- galaxy-dev - lists.galaxyproject.org

large files
by Juan Perin 10 Nov '09

10 Nov '09

Uploading files through the browser, in our case, is ultimately unnecessary or inefficient. The data we get will be on the same machine hosting Galaxy. I'd like to be able to move data into a users workspace within the browser without having to use the browser. This is especially the case for very large FASTQ files that we're getting from NGS experiments. Is there a way to do this? I'm not finding much documentation on this matter, and it would greatly increase the utility of Galaxy for us. Thanks! Juan Perin

2 1

Samtools configuration
by juan perin 10 Nov '09

10 Nov '09

Hi again, I'm now stuck trying to get the samtools app's to work. I've finally gotten the bwa and bowtie tools to run an alignment, but my attempts to convert the resulting sam file to bam, using sam_to_bam fails. The error I get in the browser is: An error occurred running this job: *No sequences are available for 'hg18', request them by reporting this error.* The error, (after searching through the output for the command), seemed to suggest that I was missing an 'egg': This was the output: python /home/perin/galaxy-dist/tools/samtools/sam_to_bam.py --input1=/home/perin/galaxy-dist/database/files/000/dataset_70.dat --dbkey=hg18 --ref_file="None" --output1=/home/perin/galaxy-dist/database/files/000/dataset_72.dat --index_dir=/home/perin/galaxy-dist/tool-data Traceback (most recent call last): File "/home/perin/galaxy-dist/tools/samtools/sam_to_bam.py", line 17, in ? from galaxy import eggs ImportError: No module named galaxy I'm guessing I'm either missing a config parameter that tells samtools how to work, or that I need to scramble another egg. Not sure, however, and was hoping for some help. I can't seem to find anything on the web. Thanks in advance. Juan Perin

5 9

RPy dependency and paths
by SHAUN WEBB 10 Nov '09

10 Nov '09

Hi, we are trying to install a local version of Galaxy on a computing cluster using sge but there are a few issues with dependencies and setting paths. For instance we can get gsummary.py to run on the command line by manually setting PYTHONPATH to the RPy area, however within Galaxy the following error is returned: File "/exports/work/biology_cell_galaxy/galaxy/tools/stats/gsummary.py", line 4, in ? from rpy import * ImportError: No module named rpy Is there a preferred way to set the PYTHONPATH environment variable? I see references to it in setup_paths.sh, but I'm not sure when/if this gets run. It appears that the PYTHONPATH is ignored by setup.sh and by run.sh. run.sh calls python with environment disabled (-E). Even with -E removed the PYTHONPATH appears not to get through. The error is the same on the command line with PYTHONPATH undefined. It is clear the problem is getting Galaxy to respect the PYTHONPATH. Any help would be greatly appreciated. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

3 2

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

2 1

[hg] galaxy 2995: Incorporate latest grid features into managing...
by Greg Von Kuster 10 Nov '09

10 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>

1 0

[hg] galaxy 2994: Make pages grid compatible with new grid frame...
by Greg Von Kuster 10 Nov '09

10 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 10 Nov '09

10 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 2992: code cleanup.. removed unused methods
by Greg Von Kuster 10 Nov '09

10 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 2993: Fixed some functional tests related to the pre...
by Greg Von Kuster 10 Nov '09

10 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 2991: remove unused MyghtyUtils egg
by Greg Von Kuster 10 Nov '09

10 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