November 2009 - galaxy-dev - lists.galaxyproject.org

Command not found error from NGS QC and manipulation tools
by Vipin TS 10 Nov '09

10 Nov '09

Hi all, I incorporated *NGS: QC and manipulation* tool tracks to my galaxy server. But I have been failing to run those tools in my local instance. From the error message I found that few of the file/script are missing in the tool directory. Here is the list of tools shows error message while running: Quality format converter ('fastq_quality_converter' command not found) Compute quality statistics ('fastx_quality_stats' command not found) Draw quality score boxplot ('fastq_quality_boxplot_graph.sh' not found) Draw nucleotides distribution chart ('fastx_nucleotide_distribution_graph.sh' not found) In the Galaxy-central source repository I am not finding such a file/script associated with these tools ( http://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastx_toolkit/) In the main galaxy server these tools are working perfectly. Please let me know if I did any mistake from these observations. Many thanks, Vipin T S

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[hg] galaxy 2995: Incorporate latest grid features into managing...
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9f485a539bfb changeset: 2995:9f485a539bfb user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Nov 09 23:00:55 2009 -0500 description: Incorporate latest grid features into managing users, groups and roles from the admin view. diffstat: lib/galaxy/web/controllers/admin.py | 436 +++++++++++++++----- templates/admin/dataset_security/deleted_groups.mako | 101 ---- templates/admin/dataset_security/deleted_roles.mako | 103 ---- templates/admin/dataset_security/group.mako | 83 --- templates/admin/dataset_security/group/grid.mako | 1 + templates/admin/dataset_security/group/group.mako | 83 +++ templates/admin/dataset_security/group/group_create.mako | 87 ++++ templates/admin/dataset_security/group/group_rename.mako | 34 + templates/admin/dataset_security/group_create.mako | 87 ---- templates/admin/dataset_security/group_rename.mako | 34 - templates/admin/dataset_security/groups.mako | 107 ----- templates/admin/dataset_security/role.mako | 117 ----- templates/admin/dataset_security/role/grid.mako | 1 + templates/admin/dataset_security/role/role.mako | 117 +++++ templates/admin/dataset_security/role/role_create.mako | 94 ++++ templates/admin/dataset_security/role/role_rename.mako | 41 + templates/admin/dataset_security/role_create.mako | 94 ---- templates/admin/dataset_security/role_rename.mako | 41 - templates/admin/dataset_security/roles.mako | 109 ----- templates/admin/user/grid.mako | 225 +---------- templates/grid_base.mako | 11 +- test/base/twilltestcase.py | 32 +- test/functional/test_history_functions.py | 4 +- test/functional/test_security_and_libraries.py | 102 ++-- tool_conf.xml.main | 52 ++- 25 files changed, 914 insertions(+), 1282 deletions(-) diffs (2900 lines): diff -r 1a438bb4dac2 -r 9f485a539bfb lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Nov 09 16:55:52 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Nov 09 23:00:55 2009 -0500 @@ -2,20 +2,31 @@ from datetime import datetime, timedelta from galaxy import util, datatypes from galaxy.web.base.controller import * +from galaxy.util.odict import odict from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids import logging log = logging.getLogger( __name__ ) +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + class UserListGrid( grids.Grid ): - class EmailColumn( grids.GridColumn ): + class EmailColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): return user.email - class UserNameColumn( grids.GridColumn ): + class UserNameColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): if user.username: return user.username return 'not set' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" class GroupsColumn( grids.GridColumn ): def get_value( self, trans, grid, user ): if user.groups: @@ -36,56 +47,242 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class DeletedColumn( grids.GridColumn ): + 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 + # Grid definition title = "Users" model_class = model.User template='/admin/user/grid.mako' + default_sort_key = "email" columns = [ - EmailColumn( "Email", link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True ), - UserNameColumn( "User Name", attach_popup=False ), + EmailColumn( "Email", + key="email", + model_class=model.User, + link=( lambda item: dict( operation="information", id=item.id ) ), + attach_popup=True, + filterable="advanced" ), + UserNameColumn( "User Name", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), GroupsColumn( "Groups", attach_popup=False ), RolesColumn( "Roles", attach_popup=False ), ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), - # Valid for filtering but invisible - grids.GridColumn( "Deleted", key="deleted", visible=False ) + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create' ) ) ] operations = [ grids.GridOperation( "Manage Roles & Groups", condition=( lambda item: not item.deleted ), allow_multiple=False ) - ] #TODO: enhance to account for trans.app.config.allow_user_deletion here so that we can eliminate these operations if # the setting is False operations.append( grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False ) ) operations.append( grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ) ) - operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ) + operations.append( grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + operations.append( grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True ) ) + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), + grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( email="All", username="All", deleted="False", purged="False" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return trans.user + def build_initial_query( self, session ): + return session.query( self.model_class ) + +class RoleListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + if role.description: + return role.description + return '' + class TypeColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.type + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.deleted: + return "deleted" + return "" + class DeletedColumn( grids.GridColumn ): + 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 GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.groups: + return len( role.groups ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.users: + return len( role.users ) + return 0 + + # Grid definition + title = "Roles" + model_class = model.Role + template='/admin/dataset_security/role/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( controller="admin", action="role", id=item.id ) ), + model_class=model.Role, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + key='description', + model_class=model.Role, + attach_popup=False, + filterable="advanced" ), + TypeColumn( "Type", + key='type', + model_class=model.Role, + attach_popup=False, + filterable="advanced" ), + GroupsColumn( "Groups", attach_popup=False ), + 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" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ), + grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( deleted=False ) + default_filter = dict( name="All", deleted="False", description="All", type="All" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True def get_current_item( self, trans ): - return trans.user + return None def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwargs ): - email_filter = kwargs.get( "email_filter", None ) - if email_filter: - if email_filter == 'all': - return query - else: - return query.filter( or_( trans.app.model.User.table.c.email.like( '%s' % email_filter.lower() + '%' ), - trans.app.model.User.table.c.email.like( '%s' % email_filter.upper() + '%' ) ) ) - elif query.count() > 200: - return query.filter( or_( trans.app.model.User.table.c.email.like( 'A%' ), - trans.app.model.User.table.c.email.like( 'a%' ) ) ) - return query + return query.filter( model.Role.type != model.Role.types.PRIVATE ) + +class GroupListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, group ): + return group.name + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.deleted: + return "deleted" + return "" + class DeletedColumn( grids.GridColumn ): + 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 RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.roles: + return len( group.roles ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.members: + return len( group.members ) + return 0 + + # Grid definition + title = "Groups" + model_class = model.Group + template='/admin/dataset_security/group/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( controller="admin", action="group", id=item.id ) ), + model_class=model.Group, + attach_popup=True, + filterable="advanced" ), + UsersColumn( "Users", attach_popup=False ), + 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" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new group", dict( controller='admin', action='groups', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True ), + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True ), + grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( name="All", deleted="False" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) class Admin( BaseController ): user_list_grid = UserListGrid() + role_list_grid = RoleListGrid() + group_list_grid = GroupListGrid() @web.expose @web.require_admin @@ -117,17 +314,23 @@ # Galaxy Role Stuff @web.expose @web.require_admin - def roles( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - roles = trans.sa_session.query( trans.app.model.Role ).filter( and_( trans.app.model.Role.table.c.deleted==False, - trans.app.model.Role.table.c.type != trans.app.model.Role.types.PRIVATE ) ) \ - .order_by( trans.app.model.Role.table.c.name ) - return trans.fill_template( '/admin/dataset_security/roles.mako', - roles=roles, - msg=msg, - messagetype=messagetype ) + def roles( self, trans, **kwargs ): + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "roles": + return self.role( trans, **kwargs ) + if operation == "create": + return self.create_role( trans, **kwargs ) + if operation == "delete": + return self.mark_role_deleted( trans, **kwargs ) + if operation == "undelete": + return self.undelete_role( trans, **kwargs ) + if operation == "purge": + return self.purge_role( trans, **kwargs ) + if operation == "manage users & groups": + return self.role( trans, **kwargs ) + # Render the list view + return self.role_list_grid( trans, **kwargs ) @web.expose @web.require_admin def create_role( self, trans, **kwd ): @@ -164,7 +367,7 @@ ( group.name, role.name, len( in_users ), len( in_groups ) ) else: msg = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) - trans.response.send_redirect( web.url_for( controller='admin', action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='roles', message=util.sanitize_text( msg ), status='done' ) ) trans.response.send_redirect( web.url_for( controller='admin', action='create_role', msg=util.sanitize_text( msg ), messagetype='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ @@ -176,7 +379,7 @@ .filter( trans.app.model.Group.table.c.deleted==False ) \ .order_by( trans.app.model.Group.table.c.name ): out_groups.append( ( group.id, group.name ) ) - return trans.fill_template( '/admin/dataset_security/role_create.mako', + return trans.fill_template( '/admin/dataset_security/role/role_create.mako', in_users=[], out_users=out_users, in_groups=[], @@ -189,7 +392,7 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) ) + role = get_role( trans, params.id ) if params.get( 'role_members_edit_button', False ): in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] for ura in role.users: @@ -210,7 +413,7 @@ trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups ) trans.sa_session.refresh( role ) msg = "Role '%s' has been updated with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype=messagetype ) ) + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status=messagetype ) ) elif params.get( 'rename', False ): if params.rename == 'submitted': old_name = role.name @@ -218,17 +421,17 @@ new_description = util.restore_text( params.description ) if not new_name: msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first(): msg = 'A role with that name already exists' - return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype='error' ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) else: role.name = new_name role.description = new_description role.flush() msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) - return trans.fill_template( '/admin/dataset_security/role_rename.mako', role=role, msg=msg, messagetype=messagetype ) + return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype=messagetype ) in_users = [] out_users = [] in_groups = [] @@ -273,7 +476,7 @@ library_dataset_actions[ library ][ folder_path ].append( dp.action ) except: library_dataset_actions[ library ][ folder_path ] = [ dp.action ] - return trans.fill_template( '/admin/dataset_security/role.mako', + return trans.fill_template( '/admin/dataset_security/role/role.mako', role=role, in_users=in_users, out_users=out_users, @@ -286,33 +489,20 @@ @web.require_admin def mark_role_deleted( self, trans, **kwd ): params = util.Params( kwd ) - role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) ) + role = get_role( trans, params.id ) role.deleted = True role.flush() - msg = "Role '%s' has been marked as deleted." % role.name - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def deleted_roles( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - roles = trans.sa_session.query( trans.app.model.Role ) \ - .filter( trans.app.model.Role.table.c.deleted==True ) \ - .order_by( trans.app.model.Role.table.c.name ) - return trans.fill_template( '/admin/dataset_security/deleted_roles.mako', - roles=roles, - msg=msg, - messagetype=messagetype ) + message = "Role '%s' has been marked as deleted." % role.name + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def undelete_role( self, trans, **kwd ): params = util.Params( kwd ) - role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) ) + role = get_role( trans, params.id ) role.deleted = False role.flush() - msg = "Role '%s' has been marked as not deleted." % role.name - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) + message = "Role '%s' has been marked as not deleted." % role.name + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def purge_role( self, trans, **kwd ): @@ -324,11 +514,10 @@ # - GroupRoleAssociations where role_id == Role.id # - DatasetPermissionss where role_id == Role.id params = util.Params( kwd ) - role = trans.sa_session.query( trans.app.model.Role ).get( int( params.role_id ) ) + role = get_role( trans, params.id ) if not role.deleted: - # We should never reach here, but just in case there is a bug somewhere... - msg = "Role '%s' has not been deleted, so it cannot be purged." % role.name - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='error' ) ) + message = "Role '%s' has not been deleted, so it cannot be purged." % role.name + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='error' ) ) # Delete UserRoleAssociations for ura in role.users: user = trans.sa_session.query( trans.app.model.User ).get( ura.user_id ) @@ -353,54 +542,60 @@ for dp in role.dataset_actions: trans.sa_session.delete( dp ) dp.flush() - msg = "The following have been purged from the database for role '%s': " % role.name - msg += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss." - trans.response.send_redirect( web.url_for( action='deleted_roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) + message = "The following have been purged from the database for role '%s': " % role.name + message += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss." + trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) # Galaxy Group Stuff @web.expose @web.require_admin - def groups( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - groups = trans.sa_session.query( trans.app.model.Group ) \ - .filter( trans.app.model.Group.table.c.deleted==False ) \ - .order_by( trans.app.model.Group.table.c.name ) - return trans.fill_template( '/admin/dataset_security/groups.mako', - groups=groups, - msg=msg, - messagetype=messagetype ) + def groups( self, trans, **kwargs ): + if 'operation' in kwargs: + operation = kwargs['operation'].lower() + if operation == "groups": + return self.group( trans, **kwargs ) + if operation == "create": + return self.create_group( trans, **kwargs ) + if operation == "delete": + return self.mark_group_deleted( trans, **kwargs ) + if operation == "undelete": + return self.undelete_group( trans, **kwargs ) + if operation == "purge": + return self.purge_group( trans, **kwargs ) + if operation == "manage users & roles": + return self.group( trans, **kwargs ) + # Render the list view + return self.group_list_grid( trans, **kwargs ) @web.expose @web.require_admin def group( self, trans, **kwd ): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) ) + group = get_group( trans, params.id ) if params.get( 'group_roles_users_edit_button', False ): in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in util.listify( params.in_roles ) ] in_users = [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in util.listify( params.in_users ) ] trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=in_roles, users=in_users ) trans.sa_session.refresh( group ) msg += "Group '%s' has been updated with %d associated roles and %d associated users" % ( group.name, len( in_roles ), len( in_users ) ) - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype=messagetype ) ) + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status=messagetype ) ) if params.get( 'rename', False ): if params.rename == 'submitted': old_name = group.name new_name = util.restore_text( params.name ) if not new_name: msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first(): msg = 'A group with that name already exists' - return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype='error' ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) else: group.name = new_name group.flush() msg = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - return trans.fill_template( '/admin/dataset_security/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) in_roles = [] out_roles = [] in_users = [] @@ -420,7 +615,7 @@ else: out_users.append( ( user.id, user.email ) ) msg += 'Group %s is currently associated with %d roles and %d users' % ( group.name, len( in_roles ), len( in_users ) ) - return trans.fill_template( '/admin/dataset_security/group.mako', + return trans.fill_template( '/admin/dataset_security/group/group.mako', group=group, in_roles=in_roles, out_roles=out_roles, @@ -455,7 +650,7 @@ gra = trans.app.model.GroupRoleAssociation( group, role ) gra.flush() msg = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) ) - trans.response.send_redirect( web.url_for( controller='admin', action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='groups', message=util.sanitize_text( msg ), status='done' ) ) trans.response.send_redirect( web.url_for( controller='admin', action='create_group', msg=util.sanitize_text( msg ), messagetype='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ @@ -467,7 +662,7 @@ .filter( trans.app.model.Role.table.c.deleted==False ) \ .order_by( trans.app.model.Role.table.c.name ): out_roles.append( ( role.id, role.name ) ) - return trans.fill_template( '/admin/dataset_security/group_create.mako', + return trans.fill_template( '/admin/dataset_security/group/group_create.mako', in_users=[], out_users=out_users, in_roles=[], @@ -478,44 +673,31 @@ @web.require_admin def mark_group_deleted( self, trans, **kwd ): params = util.Params( kwd ) - group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) ) + group = get_group( trans, params.id ) group.deleted = True group.flush() msg = "Group '%s' has been marked as deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def deleted_groups( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - groups = trans.sa_session.query( trans.app.model.Group ) \ - .filter( trans.app.model.Group.table.c.deleted==True ) \ - .order_by( trans.app.model.Group.table.c.name ) - return trans.fill_template( '/admin/dataset_security/deleted_groups.mako', - groups=groups, - msg=msg, - messagetype=messagetype ) + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) @web.expose @web.require_admin def undelete_group( self, trans, **kwd ): params = util.Params( kwd ) - group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) ) + group = get_group( trans, params.id ) group.deleted = False group.flush() msg = "Group '%s' has been marked as not deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) @web.expose @web.require_admin def purge_group( self, trans, **kwd ): # This method should only be called for a Group that has previously been deleted. # Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations. params = util.Params( kwd ) - group = trans.sa_session.query( trans.app.model.Group ).get( int( params.group_id ) ) + group = get_group( trans, params.id ) if not group.deleted: # We should never reach here, but just in case there is a bug somewhere... msg = "Group '%s' has not been deleted, so it cannot be purged." % group.name - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='error' ) ) + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='error' ) ) # Delete UserGroupAssociations for uga in group.users: trans.sa_session.delete( uga ) @@ -525,8 +707,8 @@ trans.sa_session.delete( gra ) gra.flush() # Delete the Group - msg = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name - trans.response.send_redirect( web.url_for( action='deleted_groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) + message = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) # Galaxy User Stuff @web.expose @@ -645,11 +827,12 @@ message = "No user ids received for deleting" trans.response.send_redirect( web.url_for( action='users', message=message, status='error' ) ) ids = util.listify( id ) + message = "Deleted %d users: " % len( ids ) for user_id in ids: user = get_user( trans, user_id ) user.deleted = True user.flush() - message = "Deleted %d users" % len( ids ) + message += " %s " % user.email trans.response.send_redirect( web.url_for( action='users', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin @@ -660,13 +843,15 @@ trans.response.send_redirect( web.url_for( action='users', message=message, status='error' ) ) ids = util.listify( id ) count = 0 + undeleted_users = "" for user_id in ids: user = get_user( trans, user_id ) if user.deleted: user.deleted = False user.flush() count += 1 - message = "Undeleted %d users" % count + undeleted_users += " %s" % user.email + message = "Undeleted %d users: %s" % ( count, undeleted_users ) trans.response.send_redirect( web.url_for( action='users', message=util.sanitize_text( message ), status='done' ) ) @@ -691,6 +876,7 @@ message=util.sanitize_text( message ), status='error' ) ) ids = util.listify( id ) + message = "Purged %d users: " % len( ids ) for user_id in ids: user = get_user( trans, user_id ) if not user.deleted: @@ -726,7 +912,7 @@ # Purge the user user.purged = True user.flush() - message = "Purged %d users" % len( ids ) + message += "%s " % user.email trans.response.send_redirect( web.url_for( controller='admin', action='users', message=util.sanitize_text( message ), @@ -750,6 +936,8 @@ return self.create_new_user( trans, **kwargs ) if operation == "information": return self.user_info( trans, **kwargs ) + if operation == "manage roles & groups": + return self.user( trans, **kwargs ) # Render the list view return self.user_list_grid( trans, **kwargs ) @web.expose @@ -774,6 +962,14 @@ admin_view=True, **kwd ) ) @web.expose @web.require_admin + def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ): + """Return autocomplete data for user emails""" + ac_data = "" + for user in trans.sa_session.query( User ).filter_by( deleted=False ).filter( func.lower( User.email ).like( q.lower() + "%" ) ): + ac_data = ac_data + user.email + "\n" + return ac_data + @web.expose + @web.require_admin def user( self, trans, **kwd ): user_id = kwd.get( 'id', None ) message = '' @@ -932,5 +1128,21 @@ id = trans.security.decode_id( id ) user = trans.sa_session.query( model.User ).get( id ) if not user: - err+msg( "User not found" ) + return trans.show_error_message( "User not found for id (%s)" % str( id ) ) return user +def get_role( trans, id ): + """Get a Role from the database by id.""" + # Load user from database + id = trans.security.decode_id( id ) + role = trans.sa_session.query( model.Role ).get( id ) + if not role: + return trans.show_error_message( "Role not found for id (%s)" % str( id ) ) + return role +def get_group( trans, id ): + """Get a Group from the database by id.""" + # Load user from database + id = trans.security.decode_id( id ) + group = trans.sa_session.query( model.Group ).get( id ) + if not group: + return trans.show_error_message( "Group not found for id (%s)" % str( id ) ) + return group diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/deleted_groups.mako --- a/templates/admin/dataset_security/deleted_groups.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,101 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -## Render a row -<%def name="render_row( group, ctr, anchored, curr_anchor )"> - %if ctr % 2 == 1: - <tr class="odd_row"> - %else: - <tr> - %endif - <td> - ${group.name} - <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${group.id}-popup"> - <a class="action-button" href="${h.url_for( action='undelete_group', group_id=group.id )}">Undelete</a> - <a class="action-button" href="${h.url_for( action='purge_group', group_id=group.id )}">Purge</a> - </div> - </td> - <td> - ${len( group.members )} - </td> - <td> - ${len( group.roles )} - %if not anchored: - <a name="${curr_anchor}"></a> - <div style="float: right;"><a href="#TOP">top</a></div> - %endif - </td> - </tr> -</%def> - -<a name="TOP"><h2>Deleted Groups</h2></a> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -## TODO: make this a grid - -%if not groups: - There are no deleted Galaxy groups -%else: - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <% - render_quick_find = groups.count() > 200 - ctr = 0 - %> - %if render_quick_find: - <% - anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] - anchor_loc = 0 - anchored = False - curr_anchor = 'A' - %> - <tr style="background: #EEE"> - <td colspan="3" style="text-align: center; border-bottom: 1px solid #D8B365"> - Jump to letter: - %for a in anchors: - | <a href="#${a}">${a}</a> - %endfor - </td> - </tr> - %endif - <tr class="header"> - <td>Name</td> - <td>Users</td> - <td>Roles</td> - </tr> - %for ctr, group in enumerate( groups ): - %if render_quick_find and not group.name.upper().startswith( curr_anchor ): - <% anchored = False %> - %endif - %if render_quick_find and group.name.upper().startswith( curr_anchor ): - %if not anchored: - ${render_row( group, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( group, ctr, anchored, curr_anchor )} - %endif - %elif render_quick_find: - %for anchor in anchors[ anchor_loc: ]: - %if group.name.upper().startswith( anchor ): - %if not anchored: - <% curr_anchor = anchor %> - ${render_row( group, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( group, ctr, anchored, curr_anchor )} - %endif - <% - anchor_loc = anchors.index( anchor ) - break - %> - %endif - %endfor - %else: - ${render_row( group, ctr, True, '' )} - %endif - %endfor - </table> -%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/deleted_roles.mako --- a/templates/admin/dataset_security/deleted_roles.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,103 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -## Render a row -<%def name="render_row( role, ctr, anchored, curr_anchor )"> - %if ctr % 2 == 1: - <tr class="odd_row"> - %else: - <tr> - %endif - <td> - ${role.name} - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( action='undelete_role', role_id=role.id )}">Undelete</a> - <a class="action-button" href="${h.url_for( action='purge_role', role_id=role.id )}">Purge</a> - </div> - </td> - <td>${role.description}</td> - <td>${role.type}</td> - <td> - ${len( role.users )} - </td> - <td> - ${len( role.groups )} - %if not anchored: - <a name="${curr_anchor}"></a> - <div style="float: right;"><a href="#TOP">top</a></div> - %endif - </td> - </tr> -</%def> - -<a name="TOP"><h2>Deleted Roles</h2></a> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -%if not roles: - There are no deleted Galaxy roles -%else: - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <% - render_quick_find = roles.count() > 200 - ctr = 0 - %> - %if render_quick_find: - <% - anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] - anchor_loc = 0 - anchored = False - curr_anchor = 'A' - %> - <tr style="background: #EEE"> - <td colspan="3" style="text-align: center; border-bottom: 1px solid #D8B365"> - Jump to letter: - %for a in anchors: - | <a href="#${a}">${a}</a> - %endfor - </td> - </tr> - %endif - <tr class="header"> - <td>Name</td> - <td>Description</td> - <td>Type</td> - <td>Users</td> - <td>Groups</td> - </tr> - %for ctr, role in enumerate( roles ): - %if render_quick_find and not role.name.upper().startswith( curr_anchor ): - <% anchored = False %> - %endif - %if render_quick_find and role.name.upper().startswith( curr_anchor ): - %if not anchored: - ${render_row( role, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( role, ctr, anchored, curr_anchor )} - %endif - %elif render_quick_find: - %for anchor in anchors[ anchor_loc: ]: - %if role.name.upper().startswith( anchor ): - %if not anchored: - <% curr_anchor = anchor %> - ${render_row( role, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( role, ctr, anchored, curr_anchor )} - %endif - <% - anchor_loc = anchors.index( anchor ) - break - %> - %endif - %endfor - %else: - ${render_row( role, ctr, True, '' )} - %endif - %endfor - </table> -%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group.mako --- a/templates/admin/dataset_security/group.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,83 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -<%def name="render_select( name, options )"> - <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> - %for option in options: - <option value="${option[0]}">${option[1]}</option> - %endfor - </select> -</%def> - -<script type="text/javascript"> -$().ready(function() { - $('#roles_add_button').click(function() { - return !$('#out_roles option:selected').remove().appendTo('#in_roles'); - }); - $('#roles_remove_button').click(function() { - return !$('#in_roles option:selected').remove().appendTo('#out_roles'); - }); - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('form#associate_group_role_user').submit(function() { - $('#in_roles option').each(function(i) { - $(this).attr("selected", "selected"); - }); - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); - }); - }); -}); -</script> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Group '${group.name}'</div> - <div class="toolFormBody"> - <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='group', group_id=group.id )}" method="post" > - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Roles associated with '${group.name}'</label> - ${render_select( "in_roles", in_roles )}<br/> - <input type="submit" id="roles_remove_button" value=">>"/> - </div> - <div> - <label>Roles not associated with '${group.name}'</label> - ${render_select( "out_roles", out_roles )}<br/> - <input type="submit" id="roles_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Users associated with '${group.name}'</label> - ${render_select( "in_users", in_users )}<br/> - <input type="submit" id="users_remove_button" value=">>"/> - </div> - <div> - <label>Users not associated with '${group.name}'</label> - ${render_select( "out_users", out_users )}<br/> - <input type="submit" id="users_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <input type="submit" name="group_roles_users_edit_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/group/grid.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,1 @@ +<%inherit file="/grid_base.mako"/> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group/group.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/group/group.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,83 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#roles_add_button').click(function() { + return !$('#out_roles option:selected').remove().appendTo('#in_roles'); + }); + $('#roles_remove_button').click(function() { + return !