details: http://www.bx.psu.edu/hg/galaxy/rev/d6a527033f2c changeset: 3644:d6a527033f2c user: Greg Von Kuster greg@bx.psu.edu date: Wed Apr 14 09:38:35 2010 -0400 description: Since the handle to the tag handler has been moved to the app, eliminate the now unnecessary import of a specific tag handler from the grid helper. Clean up the grid helpr code, pass trans to methods instead of trans.sa_session so that methods can get other items from trans ( like the tag hendler ). Eliminate a seemingly unnecessary import in grid_base.mako that tightly coupled the template to the model.
diffstat:
lib/galaxy/web/framework/helpers/grids.py | 85 ++++++++++-------------------- templates/grid_base.mako | 1 - 2 files changed, 28 insertions(+), 58 deletions(-)
diffs (351 lines):
diff -r 99782dc9d022 -r d6a527033f2c lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Apr 13 20:21:57 2010 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Apr 14 09:38:35 2010 -0400 @@ -3,7 +3,6 @@
from galaxy.web.base import controller from galaxy.web.framework.helpers import iff -from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict @@ -21,9 +20,7 @@ model_class = None template = "grid_base.mako" async_template = "grid_base_async.mako" - use_async = False - global_actions = [] columns = [] operations = [] @@ -32,10 +29,8 @@ default_filter = {} default_sort_key = None preserve_state = False - use_paging = False num_rows_per_page = 25 - # Set preference names. cur_filter_pref_name = ".filter" cur_sort_key_pref_name = ".sort_key" @@ -47,12 +42,10 @@ if operation.allow_multiple: self.has_multiple_item_operations = True break - def __call__( self, trans, **kwargs ): status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) session = trans.sa_session - # Build a base filter and sort key that is the combination of the saved state and defaults. Saved state takes preference over defaults. base_filter = {} if self.default_filter: @@ -63,24 +56,19 @@ if pref_name in trans.get_user().preferences: saved_filter = from_json_string( trans.get_user().preferences[pref_name] ) base_filter.update( saved_filter ) - pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name ) if pref_name in trans.get_user().preferences: base_sort_key = from_json_string( trans.get_user().preferences[pref_name] ) - # Build initial query query = self.build_initial_query( session ) query = self.apply_default_filter( trans, query, **kwargs ) - # Maintain sort state in generated urls extra_url_args = {} - # Determine whether use_default_filter flag is set. use_default_filter_str = kwargs.get( 'use_default_filter' ) use_default_filter = False if use_default_filter_str: use_default_filter = ( use_default_filter_str.lower() == 'true' ) - # Process filtering arguments to (a) build a query that represents the filter and (b) builds a # dictionary that denotes the current filter. cur_filter_dict = {} @@ -96,7 +84,6 @@ column_filter = kwargs.get( "f-" + column.key ) elif column.key in base_filter: column_filter = base_filter.get( column.key ) - # Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings. def from_json_string_recurse(item): decoded_list = [] @@ -115,8 +102,7 @@ for element in item: a_list = from_json_string_recurse( element ) decoded_list = decoded_list + a_list - return decoded_list - + return decoded_list # If column filter found, apply it. if column_filter is not None: # TextColumns may have a mix of json and strings. @@ -131,7 +117,7 @@ if column_filter == '': continue # Update query. - query = column.filter( trans.sa_session, trans.get_user(), query, column_filter ) + query = column.filter( trans, trans.get_user(), query, column_filter ) # Upate current filter dict. cur_filter_dict[ column.key ] = column_filter # Carry filter along to newly generated urls; make sure filter is a string so @@ -147,7 +133,6 @@ if not isinstance( column_filter, basestring ): column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") - # Process sort arguments. sort_key = sort_order = None if 'sort' in kwargs: @@ -167,10 +152,8 @@ # See reason for not using lower() to do case-insensitive search. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key - # There might be a current row current_item = self.get_current_item( trans ) - # Process page number. if self.use_paging: if 'page' in kwargs: @@ -196,8 +179,6 @@ # Defaults. page_num = 1 num_pages = 1 - - # Preserve grid state: save current filter and sort key. if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) @@ -207,14 +188,12 @@ pref_name = unicode( self.__class__.__name__ + self.cur_sort_key_pref_name ) trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) ) trans.sa_session.flush() - # Log grid view. context = unicode( self.__class__.__name__ ) params = cur_filter_dict.copy() params['sort'] = sort_key params['async'] = ( 'async' in kwargs ) trans.log_action( trans.get_user(), unicode( "grid.view"), context, params ) - # Render grid. def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another @@ -235,7 +214,6 @@ else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - use_panels = ( 'use_panels' in kwargs ) and ( kwargs['use_panels'] == True ) async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ 'True', 'true'] ) ) return trans.fill_template( iff( async_request, self.async_template, self.template), @@ -254,9 +232,9 @@ message_type = status, message = message, use_panels=use_panels, - # Pass back kwargs so that grid template can set and use args without grid explicitly having to pass them. - kwargs=kwargs - ) + # Pass back kwargs so that grid template can set and use args without + # grid explicitly having to pass them. + kwargs=kwargs ) def get_ids( self, **kwargs ): id = [] if 'id' in kwargs: @@ -270,7 +248,6 @@ except: error( "Invalid id" ) return id - # ---- Override these ---------------------------------------------------- def handle_operation( self, trans, operation, ids ): pass @@ -315,7 +292,7 @@ if self.link and self.link( item ): return self.link( item ) return None - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to reflect the column filter. """ if column_filter == "All": pass @@ -335,15 +312,14 @@
