- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3615: Fix unicode bug for large files. Fixes #244
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/61f1556d6e88 changeset: 3615:61f1556d6e88 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Apr 06 12:10:20 2010 -0400 description: Fix unicode bug for large files. Fixes #244 diffstat: templates/dataset/large_file.mako | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (10 lines): diff -r 44366a1123b0 -r 61f1556d6e88 templates/dataset/large_file.mako --- a/templates/dataset/large_file.mako Tue Apr 06 09:24:33 2010 -0400 +++ b/templates/dataset/large_file.mako Tue Apr 06 12:10:20 2010 -0400 @@ -7,5 +7,5 @@ </div> <pre> -${ truncated_data | h } +${ unicode( truncated_data, 'utf-8' ) | h } </pre>

1 0

[hg] galaxy 3614: lims: delete/undelete request bug fixed. all s...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/44366a1123b0 changeset: 3614:44366a1123b0 user: rc date: Tue Apr 06 09:24:33 2010 -0400 description: lims: delete/undelete request bug fixed. all samples are also deleted when a request is deleted. diffstat: lib/galaxy/web/controllers/requests.py | 8 ++++++++ lib/galaxy/web/controllers/requests_admin.py | 8 ++++++++ 2 files changed, 16 insertions(+), 0 deletions(-) diffs (50 lines): diff -r 6f7528445c64 -r 44366a1123b0 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Apr 05 15:11:04 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Tue Apr 06 09:24:33 2010 -0400 @@ -924,6 +924,10 @@ else: request.deleted = True trans.sa_session.add( request ) + # delete all the samples belonging to this request + for s in request.samples: + s.deleted = True + trans.sa_session.add( s ) trans.sa_session.flush() if not len(delete_failed): message = '%i request(s) has been deleted.' % len(id_list) @@ -951,6 +955,10 @@ **kwd) ) request.deleted = False trans.sa_session.add( request ) + # undelete all the samples belonging to this request + for s in request.samples: + s.deleted = False + trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests', action='list', diff -r 6f7528445c64 -r 44366a1123b0 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Apr 05 15:11:04 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Apr 06 09:24:33 2010 -0400 @@ -385,6 +385,10 @@ **kwd) ) request.deleted = True trans.sa_session.add( request ) + # delete all the samples belonging to this request + for s in request.samples: + s.deleted = True + trans.sa_session.add( s ) trans.sa_session.flush() message = '%i request(s) has been deleted.' % len(id_list) status = 'done' @@ -407,6 +411,10 @@ **kwd) ) request.deleted = False trans.sa_session.add( request ) + # undelete all the samples belonging to this request + for s in request.samples: + s.deleted = False + trans.sa_session.add( s ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list',

1 0

[hg] galaxy 3613: trackster: don't allow adding of datasets in e...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6f7528445c64 changeset: 3613:6f7528445c64 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Apr 05 15:11:04 2010 -0400 description: trackster: don't allow adding of datasets in error state diffstat: lib/galaxy/web/controllers/tracks.py | 10 ++++++---- 1 files changed, 6 insertions(+), 4 deletions(-) diffs (23 lines): diff -r 7bdc5202c67e -r 6f7528445c64 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Mon Apr 05 14:15:19 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Apr 05 15:11:04 2010 -0400 @@ -61,13 +61,15 @@ grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ), grids.GridColumn( "Filetype", key="extension" ), ] + + def build_initial_query( self, session ): + return session.query( self.model_class ).join( model.History.table).join( model.Dataset.table ) def apply_default_filter( self, trans, query, **kwargs ): if self.available_tracks is None: self.available_tracks = trans.app.datatypes_registry.get_available_tracks() - return query.select_from( model.HistoryDatasetAssociation.table \ - .join( model.History.table ) ) \ - .filter( model.History.user == trans.user ) \ - .filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) + return query.filter( model.History.user == trans.user ) \ + .filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \ + .filter( model.Dataset.state != "error") class TracksController( BaseController ): """

1 0

[hg] galaxy 3612: merged to 3610:23fb19105d96
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7bdc5202c67e changeset: 3612:7bdc5202c67e user: fubar: ross Lazarus at gmail period com date: Mon Apr 05 14:15:19 2010 -0400 description: merged to 3610:23fb19105d96 diffstat: lib/galaxy/model/__init__.py | 4 +- lib/galaxy/tools/actions/__init__.py | 13 + lib/galaxy/web/controllers/admin.py | 205 +--- lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/forms.py | 100 +- lib/galaxy/web/controllers/history.py | 7 +- lib/galaxy/web/controllers/library.py | 16 +- lib/galaxy/web/controllers/library_admin.py | 46 +- lib/galaxy/web/controllers/library_common.py | 548 +++++++------- lib/galaxy/web/controllers/requests.py | 164 ++-- lib/galaxy/web/controllers/requests_admin.py | 298 +++--- lib/galaxy/web/controllers/root.py | 32 +- lib/galaxy/web/controllers/user.py | 442 ++++------ lib/galaxy/web/framework/__init__.py | 11 +- static/images/fugue/plus-white.png | 0 static/june_2007_style/base.css.tmpl | 6 + static/june_2007_style/blue/base.css | 2 +- static/scripts/galaxy.base.js | 87 +- static/scripts/packed/galaxy.base.js | 2 +- templates/admin/dataset_security/group/group.mako | 4 +- templates/admin/dataset_security/group/group_create.mako | 4 +- templates/admin/dataset_security/group/group_rename.mako | 4 +- templates/admin/dataset_security/role/role.mako | 4 +- templates/admin/dataset_security/role/role_create.mako | 4 +- templates/admin/dataset_security/role/role_rename.mako | 4 +- templates/admin/forms/create_form.mako | 4 +- templates/admin/forms/edit_form.mako | 4 +- templates/admin/forms/show_form_read_only.mako | 4 +- templates/admin/jobs.mako | 4 +- templates/admin/library/new_library.mako | 4 +- templates/admin/memdump.mako | 4 +- templates/admin/reload_tool.mako | 4 +- templates/admin/requests/add_states.mako | 4 +- templates/admin/requests/create_request_type.mako | 4 +- templates/admin/requests/edit_request.mako | 4 +- templates/admin/requests/edit_request_type.mako | 4 +- templates/admin/requests/events.mako | 4 +- templates/admin/requests/get_data.mako | 4 +- templates/admin/requests/new_request.mako | 4 +- templates/admin/requests/reject.mako | 4 +- templates/admin/requests/show_request.mako | 4 +- templates/admin/requests/view_request_type.mako | 4 +- templates/admin/samples/bar_codes.mako | 4 +- templates/admin/samples/events.mako | 4 +- templates/admin/user/create.mako | 43 - templates/admin/user/reset_password.mako | 4 +- templates/admin/user/user.mako | 4 +- templates/dataset/edit_attributes.mako | 10 +- templates/history/sharing.mako | 4 +- templates/library/browse_libraries.mako | 4 +- templates/library/common/browse_library.mako | 5 +- templates/library/common/common.mako | 2 +- templates/library/common/edit_template.mako | 4 +- templates/library/common/folder_info.mako | 4 +- templates/library/common/folder_permissions.mako | 4 +- templates/library/common/ldda_edit_info.mako | 11 +- templates/library/common/ldda_info.mako | 4 +- templates/library/common/ldda_permissions.mako | 4 +- templates/library/common/library_dataset_info.mako | 4 +- templates/library/common/library_dataset_permissions.mako | 4 +- templates/library/common/library_info.mako | 4 +- templates/library/common/library_permissions.mako | 4 +- templates/library/common/new_folder.mako | 4 +- templates/library/common/select_template.mako | 4 +- templates/library/common/upload.mako | 4 +- templates/mobile/manage_library.mako | 4 +- templates/requests/edit_request.mako | 4 +- templates/requests/events.mako | 4 +- templates/requests/new_request.mako | 4 +- templates/requests/show_data.mako | 4 +- templates/requests/show_request.mako | 4 +- templates/root/index.mako | 3 - templates/sample/sample_events.mako | 4 +- templates/tool_form.mako | 5 +- templates/user/edit_address.mako | 4 +- templates/user/index.mako | 16 +- templates/user/info.mako | 4 +- templates/user/login.mako | 53 +- templates/user/logout.mako | 6 + templates/user/new_address.mako | 4 +- templates/user/register.mako | 122 +- templates/user/reset_password.mako | 4 +- templates/webapps/galaxy/base_panels.mako | 10 +- test/base/twilltestcase.py | 82 +- test/functional/test_admin_features.py | 25 +- 85 files changed, 1264 insertions(+), 1322 deletions(-) diffs (truncated from 5963 to 3000 lines): diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/model/__init__.py Mon Apr 05 14:15:19 2010 -0400 @@ -1348,8 +1348,8 @@ # Since we do not have contents, set checkbox value to False value = False else: - # Set other field types to empty string - value = '' + # Set other field types to the default value of the field + value = field['default'] # create the field widget field_widget = eval( field[ 'type' ] )( field_name ) if field[ 'type' ] == 'TextField': diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Mon Apr 05 14:15:19 2010 -0400 @@ -107,14 +107,27 @@ Makes a copy of input dictionary from_dict such that all values that are dictionaries result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle other complex types ( e.g., lists, etc ), but not sure... + Yes, we need to handle lists (and now are)... """ copy_from_dict = {} for key, value in from_dict.items(): if type( value ).__name__ == 'dict': copy_from_dict[ key ] = make_dict_copy( value ) + elif isinstance( value, list ): + copy_from_dict[ key ] = make_list_copy( value ) else: copy_from_dict[ key ] = value return copy_from_dict + def make_list_copy( from_list ): + new_list = [] + for value in from_list: + if isinstance( value, dict ): + new_list.append( make_dict_copy( value ) ) + elif isinstance( value, list ): + new_list.append( make_list_copy( value ) ) + else: + new_list.append( value ) + return new_list def wrap_values( inputs, input_values ): # Wrap tool inputs as necessary for input in inputs.itervalues(): diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Apr 05 14:15:19 2010 -0400 @@ -263,9 +263,9 @@ @web.require_admin def index( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - return trans.fill_template( '/admin/index.mako', msg=msg, messagetype=messagetype ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/admin/index.mako', message=message, status=status ) @web.expose @web.require_admin def center( self, trans, **kwd ): @@ -274,17 +274,17 @@ @web.require_admin def reload_tool( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, msg=msg, messagetype=messagetype ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, message=message, status=status ) @web.expose @web.require_admin def tool_reload( self, trans, tool_version=None, **kwd ): params = util.Params( kwd ) tool_id = params.tool_id self.app.toolbox.reload( tool_id ) - msg = 'Reloaded tool: ' + tool_id - return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, msg=msg, messagetype='done' ) + message = 'Reloaded tool: ' + tool_id + return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, message=message, status='done' ) # Galaxy Role Stuff @web.expose @@ -312,8 +312,8 @@ @web.require_admin def create_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_role_button', False ): name = util.restore_text( params.name ) description = util.restore_text( params.description ) @@ -321,9 +321,9 @@ in_groups = util.listify( params.get( 'in_groups', [] ) ) create_group_for_role = params.get( 'create_group_for_role', 'no' ) if not name or not description: - msg = "Enter a valid name and a description" + message = "Enter a valid name and a description" elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first(): - msg = "A role with that name already exists" + message = "A role with that name already exists" else: # Create the role role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN ) @@ -340,13 +340,13 @@ # Create the group group = trans.app.model.Group( name=name ) trans.sa_session.add( group ) - msg = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ + message = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ ( 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 ) ) + message = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) trans.sa_session.flush() - 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' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='roles', message=util.sanitize_text( message ), status='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='create_role', message=util.sanitize_text( message ), status='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ .filter( trans.app.model.User.table.c.deleted==False ) \ @@ -362,39 +362,39 @@ out_users=out_users, in_groups=[], out_groups=out_groups, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def rename_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) role = get_role( trans, params.id ) if params.get( 'rename_role_button', False ): old_name = role.