$('#in_roles option:selected').remove().appendTo('#out_roles'); + }); + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('form#associate_group_role_user').submit(function() { + $('#in_roles option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Group '${group.name}'</div> + <div class="toolFormBody"> + <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='group', group_id=group.id )}" method="post" > + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Roles associated with '${group.name}'</label> + ${render_select( "in_roles", in_roles )}<br/> + <input type="submit" id="roles_remove_button" value=">>"/> + </div> + <div> + <label>Roles not associated with '${group.name}'</label> + ${render_select( "out_roles", out_roles )}<br/> + <input type="submit" id="roles_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with '${group.name}'</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + </div> + <div> + <label>Users not associated with '${group.name}'</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <input type="submit" name="group_roles_users_edit_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group/group_create.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/group/group_create.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,87 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#roles_add_button').click(function() { + return !$('#out_roles option:selected').remove().appendTo('#in_roles'); + }); + $('#roles_remove_button').click(function() { + return !$('#in_roles option:selected').remove().appendTo('#out_roles'); + }); + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('form#associate_group_role_user').submit(function() { + $('#in_roles option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create Group</div> + <div class="toolFormBody"> + <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='create_group' )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Roles associated with new group</label> + ${render_select( "in_roles", in_roles )}<br/> + <input type="submit" id="roles_remove_button" value=">>"/> + </div> + <div> + <label>Roles not associated with new group</label> + ${render_select( "out_roles", out_roles )}<br/> + <input type="submit" id="roles_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with new group</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + </div> + <div> + <label>Users not associated with new group</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <input type="submit" name="create_group_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group/group_rename.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/group/group_rename.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,34 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change group name</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='group' )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${group.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${ trans.security.encode_id( group.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <input type="submit" name="rename_group_button" value="Save"/> + </form> + </div> +</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group_create.mako --- a/templates/admin/dataset_security/group_create.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -<%def name="render_select( name, options )"> - <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> - %for option in options: - <option value="${option[0]}">${option[1]}</option> - %endfor - </select> -</%def> - -<script type="text/javascript"> -$().ready(function() { - $('#roles_add_button').click(function() { - return !$('#out_roles option:selected').remove().appendTo('#in_roles'); - }); - $('#roles_remove_button').click(function() { - return !$('#in_roles option:selected').remove().appendTo('#out_roles'); - }); - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('form#associate_group_role_user').submit(function() { - $('#in_roles option').each(function(i) { - $(this).attr("selected", "selected"); - }); - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); - }); - }); -}); -</script> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Group</div> - <div class="toolFormBody"> - <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='create_group' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <input name="name" type="textfield" value="" size=40"/> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Roles associated with new group</label> - ${render_select( "in_roles", in_roles )}<br/> - <input type="submit" id="roles_remove_button" value=">>"/> - </div> - <div> - <label>Roles not associated with new group</label> - ${render_select( "out_roles", out_roles )}<br/> - <input type="submit" id="roles_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Users associated with new group</label> - ${render_select( "in_users", in_users )}<br/> - <input type="submit" id="users_remove_button" value=">>"/> - </div> - <div> - <label>Users not associated with new group</label> - ${render_select( "out_users", out_users )}<br/> - <input type="submit" id="users_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <input type="submit" name="create_group_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/group_rename.mako --- a/templates/admin/dataset_security/group_rename.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change group name</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='group' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${group.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="group_id" value="${group.id}"/> - </div> - <div style="clear: both"></div> - </div> - <input type="submit" name="rename_group_button" value="Save"/> - </form> - </div> -</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/groups.mako --- a/templates/admin/dataset_security/groups.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,107 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -## Render a row -<%def name="render_row( group, ctr, anchored, curr_anchor )"> - %if ctr % 2 == 1: - <tr class="odd_row"> - %else: - <tr> - %endif - <td> - <a href="${h.url_for( controller='admin', action='group', group_id=group.id )}">${group.name}</a> - <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${group.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='group', rename=True, group_id=group.id )}">Rename this group</a> - <a class="action-button" href="${h.url_for( controller='admin', action='group', group_id=group.id )}">Change associated users and roles</a> - <a class="action-button" href="${h.url_for( controller='admin', action='mark_group_deleted', group_id=group.id )}">Mark group deleted</a> - </div> - </td> - <td> - ${len( group.members )} - </td> - <td> - ${len( group.roles )} - %if not anchored: - <a name="${curr_anchor}"></a> - <div style="float: right;"><a href="#TOP">top</a></div> - %endif - </td> - </tr> -</%def> - -<a name="TOP"><h2>Groups</h2></a> - -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='admin', action='create_group' )}">Create a new group</a></li> - <li><a class="action-button" href="${h.url_for( controller='admin', action='deleted_groups' )}">Manage deleted groups</a></li> -</ul> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -## TODO: make this a grid - -%if not groups: - There are no Galaxy groups -%else: - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <% - render_quick_find = groups.count() > 200 - ctr = 0 - %> - %if render_quick_find: - <% - anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] - anchor_loc = 0 - anchored = False - curr_anchor = 'A' - %> - <tr style="background: #EEE"> - <td colspan="3" style="border-bottom: 1px solid #D8B365; text-align: center;"> - Jump to letter: - %for a in anchors: - | <a href="#${a}">${a}</a> - %endfor - </td> - </tr> - %endif - <tr class="header"> - <td>Name</td> - <td>Users</td> - <td>Roles</td> - </tr> - %for ctr, group in enumerate( groups ): - %if render_quick_find and not group.name.upper().startswith( curr_anchor ): - <% anchored = False %> - %endif - %if render_quick_find and group.name.upper().startswith( curr_anchor ): - %if not anchored: - ${render_row( group, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( group, ctr, anchored, curr_anchor )} - %endif - %elif render_quick_find: - %for anchor in anchors[ anchor_loc: ]: - %if group.name.upper().startswith( anchor ): - %if not anchored: - <% curr_anchor = anchor %> - ${render_row( group, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( group, ctr, anchored, curr_anchor )} - %endif - <% - anchor_loc = anchors.index( anchor ) - break - %> - %endif - %endfor - %else: - ${render_row( group, ctr, True, '' )} - %endif - %endfor - </table> -%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role.mako --- a/templates/admin/dataset_security/role.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -<%def name="render_select( name, options )"> - <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> - %for option in options: - <option value="${option[0]}">${option[1]}</option> - %endfor - </select> -</%def> - -<script type="text/javascript"> -$().ready(function() { - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('#groups_add_button').click(function() { - return !$('#out_groups option:selected').remove().appendTo('#in_groups'); - }); - $('#groups_remove_button').click(function() { - return !$('#in_groups option:selected').remove().appendTo('#out_groups'); - }); - $('form#associate_role_user_group').submit(function() { - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); - }); - $('#in_groups option').each(function(i) { - $(this).attr("selected", "selected"); - }); - }); -}); -</script> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Role '${role.name}'</div> - <div class="toolFormBody"> - <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='role', role_id=role.id )}" method="post" > - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Users associated with '${role.name}'</label> - ${render_select( "in_users", in_users )}<br/> - <input type="submit" id="users_remove_button" value=">>"/> - </div> - <div> - <label>Users not associated with '${role.name}'</label> - ${render_select( "out_users", out_users )}<br/> - <input type="submit" id="users_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Groups associated with '${role.name}'</label> - ${render_select( "in_groups", in_groups )}<br/> - <input type="submit" id="groups_remove_button" value=">>"/> - </div> - <div> - <label>Groups not associated with '${role.name}'</label> - ${render_select( "out_groups", out_groups )}<br/> - <input type="submit" id="groups_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <input type="submit" name="role_members_edit_button" value="Save"/> - </div> - </form> - </div> -</div> -<br clear="left"/> -<br/> -%if len( library_dataset_actions ) > 0: - <h3>Data library datasets associated with role '${role.name}'</h3> - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr> - <td> - <ul> - %for ctr, library, in enumerate( library_dataset_actions.keys() ): - <li> - <img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - ${library.name} - <ul> - %for folder_path, permissions in library_dataset_actions[ library ].items(): - <li> - <img src="/static/images/silk/folder_page.png" class="rowIcon"/> - ${folder_path} - <ul> - % for permission in permissions: - <ul> - <li>${permission}</li> - </ul> - %endfor - </ul> - </li> - %endfor - </ul> - </li> - %endfor - </ul> - </td> - </tr> - </table> -%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/role/grid.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,1 @@ +<%inherit file="/grid_base.mako"/> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role/role.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/role/role.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,117 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('#groups_add_button').click(function() { + return !$('#out_groups option:selected').remove().appendTo('#in_groups'); + }); + $('#groups_remove_button').click(function() { + return !$('#in_groups option:selected').remove().appendTo('#out_groups'); + }); + $('form#associate_role_user_group').submit(function() { + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_groups option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Role '${role.name}'</div> + <div class="toolFormBody"> + <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='role', role_id=role.id )}" method="post" > + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with '${role.name}'</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + </div> + <div> + <label>Users not associated with '${role.name}'</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Groups associated with '${role.name}'</label> + ${render_select( "in_groups", in_groups )}<br/> + <input type="submit" id="groups_remove_button" value=">>"/> + </div> + <div> + <label>Groups not associated with '${role.name}'</label> + ${render_select( "out_groups", out_groups )}<br/> + <input type="submit" id="groups_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <input type="submit" name="role_members_edit_button" value="Save"/> + </div> + </form> + </div> +</div> +<br clear="left"/> +<br/> +%if len( library_dataset_actions ) > 0: + <h3>Data library datasets associated with role '${role.name}'</h3> + <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> + <tr> + <td> + <ul> + %for ctr, library, in enumerate( library_dataset_actions.keys() ): + <li> + <img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> + ${library.name} + <ul> + %for folder_path, permissions in library_dataset_actions[ library ].items(): + <li> + <img src="/static/images/silk/folder_page.png" class="rowIcon"/> + ${folder_path} + <ul> + % for permission in permissions: + <ul> + <li>${permission}</li> + </ul> + %endfor + </ul> + </li> + %endfor + </ul> + </li> + %endfor + </ul> + </td> + </tr> + </table> +%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role/role_create.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/role/role_create.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,94 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +<%def name="render_select( name, options )"> + <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> + %for option in options: + <option value="${option[0]}">${option[1]}</option> + %endfor + </select> +</%def> + +<script type="text/javascript"> +$().ready(function() { + $('#groups_add_button').click(function() { + return !$('#out_groups option:selected').remove().appendTo('#in_groups'); + }); + $('#groups_remove_button').click(function() { + return !$('#in_groups option:selected').remove().appendTo('#out_groups'); + }); + $('#users_add_button').click(function() { + return !$('#out_users option:selected').remove().appendTo('#in_users'); + }); + $('#users_remove_button').click(function() { + return !$('#in_users option:selected').remove().appendTo('#out_users'); + }); + $('form#associate_role_group_user').submit(function() { + $('#in_groups option').each(function(i) { + $(this).attr("selected", "selected"); + }); + $('#in_users option').each(function(i) { + $(this).attr("selected", "selected"); + }); + }); +}); +</script> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create Role</div> + <div class="toolFormBody"> + <form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for( action='create_role' )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Groups associated with new role</label> + ${render_select( "in_groups", in_groups )}<br/> + <input type="submit" id="groups_remove_button" value=">>"/> + </div> + <div> + <label>Groups not associated with new role</label> + ${render_select( "out_groups", out_groups )}<br/> + <input type="submit" id="groups_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <div style="float: left; margin-right: 10px;"> + <label>Users associated with new role</label> + ${render_select( "in_users", in_users )}<br/> + <input type="submit" id="users_remove_button" value=">>"/> + </div> + <div> + <label>Users not associated with new role</label> + ${render_select( "out_users", out_users )}<br/> + <input type="submit" id="users_add_button" value="<<"/> + </div> + </div> + <div class="form-row"> + <input type="checkbox" name="create_group_for_role" value="yes" />Create a new group of the same name for this role + </div> + <div class="form-row"> + <input type="submit" name="create_role_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role/role_rename.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/dataset_security/role/role_rename.mako Mon Nov 09 23:00:55 2009 -0500 @@ -0,0 +1,41 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change role name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='role' )}" method="post" > + <div class="form-row"> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${role.