class TextColumn( GridColumn ): """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to filter using free text, case independence. """ if column_filter == "All": pass elif column_filter: - query = query.filter( self.get_filter( user, column_filter ) ) + query = query.filter( self.get_filter( trans, user, column_filter ) ) return query - - def get_filter( self, user, column_filter ): + def get_filter( self, trans, user, column_filter ): """ Returns a SQLAlchemy criterion derived from column_filter. """ if isinstance( column_filter, basestring ): return self.get_single_filter( user, column_filter ) @@ -352,7 +328,6 @@ for filter in column_filter: clause_list.append( self.get_single_filter( user, filter ) ) return and_( *clause_list ) - def get_single_filter( self, user, a_filter ): """ Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """ model_class_key_field = getattr( self.model_class, self.key ) @@ -364,12 +339,10 @@ GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) self.sortable = False self.model_annotation_association_class = model_annotation_association_class - def get_value( self, trans, grid, item ): """ Returns item annotation. """ annotation = self.get_item_annotation_str( trans.sa_session, item.user, item ) return iff( annotation, annotation, "" ) - def get_single_filter( self, user, a_filter ): """ Filter by annotation and annotation owner. """ return self.model_class.annotations.any( @@ -390,20 +363,19 @@ def get_value( self, trans, grid, item ): return trans.fill_template( "/tagging_common.mako", tag_type="community", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter", use_toggle_link=True ) - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ if column_filter == "All": pass elif column_filter: - query = query.filter( self.get_filter( user, column_filter ) ) + query = query.filter( self.get_filter( trans, user, column_filter ) ) return query - def get_filter( self, user, column_filter ): + def get_filter( self, trans, user, column_filter ): # Parse filter to extract multiple tags. - tag_handler = GalaxyTagHandler() if isinstance( column_filter, list ): # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. column_filter = ",".join( column_filter ) - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + raw_tags = trans.app.tag_handler.parse_tags( column_filter.encode( "utf-8" ) ) clause_list = [] for name, value in raw_tags.items(): if name: @@ -417,15 +389,21 @@ class IndividualTagsColumn( CommunityTagsColumn ): """ Column that supports individual tags. """ def get_value( self, trans, grid, item ): - return trans.fill_template( "/tagging_common.mako", tag_type="individual", trans=trans, user=trans.get_user(), tagged_item=item, elt_context=self.grid_name, - in_form=True, input_size="20", tag_click_fn="add_tag_to_grid_filter", use_toggle_link=True ) - def get_filter( self, user, column_filter ): + return trans.fill_template( "/tagging_common.mako", + tag_type="individual", + user=trans.user, + tagged_item=item, + elt_context=self.grid_name, + in_form=True, + input_size="20", + tag_click_fn="add_tag_to_grid_filter", + use_toggle_link=True ) + def get_filter( self, trans, user, column_filter ): # Parse filter to extract multiple tags. - tag_handler = GalaxyTagHandler() if isinstance( column_filter, list ): # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. column_filter = ",".join( column_filter ) - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + raw_tags = trans.app.tag_handler.parse_tags( column_filter.encode( "utf-8" ) ) clause_list = [] for name, value in raw_tags.items(): if name: @@ -441,7 +419,7 @@ def __init__( self, col_name, cols_to_filter, key, visible, filterable="default" ): GridColumn.__init__( self, col_name, key=key, visible=visible, filterable=filterable) self.cols_to_filter = cols_to_filter - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ if column_filter == "All": return query @@ -450,15 +428,14 @@ for filter in column_filter: part_clause_list = [] for column in self.cols_to_filter: - part_clause_list.append( column.get_filter( user, filter ) ) + part_clause_list.append( column.get_filter( trans, user, filter ) ) clause_list.append( or_( *part_clause_list ) ) complete_filter = and_( *clause_list ) else: clause_list = [] for column in self.cols_to_filter: - clause_list.append( column.get_filter( user, column_filter ) ) + clause_list.append( column.get_filter( trans, user, column_filter ) ) complete_filter = or_( *clause_list ) - return query.filter( complete_filter )
class OwnerColumn( TextColumn ): @@ -495,7 +472,6 @@ # Delete items cannot be shared. if item.deleted: return "" - # Build a list of sharing for this item. sharing_statuses = [] if item.users_shared_with: @@ -505,13 +481,11 @@ if item.published: sharing_statuses.append( "Published" ) return ", ".join( sharing_statuses ) - def get_link( self, trans, grid, item ): if not item.deleted and ( item.users_shared_with or item.importable or item.published ): return dict( operation="share or publish", id=item.id ) return None - - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to filter histories by sharing status. """ if column_filter == "All": pass @@ -526,7 +500,6 @@ elif column_filter == "published": query = query.filter( self.model_class.published == True ) return query - def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ accepted_filter_labels_and_vals = odict() @@ -560,7 +533,6 @@ return temp else: return dict( operation=self.label, id=item.id ) - def allowed( self, item ): if self.condition: return self.condition( item ) @@ -586,4 +558,3 @@ for k, v in self.args.items(): rval[ "f-" + k ] = v return rval - diff -r 99782dc9d022 -r d6a527033f2c templates/grid_base.mako --- a/templates/grid_base.mako Tue Apr 13 20:21:57 2010 -0400 +++ b/templates/grid_base.mako Wed Apr 14 09:38:35 2010 -0400 @@ -1,6 +1,5 @@ <%! from galaxy.web.framework.helpers.grids import TextColumn - from galaxy.model import History, HistoryDatasetAssociation, User, Role, Group import galaxy.util def inherit(context): if context.get('use_panels'):