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) if not new_name: - msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) + message = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status='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/role_rename.mako', role=role, msg=msg, messagetype='error' ) + message = 'A role with that name already exists' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status='error' ) else: role.name = new_name role.description = new_description trans.sa_session.add( role ) trans.sa_session.flush() - msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) - 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 ) + message = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status=status ) @web.expose @web.require_admin def manage_users_and_groups_for_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) 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 ) ] @@ -414,8 +414,8 @@ in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] 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', message=util.sanitize_text( msg ), status=messagetype ) ) + message = "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', message=util.sanitize_text( message ), status=status ) ) in_users = [] out_users = [] in_groups = [] @@ -467,8 +467,8 @@ in_groups=in_groups, out_groups=out_groups, library_dataset_actions=library_dataset_actions, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def mark_role_deleted( self, trans, **kwd ): @@ -554,39 +554,39 @@ @web.require_admin def rename_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) group = get_group( trans, params.id ) if params.get( 'rename_group_button', False ): 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/group_rename.mako', group=group, msg=msg, messagetype='error' ) + message = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status='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/group_rename.mako', group=group, msg=msg, messagetype='error' ) + message = 'A group with that name already exists' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status='error' ) else: group.name = new_name trans.sa_session.add( group ) trans.sa_session.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/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) + message = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status=status ) @web.expose @web.require_admin def manage_users_and_roles_for_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) 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', message=util.sanitize_text( msg ), status=messagetype ) ) + message += "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', message=util.sanitize_text( message ), status=status ) ) in_roles = [] out_roles = [] in_users = [] @@ -605,29 +605,29 @@ in_users.append( ( user.id, user.email ) ) 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 ) ) + message += '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/group.mako', group=group, in_roles=in_roles, out_roles=out_roles, in_users=in_users, out_users=out_users, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def create_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_group_button', False ): name = util.restore_text( params.name ) in_users = util.listify( params.get( 'in_users', [] ) ) in_roles = util.listify( params.get( 'in_roles', [] ) ) if not name: - msg = "Enter a valid name" + message = "Enter a valid name" elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): - msg = "A group with that name already exists" + message = "A group with that name already exists" else: # Create the group group = trans.app.model.Group( name=name ) @@ -643,9 +643,9 @@ gra = trans.app.model.GroupRoleAssociation( group, role ) trans.sa_session.add( gra ) trans.sa_session.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', 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' ) ) + message = "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', message=util.sanitize_text( message ), status='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='create_group', message=util.sanitize_text( message ), status='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ .filter( trans.app.model.User.table.c.deleted==False ) \ @@ -661,8 +661,8 @@ out_users=out_users, in_roles=[], out_roles=out_roles, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def mark_group_deleted( self, trans, **kwd ): @@ -671,8 +671,8 @@ group.deleted = True trans.sa_session.add( group ) trans.sa_session.flush() - msg = "Group '%s' has been marked as deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) + message = "Group '%s' has been marked as deleted." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def undelete_group( self, trans, **kwd ): @@ -681,8 +681,8 @@ group.deleted = False trans.sa_session.add( group ) trans.sa_session.flush() - msg = "Group '%s' has been marked as not deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) + message = "Group '%s' has been marked as not deleted." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def purge_group( self, trans, **kwd ): @@ -692,8 +692,8 @@ 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', message=util.sanitize_text( msg ), status='error' ) ) + message = "Group '%s' has not been deleted, so it cannot be purged." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='error' ) ) # Delete UserGroupAssociations for uga in group.users: trans.sa_session.delete( uga ) @@ -711,69 +711,6 @@ return trans.response.send_redirect( web.url_for( controller='user', action='create', admin_view=True ) ) - email = '' - password = '' - confirm = '' - subscribe = False - email_filter = kwargs.get( 'email_filter', 'A' ) - if 'user_create_button' in kwargs: - message = '' - status = '' - email = kwargs.get( 'email' , None ) - password = kwargs.get( 'password', None ) - confirm = kwargs.get( 'confirm', None ) - subscribe = kwargs.get( 'subscribe', None ) - if not email: - message = 'Enter a valid email address' - elif not password: - message = 'Enter a valid password' - elif not confirm: - message = 'Confirm the password' - elif len( email ) == 0 or "@" not in email or "." not in email: - message = 'Enter a real email address' - elif len( email) > 255: - message = 'Email address exceeds maximum allowable length' - elif trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first(): - message = 'User with that email already exists' - elif len( password ) < 6: - message = 'Use a password of at least 6 characters' - elif password != confirm: - message = 'Passwords do not match' - if message: - trans.response.send_redirect( web.url_for( controller='admin', - action='users', - email_filter=email_filter, - message=util.sanitize_text( message ), - status='error' ) ) - else: - user = trans.app.model.User( email=email ) - user.set_password_cleartext( password ) - if trans.app.config.use_remote_user: - user.external = True - trans.sa_session.add( user ) - trans.sa_session.flush() - trans.app.security_agent.create_private_user_role( user ) - trans.app.security_agent.user_set_default_permissions( user, history=False, dataset=False ) - message = 'Created new user account (%s)' % user.email - status = 'done' - #subscribe user to email list - if subscribe: - mail = os.popen( "%s -t" % trans.app.config.sendmail_path, 'w' ) - mail.write( "To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list." % ( trans.app.config.mailing_join_addr, email ) ) - if mail.close(): - message + ". However, subscribing to the mailing list has failed." - status = 'error' - trans.response.send_redirect( web.url_for( controller='admin', - action='users', - email_filter=email_filter, - message=util.sanitize_text( message ), - status=status ) ) - return trans.fill_template( '/admin/user/create.mako', - email_filter=email_filter, - email=email, - password=password, - confirm=confirm, - subscribe=subscribe ) @web.expose @web.require_admin def reset_user_password( self, trans, **kwd ): @@ -916,7 +853,7 @@ status='done' ) ) @web.expose @web.require_admin - def users( self, trans, **kwargs ): + def users( self, trans, **kwargs ): if 'operation' in kwargs: operation = kwargs['operation'].lower() if operation == "roles": @@ -1035,8 +972,8 @@ out_roles=out_roles, in_groups=in_groups, out_groups=out_groups, - msg=message, - messagetype=status ) + message=message, + status=status ) @web.expose @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): @@ -1083,11 +1020,11 @@ def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, **kwd ): deleted = [] msg = None - messagetype = None + status = None job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' - messagetype = 'error' + status = 'error' elif job_ids: if stop_msg[-1] not in string.punctuation: stop_msg += '.' @@ -1100,7 +1037,7 @@ msg += 's' msg += ' for deletion: ' msg += ', '.join( deleted ) - messagetype = 'done' + status = 'done' cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, @@ -1116,7 +1053,7 @@ last_updated[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) - return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype ) + return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, status = status ) ## ---- Utility methods ------------------------------------------------------- diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Mon Apr 05 14:15:19 2010 -0400 @@ -352,7 +352,7 @@ return open( data.file_name ) if os.path.exists( data.file_name ): max_peek_size = 1000000 # 1 MB - if preview and os.stat( data.file_name ).st_size > max_peek_size: + if preview and (not isinstance(data.datatype, datatypes.binary.Binary)) and os.stat( data.file_name ).st_size > max_peek_size: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", truncated_data = open( data.file_name ).read(max_peek_size), diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon Apr 05 14:15:19 2010 -0400 @@ -72,7 +72,8 @@ 'required': False, 'type': BaseField.form_field_types()[0], 'selectlist': [], - 'layout': 'none' } + 'layout': 'none', + 'default': '' } forms_grid = FormsGrid() @web.expose @@ -101,8 +102,8 @@ except: return trans.response.send_redirect( web.url_for( controller='forms', action='manage', - msg='Invalid form', - messagetype='error' ) ) + message='Invalid form', + status='error' ) ) return trans.fill_template( '/admin/forms/show_form_read_only.mako', form=fdc.latest_form ) def __form_types_widget(self, trans, selected='none'): @@ -126,16 +127,16 @@ @web.require_admin def new( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) self.