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${role.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( role.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <input type="submit" name="rename_role_button" value="Save"/> + </form> + </div> +</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role_create.mako --- a/templates/admin/dataset_security/role_create.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -<%def name="render_select( name, options )"> - <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> - %for option in options: - <option value="${option[0]}">${option[1]}</option> - %endfor - </select> -</%def> - -<script type="text/javascript"> -$().ready(function() { - $('#groups_add_button').click(function() { - return !$('#out_groups option:selected').remove().appendTo('#in_groups'); - }); - $('#groups_remove_button').click(function() { - return !$('#in_groups option:selected').remove().appendTo('#out_groups'); - }); - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('form#associate_role_group_user').submit(function() { - $('#in_groups option').each(function(i) { - $(this).attr("selected", "selected"); - }); - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); - }); - }); -}); -</script> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Role</div> - <div class="toolFormBody"> - <form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for( action='create_role' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <input name="name" type="textfield" value="" size=40"/> - </div> - <div class="form-row"> - <label>Description:</label> - <input name="description" type="textfield" value="" size=40"/> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Groups associated with new role</label> - ${render_select( "in_groups", in_groups )}<br/> - <input type="submit" id="groups_remove_button" value=">>"/> - </div> - <div> - <label>Groups not associated with new role</label> - ${render_select( "out_groups", out_groups )}<br/> - <input type="submit" id="groups_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Users associated with new role</label> - ${render_select( "in_users", in_users )}<br/> - <input type="submit" id="users_remove_button" value=">>"/> - </div> - <div> - <label>Users not associated with new role</label> - ${render_select( "out_users", out_users )}<br/> - <input type="submit" id="users_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <input type="checkbox" name="create_group_for_role" value="yes" />Create a new group of the same name for this role - </div> - <div class="form-row"> - <input type="submit" name="create_role_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/role_rename.mako --- a/templates/admin/dataset_security/role_rename.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change role name and description</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='role' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${role.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${role.description}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="role_id" value="${role.id}"/> - </div> - <div style="clear: both"></div> - </div> - <input type="submit" name="rename_role_button" value="Save"/> - </form> - </div> -</div> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/dataset_security/roles.mako --- a/templates/admin/dataset_security/roles.mako Mon Nov 09 16:55:52 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -## Render a row -<%def name="render_row( role, ctr, anchored, curr_anchor )"> - %if ctr % 2 == 1: - <tr class="odd_row"> - %else: - <tr> - %endif - <td> - <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a> - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='role', rename=True, role_id=role.id )}">Rename this role</a> - <a class="action-button" href="${h.url_for( controller='admin', action='role', role_id=role.id )}">Change associated users and groups</a> - <a class="action-button" href="${h.url_for( controller='admin', action='mark_role_deleted', role_id=role.id )}">Mark role deleted</a> - </div> - </td> - <td>${role.description}</td> - <td>${role.type}</td> - <td> - ${len( role.users )} - </td> - <td> - ${len( role.groups )} - %if not anchored: - <a name="${curr_anchor}"></a> - <div style="float: right;"><a href="#TOP">top</a></div> - %endif - </td> - </tr> -</%def> - -<a name="TOP"><h2>Roles</h2></a> - -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='admin', action='create_role' )}">Create a new role</a></li> - <li><a class="action-button" href="${h.url_for( controller='admin', action='deleted_roles' )}">Manage deleted roles</a></li> -</ul> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -%if not roles: - There are no non-private Galaxy roles -%else: - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <% - render_quick_find = roles.count() > 200 - ctr = 0 - %> - %if render_quick_find: - <% - anchors = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] - anchor_loc = 0 - anchored = False - curr_anchor = 'A' - %> - <tr style="background: #EEE"> - <td colspan="4" style="text-align: center; border-bottom: 1px solid #D8B365"> - Jump to letter: - %for a in anchors: - | <a href="#${a}">${a}</a> - %endfor - </td> - </tr> - %endif - <tr class="header"> - <td>Name</td> - <td>Description</td> - <td>Type</td> - <td>Users</td> - <td>Groups</td> - </tr> - %for ctr, role in enumerate( roles ): - %if render_quick_find and not role.name.upper().startswith( curr_anchor ): - <% anchored = False %> - %endif - %if render_quick_find and role.name.upper().startswith( curr_anchor ): - %if not anchored: - ${render_row( role, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( role, ctr, anchored, curr_anchor )} - %endif - %elif render_quick_find: - %for anchor in anchors[ anchor_loc: ]: - %if role.name.upper().startswith( anchor ): - %if not anchored: - <% curr_anchor = anchor %> - ${render_row( role, ctr, anchored, curr_anchor )} - <% anchored = True %> - %else: - ${render_row( role, ctr, anchored, curr_anchor )} - %endif - <% - anchor_loc = anchors.index( anchor ) - break - %> - %endif - %endfor - %else: - ${render_row( role, ctr, True, '' )} - %endif - %endfor - </table> -%endif diff -r 1a438bb4dac2 -r 9f485a539bfb templates/admin/user/grid.mako --- a/templates/admin/user/grid.mako Mon Nov 09 16:55:52 2009 -0500 +++ b/templates/admin/user/grid.mako Mon Nov 09 23:00:55 2009 -0500 @@ -1,224 +1,1 @@ -<%inherit file="/base.mako"/> -<%def name="title()">${grid.title}</%def> -<% from galaxy import util %> - -%if message: - <p> - <div class="${message_type}message transient-message">${util.restore_text( message )}</div> - <div style="clear: both"></div> - </p> -%endif - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -%if grid.standard_filters: - <div class="grid-header"> - <h2>${grid.title}</h2> - <span class="title">Filter:</span> - %for i, filter in enumerate( grid.standard_filters ): - %if i > 0: - <span>|</span> - %endif - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endfor - </div> -%endif - -<ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='admin', action='users', operation='create' )}">Create a new user</a></li> -</ul> - -%if query.count() == 0: - No users were returned for the current query. Click the Show all users button or a letter below. -%endif: -<% - letters = ['A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] -%> -<div class="toolFormBody"> - <div class="form-row"> - <a class="action-button" href="${h.url_for( controller='admin', action='users', email_filter='all' )}"><span>Show all users</span></a> - <div class="toolParamHelp" style="clear: both;"> - Default behavior is displaying only users whose email begins with 'a' if there are more than 200 total users - </div> - </div> - <div class="form-row"> - <label>Show only users whose email starts with:</label> - %for letter in letters: - | <a href="${h.url_for( controller='admin', action='users', email_filter=letter )}">${letter}</a> - %endfor - <div style="clear: both"></div> - </div> - <form name="user_actions" action="${url()}" method="post"> - <table class="grid"> - <thead> - <tr> - <th></th> - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody> - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## Item selection column - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - %> - %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}${extra}</a> </td> - %else: - <td >${v}${extra}</td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ) and operation.allow_popup: - <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - %if grid.operations: - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected users: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> - %endif - </table> - </form> -</div> +<%inherit file="/grid_base.mako"/> diff -r 1a438bb4dac2 -r 9f485a539bfb templates/grid_base.mako --- a/templates/grid_base.mako Mon Nov 09 16:55:52 2009 -0500 +++ b/templates/grid_base.mako Mon Nov 09 23:00:55 2009 -0500 @@ -1,5 +1,6 @@ <%! - from galaxy.model import History, HistoryDatasetAssociation + from galaxy.model import History, HistoryDatasetAssociation, User, Role, Group + import galaxy.util def inherit(context): if context.get('use_panels'): return '/base_panels.mako' @@ -11,7 +12,7 @@ ## Render the grid's basic elements. Each of these elements can be subclassed. %if message: <p> - <div class="${message_type}message transient-message">${message}</div> + <div class="${message_type}message transient-message">${util.restore_text( message )}</div> <div style="clear: both"></div> </p> %endif @@ -303,6 +304,12 @@ items_plural = "histories" elif grid.model_class == HistoryDatasetAssociation: items_plural = "datasets" + elif grid.model_class == User: + items_plural = "users" + elif grid.model_class == Role: + items_plural = "roles" + elif grid.model_class == Group: + items_plural = "groups" %> %if num_pages > 1: <tr> diff -r 1a438bb4dac2 -r 9f485a539bfb test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 09 16:55:52 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 09 23:00:55 2009 -0500 @@ -672,7 +672,8 @@ self.check_page_for_string( "The user information has been updated with the changes." ) for value in info_values: self.check_page_for_string( value ) - def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id=2 ): # role.id = 2 is Private Role for test2(a)bx.psu.edu + def user_set_default_permissions( self, permissions_out=[], permissions_in=[], role_id='2' ): + # role.id = 2 is Private Role for test2(a)bx.psu.edu # NOTE: Twill has a bug that requires the ~/user/permissions page to contain at least 1 option value # in each select list or twill throws an exception, which is: ParseError: OPTION outside of SELECT # Due to this bug, we'll bypass visiting the page, and simply pass the permissions on to the @@ -921,6 +922,7 @@ # Tests associated with users def create_new_account_as_admin( self, email='test4(a)bx.psu.edu', password='testuser' ): """Create a new account for another user""" + # TODO: fix this so that it uses the form rather than the following URL. self.home() self.visit_url( "%s/user/create?admin_view=True&email=%s&password=%s&confirm=%s&create_user_button=Submit&subscribe=False" \ % ( self.url, email, password, password ) ) @@ -983,7 +985,13 @@ self.home() # Tests associated with roles - def create_role( self, name='Role One', description="This is Role One", in_user_ids=[], in_group_ids=[], create_group_for_role='no', private_role='' ): + def create_role( self, + name='Role One', + description="This is Role One", + in_user_ids=[], + in_group_ids=[], + create_group_for_role='no', + private_role='' ): """Create a new role""" url = "%s/admin/create_role?create_role_button=Save&name=%s&description=%s" % ( self.url, name.replace( ' ', '+' ), description.replace( ' ', '+' ) ) if in_user_ids: @@ -1017,7 +1025,7 @@ def rename_role( self, role_id, name='Role One Renamed', description='This is Role One Re-described' ): """Rename a role""" self.home() - self.visit_url( "%s/admin/role?rename=True&role_id=%s" % ( self.url, role_id ) ) + self.visit_url( "%s/admin/role?rename=True&id=%s" % ( self.url, role_id ) ) self.check_page_for_string( 'Change role name and description' ) tc.fv( "1", "name", name ) tc.fv( "1", "description", description ) @@ -1026,28 +1034,28 @@ def mark_role_deleted( self, role_id, role_name ): """Mark a role as deleted""" self.home() - self.visit_url( "%s/admin/mark_role_deleted?role_id=%s" % ( self.url, role_id ) ) + self.visit_url( "%s/admin/roles?operation=delete&id=%s" % ( self.url, role_id ) ) check_str = "Role '%s' has been marked as deleted" % role_name self.check_page_for_string( check_str ) self.home() def undelete_role( self, role_id, role_name ): """Undelete an existing role""" self.home() - self.visit_url( "%s/admin/undelete_role?role_id=%s" % ( self.url, role_id ) ) + self.visit_url( "%s/admin/roles?operation=undelete&id=%s" % ( self.url, role_id ) ) check_str = "Role '%s' has been marked as not deleted" % role_name self.check_page_for_string( check_str ) self.home() def purge_role( self, role_id, role_name ): """Purge an existing role""" self.home() - self.visit_url( "%s/admin/purge_role?role_id=%s" % ( self.url, role_id ) ) + self.visit_url( "%s/admin/roles?operation=purge&id=%s" % ( self.url, role_id ) ) check_str = "The following have been purged from the database for role '%s': " % role_name check_str += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss." self.check_page_for_string( check_str ) self.home() def associate_users_and_groups_with_role( self, role_id, role_name, user_ids=[], group_ids=[] ): self.home() - url = "%s/admin/role?role_id=%s&role_members_edit_button=Save" % ( self.url, role_id ) + url = "%s/admin/role?id=%s&role_members_edit_button=Save" % ( self.url, role_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) if group_ids: @@ -1076,14 +1084,14 @@ def rename_group( self, group_id, name='Group One Renamed' ): """Rename a group""" self.home() - self.visit_url( "%s/admin/group?rename=True&group_id=%s" % ( self.url, group_id ) ) + self.visit_url( "%s/admin/group?rename=True&id=%s" % ( self.url, group_id ) ) self.check_page_for_string( 'Change group name' ) tc.fv( "1", "name", name ) tc.submit( "rename_group_button" ) self.home() def associate_users_and_roles_with_group( self, group_id, group_name, user_ids=[], role_ids=[] ): self.home() - url = "%s/admin/group?group_id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) + url = "%s/admin/group?id=%s&group_roles_users_edit_button=Save" % ( self.url, group_id ) if user_ids: url += "&in_users=%s" % ','.join( user_ids ) if role_ids: @@ -1095,21 +1103,21 @@ def mark_group_deleted( self, group_id, group_name ): """Mark a group as deleted""" self.home() - self.visit_url( "%s/admin/mark_group_deleted?group_id=%s" % ( self.url, group_id ) ) + self.visit_url( "%s/admin/groups?operation=delete&id=%s" % ( self.url, group_id ) ) check_str = "Group '%s' has been marked as deleted" % group_name self.check_page_for_string( check_str ) self.home() def undelete_group( self, group_id, group_name ): """Undelete an existing group""" self.home() - self.visit_url( "%s/admin/undelete_group?group_id=%s" % ( self.url, group_id ) ) + self.visit_url( "%s/admin/groups?operation=undelete&id=%s" % ( self.url, group_id ) ) check_str = "Group '%s' has been marked as not deleted" % group_name self.check_page_for_string( check_str ) self.home() def purge_group( self, group_id, group_name ): """Purge an existing group""" self.home() - self.visit_url( "%s/admin/purge_group?group_id=%s" % ( self.url, group_id ) ) + self.visit_url( "%s/admin/groups?operation=purge&id=%s" % ( self.url, group_id ) ) check_str = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group_name self.check_page_for_string( check_str ) self.home() diff -r 1a438bb4dac2 -r 9f485a539bfb test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Nov 09 16:55:52 2009 -0500 +++ b/test/functional/test_history_functions.py Mon Nov 09 23:00:55 2009 -0500 @@ -780,8 +780,8 @@ self.delete_history( id=self.security.encode_id( history4.id ) ) self.delete_history( id=self.security.encode_id( history5.id ) ) # Eliminate Sharing role for: test(a)bx.psu.edu, test2(a)bx.psu.edu - self.mark_role_deleted( str( sharing_role.id ), sharing_role.name ) - self.purge_role( str( sharing_role.id ), sharing_role.name ) + self.mark_role_deleted( self.security.encode_id( sharing_role.id ), sharing_role.name ) + self.purge_role( self.security.encode_id( sharing_role.id ), sharing_role.name ) # Manually delete the sharing role from the database sa_session.refresh( sharing_role ) sa_session.delete( sharing_role ) diff -r 1a438bb4dac2 -r 9f485a539bfb test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Nov 09 16:55:52 2009 -0500 +++ b/test/functional/test_security_and_libraries.py Mon Nov 09 23:00:55 2009 -0500 @@ -327,8 +327,12 @@ name = 'Role One' description = "This is Role Ones description" user_ids=[ str( admin_user.id ), str( regular_user1.id ), str( regular_user3.id ) ] - self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=[], - create_group_for_role='yes', private_role=admin_user.email ) + self.create_role( name=name, + description=description, + in_user_ids=user_ids, + in_group_ids=[], + create_group_for_role='yes', + private_role=admin_user.email ) # Get the role object for later tests global role_one role_one = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() @@ -352,13 +356,13 @@ # Rename the role rename = "Role One's been Renamed" redescription="This is Role One's Re-described" - self.rename_role( str( role_one.id ), name=rename, description=redescription ) + self.rename_role( self.security.encode_id( role_one.id ), name=rename, description=redescription ) self.home() self.visit_page( 'admin/roles' ) self.check_page_for_string( rename ) self.check_page_for_string( redescription ) # Reset the role back to the original name and description - self.rename_role( str( role_one.id ), name=name, description=description ) + self.rename_role( self.security.encode_id( role_one.id ), name=name, description=description ) def test_050_create_group( self ): """Testing creating new group with 3 members and 1 associated role, then renaming it""" name = "Group One's Name" @@ -384,12 +388,12 @@ % ( len( group_one.roles ), group_one.id, len( role_ids ) ) ) # Rename the group rename = "Group One's been Renamed" - self.rename_group( str( group_one.id ), name=rename, ) + self.rename_group( self.security.encode_id( group_one.id ), name=rename, ) self.home() self.visit_page( 'admin/groups' ) self.check_page_for_string( rename ) # Reset the group back to the original name - self.rename_group( str( group_one.id ), name=name ) + self.rename_group( self.security.encode_id( group_one.id ), name=name ) def test_055_add_members_and_role_to_group( self ): """Testing editing user membership and role associations of an existing group""" name = 'Group Two' @@ -405,10 +409,12 @@ if group_two.roles: raise AssertionError( '%d GroupRoleAssociations were created for group id %d when it was created ( should have been 0 )' \ % ( len( group_two.roles ), group_two.id ) ) - group_two_id = str( group_two.id ) user_ids = [ str( regular_user1.id ) ] role_ids = [ str( role_one.id ) ] - self.associate_users_and_roles_with_group( group_two.id, group_two.name, user_ids=user_ids, role_ids=role_ids ) + self.associate_users_and_roles_with_group( self.security.encode_id( group_two.id ), + group_two.name, + user_ids=user_ids, + role_ids=role_ids ) def test_060_create_role_with_user_and_group_associations( self ): """Testing creating a role with user and group associations""" # NOTE: To get this to work with twill, all select lists on the ~/admin/role page must contain at least @@ -421,7 +427,11 @@ group_ids=[ str( group_two.id ) ] private_role=admin_user.email # Create the role - self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=group_ids, private_role=private_role ) + self.create_role( name=name, + description=description, + in_user_ids=user_ids, + in_group_ids=group_ids, + private_role=private_role ) # Get the role object for later tests global role_two role_two = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() @@ -451,7 +461,11 @@ user_ids=[] group_ids=[] private_role=admin_user.email - self.create_role( name=name, description=description, in_user_ids=user_ids, in_group_ids=group_ids, private_role=private_role ) + self.create_role( name=name, + description=description, + in_user_ids=user_ids, + in_group_ids=group_ids, + private_role=private_role ) # Get the role object for later tests global role_three role_three = sa_session.query( galaxy.model.Role ).filter( galaxy.model.Role.table.c.name==name ).first() @@ -466,8 +480,11 @@ for uga in admin_user.groups: group_ids.append( str( uga.group_id ) ) check_str = "User '%s' has been updated with %d associated roles and %d associated groups" % ( admin_user.email, len( role_ids ), len( group_ids ) ) - self.associate_roles_and_groups_with_user( self.security.encode_id( admin_user.id ), str( admin_user.email ), - in_role_ids=role_ids, in_group_ids=group_ids, check_str=check_str ) + self.associate_roles_and_groups_with_user( self.security.encode_id( admin_user.id ), + str( admin_user.email ), + in_role_ids=role_ids, + in_group_ids=group_ids, + check_str=check_str ) sa_session.refresh( admin_user ) # admin_user should now be associated with 4 roles: private, role_one, role_two, role_three if len( admin_user.roles ) != 4: @@ -1374,7 +1391,7 @@ self.home() self.visit_url( '%s/admin/groups' % self.url ) self.check_page_for_string( group_two.name ) - self.mark_group_deleted( str( group_two.id ), group_two.name ) + self.mark_group_deleted( self.security.encode_id( group_two.id ), group_two.name ) sa_session.refresh( group_two ) if not group_two.deleted: raise AssertionError( '%s was not correctly marked as deleted.' % group_two.name ) @@ -1386,7 +1403,7 @@ def test_175_undelete_group( self ): """Testing undeleting a deleted group""" # Logged in as admin_user - self.undelete_group( str( group_two.id ), group_two.name ) + self.undelete_group( self.security.encode_id( group_two.id ), group_two.name ) sa_session.refresh( group_two ) if group_two.deleted: raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name ) @@ -1396,7 +1413,7 @@ self.home() self.visit_url( '%s/admin/roles' % self.url ) self.check_page_for_string( role_two.name ) - self.mark_role_deleted( str( role_two.id ), role_two.name ) + self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name ) sa_session.refresh( role_two ) if not role_two.deleted: raise AssertionError( '%s was not correctly marked as deleted.' % role_two.name ) @@ -1408,7 +1425,7 @@ def test_185_undelete_role( self ): """Testing undeleting a deleted role""" # Logged in as admin_user - self.undelete_role( str( role_two.id ), role_two.name ) + self.undelete_role( self.security.encode_id( role_two.id ), role_two.name ) def test_190_mark_dataset_deleted( self ): """Testing marking a library dataset as deleted""" # Logged in as admin_user @@ -1541,59 +1558,57 @@ def test_235_purge_group( self ): """Testing purging a group""" # Logged in as admin_user - group_id = str( group_two.id ) - self.mark_group_deleted( group_id, group_two.name ) - self.purge_group( group_id, group_two.name ) + self.mark_group_deleted( self.security.encode_id( group_two.id ), group_two.name ) + self.purge_group( self.security.encode_id( group_two.id ), group_two.name ) # Make sure there are no UserGroupAssociations uga = sa_session.query( galaxy.model.UserGroupAssociation ) \ - .filter( galaxy.model.UserGroupAssociation.table.c.group_id == group_id ) \ + .filter( galaxy.model.UserGroupAssociation.table.c.group_id == group_two.id ) \ .first() if uga: - raise AssertionError( "Purging the group did not delete the UserGroupAssociations for group_id '%s'" % group_id ) + raise AssertionError( "Purging the group did not delete the UserGroupAssociations for group_id '%s'" % group_two.id ) # Make sure there are no GroupRoleAssociations gra = sa_session.query( galaxy.model.GroupRoleAssociation ) \ - .filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group_id ) \ + .filter( galaxy.model.GroupRoleAssociation.table.c.group_id == group_two.id ) \ .first() if gra: - raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id ) + raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_two.id ) # Undelete the group for later test runs - self.undelete_group( group_id, group_two.name ) + self.undelete_group( self.security.encode_id( group_two.id ), group_two.name ) def test_240_purge_role( self ): """Testing purging a role""" # Logged in as admin_user - role_id = str( role_two.id ) - self.mark_role_deleted( role_id, role_two.name ) - self.purge_role( role_id, role_two.name ) + self.mark_role_deleted( self.security.encode_id( role_two.id ), role_two.name ) + self.purge_role( self.security.encode_id( role_two.id ), role_two.name ) # Make sure there are no UserRoleAssociations uras = sa_session.query( galaxy.model.UserRoleAssociation ) \ - .filter( galaxy.model.UserRoleAssociation.table.c.role_id == role_id ) \ + .filter( galaxy.model.UserRoleAssociation.table.c.role_id == role_two.id ) \ .all() if uras: - raise AssertionError( "Purging the role did not delete the UserRoleAssociations for role_id '%s'" % role_id ) + raise AssertionError( "Purging the role did not delete the UserRoleAssociations for role_id '%s'" % role_two.id ) # Make sure there are no DefaultUserPermissions associated with the Role dups = sa_session.query( galaxy.model.DefaultUserPermissions ) \ - .filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role_id ) \ + .filter( galaxy.model.DefaultUserPermissions.table.c.role_id == role_two.id ) \ .all() if dups: - raise AssertionError( "Purging the role did not delete the DefaultUserPermissions for role_id '%s'" % role_id ) + raise AssertionError( "Purging the role did not delete the DefaultUserPermissions for role_id '%s'" % role_two.id ) # Make sure there are no DefaultHistoryPermissions associated with the Role dhps = sa_session.query( galaxy.model.DefaultHistoryPermissions ) \ - .filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role_id ) \ + .filter( galaxy.model.DefaultHistoryPermissions.table.c.role_id == role_two.id ) \ .all() if dhps: - raise AssertionError( "Purging the role did not delete the DefaultHistoryPermissions for role_id '%s'" % role_id ) + raise AssertionError( "Purging the role did not delete the DefaultHistoryPermissions for role_id '%s'" % role_two.id ) # Make sure there are no GroupRoleAssociations gra = sa_session.query( galaxy.model.GroupRoleAssociation ) \ - .filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role_id ) \ + .filter( galaxy.model.GroupRoleAssociation.table.c.role_id == role_two.id ) \ .first() if gra: - raise AssertionError( "Purging the role did not delete the GroupRoleAssociations for role_id '%s'" % role_id ) + raise AssertionError( "Purging the role did not delete the GroupRoleAssociations for role_id '%s'" % role_two.id ) # Make sure there are no DatasetPermissionss dp = sa_session.query( galaxy.model.DatasetPermissions ) \ - .filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ) \ + .filter( galaxy.model.DatasetPermissions.table.c.role_id == role_two.id ) \ .first() if dp: - raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id ) + raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_two.id ) def test_245_manually_unpurge_role( self ): """Testing manually un-purging a role""" # Logged in as admin_user @@ -1601,7 +1616,7 @@ # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call role_two.purged = False role_two.flush() - self.undelete_role( str( role_two.id ), role_two.name ) + self.undelete_role( self.security.encode_id( role_two.id ), role_two.name ) def test_250_purge_library( self ): """Testing purging a library""" # Logged in as admin_user @@ -1815,8 +1830,8 @@ # Eliminate all non-private roles ################## for role in [ role_one, role_two, role_three ]: - self.mark_role_deleted( str( role.id ), role.name ) - self.purge_role( str( role.id ), role.name ) + self.mark_role_deleted( self.security.encode_id( role.id ), role.name ) + self.purge_role( self.security.encode_id( role.id ), role.name ) # Manually delete the role from the database sa_session.refresh( role ) sa_session.delete( role ) @@ -1825,8 +1840,8 @@ # Eliminate all groups ################## for group in [ group_zero, group_one, group_two ]: - self.mark_group_deleted( str( group.id ), group.name ) - self.purge_group( str( group.id ), group.name ) + self.mark_group_deleted( self.security.encode_id( group.id ), group.name ) + self.purge_group( self.security.encode_id( group.id ), group.name ) # Manually delete the group from the database sa_session.refresh( group ) sa_session.delete( group ) @@ -1846,7 +1861,6 @@ # Change DefaultHistoryPermissions for regular_user1 back to the default permissions_in = [ 'DATASET_MANAGE_PERMISSIONS' ] permissions_out = [ 'DATASET_ACCESS' ] - role_id = str( regular_user1_private_role.id ) - self.user_set_default_permissions( permissions_in=permissions_in, permissions_out=permissions_out, role_id=role_id ) + self.user_set_default_permissions( permissions_in=permissions_in, permissions_out=permissions_out, role_id=str( regular_user1_private_role.id ) ) self.logout() self.login( email=admin_user.email ) diff -r 1a438bb4dac2 -r 9f485a539bfb tool_conf.xml.main --- a/tool_conf.xml.main Mon Nov 09 16:55:52 2009 -0500 +++ b/tool_conf.xml.main Mon Nov 09 23:00:55 2009 -0500 @@ -8,6 +8,7 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> + <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> </section> @@ -27,6 +28,7 @@ <tool file="filters/catWrapper.xml" /> <tool file="filters/condense_characters.xml" /> <tool file="filters/convert_characters.xml" /> + <tool file="filters/mergeCols.xml" /> <tool file="filters/CreateInterval.xml" /> <tool file="filters/cutWrapper.xml" /> <tool file="filters/changeCase.xml" /> @@ -34,15 +36,17 @@ <tool file="filters/remove_beginning.xml" /> <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> </section> <section name="Convert Formats" id="convert"> <tool file="filters/bed2gff.xml" /> <tool file="fasta_tools/fasta_to_tabular.xml" /> <tool file="filters/gff2bed.xml" /> <tool file="maf/maf_to_bed.xml" /> - <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_interval.xml" /> <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> </section> <section name="FASTA manipulation" id="fasta_manipulation"> <tool file="fasta_tools/fasta_compute_length.xml" /> @@ -50,6 +54,9 @@ <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> <tool file="fasta_tools/fasta_to_tabular.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fasta_formatter.xml" /> + <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> </section> <section name="Filter and Sort" id="filter"> <tool file="stats/filtering.xml" /> @@ -80,9 +87,7 @@ <tool file="maf/maf_limit_size.xml"/> <tool file="maf/maf_by_block_number.xml"/> <tool file="maf/maf_filter.xml"/> -  </section> <section name="Get Genomic Scores" id="scores"> <tool file="stats/wiggle_to_simple.xml" /> @@ -90,7 +95,7 @@ <tool file="extract/phastOdds/phastOdds_tool.xml" /> </section> <section name="Operate on Genomic Intervals" id="bxops"> - <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/intersect.xml" /> <tool file="new_operations/subtract.xml" /> <tool file="new_operations/merge.xml" /> <tool file="new_operations/concat.xml" /> @@ -147,12 +152,6 @@ <tool file="taxonomy/lca.xml" /> <tool file="taxonomy/poisson2test.xml" /> </section> - <section name="Short Read Analysis" id="short_read_analysis"> - <tool file="metag_tools/short_reads_figure_score.xml" /> - <tool file="metag_tools/short_reads_trim_seq.xml" /> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> - </section> <section name="EMBOSS" id="EMBOSSLite"> <tool file="emboss_5/emboss_antigenic.xml" /> <tool file="emboss_5/emboss_backtranseq.xml" /> @@ -262,4 +261,37 @@ <tool file="emboss_5/emboss_wordcount.xml" /> <tool file="emboss_5/emboss_wordmatch.xml" /> </section> + <label text="NGS Toolbox Beta" id="ngs" /> + <section name="NGS: QC and manipulation" id="cshl_library_information"> + <label text="Generic FASTQ data" id="fastq" /> + <tool file="next_gen_conversion/fastq_gen_conv.xml" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> + <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="metag_tools/split_paired_reads.xml" /> + <label text="Roche-454 data" id="454" /> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + <label text="AB-SOLiD data" id="solid" /> + <tool file="next_gen_conversion/solid_to_fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> +  + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + </section> + <section name="NGS: SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> + </section> </toolbox>

