
|
||||
# specify a general operation that acts on the full grid
|
||||
# this should be a function returning a dictionary with parameters
|
||||
# to pass to the URL, similar to GridColumn links:
|
||||
# global_operation=(lambda: dict(operation="download")
|
||||
self.global_operation = global_operation
|
||||
|
||||
def get_url_args(self, item):
|
||||
if self.url_args:
|
||||
if callable(self.url_args):
|
||||
url_args = self.url_args(item)
|
||||
else:
|
||||
url_args = dict(self.url_args)
|
||||
url_args["id"] = item.id
|
||||
return url_args
|
||||
else:
|
||||
return dict(operation=self.label, id=item.id)
|
||||
|
||||
def allowed(self, item):
|
||||
if self.condition:
|
||||
return bool(self.condition(item))
|
||||
else:
|
||||
return True
|
||||
|
||||
|
||||
class DisplayByUsernameAndSlugGridOperation(GridOperation):
|
||||
"""Operation to display an item by username and slug."""
|
||||
|
||||
def get_url_args(self, item):
|
||||
return {"action": "display_by_username_and_slug", "username": item.user.username, "slug": item.slug}
|
||||
|
||||
|
||||
class GridAction:
|
||||
def __init__(self, label=None, url_args=None, target=None):
|
||||
self.label = label
|
||||
self.url_args = url_args
|
||||
self.target = target
|
||||
|
||||
|
||||
class GridColumnFilter:
|
||||
def __init__(self, label, args=None):
|
||||
self.label = label
|
||||
self.args = args
|
||||
|
||||
def get_url_args(self):
|
||||
rval = {}
|
||||
for k, v in self.args.items():
|
||||
rval[f"f-{k}"] = v
|
||||
return rval
|
||||
|
||||
|
||||
class GridData:
|
||||
"""
|
||||
Specifies the content a grid (data table).
|
||||
|
||||
@@ -245,7 +245,7 @@ class GroupListGrid(grids.GridData):
|
||||
grids.GridColumn("Name", key="name"),
|
||||
UsersColumn("Users", key="users"),
|
||||
RolesColumn("Roles", key="roles"),
|
||||
grids.DeletedColumn("Deleted", key="deleted", escape=False),
|
||||
grids.GridColumn("Deleted", key="deleted", escape=False),
|
||||
grids.GridColumn("Last Updated", key="update_time"),
|
||||
]
|
||||
|
||||
|
||||
Reference in New Issue
Block a user