__imported_from_file = False if params.get( 'create_form_button', False ): - fd, msg = self.__save_form( trans, fdc_id=None, **kwd ) + fd, message = self.__save_form( trans, fdc_id=None, **kwd ) if not fd: return trans.response.send_redirect( web.url_for( controller='forms', action='new', - msg=msg, - messagetype='error', + message=message, + status='error', name=util.restore_text( params.get( 'name', '' ) ), description=util.restore_text( params.get( 'description', '' ) ) )) self.__get_saved_form( fd ) @@ -157,8 +158,8 @@ ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', inputs=inputs, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) def __delete( self, trans, **kwd ): id_list = util.listify( kwd['id'] ) delete_failed = [] @@ -204,8 +205,8 @@ edit_template() method in the library_common controller. ''' params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( trans.security.decode_id(kwd['id']) ) except: @@ -218,22 +219,22 @@ # Save changes # if params.get( 'save_changes_button', False ): - fd_new, msg = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd ) + fd_new, message = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd ) # if validation error encountered while saving the form, show the # unsaved form, with the error message if not fd_new: current_form = self.__get_form( trans, **kwd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype='error', response_redirect=response_redirect, **kwd ) + message=message, status='error', response_redirect=response_redirect, **kwd ) # everything went fine. form saved successfully. Show the saved form or redirect # to response_redirect if appropriate. if response_redirect: return trans.response.send_redirect( response_redirect ) fd = fd_new current_form = self.__get_saved_form( fd ) - msg = "The form '%s' has been updated with the changes." % fd.name + message = "The form '%s' has been updated with the changes." % fd.name return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add a layout grid # @@ -242,7 +243,7 @@ current_form['layout'].append('') # show the form again return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Delete a layout grid # @@ -251,7 +252,7 @@ index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1 del current_form['layout'][index] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add a field # @@ -260,7 +261,7 @@ current_form['fields'].append( self.empty_field ) # show the form again with one empty field return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Delete a field # @@ -270,33 +271,33 @@ index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1 del current_form['fields'][index] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add SelectField option # elif 'Add' in kwd.values(): - return self.__add_selectbox_option(trans, fd, msg, messagetype, response_redirect=response_redirect, **kwd) + return self.__add_selectbox_option(trans, fd, message, status, response_redirect=response_redirect, **kwd) # # Remove SelectField option # elif 'Remove' in kwd.values(): - return self.__remove_selectbox_option(trans, fd, msg, messagetype, response_redirect=response_redirect, **kwd) + return self.__remove_selectbox_option(trans, fd, message, status, response_redirect=response_redirect, **kwd) # # Refresh page # elif params.get( 'refresh', False ): current_form = self.__get_form( trans, **kwd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Show the form for editing # else: current_form = self.__get_saved_form( fd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) - def __add_selectbox_option( self, trans, fd, msg, messagetype, response_redirect=None, **kwd ): + def __add_selectbox_option( self, trans, fd, message, status, response_redirect=None, **kwd ): ''' This method adds a selectbox option. The kwd dict searched for the field index which needs to be removed @@ -312,13 +313,13 @@ if index == -1: # something wrong happened return self.__show( trans=trans, form=fd, current_form=current_form, - msg='Error in adding selectfield option', - messagetype='error', response_redirect=response_redirect, **kwd ) + message='Error in adding selectfield option', + status='error', response_redirect=response_redirect, **kwd ) # add an empty option current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) - def __remove_selectbox_option( self, trans, fd, msg, messagetype, response_redirect=None, **kwd ): + message=message, status=status, response_redirect=response_redirect, **kwd ) + def __remove_selectbox_option( self, trans, fd, message, status, response_redirect=None, **kwd ): ''' This method removes a selectbox option. The kwd dict searched for the field index and option index which needs to be removed @@ -335,12 +336,12 @@ if option == -1: # something wrong happened return self.__show( trans=trans, form=fd, current_form=current_form, - msg='Error in removing selectfield option', - messagetype='error', response_redirect=response_redirect, **kwd ) + message='Error in removing selectfield option', + status='error', response_redirect=response_redirect, **kwd ) # remove the option del current_form[ 'fields' ][ index ][ 'selectlist' ][ option ] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) def __get_field(self, index, **kwd): @@ -354,6 +355,7 @@ required = params.get( 'field_required_%i' % index, False ) field_type = util.restore_text( params.get( 'field_type_%i' % index, '' ) ) layout = params.get( 'field_layout_%i' % index, '' ) + default = params.get( 'field_default_%i' % index, '' ) if field_type == 'SelectField': selectlist = self.__get_selectbox_options(index, **kwd) return {'label': name, @@ -362,13 +364,15 @@ 'required': required, 'type': field_type, 'selectlist': selectlist, - 'layout': layout } + 'layout': layout, + 'default': default } return {'label': name, 'helptext': helptext, 'visible': True, 'required': required, 'type': field_type, - 'layout': layout} + 'layout': layout, + 'default': default} def __get_selectbox_options(self, index, **kwd): ''' This method gets all the options entered by the user for field when @@ -453,7 +457,8 @@ 'required': row[3], 'type': row[4], 'selectlist': options, - 'layout':row[6]}) + 'layout':row[6], + 'default': row[7]}) layouts.add(row[6]) else: for row in reader: @@ -463,7 +468,8 @@ 'visible': row[2], 'required': row[3], 'type': row[4], - 'selectlist': options}) + 'selectlist': options, + 'default': row[7]}) except: return trans.response.send_redirect( web.url_for( controller='forms', action='new', @@ -491,9 +497,9 @@ This method saves the current form ''' # check the form for invalid inputs - flag, msg = self.__validate_form(**kwd) + flag, message = self.__validate_form(**kwd) if not flag: - return None, msg + return None, message current_form = self.__get_form( trans, **kwd ) # validate fields for field in current_form[ 'fields' ]: @@ -517,8 +523,8 @@ fdc.latest_form = fd trans.sa_session.add( fdc ) trans.sa_session.flush() - msg = "The new form named '%s' has been created. " % (fd.name) - return fd, msg + message = "The new form named '%s' has been created. " % (fd.name) + return fd, message class FieldUI(object): def __init__(self, trans, layout_grids, index, field=None, field_type=None, form_type=None): @@ -549,7 +555,9 @@ if layout_grids: self.layout_selectbox = SelectField('field_layout_'+str(index)) for index, grid_name in enumerate(layout_grids): - self.layout_selectbox.add_option("%i. %s" %(index+1, grid_name), index) + self.layout_selectbox.add_option("%i. %s" %(index+1, grid_name), index) + # default value + self.default = TextField('field_default_'+str(index), 40, '') if field: self.fill(trans, field, field_type, form_type) def fill(self, trans, field, field_type=None, form_type=None): @@ -557,6 +565,8 @@ self.label.value = field['label'] # helptext self.helptext.value = field['helptext'] + # default value + self.default.value = field['default'] # type self.fieldtype = SelectField('field_type_'+str(self.index), refresh_on_change=True, @@ -608,18 +618,20 @@ return [( 'Label', self.label ), ( 'Help text', self.helptext ), ( 'Type', self.fieldtype, self.selectbox_options), + ( 'Default value', self.default ), ( '', self.required), ( 'Select the grid layout to place this field', self.layout_selectbox)] return [( 'Label', self.label ), ( 'Help text', self.helptext ), ( 'Type', self.fieldtype, self.selectbox_options), + ( 'Default value', self.default ), ( '', self.required)] def __repr__(self): return str(self.index)+'.'+self.label def label(self): return str(self.index)+'.'+self.label - def __show( self, trans, form, current_form, msg='', messagetype='done', response_redirect=None, **kwd ): + def __show( self, trans, form, current_form, message='', status='done', response_redirect=None, **kwd ): ''' This method displays the form and any of the changes made to it, The empty_form param allows for this method to simulate clicking @@ -650,8 +662,8 @@ field_details=field_details, form=form, field_types=BaseField.form_field_types(), - msg=msg, - messagetype=messagetype, + message=message, + status=status, current_form_type=current_form[ 'type' ], layout_grids=form_layout, response_redirect=response_redirect ) diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Mon Apr 05 14:15:19 2010 -0400 @@ -648,8 +648,11 @@ elif 'unshare_user' in kwargs: user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwargs[ 'unshare_user' ] ) ) if not user: - msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) - return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' ) + message = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) + return trans.fill_template( 'history/sharing.mako', + histories=histories, + message=message, + status='error' ) husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=user, history=history ).all() if husas: for husa in husas: diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/library.py Mon Apr 05 14:15:19 2010 -0400 @@ -10,17 +10,17 @@ @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) return trans.fill_template( "/library/index.mako", default_action=params.get( 'default_action', None ), - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def browse_libraries( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) current_user_roles = trans.get_current_user_roles() all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted==False ) \ @@ -32,5 +32,5 @@ return trans.fill_template( '/library/browse_libraries.mako', libraries=authorized_libraries, default_action=params.get( 'default_action', None ), - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Apr 05 14:15:19 2010 -0400 @@ -92,8 +92,8 @@ @web.require_admin def create_library( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_library_button', False ): name = util.restore_text( params.get( 'name', 'No name' ) ) description = util.restore_text( params.get( 'description', '' ) ) @@ -105,14 +105,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - msg = "The new library named '%s' has been created" % library.name + message = "The new library named '%s' has been created" % library.name return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( library.id ), - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) + message=util.sanitize_text( message ), + status='done' ) ) + return trans.fill_template( '/admin/library/new_library.mako', message=message, status=status ) @web.expose @web.require_admin def purge_library( self, trans, **kwd ): @@ -146,20 +146,20 @@ trans.sa_session.add( library_folder ) trans.sa_session.flush() if not library.deleted: - msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) + message = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', - message=util.sanitize_text( msg ), + message=util.sanitize_text( message ), status='error' ) ) else: purge_folder( library.root_folder ) library.purged = True trans.sa_session.add( library ) trans.sa_session.flush() - msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name + message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', - message=util.sanitize_text( msg ), + message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin @@ -176,8 +176,8 @@ 'folder': trans.app.model.LibraryFolder, 'library_dataset': trans.app.model.LibraryDataset } if item_type not in item_types: - msg = 'Bad item_type specified: %s' % str( item_type ) - messagetype = 'error' + message = 'Bad item_type specified: %s' % str( item_type ) + status = 'error' else: if item_type == 'library_dataset': item_desc = 'Dataset' @@ -187,18 +187,18 @@ library_item.deleted = True trans.sa_session.add( library_item ) trans.sa_session.flush() - msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) - messagetype = 'done' + message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) + status = 'done' if item_type == 'library': - return self.browse_libraries( trans, message=msg, status=messagetype ) + return self.browse_libraries( trans, message=message, status=status ) else: return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=library_id, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) ) + message=message, + status=status ) ) @web.expose @web.require_admin def undelete_library_item( self, trans, library_id, item_id, item_type, **kwd ): @@ -208,7 +208,7 @@ 'folder': trans.app.model.LibraryFolder, 'library_dataset': trans.app.model.LibraryDataset } if item_type not in item_types: - msg = 'Bad item_type specified: %s' % str( item_type ) + message = 'Bad item_type specified: %s' % str( item_type ) status = ERROR else: if item_type == 'library_dataset': @@ -217,21 +217,21 @@ item_desc = item_type.capitalize() library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) if library_item.purged: - msg = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) + message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) status = ERROR else: library_item.deleted = False trans.sa_session.add( library_item ) trans.sa_session.flush() - msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) + message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) status = SUCCESS if item_type == 'library': - return self.browse_libraries( trans, message=msg, status=status ) + return self.browse_libraries( trans, message=message, status=status ) else: return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=library_id, show_deleted=show_deleted, - msg=msg, - messagetype=status ) ) + message=message, + status=status ) ) diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Mon Apr 05 14:15:19 2010 -0400 @@ -79,18 +79,18 @@ @web.expose def browse_library( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) library_id = params.get( 'id', None ) if not library_id: # To handle bots - msg = "You must specify a library id." - messagetype = 'error' + message = "You must specify a library id." + status = 'error' library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) if not library: # To handle bots - msg = "Invalid library id ( %s )." % str( library_id ) - messagetype = 'error' + message = "Invalid library id ( %s )." % str( library_id ) + status = 'error' else: # If use_panels is True, the library is being accessed via an external link # which did not originate from within the Galaxy instance, and the library will @@ -100,12 +100,12 @@ created_ldda_ids = params.get( 'created_ldda_ids', '' ) hidden_folder_ids = util.listify( params.get( 'hidden_folder_ids', '' ) ) current_user_roles = trans.get_current_user_roles() - if created_ldda_ids and not msg: - msg = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \ + if created_ldda_ids and not message: + message = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \ ( len( created_ldda_ids.split( ',' ) ), library.name ) - msg += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the " - msg += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." - messagetype = "info" + message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the " + message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." + status = "info" return trans.fill_template( '/library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, @@ -115,19 +115,19 @@ show_deleted=show_deleted, comptypes=comptypes, current_user_roles=current_user_roles, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) return trans.response.send_redirect( web.url_for( use_panels=use_panels, controller=cntrller, action='browse_libraries', default_action=params.get( 'default_action', None ), - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) @web.expose def library_info( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -140,8 +140,8 @@ old_name = library.name new_name = util.restore_text( params.get( 'name', 'No name' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype='error' + message = 'Enter a valid name' + status='error' else: new_description = util.restore_text( params.get( 'description', '' ) ) new_synopsis = util.restore_text( params.get( 'synopsis', '' ) ) @@ -155,15 +155,15 @@ library.root_folder.description = new_description trans.sa_session.add_all( ( library, library.root_folder ) ) trans.sa_session.flush() - msg = "The information has been updated." + message = "The information has been updated." return trans.response.send_redirect( web.url_for( controller='library_common', action='library_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) return trans.fill_template( '/library/common/library_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -173,13 +173,13 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def library_permissions( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -195,15 +195,15 @@ trans.sa_session.refresh( library ) # Copy the permissions to the root folder trans.app.security_agent.copy_library_permissions( library, library.root_folder ) - msg = "Permissions updated for library '%s'" % library.name + message = "Permissions updated for library '%s'" % library.name return trans.response.send_redirect( web.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_permissions.mako', cntrller=cntrller, @@ -212,26 +212,26 @@ current_user_roles=current_user_roles, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) parent_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( parent_id ) ) if not parent_folder: - msg = "Invalid parent folder id (%s) specified" % str( parent_id ) + message = "Invalid parent folder id (%s) specified" % str( parent_id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if params.get( 'new_folder_button', False ): new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), description=util.restore_text( params.description ) ) @@ -252,8 +252,8 @@ widgets = new_folder.get_template_widgets( trans ) if info_association: current_user_roles = trans.get_current_user_roles() - msg = "The new folder named '%s' has been added to the data library. " % new_folder.name - msg += "Additional information about this folder may be added using the inherited template." + message = "The new folder named '%s' has been added to the data library. " % new_folder.name + message += "Additional information about this folder may be added using the inherited template." return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -264,18 +264,18 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype='done' ) + message=message, + status='done' ) # If not inheritable info_association, redirect to the library. - msg = "The new folder named '%s' has been added to the data library." % new_folder.name + message = "The new folder named '%s' has been added to the data library." % new_folder.name return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) # We do not render any template widgets on creation pages since saving the info_association # cannot occur before the associated item is saved. return trans.fill_template( '/library/common/new_folder.mako', @@ -284,13 +284,13 @@ library_id=library_id, folder=parent_folder, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def folder_info( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) @@ -306,18 +306,18 @@ new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) if not new_name: - msg = 'Enter a valid name' - messagetype='error' + message = 'Enter a valid name' + status='error' else: folder.name = new_name folder.description = new_description trans.sa_session.add( folder ) trans.sa_session.flush() - msg = "The information has been updated." - messagetype='done' + message = "The information has been updated." + status='done' else: - msg = "You are not authorized to edit this folder" - messagetype='error' + message = "You are not authorized to edit this folder" + status='error' return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -328,26 +328,26 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def folder_permissions( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) if not folder: - msg = "Invalid folder specified, id: %s" % str( id ) + message = "Invalid folder specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() if params.get( 'update_roles_button', False ): # The user clicked the Save button on the 'Associate With Roles' form @@ -361,11 +361,11 @@ permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles trans.app.security_agent.set_all_library_permissions( folder, permissions ) trans.sa_session.refresh( folder ) - msg = 'Permissions updated for folder %s' % folder.name - messagetype='done' + message = 'Permissions updated for folder %s' % folder.name + status='done' else: - msg = "You are not authorized to manage permissions on this folder" - messagetype = "error" + message = "You are not authorized to manage permissions on this folder" + status = "error" return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, @@ -373,8 +373,8 @@ id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # If the library is public all roles are legitimate, but if the library is restricted, only those # roles associated with the LIBRARY_ACCESS permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -387,26 +387,26 @@ current_user_roles=current_user_roles, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) + message = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): dbkey = dbkey[0] @@ -424,14 +424,14 @@ if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) trans.sa_session.flush() - msg = "Data type changed for library dataset '%s'" % ldda.name - messagetype = 'done' + message = "Data type changed for library dataset '%s'" % ldda.name + status = 'done' else: - msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - messagetype = 'error' + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to change the data type of dataset '%s'" % ldda.name + status = 'error' elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): @@ -440,8 +440,8 @@ new_info = util.restore_text( params.get( 'info', '' ) ) new_message = util.restore_text( params.get( 'message', '' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' + message = 'Enter a valid name' + status = 'error' else: ldda.name = new_name ldda.info = new_info @@ -459,11 +459,11 @@ ldda.metadata.dbkey = dbkey ldda.datatype.after_setting_metadata( ldda ) trans.sa_session.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' + message = 'Attributes updated for library dataset %s' % ldda.name + status = 'done' else: - msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name + status = 'error' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): @@ -475,11 +475,11 @@ ldda.datatype.set_meta( ldda ) ldda.datatype.after_setting_metadata( ldda ) trans.sa_session.