details: http://www.bx.psu.edu/hg/galaxy/rev/390dfb039df7 changeset: 3353:390dfb039df7 user: jeremy goecks <jeremy.goecks@emory.edu> date: Mon Feb 08 09:53:20 2010 -0500 description: Refactoring grid code: moved numerous grid column definitions from controller.py to grids.py diffstat: lib/galaxy/web/base/controller.py | 83 -------------------------- lib/galaxy/web/controllers/admin.py | 6 +- lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/history.py | 8 +- lib/galaxy/web/controllers/library_admin.py | 2 +- lib/galaxy/web/controllers/page.py | 28 ++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 4 +- lib/galaxy/web/controllers/workflow.py | 4 +- lib/galaxy/web/framework/helpers/grids.py | 89 ++++++++++++++++++++++++++- 10 files changed, 113 insertions(+), 115 deletions(-) diffs (465 lines): diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/base/controller.py Mon Feb 08 09:53:20 2010 -0500 @@ -9,41 +9,10 @@ from galaxy.web import error, form, url_for from galaxy.model.orm import * from galaxy.web.framework.helpers import grids -from galaxy.util.odict import odict from Cheetah.Template import Template log = logging.getLogger( __name__ ) - -# Useful columns in many grids used by controllers. - -class OwnerColumn( grids.TextColumn ): - """ Column that lists item's owner. """ - def get_value( self, trans, grid, item ): - return item.user.username - -class PublicURLColumn( grids.TextColumn ): - """ Column displays item's public URL based on username and slug. """ - def get_link( self, trans, grid, item ): - if item.user.username and item.slug: - return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) - elif not item.user.username: - # TODO: provide link to set username. - return None - elif not item.user.slug: - # TODO: provide link to set slg - return None - -class DeletedColumn( grids.GridColumn ): - """ Column that tracks and filters for items with deleted attribute. """ - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class BaseController( object ): """ @@ -138,58 +107,6 @@ return True Root = BaseController - -class SharingStatusColumn( grids.GridColumn ): - """ Grid column to indicate sharing status. """ - def get_value( self, trans, grid, item ): - # Delete items cannot be shared. - if item.deleted: - return "" - - # Build a list of sharing for this item. - sharing_statuses = [] - if item.users_shared_with: - sharing_statuses.append( "Shared" ) - if item.importable: - sharing_statuses.append( "Accessible" ) - 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 ): - """ Modify query to filter histories by sharing status. """ - if column_filter == "All": - pass - elif column_filter: - if column_filter == "private": - query = query.filter( self.model_class.users_shared_with == None ) - query = query.filter( self.model_class.importable == False ) - elif column_filter == "shared": - query = query.filter( self.model_class.users_shared_with != None ) - elif column_filter == "accessible": - query = query.filter( self.model_class.importable == True ) - 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() - accepted_filter_labels_and_vals["private"] = "private" - accepted_filter_labels_and_vals["shared"] = "shared" - accepted_filter_labels_and_vals["accessible"] = "accessible" - accepted_filter_labels_and_vals["published"] = "published" - accepted_filter_labels_and_vals["all"] = "All" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class Sharable: """ Mixin for a controller that manages and item that can be shared. """ diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -71,7 +71,7 @@ LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -159,7 +159,7 @@ UsersColumn( "Users", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -225,7 +225,7 @@ RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,7 +44,7 @@ model_class=model.FormDefinition, filterable="advanced" ), TypeColumn( "Type" ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Feb 08 09:53:20 2010 -0500 @@ -44,11 +44,11 @@ attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( @@ -118,7 +118,7 @@ return query.filter( model.HistoryUserShareAssociation.user == trans.user ) class HistoryAllPublishedGrid( grids.Grid ): - class NameURLColumn( PublicURLColumn, NameColumn ): + class NameURLColumn( grids.PublicURLColumn, NameColumn ): pass title = "Published Histories" @@ -128,7 +128,7 @@ use_async = True columns = [ NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -52,7 +52,7 @@ grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Feb 08 09:53:20 2010 -0500 @@ -16,7 +16,7 @@ class PageListGrid( grids.Grid ): # Custom column. - class URLColumn( PublicURLColumn ): + class URLColumn( grids.PublicURLColumn ): def get_value( self, trans, grid, item ): return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) @@ -30,7 +30,7 @@ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -62,8 +62,8 @@ default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] @@ -100,8 +100,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -144,8 +144,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -167,8 +167,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -192,8 +192,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -212,8 +212,8 @@ grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests.py Mon Feb 08 09:53:20 2010 -0500 @@ -95,7 +95,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), TypeColumn( "Type" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Feb 08 09:53:20 2010 -0500 @@ -107,7 +107,7 @@ TypeColumn( "Type", link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ), ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -184,7 +184,7 @@ link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.request_form.id ) ) ), ), SampleFormColumn( "Sample Form", link=( lambda item: iff( item.deleted, None, dict( operation="view_form", id=item.sample_form.id ) ) ), ), - DeletedColumn( "Deleted", + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/controllers/workflow.py Mon Feb 08 09:53:20 2010 -0500 @@ -59,8 +59,8 @@ default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), + grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] diff -r aa81684b9275 -r 390dfb039df7 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:03:07 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Feb 08 09:53:20 2010 -0500 @@ -5,6 +5,7 @@ from galaxy.tags.tag_handler import TagHandler from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.odict import odict import sys, logging, math @@ -329,8 +330,8 @@ accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters -# Generic column that employs freetext and, hence, supports freetext, case-independent filtering. class TextColumn( GridColumn ): + """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ def filter( self, db_session, user, query, column_filter ): """ Modify query to filter using free text, case independence. """ if column_filter == "All": @@ -350,8 +351,8 @@ clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) return and_( *clause_list ) -# Column that supports community tags. class CommunityTagsColumn( TextColumn ): + """ Column that supports community tags. """ def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class @@ -386,8 +387,8 @@ clause_list.append( self.model_class.tags.any( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ) ) ) return and_( *clause_list ) -# Column that supports individual tags. 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" ) @@ -408,8 +409,8 @@ clause_list.append( self.model_class.tags.any( and_( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ), self.model_tag_association_class.user == user ) ) ) return and_( *clause_list ) -# Column that performs multicolumn filtering. class MulticolFilterColumn( TextColumn ): + """ Column that performs multicolumn filtering. """ 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 @@ -432,6 +433,86 @@ complete_filter = or_( *clause_list ) return query.filter( complete_filter ) + +class OwnerColumn( TextColumn ): + """ Column that lists item's owner. """ + def get_value( self, trans, grid, item ): + return item.user.username + +class PublicURLColumn( TextColumn ): + """ Column displays item's public URL based on username and slug. """ + def get_link( self, trans, grid, item ): + if item.user.username and item.slug: + return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) + elif not item.user.username: + # TODO: provide link to set username. + return None + elif not item.user.slug: + # TODO: provide link to set slg + return None + +class DeletedColumn( GridColumn ): + """ Column that tracks and filters for items with deleted attribute. """ + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" } + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters + +class SharingStatusColumn( GridColumn ): + """ Grid column to indicate sharing status. """ + def get_value( self, trans, grid, item ): + # Delete items cannot be shared. + if item.deleted: + return "" + + # Build a list of sharing for this item. + sharing_statuses = [] + if item.users_shared_with: + sharing_statuses.append( "Shared" ) + if item.importable: + sharing_statuses.append( "Accessible" ) + 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 ): + """ Modify query to filter histories by sharing status. """ + if column_filter == "All": + pass + elif column_filter: + if column_filter == "private": + query = query.filter( self.model_class.users_shared_with == None ) + query = query.filter( self.model_class.importable == False ) + elif column_filter == "shared": + query = query.filter( self.model_class.users_shared_with != None ) + elif column_filter == "accessible": + query = query.filter( self.model_class.importable == True ) + 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() + accepted_filter_labels_and_vals["private"] = "private" + accepted_filter_labels_and_vals["shared"] = "shared" + accepted_filter_labels_and_vals["accessible"] = "accessible" + accepted_filter_labels_and_vals["published"] = "published" + accepted_filter_labels_and_vals["all"] = "All" + accepted_filters = [] + for label, val in accepted_filter_labels_and_vals.items(): + args = { self.key: val } + accepted_filters.append( GridColumnFilter( label, args) ) + return accepted_filters class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False, confirm=None ):