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[hg] galaxy 2994: Make pages grid compatible with new grid frame...
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1a438bb4dac2 changeset: 2994:1a438bb4dac2 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 16:55:52 2009 -0500 description: Make pages grid compatible with new grid framework. diffstat: lib/galaxy/web/controllers/page.py | 118 ++++----------------------------------- templates/grid_base.mako | 2 +- templates/grid_common.mako | 2 +- 3 files changed, 15 insertions(+), 107 deletions(-) diffs (171 lines): diff -r 50c64a663d24 -r 1a438bb4dac2 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Nov 09 16:40:59 2009 -0500 +++ b/lib/galaxy/web/controllers/page.py Mon Nov 09 16:55:52 2009 -0500 @@ -33,9 +33,9 @@ model_class = model.Page default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Title", key="title", attach_popup=True ), + grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="standard" ), PublicURLColumn( "Public URL" ), - grids.GridColumn( "Published", key="published", format=format_bool ), + grids.GridColumn( "Published", key="published", format=format_bool, filterable="advanced" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -68,120 +68,28 @@ ] def apply_default_filter( self, trans, query, **kwargs ): return query.filter_by( deleted=False, published=True ) - -# Custom column types -class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup, filterable ): - grids.GridColumn.__init__(self, key, link, attach_popup) - def get_value( self, trans, grid, history ): + +class NameColumn( grids.TextColumn ): + def get_value(self, trans, grid, history): return history.get_display_name() - - def filter( self, db_session, query, column_filter ): - """ Modify query to filter histories by name. """ - if column_filter == "All": - pass - elif column_filter: - query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) - 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["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - -class TagsColumn( grids.GridColumn ): - def __init__( self, col_name, key, filterable ): - grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) - # Tags cannot be sorted. - self.sortable = False - self.tag_elt_id_gen = 0 - def get_value( self, trans, grid, history ): - self.tag_elt_id_gen += 1 - elt_id="tagging-elt" + str( self.tag_elt_id_gen ) - div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, - elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) - def filter( self, db_session, query, column_filter ): - """ Modify query to filter histories by tag. """ - if column_filter == "All": - pass - elif column_filter: - # Parse filter to extract multiple tags. - tag_handler = TagHandler() - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) - for name, value in raw_tags.items(): - if name: - # Search for tag names. - query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) - if value: - # Search for tag values. - query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) - 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["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - -class FreeTextSearchColumn( grids.GridColumn ): - def filter( self, db_session, query, column_filter ): - """ Modify query to search tags and history names. """ - if column_filter == "All": - pass - elif column_filter: - # Build tags filter. - tag_handler = TagHandler() - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) - tags_filter = None - for name, value in raw_tags.items(): - if name: - # Search for tag names. - tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) - if value: - # Search for tag values. - tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) - - # Build history name filter. - history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) - - # Apply filters to query. - if tags_filter: - query = query.filter( or_( tags_filter, history_name_filter ) ) - else: - query = query.filter( history_name_filter ) - 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["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class HistorySelectionGrid( grids.Grid ): # Grid definition. - template='/page/history_selection_grid.mako' title = "Saved Histories" model_class = model.History default_sort_key = "-update_time" columns = [ - NameColumn( "Name", key="name", filterable=True ), - TagsColumn( "Tags", key="tags", filterable=True), + NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), + grids.TagsColumn( "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. - FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", visible=False, filterable="standard" ) + ) class PageController( BaseController ): diff -r 50c64a663d24 -r 1a438bb4dac2 templates/grid_base.mako --- a/templates/grid_base.mako Mon Nov 09 16:40:59 2009 -0500 +++ b/templates/grid_base.mako Mon Nov 09 16:55:52 2009 -0500 @@ -286,7 +286,7 @@ if operation.target: target = "target='" + operation.target + "'" %> - <a class="action-button" ${target} href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> + <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> %endif %endfor </div> diff -r 50c64a663d24 -r 1a438bb4dac2 templates/grid_common.mako --- a/templates/grid_common.mako Mon Nov 09 16:40:59 2009 -0500 +++ b/templates/grid_common.mako Mon Nov 09 16:55:52 2009 -0500 @@ -60,7 +60,7 @@ %if i > 0: <span>|</span> %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: + %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: <span class="filter" style="font-style: italic">${filter.label}</span> %else: <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span>