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' + message = 'Attributes updated for library dataset %s' % ldda.name + status = 'done' else: - msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name + status = 'error' if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability @@ -499,26 +499,26 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) + message = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) # See if we have any associated templates widgets = [] @@ -536,13 +536,13 @@ current_user_roles=current_user_roles, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ids = util.listify( id ) @@ -550,15 +550,15 @@ for id in [ trans.security.decode_id( id ) for id in ids ]: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( id ) if ldda is None: - msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) + message = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) lddas.append( ldda ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) # If access to the dataset is restricted, then use the roles associated with the DATASET_ACCESS permission to @@ -577,7 +577,7 @@ if cntrller=='library_admin' or ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \ trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ): a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action ) - permissions, in_roles, error, msg = \ + permissions, in_roles, error, message = \ trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **kwd ) for ldda in lddas: # Set the DATASET permissions on the Dataset. @@ -601,13 +601,13 @@ trans.app.security_agent.set_all_library_permissions( ldda, permissions ) trans.sa_session.refresh( ldda ) if error: - messagetype = 'error' + status = 'error' else: - msg = 'Permissions have been updated on %d datasets.' % len( lddas ) - messagetype= 'done' + message = 'Permissions have been updated on %d datasets.' % len( lddas ) + status= 'done' else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to change the permissions of dataset '%s'" % ldda.name + status = 'error' return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, use_panels=use_panels, @@ -615,8 +615,8 @@ library_id=library_id, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) if len( ids ) > 1: # Ensure that the permissions across all library items are identical, otherwise we can't update them together. check_list = [] @@ -634,15 +634,15 @@ if not check_list: check_list = permissions if permissions != check_list: - msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' + message = 'The datasets you selected do not have identical permissions, so they can not be updated together' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) # Display permission form, permissions will be updated for all lddas simultaneously. return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, @@ -651,13 +651,13 @@ library_id=library_id, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) deleted = util.string_as_bool( params.get( 'deleted', False ) ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) dbkey = params.get( 'dbkey', '?' ) @@ -694,10 +694,10 @@ error = None if roles: vars = dict( DATASET_ACCESS_in=roles ) - permissions, in_roles, error, msg = \ + permissions, in_roles, error, message = \ trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **vars ) if error: - messagetype = 'error' + status = 'error' trans.response.send_redirect( web.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, @@ -706,8 +706,8 @@ replace_id=replace_id, upload_option=upload_option, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) else: # See if we have any inherited templates, but do not inherit contents. @@ -731,16 +731,16 @@ ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] created_ldda_ids=",".join( ldda_id_list ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder - msg = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) else: - msg = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) if cntrller == 'library_admin': - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." - messagetype='done' + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + status='done' else: # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need # to check one of them to see if the current user can manage permissions on them. @@ -749,7 +749,7 @@ if replace_dataset: default_action = '' else: - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: default_action = 'add' @@ -760,21 +760,21 @@ default_action=default_action, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) else: created_ldda_ids = '' - msg = "Upload failed" - messagetype='error' + message = "Upload failed" + status='error' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) if info_association and info_association.inheritable: @@ -819,8 +819,8 @@ history=history, widgets=widgets, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ): # Set up the traditional tool state/params tool_id = 'upload1' @@ -836,8 +836,8 @@ params = util.Params( kwd ) # is this filetoolparam safe? show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) server_dir = util.restore_text( params.get( 'server_dir', '' ) ) if replace_dataset not in [ None, 'None' ]: replace_id = trans.security.encode_id( replace_dataset.id ) @@ -860,21 +860,21 @@ else: full_dir = os.path.join( import_dir, trans.user.email, server_dir ) if import_dir: - msg = 'Select a directory' + message = 'Select a directory' else: - msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc + message = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc # Proceed with (mostly) regular upload processing precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller ) if upload_option == 'upload_file': tool_params = upload_common.persist_uploads( tool_params ) uploaded_datasets = upload_common.get_uploaded_datasets( trans, cntrller, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) elif upload_option == 'upload_directory': - uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, message = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, message ) elif upload_option == 'upload_paths': - uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, message = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, err_redirect, message ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if upload_option == 'upload_file' and not uploaded_datasets: - msg = 'Select a file, enter a URL or enter text' + message = 'Select a file, enter a URL or enter text' err_redirect = True if err_redirect: trans.response.send_redirect( web.url_for( controller='library_common', @@ -885,8 +885,8 @@ replace_id=replace_id, upload_option=upload_option, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) @@ -909,7 +909,7 @@ trans.sa_session.add( uploaded_dataset.data ) trans.sa_session.flush() return uploaded_dataset - def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): + def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, message ): files = [] try: for entry in os.listdir( full_dir ): @@ -925,23 +925,23 @@ if os.path.isfile( path ): files.append( path ) except Exception, e: - msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) + message = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message if not files: - msg = "The directory '%s' contains no valid files" % full_dir + message = "The directory '%s' contains no valid files" % full_dir err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message uploaded_datasets = [] for file in files: name = os.path.basename( file ) uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, file, 'server_dir', library_bunch ) ) return uploaded_datasets, None, None - def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, err_redirect, msg ): + def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, err_redirect, message ): if params.get( 'filesystem_paths', '' ) == '': - msg = "No paths entered in the upload form" + message = "No paths entered in the upload form" err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message preserve_dirs = True if params.get( 'dont_preserve_dirs', False ): preserve_dirs = False @@ -974,16 +974,16 @@ library_bunch, in_folder ) ) if bad_paths: - msg = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) + message = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message return uploaded_datasets, None, None @web.expose def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ): params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) replace_id = params.get( 'replace_id', None ) if replace_id: @@ -994,14 +994,14 @@ history = trans.get_history() trans.sa_session.refresh( history ) if not history.active_datasets: - msg = 'Your current history is empty' + message = 'Your current history is empty' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if params.get( 'add_history_datasets_to_library_button', False ): hda_ids = util.listify( hda_ids ) if hda_ids: @@ -1021,28 +1021,28 @@ # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda ) else: - msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) + message = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if created_ldda_ids: created_ldda_ids = created_ldda_ids.lstrip( ',' ) ldda_id_list = created_ldda_ids.split( ',' ) total_added = len( ldda_id_list ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder - msg = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) else: - msg = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) if cntrller == 'library_admin': - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." else: # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need # to check one of them to see if the current user can manage permissions on them. @@ -1052,7 +1052,7 @@ if replace_dataset: default_action = '' else: - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: default_action = 'add' @@ -1062,11 +1062,11 @@ id=library_id, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) else: - msg = 'Select at least one dataset from the list of active datasets in your current history' - messagetype = 'error' + message = 'Select at least one dataset from the list of active datasets in your current history' + status = 'error' last_used_build = folder.genome_build upload_option = params.get( 'upload_option', 'import_from_history' ) # Send list of data formats to the form so the "extension" select list can be populated dynamically @@ -1091,8 +1091,8 @@ history=history, widgets=[], show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ): """Catches the dataset id and displays file contents as directed""" @@ -1101,8 +1101,8 @@ use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) - messagetype = 'error' + message = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) + status = 'error' else: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) ext = ldda.extension @@ -1123,33 +1123,33 @@ try: return open( ldda.file_name ) except: - msg = 'This dataset contains no content' + message = 'This dataset contains no content' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) @web.expose def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( id ) ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + message = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() # See if we have any associated templates widgets = [] @@ -1163,18 +1163,18 @@ new_name = util.restore_text( params.get( 'name', '' ) ) new_info = util.restore_text( params.get( 'info', '' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' + message = 'Enter a valid name' + status = 'error' else: library_dataset.name = new_name library_dataset.info = new_info trans.sa_session.add( library_dataset ) trans.sa_session.flush() - msg = "The information has been updated." - messagetype = 'done' + message = "The information has been updated." + status = 'done' else: - msg = "You are not authorized to change the attributes of this dataset" - messagetype = "error" + message = "You are not authorized to change the attributes of this dataset" + status = "error" return trans.fill_template( '/library/common/library_dataset_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -1185,26 +1185,26 @@ inherited=inherited, widgets=widgets, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( id ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + message = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() if params.get( 'update_roles_button', False ): if cntrller == 'library_admin' or trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ): @@ -1223,11 +1223,11 @@ # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions ) trans.sa_session.refresh( library_dataset.library_dataset_dataset_association ) - msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name - messagetype = 'done' + message = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name + status = 'done' else: - msg = "You are not authorized to managed the permissions of this dataset" - messagetype = "error" + message = "You are not authorized to managed the permissions of this dataset" + status = "error" library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_dataset_permissions.mako', @@ -1238,53 +1238,53 @@ roles=roles, current_user_roles=current_user_roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ): # Perform an action on a list of library datasets. params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) action = params.get( 'do_action', None ) if not ldda_ids: - msg = "You must select at least one dataset" - messagetype = 'error' + message = "You must select at least one dataset" + status = 'error' elif not action: - msg = "You must select an action to perform on selected datasets" - messagetype = 'error' + message = "You must select an action to perform on selected datasets" + status = 'error' else: ldda_ids = util.listify( ldda_ids ) if action == 'import_to_history' or action == 'add': history = trans.get_history() if history is None: # Must be a bot sending a request without having a history. - msg = "You do not have a current history" + message = "You do not have a current history" return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) total_imported_lddas = 0 - msg = '' - messagetype = 'done' + message = '' + status = 'done' for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - msg += "Cannot import dataset (%s) since it's state is (%s). " % ( ldda.name, ldda.dataset.state ) - messagetype = 'error' + message += "Cannot import dataset (%s) since it's state is (%s). " % ( ldda.name, ldda.dataset.state ) + status = 'error' elif ldda.dataset.state in [ 'ok', 'error' ]: hda = ldda.to_history_dataset_association( target_history=history, add_to_history=True ) total_imported_lddas += 1 if total_imported_lddas: trans.sa_session.add( history ) trans.sa_session.flush() - msg += "%i dataset(s) have been imported into your history. " % total_imported_lddas + message += "%i dataset(s) have been imported into your history. " % total_imported_lddas elif action == 'manage_permissions': # We need the folder containing the LibraryDatasetDatasetAssociation(s) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_ids[0] ) ) @@ -1296,8 +1296,8 @@ folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=",".join( ldda_ids ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) elif action == 'delete': for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) @@ -1307,7 +1307,7 @@ ld.deleted = True trans.sa_session.add( ld ) trans.sa_session.flush() - msg = "The selected datasets have been removed from this data library" + message = "The selected datasets have been removed from this data library" elif action in ['zip','tgz','tbz']: error = False killme = string.punctuation + string.whitespace @@ -1332,13 +1332,13 @@ except (OSError, zipfile.BadZipFile): error = True log.exception( "Unable to create archive for download" ) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' except: error = True log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0]) - msg = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - messagetype = 'error' + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' if not error: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) seen = [] @@ -1374,8 +1374,8 @@ except IOError: error = True log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' continue flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths for fpath in flist: @@ -1387,8 +1387,8 @@ except IOError: error = True log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' continue else: # simple case try: @@ -1396,8 +1396,8 @@ except IOError: error = True log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' if not error: if action == 'zip': archive.close() @@ -1409,8 +1409,8 @@ except OSError: error = True log.exception( "Unable to remove temporary library download archive and directory" ) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' if not error: trans.response.set_content_type( "application/x-zip-compressed" ) trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext) @@ -1422,7 +1422,7 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream else: # unknown action - msg = '### unknown action = %s in act_on_multiple_datasets' % action + message = '### unknown action = %s in act_on_multiple_datasets' % action return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', @@ -1430,8 +1430,8 @@ use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) def get_item_and_stuff( self, trans, item_type, library_id, folder_id, ldda_id ): # Return an item, description, action and an id based on the item_type. if item_type == 'library': @@ -1450,14 +1450,14 @@ action = 'ldda_edit_info' id = ldda_id else: - msg = "Invalid library item type ( %s )" % str( item_type ) + message = "Invalid library item type ( %s )" % str( item_type ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) return item, item_desc, action, id @web.expose def add_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): @@ -1466,19 +1466,19 @@ filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) if not forms: - msg = "There are no forms on which to base the template, so create a form and then add the template." + message = "There are no forms on which to base the template, so create a form and then add the template." trans.response.send_redirect( web.url_for( controller='forms', action='new', - msg=msg, - messagetype='done', + message=message, + status='done', form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) ) else: params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) + message = util.restore_text( params.get( 'message', '' ) ) action = '' - messagetype = params.get( 'messagetype', 'done' ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # If the inheritable checkbox is checked, the param will be in the request inheritable = CheckboxField.is_checked( params.get( 'inheritable', '' ) ) @@ -1497,7 +1497,7 @@ assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, form, form_values ) trans.sa_session.add( assoc ) trans.sa_session.flush() - msg = 'A template based on the form "%s" has been added to this %s.' % ( form.name, item_desc ) + message = 'A template based on the form "%s" has been added to this %s.' % ( form.name, item_desc ) trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1506,11 +1506,11 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=msg, - messagetype='done' ) ) + message=message, + status='done' ) ) else: - msg = "Select a form on which to base the template." - messagetype = "error" + message = "Select a form on which to base the template." + status = "error" def generate_template_stuff( trans, forms, form_id ): # Returns the following: # - a list of template ids @@ -1555,22 +1555,22 @@ template_select_list=template_select_list, inheritable_checked=inheritable, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) info_association, inherited = item.get_info_association( restrict=True ) if info_association: if info_association.inheritable: - msg = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc else: - msg = "The template for this %s will now be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will now be inherited to contained folders and datasets." % item_desc info_association.inheritable = not( info_association.inheritable ) trans.sa_session.add( info_association ) trans.sa_session.flush() @@ -1582,16 +1582,16 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) @web.expose def edit_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, edited=False, **kwd ): # Edit the template itself, keeping existing field contents, if any. params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # An info_association must exist at this point info_association, inherited = item.get_info_association( restrict=True ) @@ -1605,7 +1605,7 @@ info_association.template = fdc.latest_form trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = "The template for this %s has been updated with your changes." % item_desc + message = "The template for this %s has been updated with your changes." % item_desc return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1614,8 +1614,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) # "template" is a FormDefinition, so since we're changing it, we need to use the latest version of it. vars = dict( id=trans.security.encode_id( template.form_definition_current_id ), response_redirect=web.url_for( controller='library_common', @@ -1634,8 +1634,8 @@ params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # Save updated template field contents field_contents = [] @@ -1681,7 +1681,7 @@ info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, template, form_values ) trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = 'The information has been updated.' + message = 'The information has been updated.' return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1690,8 +1690,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) @web.expose def delete_template( self, trans, cntrller, item_type, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): # Only adding a new template to a library or folder is currently allowed. Editing an existing template is @@ -1699,19 +1699,19 @@ params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) info_association, inherited = item.get_info_association() if not info_association: - msg = "There is no template for this %s" % item_type - messagetype = 'error' + message = "There is no template for this %s" % item_type + status = 'error' else: info_association.deleted = True trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = 'The template for this %s has been deleted.' % item_type - messagetype = 'done' + message = 'The template for this %s has been deleted.' % item_type + status = 'done' return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1720,8 +1720,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # ---- Utility methods ------------------------------------------------------- diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Mon Apr 05 14:15:19 2010 -0400 @@ -164,7 +164,7 @@ elif operation == "events": return self.