1 0

[hg] galaxy 2990: Fixed a checkbox bug in request & user_info
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a2dee187b2b6 changeset: 2990:a2dee187b2b6 user: rc date: Mon Nov 09 16:15:52 2009 -0500 description: Fixed a checkbox bug in request & user_info Resolved bitbucket issue 221: now there is a reject option for an admin to move a request to an unsubmitted state diffstat: lib/galaxy/model/__init__.py | 6 +- lib/galaxy/web/controllers/admin.py | 3 +- lib/galaxy/web/controllers/requests.py | 6 +- lib/galaxy/web/controllers/requests_admin.py | 32 ++++++++++- lib/galaxy/web/controllers/user.py | 42 +++++++++++--- lib/galaxy/web/form_builder.py | 8 ++ templates/admin/requests/show_request.mako | 13 +++- templates/requests/show_request.mako | 2 +- templates/user/address.mako | 80 -------------------------- templates/user/info.mako | 46 ++++++++------ test/base/twilltestcase.py | 4 + test/functional/test_forms_and_requests.py | 12 ++++ test/functional/test_user_info.py | 29 ++++++--- 13 files changed, 154 insertions(+), 129 deletions(-) diffs (579 lines): diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/model/__init__.py Mon Nov 09 16:15:52 2009 -0500 @@ -1170,7 +1170,7 @@ else: field_widget.add_option( option, option ) elif field[ 'type' ] == 'CheckboxField': - field_widget.checked = value + field_widget.set_checked( value ) if field[ 'required' ] == 'required': req = 'Required' else: @@ -1231,7 +1231,9 @@ self.values = form_values self.bar_code = bar_code def current_state(self): - return self.events[0].state + if self.events: + return self.events[0].state + return None class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None): diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Mon Nov 09 16:15:52 2009 -0500 @@ -760,7 +760,6 @@ information, public username, reset password & other user information obtained during registration ''' - print 'KWD', kwd user_id = kwd.get( 'id', None ) if not user_id: message += "Invalid user id (%s) received" % str( user_id ) @@ -772,7 +771,7 @@ return trans.response.send_redirect( web.url_for( controller='user', action='show_info', user_id=user.id, - admin_view=True ) ) + admin_view=True, **kwd ) ) @web.expose @web.require_admin def user( self, trans, **kwd ): diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Mon Nov 09 16:15:52 2009 -0500 @@ -85,7 +85,7 @@ return self.__show_request(trans, id, kwargs.get('add_sample', False)) elif operation == "submit": id = trans.security.decode_id(kwargs['id']) - return self.__submit(trans, id) + return self.__submit_request(trans, id) elif operation == "delete": id = trans.security.decode_id(kwargs['id']) return self.__delete_request(trans, id) @@ -642,6 +642,8 @@ values.append('') else: values.append(int(value)) + elif field['type'] == 'CheckboxField': + values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) else: values.append(util.restore_text(params.get('field_%i' % index, ''))) form_values = trans.app.model.FormValues(request_type.request_form, values) @@ -799,7 +801,7 @@ status='done', message='The request <b>%s</b> has been undeleted.' % request.name, **kwd) ) - def __submit(self, trans, id): + def __submit_request(self, trans, id): try: request = trans.sa_session.query( trans.app.model.Request ).get( id ) except: diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Nov 09 16:15:52 2009 -0500 @@ -37,6 +37,7 @@ operations = [ grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ), grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Reject", allow_multiple=False, condition=( lambda item: not item.deleted and item.submitted() ) ), grids.GridOperation( "Delete", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), ] @@ -94,7 +95,7 @@ return self.__show_request(trans, id, status, message) elif operation == "submit": id = trans.security.decode_id(kwargs['id']) - return self.__submit(trans, id) + return self.__submit_request(trans, id) elif operation == "edit": id = trans.security.decode_id(kwargs['id']) return self.__edit_request(trans, id) @@ -104,6 +105,9 @@ elif operation == "undelete": id = trans.security.decode_id(kwargs['id']) return self.__undelete_request(trans, id) + elif operation == "reject": + id = trans.security.decode_id(kwargs['id']) + return self.__reject_request(trans, id) if 'show_filter' in kwargs.keys(): if kwargs['show_filter'] == 'All': self.request_grid.default_filter = {} @@ -226,7 +230,7 @@ status='done', message='The request <b>%s</b> has been undeleted.' % request.name, **kwd) ) - def __submit(self, trans, id): + def __submit_request(self, trans, id): try: request = trans.sa_session.query( trans.app.model.Request ).get( id ) except: @@ -582,6 +586,8 @@ values.append('') else: values.append(int(value)) + elif field['type'] == 'CheckboxField': + values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) else: values.append(util.restore_text(params.get('field_%i' % index, ''))) form_values = trans.app.model.FormValues(request_type.request_form, values) @@ -690,6 +696,28 @@ action='list', show_filter=trans.app.model.Request.states.SUBMITTED, **kwd) ) + def __reject_request(self, trans, id): + try: + request = trans.sa_session.query( trans.app.model.Request ).get( id ) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # change request's submitted field + request.state = request.states.UNSUBMITTED + request.flush() + kwd = {} + kwd['id'] = trans.security.encode_id(request.id) + kwd['status'] = 'done' + kwd['message'] = 'The request <b>%s</b> is now unsubmitted.' % request.name + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + show_filter=trans.app.model.Request.states.UNSUBMITTED, + **kwd) ) def __update_samples(self, request, **kwd): ''' This method retrieves all the user entered sample information and diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Mon Nov 09 16:15:52 2009 -0500 @@ -168,7 +168,7 @@ username = util.restore_text( params.get('username', '') ) password = util.restore_text( params.get('password', '') ) confirm = util.restore_text( params.get('confirm', '') ) - subscribe = params.get('subscribe', False) + subscribe = CheckboxField.is_checked( params.get('subscribe', '') ) admin_view = params.get('admin_view', 'False') msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -241,10 +241,10 @@ # get all the user information forms user_info_forms = get_all_forms( trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.USER_INFO ) - # if there are no user forms available then there is nothing to save - if not len( user_info_forms ): - return if new_user: + # if there are no user forms available then there is nothing to save + if not len( user_info_forms ): + return user_info_type = params.get( 'user_info_select', 'none' ) try: user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(user_info_type)) @@ -254,7 +254,25 @@ msg='Invalid user information form id', messagetype='error') ) else: - user_info_form = user.values.form_definition + if user.values: + user_info_form = user.values.form_definition + else: + # user was created before any of the user_info forms were created + if len(user_info_forms) > 1: + # when there are multiple user_info forms and the user or admin + # can change the user_info form + user_info_type = params.get( 'user_info_select', 'none' ) + try: + user_info_form = trans.sa_session.query( trans.app.model.FormDefinition ).get(int(user_info_type)) + except: + return trans.response.send_redirect( web.url_for( controller='user', + action=action, + msg='Invalid user information form id', + messagetype='error') ) + else: + # when there is only one user_info form then there is no way + # to change the user_info form + user_info_form = user_info_forms[0] values = [] for index, field in enumerate(user_info_form.fields): if field['type'] == 'AddressField': @@ -278,13 +296,17 @@ values.append('') else: values.append(int(value)) + elif field['type'] == 'CheckboxField': + values.append(CheckboxField.is_checked( params.get('field_%i' % index, '') )) else: values.append(util.restore_text(params.get('field_%i' % index, ''))) - if new_user: + if new_user or not user.values: + # new user or existing form_values = trans.app.model.FormValues(user_info_form, values) form_values.flush() user.values = form_values - else: # editing the user info of an existing user + elif user.values: + # editing the user info of an existing user with existing user info user.values.content = values user.values.flush() user.flush() @@ -340,7 +362,7 @@ if user.values: selected_user_form_id = user.values.form_definition.id else: - selected_user_form_id = 'none' + selected_user_form_id = params.get( 'user_info_select', 'none' ) else: selected_user_form_id = params.get( 'user_info_select', 'none' ) # when there are more than one user information forms then show a select box @@ -428,10 +450,12 @@ addresses = [address for address in user.addresses if address.deleted] else: addresses = [address for address in user.addresses if not address.deleted] + user_info_forms = get_all_forms( trans, filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.USER_INFO ) return trans.fill_template( '/user/info.mako', user=user, admin_view=admin_view, user_info_select=user_info_select, user_info_form=user_info_form, widgets=widgets, - login_info=login_info, + login_info=login_info, user_info_forms=user_info_forms, addresses=addresses, show_filter=show_filter, msg=msg, messagetype=messagetype) @web.expose diff -r 1612a5f4ed62 -r a2dee187b2b6 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Mon Nov 09 15:50:12 2009 -0500 +++ b/lib/galaxy/web/form_builder.py Mon Nov 09 16:15:52 2009 -0500 @@ -118,6 +118,14 @@ return True else: return False + def set_checked(self, value): + if type(value) == type('a'): + if value.lower() in [ "yes", "true", "on" ]: + self.checked = True + else: + self.checked = False + else: + self.checked = value class FileField(BaseField): """ diff -r 1612a5f4ed62 -r a2dee187b2b6 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Mon Nov 09 15:50:12 2009 -0500 +++ b/templates/admin/requests/show_request.mako Mon Nov 09 16:15:52 2009 -0500 @@ -14,16 +14,23 @@ <ul class="manage-table-actions"> %if request.unsubmitted() and request.samples: <li> - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='submit_request', id=request.id)}"> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}"> <span>Submit request</span></a> </li> %endif + %if request.submitted(): + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='Reject', id=trans.security.encode_id(request.id))}"> + <span>Reject request</span></a> + </li> + %endif %if request.submitted() and request.samples: <li> <a class="action-button" href="${h.url_for( controller='requests_admin', action='bar_codes', request_id=request.id)}"> <span>Bar codes</span></a> </li> %endif + </ul> @@ -76,7 +83,9 @@ <td> %if sample.request.unsubmitted(): Unsubmitted - %else: + %elif not sample.current_state(): + New + %else: <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> %endif </td> diff -r 1612a5f4ed62 -r a2dee187b2b6 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Mon Nov 09 15:50:12 2009 -0500 +++ b/templates/requests/show_request.mako Mon Nov 09 16:15:52 2009 -0500 @@ -14,7 +14,7 @@ <ul class="manage-table-actions"> %if request.unsubmitted() and request.samples: <li> - <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='submit_request', id=request.id)}"> + <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}"> <span>Submit request</span></a> </li> %endif diff -r 1612a5f4ed62 -r a2dee187b2b6 templates/user/address.mako --- a/templates/user/address.mako Mon Nov 09 15:50:12 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<h2>Manage Addresses</h2> -<ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='user', action='new_address')}"> - <span>Add a new address</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='index')}"> - <span>User preferences</span></a> - </li> -</ul> -%if not trans.user.addresses: - There are no addresses -%else: -<div class="grid-header"> - ##<span class="title">Filter:</span> - %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: - <span>|</span> - %endif - %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_addresses', show_filter=filter )}"><b>${filter}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_addresses', show_filter=filter )}">${filter}</a></span> - %endif - %endfor -</div> - - -%if not addresses: - <label>There are no addresses</label> -%else: - <div class="toolForm"> - <div class="toolFormBody"> - <% trans.sa_session.refresh( trans.user ) %> - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td> - <div class="form-row"> - <label>${address.desc}</label> - ${address.get_html()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', address_id=address.id, - short_desc=address.desc, - name=address.name, institution=address.institution, - address1=address.address, city=address.city, - state=address.state, postal_code=address.postal_code, - country=address.country, phone=address.phone)}"> - <span>Edit</span></a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', address_id=address.id)}"> - <span>Delete</span></a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', address_id=address.id)}"> - <span>Undelete</span></a> - %endif - - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> - %endif - </div> - </div> -%endif \ No newline at end of file diff -r 1612a5f4ed62 -r a2dee187b2b6 templates/user/info.mako --- a/templates/user/info.mako Mon Nov 09 15:50:12 2009 -0500 +++ b/templates/user/info.mako Mon Nov 09 16:15:52 2009 -0500 @@ -76,28 +76,34 @@ <input type="submit" name="change_password_button" value="Save"> </div> </form> - %if user.values: - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > - <div class="toolFormTitle">User information</div> - %if user_info_form: - %for field in widgets: - <div class="form-row"> - <label>${field['label']}</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor - %if not user_info_select: - <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> - %endif - %endif + %if user.values or user_info_forms: + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', user_id=user.id, admin_view=admin_view )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_info_select: <div class="form-row"> - <input type="submit" name="edit_user_info_button" value="Save"> + <label>User type</label> + ${user_info_select.get_html()} </div> - </form> + %endif + + %for field in widgets: + <div class="form-row"> + <label>${field['label']}</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + %if not user_info_select: + <input type="hidden" name="user_info_select" value="${user_info_form.id}"/> + %endif + + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"> + </div> + </form> %endif <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > <div class="toolFormTitle">User Addresses</div> diff -r 1612a5f4ed62 -r a2dee187b2b6 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 09 15:50:12 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 09 16:15:52 2009 -0500 @@ -1265,6 +1265,10 @@ self.home() self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id )) self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) + def reject_request( self, request_id, request_name ): + self.home() + self.visit_url( "%s/requests_admin/list?operation=Reject&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + self.check_page_for_string( 'The request <b>%s</b> is now unsubmitted.' % request_name ) def add_bar_codes( self, request_id, request_name, bar_codes ): self.home() self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) ) diff -r 1612a5f4ed62 -r a2dee187b2b6 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Nov 09 15:50:12 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Mon Nov 09 16:15:52 2009 -0500 @@ -288,3 +288,15 @@ self.visit_url( '%s/requests_admin/list?show_filter=All' % self.url ) self.check_page_for_string( request_one.name ) self.check_page_for_string( request_two.name ) + def test_45_reject_request( self ): + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.reject_request( request_two.id, request_two.name ) + sa_session.refresh( request_two ) + # check if the request is showing in the 'unsubmitted' filter + self.home() + self.visit_url( '%s/requests_admin/list?show_filter=Unsubmitted' % self.url ) + self.check_page_for_string( request_two.name ) + # check if the request's state is now set to 'submitted' + assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" \ + % ( request_two.name, request_two.states.UNSUBMITTED ) diff -r 1612a5f4ed62 -r a2dee187b2b6 test/functional/test_user_info.py --- a/test/functional/test_user_info.py Mon Nov 09 15:50:12 2009 -0500 +++ b/test/functional/test_user_info.py Mon Nov 09 16:15:52 2009 -0500 @@ -43,6 +43,10 @@ dict(name='Name of Organization', desc='', type='TextField', + required='optional'), + dict(name='Contact for feedback', + desc='', + type='CheckboxField', required='optional')] form_one = get_latest_form(form_one_name) self.form_add_field(form_one.id, form_one.name, form_one.desc, form_one.type, field_index=len(form_one.fields), fields=fields) @@ -65,6 +69,10 @@ dict(name='Name of Organization', desc='', type='TextField', + required='optional'), + dict(name='Contact for feedback', + desc='', + type='CheckboxField', required='optional')] form_two = get_latest_form(form_two_name) self.form_add_field(form_two.id, form_two.name, form_two.desc, form_two.type, field_index=len(form_one.fields), fields=fields) @@ -75,7 +83,7 @@ self.logout() # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) - user_info_values=['Educational', 'Penn State'] + user_info_values=['Educational', 'Penn State', True] self.create_user_with_info( 'test11(a)bx.psu.edu', 'testuser', 'test11', user_info_forms='multiple', user_info_form_id=form_one.id, @@ -83,8 +91,9 @@ self.home() self.visit_page( "user/show_info" ) self.check_page_for_string( "Manage User Information" ) - for value in user_info_values: - self.check_page_for_string( value ) + self.check_page_for_string( user_info_values[0] ) + self.check_page_for_string( user_info_values[1] ) + self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' ) def test_010_user_reqistration_single_user_info_forms( self ): ''' Testing user registration with a single user info form ''' # lets delete the 'Researcher' user info form @@ -98,7 +107,7 @@ self.logout() # user a new user with 'Student' user info form form_one = get_latest_form(form_one_name) - user_info_values=['Educational', 'Penn State'] + user_info_values=['Educational', 'Penn State', True] self.create_user_with_info( 'test12(a)bx.psu.edu', 'testuser', 'test12', user_info_forms='single', user_info_form_id=form_one.id, @@ -106,8 +115,9 @@ self.home() self.visit_page( "user/show_info" ) self.check_page_for_string( "Manage User Information" ) - for value in user_info_values: - self.check_page_for_string( value ) + self.check_page_for_string( user_info_values[0] ) + self.check_page_for_string( user_info_values[1] ) + self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' ) def test_015_edit_user_info( self ): """Testing editing user info as a regular user""" self.logout() @@ -122,7 +132,7 @@ self.logout() self.login( 'test(a)bx.psu.edu' ) form_one = get_latest_form(form_one_name) - user_info_values=['Educational', 'Penn State'] + user_info_values=['Educational', 'Penn State', True] self.create_user_with_info( 'test13(a)bx.psu.edu', 'testuser', 'test13', user_info_forms='single', user_info_form_id=form_one.id, @@ -136,8 +146,9 @@ self.visit_page( page ) self.check_page_for_string( 'Manage User Information' ) self.check_page_for_string( 'test13(a)bx.psu.edu' ) - for value in user_info_values: - self.check_page_for_string( value ) + self.check_page_for_string( user_info_values[0] ) + self.check_page_for_string( user_info_values[1] ) + self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' ) # lets delete the 'Student' user info form self.login( 'test(a)bx.psu.edu' ) form_one_latest = get_latest_form(form_one_name)