__request_events( trans, **kwd ) # if there are one or more requests that has been rejected by the admin - # recently, then show a msg as a reminder to the user + # recently, then show a message as a reminder to the user rlist = trans.sa_session.query( trans.app.model.Request ) \ .filter( trans.app.model.Request.table.c.deleted==False ) \ .filter( trans.app.model.Request.table.c.user_id==trans.user.id ) @@ -182,12 +182,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = request.events @@ -238,8 +238,8 @@ return request_details def __show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) add_sample = params.get('add_sample', False) try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) @@ -279,7 +279,7 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False' ) ), - msg=msg, messagetype=messagetype ) + message=message, status=status ) def __library_widgets(self, trans, user, sample_index, libraries, sample=None, **kwd): ''' This method creates the data library & folder selectbox for creating & @@ -424,8 +424,8 @@ @web.require_login( "create/submit sequencing requests" ) def show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -503,28 +503,28 @@ edit_mode=edit_mode) elif params.get('save_samples_button', False) == 'Save': # check for duplicate sample names - msg = '' + message = '' for index in range(len(current_samples)-len(request.samples)): sample_index = index + len(request.samples) sample_name = current_samples[sample_index]['name'] if not sample_name.strip(): - msg = 'Please enter the name of sample number %i' % sample_index + message = 'Please enter the name of sample number %i' % sample_index break count = 0 for i in range(len(current_samples)): if sample_name == current_samples[i]['name']: count = count + 1 if count > 1: - msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) break - if msg: + if message: return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), current_samples = current_samples, sample_copy=self.__copy_sample(current_samples), details=details, edit_mode=edit_mode, - messagetype='error', msg=msg) + status='error', message=message) # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): @@ -542,18 +542,18 @@ trans.sa_session.add( s ) trans.sa_session.flush() else: - messagetype = 'done' - msg = 'Changes made to the sample(s) are saved. ' + status = 'done' + message = 'Changes made to the sample(s) are saved. ' for sample_index in range(len(current_samples)): sample = request.samples[sample_index] sample.name = current_samples[sample_index]['name'] sample.library = current_samples[sample_index]['library'] sample.folder = current_samples[sample_index]['folder'] if request.submitted(): - bc_msg = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) - if bc_msg: - messagetype = 'error' - msg += bc_msg + bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) + if bc_message: + status = 'error' + message += bc_message else: sample.bar_code = current_samples[sample_index]['barcode'] trans.sa_session.add( sample ) @@ -566,8 +566,8 @@ action='list', operation='show_request', id=trans.security.encode_id(request.id), - messagetype=messagetype, - msg=msg )) + status=status, + message=message )) elif params.get('edit_samples_button', False) == 'Edit samples': edit_mode = 'True' return trans.fill_template( '/requests/show_request.mako', @@ -589,15 +589,15 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details=details, libraries=libraries, - edit_mode=edit_mode, messagetype=messagetype, msg=msg) + edit_mode=edit_mode, status=status, message=message) @web.expose @web.require_login( "create/submit sequencing requests" ) def delete_sample(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) ) current_samples, details, edit_mode = self.__update_samples( request, **kwd ) sample_index = int(params.get('sample_id', 0)) @@ -639,34 +639,34 @@ @web.require_login( "create/submit sequencing requests" ) def new(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get('select_request_type', False) == 'True': return trans.fill_template( '/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) elif params.get('create', False) == 'True': if params.get('create_request_button', False) == 'Save' \ or params.get('create_request_samples_button', False) == 'Add samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' + message = 'Please enter the <b>Name</b> of the request' kwd['create'] = 'True' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + kwd['status'] = 'error' + kwd['message'] = message kwd['create_request_button'] = None kwd['create_request_samples_button'] = None return trans.response.send_redirect( web.url_for( controller='requests', action='new', **kwd) ) request = self.__save_request(trans, None, **kwd) - msg = 'The new request named <b>%s</b> has been created' % request.name + message = 'The new request named <b>%s</b> has been created' % request.name if params.get('create_request_button', False) == 'Save': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - message=msg , + message=message , status='done') ) elif params.get('create_request_samples_button', False) == 'Add samples': new_kwd = {} @@ -675,8 +675,8 @@ new_kwd['add_sample'] = True return trans.response.send_redirect( web.url_for( controller='requests', action='list', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) else: return self.__show_request_form(trans, **kwd) @@ -684,16 +684,16 @@ return self.__show_request_form(trans, **kwd) def __show_request_form(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) except: return trans.fill_template( '/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) form_values = None select_request_type = self.__select_request_type(trans, request_type.id) # list of widgets to be rendered on the request form @@ -711,8 +711,8 @@ select_request_type=select_request_type, request_type=request_type, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) def __validate(self, trans, request): ''' Validates the request entered by the user @@ -723,14 +723,14 @@ if field['required'] == 'required' and request.values.content[index] in ['', None]: empty_fields.append(field['label']) if empty_fields: - msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name for ef in empty_fields: - msg = msg + '<b>' +ef + '</b><br/>' + message = message + '<b>' +ef + '</b><br/>' return trans.response.send_redirect( web.url_for( controller='requests', action='list', operation='edit', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) )) # now check the required fields of all the samples of this request for s in request.samples: @@ -738,14 +738,14 @@ if field['required'] == 'required' and s.values.content[index] in ['', None]: empty_fields.append((s.name, field['label'])) if empty_fields: - msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name for sname, ef in empty_fields: - msg = msg + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname) + message = message + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname) return trans.response.send_redirect( web.url_for( controller='requests', action='list', operation='show_request', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) )) def __save_request(self, trans, request=None, **kwd): ''' @@ -823,8 +823,8 @@ @web.require_login( "create/submit sequencing requests" ) def edit(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -839,19 +839,19 @@ or params.get('edit_samples_button', False) == 'Edit samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + message = 'Please enter the <b>Name</b> of the request' + kwd['status'] = 'error' + kwd['message'] = message kwd['show'] = 'True' return trans.response.send_redirect( web.url_for( controller='requests', action='edit', **kwd) ) request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name + message = 'The changes made to the request named %s has been saved' % request.name if params.get('save_changes_request_button', False) == 'Save changes': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - message=msg , + message=message , status='done') ) elif params.get('edit_samples_button', False) == 'Edit samples': new_kwd = {} @@ -859,8 +859,8 @@ new_kwd['edit_samples_button'] = 'Edit samples' return trans.response.send_redirect( web.url_for( controller='requests', action='show_request', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) elif params.get('refresh', False) == 'true': return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) @@ -869,15 +869,15 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg) ) + message=message) ) params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) select_request_type = self.__select_request_type(trans, request.type.id) # list of widgets to be rendered on the request form widgets = [] @@ -901,8 +901,8 @@ request_type=request.type, request=request, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) return self.__show_request_form(trans) def __delete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) @@ -911,12 +911,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) # a request cannot be deleted once its submitted if not request.new(): @@ -926,28 +926,28 @@ trans.sa_session.add( request ) trans.sa_session.flush() if not len(delete_failed): - msg = '%i request(s) has been deleted.' % len(id_list) + message = '%i request(s) has been deleted.' % len(id_list) status = 'done' else: - msg = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed), + message = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed), len(delete_failed), str(delete_failed)) status = 'warning' return trans.response.send_redirect( web.url_for( controller='requests', action='list', status=status, - message=msg) ) + message=message) ) def __undelete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) for id in id_list: try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = False trans.sa_session.add( request ) @@ -960,12 +960,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) # check if all the required request and its sample fields have been filled self.__validate(trans, request) @@ -994,11 +994,11 @@ sample_id = int(params.get('sample_id', False)) sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id ) except: - msg = "Invalid sample ID" + message = "Invalid sample ID" return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = sample.events @@ -1015,8 +1015,8 @@ @web.require_login( "create/submit sequencing requests" ) def show_datatx_page( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) ) except: diff -r fabf48e747ae -r 7bdc5202c67e lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Apr 05 14:14:09 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Apr 05 14:15:19 2010 -0400 @@ -289,8 +289,8 @@ @web.require_admin def edit(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -305,19 +305,19 @@ or params.get('edit_samples_button', False) == 'Edit samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + message = 'Please enter the <b>Name</b> of the request' + kwd['status'] = 'error' + kwd['message'] = message kwd['show'] = 'True' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='edit', **kwd) ) request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name + message = 'The changes made to the request named %s has been saved' % request.name if params.get('save_changes_request_button', False) == 'Save changes': return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', - message=msg , + message=message , status='done') ) elif params.get('edit_samples_button', False) == 'Edit samples': new_kwd = {} @@ -325,8 +325,8 @@ new_kwd['edit_samples_button'] = 'Edit samples' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_request', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) elif params.get('refresh', False) == 'true': return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) @@ -335,15 +335,15 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg) ) + message=message) ) params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) select_request_type = self.__select_request_type(trans, request.type.id) # list of widgets to be rendered on the request form widgets = [] @@ -367,8 +367,8 @@ request_type=request.type, request=request, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) return self.__show_request_form(trans) def __delete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) @@ -376,34 +376,34 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = True trans.sa_session.add( request ) trans.sa_session.flush() - msg = '%i request(s) has been deleted.' % len(id_list) + message = '%i request(s) has been deleted.' % len(id_list) status = 'done' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status=status, - message=msg) ) + message=message) ) def __undelete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) for id in id_list: try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = False trans.sa_session.add( request ) @@ -416,20 +416,20 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) - msg = self.__validate(trans, request) - if msg: + message = self.__validate(trans, request) + if message: return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', operation='edit', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) ) ) # change the request state to 'Submitted' if request.user.email is not trans.user: @@ -456,12 +456,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) return trans.fill_template( '/admin/requests/reject.mako', request=request) @@ -477,18 +477,18 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) # validate if not params.get('comment', ''): return trans.fill_template( '/admin/requests/reject.mako', - request=request, messagetype='error', - msg='A comment is required for rejecting a request.') + request=request, status='error', + message='A comment is required for rejecting a request.') # create an event with state 'Rejected' for this request comments = util.restore_text( params.comment ) event = trans.app.model.RequestEvent(request, request.states.REJECTED, comments) @@ -503,12 +503,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = request.events @@ -547,35 +547,35 @@ @web.require_admin def new(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get('select_request_type', False) == 'True': return trans.fill_template( '/admin/requests/new_request.mako',