1 0

[hg] galaxy 2991: remove unused MyghtyUtils egg
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4e1101dc2f25 changeset: 2991:4e1101dc2f25 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 09 16:18:39 2009 -0500 description: remove unused MyghtyUtils egg diffstat: eggs.ini | 3 --- 1 files changed, 0 insertions(+), 3 deletions(-) diffs (27 lines): diff -r a2dee187b2b6 -r 4e1101dc2f25 eggs.ini --- a/eggs.ini Mon Nov 09 16:15:52 2009 -0500 +++ b/eggs.ini Mon Nov 09 16:18:39 2009 -0500 @@ -35,7 +35,6 @@ lrucache = 0.2 ;lsprof - james Mako = 0.2.5 -MyghtyUtils = 0.52 nose = 0.11.1 NoseHTML = 0.3 Paste = 1.5.1 @@ -60,7 +59,6 @@ pysqlite = _3.5.4_static MySQL_python = _5.0.67_static python_lzo = _static -flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 GeneTrack = _dev_raa786e9fc131d998e532a1aef39d108850c9e93d ; nose = .dev_r7156749efc58 @@ -86,7 +84,6 @@ GeneTrack = http://github.com/ialbert/genetrack-central/tarball/aa786e9fc131d998e532a1a… lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz Mako = http://www.makotemplates.org/downloads/Mako-0.2.5.tar.gz -MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52… nose = http://pypi.python.org/packages/source/n/nose/nose-0.11.1.tar.gz NoseHTML = http://bitbucket.org/james_taylor/nosehtml/get/c46a54d569ae.bz2 Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz

1 0

[hg] galaxy 2993: Fixed some functional tests related to the pre...
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/50c64a663d24 changeset: 2993:50c64a663d24 user: rc date: Mon Nov 09 16:40:59 2009 -0500 description: Fixed some functional tests related to the previous commit diffstat: test/base/twilltestcase.py | 6 +++++- test/functional/test_forms_and_requests.py | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diffs (28 lines): diff -r 8f47f31eb196 -r 50c64a663d24 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Nov 09 16:29:27 2009 -0500 +++ b/test/base/twilltestcase.py Mon Nov 09 16:40:59 2009 -0500 @@ -1263,7 +1263,11 @@ self.check_page_for_string( field_value ) def submit_request( self, request_id, request_name ): self.home() - self.visit_url( "%s/requests/submit_request?id=%i" % ( self.url, request_id )) + self.visit_url( "%s/requests/list?operation=Submit&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) + def submit_request_as_admin( self, request_id, request_name ): + self.home() + self.visit_url( "%s/requests_admin/list?operation=Submit&id=%s" % ( self.url, self.security.encode_id( request_id ) )) self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) def reject_request( self, request_id, request_name ): self.home() diff -r 8f47f31eb196 -r 50c64a663d24 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Mon Nov 09 16:29:27 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Mon Nov 09 16:40:59 2009 -0500 @@ -274,7 +274,7 @@ # add samples to this request self.add_samples( request_two.id, request_two.name, samples ) # submit the request - self.submit_request( request_two.id, request_two.name ) + self.submit_request_as_admin( request_two.id, request_two.name ) sa_session.refresh( request_two ) # check if the request is showing in the 'submitted' filter self.home()

1 0

[hg] galaxy 2992: code cleanup.. removed unused methods
by Greg Von Kuster 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8f47f31eb196 changeset: 2992:8f47f31eb196 user: rc date: Mon Nov 09 16:29:27 2009 -0500 description: code cleanup.. removed unused methods diffstat: lib/galaxy/web/controllers/requests.py | 39 ------------------- lib/galaxy/web/controllers/requests_admin.py | 38 ------------------- 2 files changed, 0 insertions(+), 77 deletions(-) diffs (97 lines): diff -r 4e1101dc2f25 -r 8f47f31eb196 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Nov 09 16:18:39 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Mon Nov 09 16:29:27 2009 -0500 @@ -838,45 +838,6 @@ **kwd) ) @web.expose @web.require_login( "create/submit sequencing requests" ) - def submit_request(self, trans, **kwd): - params = util.Params( kwd ) - try: - id = int(params.get('id', False)) - request = trans.sa_session.query( trans.app.model.Request ).get( id ) - except: - msg = "Invalid request ID" - log.warn( msg ) - return trans.response.send_redirect( web.url_for( controller='requests', - action='list', - status='error', - message=msg, - **kwd) ) - msg = self.__validate(trans, request) - if msg: - return trans.response.send_redirect( web.url_for( controller='requests', - action='edit', - messagetype = 'error', - msg=msg, - request_id=request.id, - show='True') ) - # get the new state - new_state = request.type.states[0] - for s in request.samples: - event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') - event.flush() - # change request's submitted field - request.state = request.states.SUBMITTED - request.flush() - kwd['id'] = trans.security.encode_id(request.id) - kwd['status'] = 'done' - kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name - return trans.response.send_redirect( web.url_for( controller='requests', - action='list', - show_filter=trans.app.model.Request.states.SUBMITTED, - **kwd) ) - - @web.expose - @web.require_login( "create/submit sequencing requests" ) def show_events(self, trans, **kwd): params = util.Params( kwd ) try: diff -r 4e1101dc2f25 -r 8f47f31eb196 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Nov 09 16:18:39 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Nov 09 16:29:27 2009 -0500 @@ -658,44 +658,6 @@ **new_kwd) ) elif params.get('refresh', False) == 'true': return self.__edit_request(trans, request.id, **kwd) - @web.expose - @web.require_admin - def submit_request(self, trans, **kwd): - params = util.Params( kwd ) - try: - id = int(params.get('id', False)) - request = trans.sa_session.query( trans.app.model.Request ).get( id ) - except: - msg = "Invalid request ID" - log.warn( msg ) - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - message=msg, - **kwd) ) - msg = self.__validate(trans, request) - if msg: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='edit', - messagetype='error', - msg=msg, - request_id=request.id, - show='True') ) - # get the new state - new_state = request.type.states[0] - for s in request.samples: - event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') - event.flush() - # change request's submitted field - request.state = request.states.SUBMITTED - request.flush() - kwd['id'] = trans.security.encode_id(request.id) - kwd['status'] = 'done' - kwd['message'] = 'The request <b>%s</b> has been submitted.' % request.name - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - show_filter=trans.app.model.Request.states.SUBMITTED, - **kwd) ) def __reject_request(self, trans, id): try: request = trans.sa_session.query( trans.app.model.Request ).get( id )

1 0

[hg] galaxy 2986: Removing unused files.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4576ebdab5c9 changeset: 2986:4576ebdab5c9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 14:49:44 2009 -0500 description: Removing unused files. diffstat: templates/grid.mako | 232 ---------------------------------------------- templates/my_data.mako | 13 -- 2 files changed, 0 insertions(+), 245 deletions(-) diffs (253 lines): diff -r cc3e5d4538db -r 4576ebdab5c9 templates/grid.mako --- a/templates/grid.mako Mon Nov 09 14:07:16 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,232 +0,0 @@ -<%! -def inherit(context): - if context.get('use_panels'): - return '/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">${grid.title}</%def> - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -<div class="grid-header"> - <h2>${grid.title}</h2> - - %if grid.global_actions: - <ul class="manage-table-actions"> - %for action in grid.global_actions: - <li> - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> - </li> - %endfor - </ul> - %endif - - %if grid.standard_filters: - <span class="title">Filter:</span> - %for i, filter in enumerate( grid.standard_filters ): - %if i > 0: - <span>|</span> - %endif - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endfor - %endif -</div> - -<form action="${url()}" method="post" > - <table class="grid"> - <thead> - <tr> - %if grid.has_multiple_item_operations: - <th></th> - %endif - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody> - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## Item selection column - %if grid.has_multiple_item_operations: - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - %endif - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - # Button class - if href and extra: - cls = "menubutton split" - elif extra: - cls = "menubutton" - else: - cls = "" - %> - %if href: - <td><div class="${cls}"><a class="label" href="${href}">${v|h}${extra}</a></div></td> - %else: - <td><div class="${cls}">${v}${extra}</div></td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <% - target = "" - if operation.target: - target = "target='" + operation.target + "'" - %> - <a class="action-button" ${target} href="${url( **operation.get_url_args( item ) )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - %if grid.has_multiple_item_operations: - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected items: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> - %endif - </table> -</form> diff -r cc3e5d4538db -r 4576ebdab5c9 templates/my_data.mako --- a/templates/my_data.mako Mon Nov 09 14:07:16 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -<%inherit file="/base.mako"/> - -<%def name="stylesheets()"> - ${h.css( "base" )} -</%def> - -<h2>Available Galaxy Data</h2> - -<ul> - <li><a href='${h.url_for( controller='history', action='list' )}'>Histories</li> - <li><a href='${h.url_for( controller='dataset', action='list' )}'>Datasets</li> -</ul> -

1 0

[hg] galaxy 2988: Fix error message displayed when setting metad...
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/62adea4325d7 changeset: 2988:62adea4325d7 user: dan date: Mon Nov 09 15:33:38 2009 -0500 description: Fix error message displayed when setting metadata_externally. e.g: Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored diffstat: scripts/set_metadata.py | 3 +++ 1 files changed, 3 insertions(+), 0 deletions(-) diffs (26 lines): diff -r ef0b9956f7d7 -r 62adea4325d7 scripts/set_metadata.py --- a/scripts/set_metadata.py Mon Nov 09 14:56:21 2009 -0500 +++ b/scripts/set_metadata.py Mon Nov 09 15:33:38 2009 -0500 @@ -8,6 +8,7 @@ import logging logging.basicConfig() +log = logging.getLogger( __name__ ) import os, sys, cPickle assert sys.version_info[:2] >= ( 2, 4 ) @@ -24,6 +25,7 @@ galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid from galaxy.util import stringify_dictionary_keys +from sqlalchemy.orm import clear_mappers def __main__(): file_path = sys.argv.pop( 1 ) @@ -48,5 +50,6 @@ simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded except Exception, e: simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow + clear_mappers() __main__()

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[hg] galaxy 2987: Bug fix.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ef0b9956f7d7 changeset: 2987:ef0b9956f7d7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 14:56:21 2009 -0500 description: Bug fix. diffstat: templates/grid_base.mako | 20 ++++++++++---------- 1 files changed, 10 insertions(+), 10 deletions(-) diffs (44 lines): diff -r 4576ebdab5c9 -r ef0b9956f7d7 templates/grid_base.mako --- a/templates/grid_base.mako Mon Nov 09 14:49:44 2009 -0500 +++ b/templates/grid_base.mako Mon Nov 09 14:56:21 2009 -0500 @@ -296,6 +296,14 @@ </tbody> <tfoot> ## Row for navigating among pages. + <% + # Mapping between item class and plural term for item. + items_plural = "items" + if grid.model_class == History: + items_plural = "histories" + elif grid.model_class == HistoryDatasetAssociation: + items_plural = "datasets" + %> %if num_pages > 1: <tr> <td></td> @@ -328,7 +336,7 @@ </select> ## Show all link. <% args = { "page" : "all" } %> - <span>| <a href="${url( args )}">Show all histories on one page</a></span> + <span>| <a href="${url( args )}">Show all ${items_plural} on one page</a></span> </td> </tr> %endif @@ -336,15 +344,7 @@ ## Grid operations. <td></td> <td colspan="100"> - <% - # Mapping between item class and plural term for item. - plural = "items" - if grid.model_class == History: - plural = "histories" - elif grid.model_class == HistoryDatasetAssociation: - plural = "datasets" - %> - For <span class="grid-selected-count"></span> selected ${plural}: + For <span class="grid-selected-count"></span> selected ${items_plural}: %for operation in grid.operations: %if operation.allow_multiple: <input type="submit" name="operation" value="${operation.label}" class="action-button">

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