1 0

[hg] galaxy 3611: Fixes to rgQC top table ordering and add offse...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/fabf48e747ae changeset: 3611:fabf48e747ae user: fubar: ross Lazarus at gmail period com date: Mon Apr 05 14:14:09 2010 -0400 description: Fixes to rgQC top table ordering and add offset so can use rgManQQ to make plots Fixes to rgManQQ to handle unsorted data - now sorts before manhattan plot diffstat: test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 4 +- test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls | 27 ++- test-data/rgtestouts/rgQC/ldp_tinywga.log | 4 +- test-data/rgtestouts/rgQC/rgQCtest1.html | 104 +++++-- test-data/rgtestouts/rgQC/tinywga.log | 4 +- test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 4 +- test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 4 +- test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 4 +- test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 4 +- tools/data_source/upload.py | 8 +- tools/rgenetics/rgManQQ.py | 9 +- tools/rgenetics/rgQC.py | 58 +--- tools/rgenetics/rgtest_one_tool.sh | 218 ++++++++++++++++++ 20 files changed, 361 insertions(+), 91 deletions(-) diffs (793 lines): diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf --- a/test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf Mon Apr 05 14:14:09 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210120) -/ModDate (D:20100325210120) +/CreationDate (D:20100405140521) +/ModDate (D:20100405140521) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls --- a/test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/MarkerDetails_rgQCtest1.xls Mon Apr 05 14:14:09 2010 -0400 @@ -1,1 +1,26 @@ -snp chrom maf a1 a2 missfrac p_hwe_all logp_hwe_all p_hwe_unaff logp_hwe_unaff N_Mendel \ No newline at end of file +snp chromosome offset maf a1 a2 missfrac p_hwe_all logp_hwe_all p_hwe_unaff logp_hwe_unaff N_Mendel +rs2283802 22 21784722 0.2593 4 2 0 0.638 0.195179 0.638 0.195179 0 +rs2267000 22 21785366 0.4259 4 2 0 1 0 1 0 0 +rs16997606 22 21794754 0.1111 1 3 0 1 0 1 0 0 +rs4820537 22 21794810 0.4444 1 3 0 0.6985 0.155834 0.6985 0.155834 0 +rs3788347 22 21797804 0.463 3 1 0 1 0 1 0 0 +rs756632 22 21799918 0.09259 4 2 0 1 0 1 0 0 +rs4820539 22 21807970 0.2778 1 3 0 0.6298 0.200797 0.6298 0.200797 0 +rs2283804 22 21820335 0.3333 1 2 0 1 0 1 0 0 +rs2267006 22 21820990 0.3333 3 1 0 1 0 1 0 0 +rs4822363 22 21821000 0.07407 4 2 0 1 0 1 0 0 +rs5751592 22 21827674 0.1667 4 2 0 1 0 1 0 0 +rs5759608 22 21832708 0.4259 2 4 0 1 0 1 0 0 +rs5759612 22 21833170 0.4259 3 1 0 1 0 1 0 0 +rs2267009 22 21860168 0.2593 3 4 0 0.638 0.195179 0.638 0.195179 0 +rs2267010 22 21864366 0.03704 3 1 0 1 0 1 0 0 +rs5759636 22 21868698 0.07407 4 2 0.025 1 0 1 0 0 +rs2071436 22 21871488 0.2593 4 2 0 0.638 0.195179 0.638 0.195179 0 +rs2267013 22 21875879 0.1111 3 1 0 1 0 1 0 0 +rs6003566 22 21889806 0.09259 3 1 0 1 0 1 0 0 +rs2256725 22 21892891 0.1111 2 1 0 1 0 1 0 0 +rs12160770 22 21892925 0.01923 1 3 0.075 1 0 1 0 0 +rs5751611 22 21896019 0.4615 2 4 0.025 0.4275 0.369064 0.4275 0.369064 0 +rs762601 22 21898858 0.3333 1 3 0 0.6657 0.176721 0.6657 0.176721 0 +rs2156921 22 21899063 0.3333 3 1 0 0.6657 0.176721 0.6657 0.176721 0 +rs4822375 22 21905642 0.3333 1 3 0 0.6657 0.176721 0.6657 0.176721 0 \ No newline at end of file diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/ldp_tinywga.log --- a/test-data/rgtestouts/rgQC/ldp_tinywga.log Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/ldp_tinywga.log Mon Apr 05 14:14:09 2010 -0400 @@ -10,7 +10,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ ldp_tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -44,5 +44,5 @@ Writing genotype bitfile to [ ldp_tinywga.bed ] Using (default) SNP-major mode -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/rgQCtest1.html --- a/test-data/rgtestouts/rgQC/rgQCtest1.html Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/rgQCtest1.html Mon Apr 05 14:14:09 2010 -0400 @@ -10,20 +10,34 @@ <body> <div class="document"> <h4> -<div>Output from Rgenetics QC report tool run at 25/03/2010 21:01:23<br> +<div>Output from Rgenetics QC report tool run at 05/04/2010 14:05:29<br> </h4> </div><div><h4>(Click any preview image to download a full sized PDF version)</h4><br><ol> <table cellpadding="5" border="0"> -<tr><td colspan="3"><a href="MarkerDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Marker QC Detail report file</a> (87 B) tab delimited</td></tr> +<tr><td colspan="3"><a href="MarkerDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Marker QC Detail report file</a> (1.4 KB) tab delimited</td></tr> <tr><td colspan="3"><a href="SubjectDetails_rgQCtest1.xls" type="application/vnd.ms-excel">Click here to download the Subject QC Detail report file</a> (1.4 KB) tab delimited</td></tr> <tr><td><a href="tinywga_All_Paged.pdf"><img src="tinywga_All_Paged-0.jpg" alt="All tinywga QC Plots joined into a single pdf" hspace="10" align="middle"> </a></td><td>All tinywga QC Plots joined into a single pdf</td><td> </td></tr> -<tr><td><a href="tinywga_All_3x3.pdf"><img src="tinywga_All_3x3.jpg" alt="All tinywga QC Plots 3 by 3 to a page" hspace="10" align="middle"> +<tr><td><a href="tinywga_All_3x3.pdf"><img src="tinywga_All_3x3-0.jpg" alt="All tinywga QC Plots 3 by 3 to a page" hspace="10" align="middle"> </a></td><td>All tinywga QC Plots 3 by 3 to a page</td><td> </td></tr> +<tr><td><a href="tinywga_logphweunaff.pdf"><img src="tinywga_logphweunaff.jpg" alt="Marker HWE" hspace="10" align="middle"> +</a></td><td>Marker HWE</td><td><a href="Ranked_Marker_HWE.xls">Worst data</a></td></tr> +<tr><td><a href="tinywga_logphweunaff_cum.pdf"><img src="tinywga_logphweunaff_cum.jpg" alt="Ranked Marker HWE" hspace="10" align="middle"> +</a></td><td>Ranked Marker HWE</td><td> </td></tr> +<tr><td><a href="QQtinywga_logphweunaff_cum.pdf"><img src="QQtinywga_logphweunaff_cum.jpg" alt="LogQQ plot Marker HWE" hspace="10" align="middle"> +</a></td><td>LogQQ plot Marker HWE</td><td> </td></tr> +<tr><td><a href="tinywga_missfrac.pdf"><img src="tinywga_missfrac.jpg" alt="Marker Missing Genotype" hspace="10" align="middle"> +</a></td><td>Marker Missing Genotype</td><td><a href="Ranked_Marker_Missing_Genotype.xls">Worst data</a></td></tr> +<tr><td><a href="tinywga_missfrac_cum.pdf"><img src="tinywga_missfrac_cum.jpg" alt="Ranked Marker Missing Genotype" hspace="10" align="middle"> +</a></td><td>Ranked Marker Missing Genotype</td><td> </td></tr> +<tr><td><a href="tinywga_maf.pdf"><img src="tinywga_maf.jpg" alt="Marker MAF" hspace="10" align="middle"> +</a></td><td>Marker MAF</td><td><a href="Ranked_Marker_MAF.xls">Worst data</a></td></tr> +<tr><td><a href="tinywga_maf_cum.pdf"><img src="tinywga_maf_cum.jpg" alt="Ranked Marker MAF" hspace="10" align="middle"> +</a></td><td>Ranked Marker MAF</td><td> </td></tr> <tr><td><a href="tinywga_fracmiss.pdf"><img src="tinywga_fracmiss.jpg" alt="Subject Missing Genotype" hspace="10" align="middle"> -</a></td><td>Subject Missing Genotype</td><td> </td></tr> +</a></td><td>Subject Missing Genotype</td><td><a href="Ranked_Subject_Missing_Genotype.xls">Worst data</a></td></tr> <tr><td><a href="tinywga_fracmiss_cum.pdf"><img src="tinywga_fracmiss_cum.jpg" alt="Ranked Subject Missing Genotype" hspace="10" align="middle"> -</a></td><td>Ranked Subject Missing Genotype</td><td><a href="Ranked_Subject_Missing_Genotype.xls">Worst data</a></td></tr> +</a></td><td>Ranked Subject Missing Genotype</td><td> </td></tr> <tr><td><a href="tinywga_s_het.pdf"><img src="tinywga_s_het.jpg" alt="Subject F Statistic" hspace="10" align="middle"> </a></td><td>Subject F Statistic</td><td> </td></tr> <tr><td><a href="tinywga_s_het_cum.pdf"><img src="tinywga_s_het_cum.jpg" alt="Ranked Subject F Statistic" hspace="10" align="middle"> @@ -35,7 +49,12 @@ <tr><td><a href="FQNormtinywga_s_het_cum.jpg">FQNormtinywga_s_het_cum.jpg</a> (30.2 KB)</td></tr> <tr><td><a href="FQNormtinywga_s_het_cum.pdf">FQNormtinywga_s_het_cum.pdf</a> (7.1 KB)</td></tr> -<tr><td><a href="MarkerDetails_rgQCtest1.xls">MarkerDetails_rgQCtest1.xls</a> (87 B)</td></tr> +<tr><td><a href="MarkerDetails_rgQCtest1.xls">MarkerDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr> +<tr><td><a href="QQtinywga_logphweunaff_cum.jpg">QQtinywga_logphweunaff_cum.jpg</a> (33.0 KB)</td></tr> +<tr><td><a href="QQtinywga_logphweunaff_cum.pdf">QQtinywga_logphweunaff_cum.pdf</a> (6.6 KB)</td></tr> +<tr><td><a href="Ranked_Marker_HWE.xls">Ranked_Marker_HWE.xls</a> (763 B)</td></tr> +<tr><td><a href="Ranked_Marker_MAF.xls">Ranked_Marker_MAF.xls</a> (564 B)</td></tr> +<tr><td><a href="Ranked_Marker_Missing_Genotype.xls">Ranked_Marker_Missing_Genotype.xls</a> (659 B)</td></tr> <tr><td><a href="Ranked_Subject_Missing_Genotype.xls">Ranked_Subject_Missing_Genotype.xls</a> (804 B)</td></tr> <tr><td><a href="SubjectDetails_rgQCtest1.xls">SubjectDetails_rgQCtest1.xls</a> (1.4 KB)</td></tr> <tr><td><a href="ldp_tinywga.bed">ldp_tinywga.bed</a> (143 B)</td></tr> @@ -55,28 +74,47 @@ <tr><td><a href="tinywga.prune.in">tinywga.prune.in</a> (140 B)</td></tr> <tr><td><a href="tinywga.prune.out">tinywga.prune.out</a> (110 B)</td></tr> <tr><td><a href="tinywga.sexcheck">tinywga.sexcheck</a> (2.5 KB)</td></tr> -<tr><td><a href="tinywga_All_3x3.jpg">tinywga_All_3x3.jpg</a> (27.6 KB)</td></tr> -<tr><td><a href="tinywga_All_3x3.pdf">tinywga_All_3x3.pdf</a> (37.4 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged-0.jpg">tinywga_All_Paged-0.jpg</a> (11.9 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged-1.jpg">tinywga_All_Paged-1.jpg</a> (29.6 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged-2.jpg">tinywga_All_Paged-2.jpg</a> (17.9 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged-3.jpg">tinywga_All_Paged-3.jpg</a> (31.4 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged-4.jpg">tinywga_All_Paged-4.jpg</a> (29.8 KB)</td></tr> -<tr><td><a href="tinywga_All_Paged.pdf">tinywga_All_Paged.pdf</a> (36.9 KB)</td></tr> +<tr><td><a href="tinywga_All_3x3-0.jpg">tinywga_All_3x3-0.jpg</a> (45.2 KB)</td></tr> +<tr><td><a href="tinywga_All_3x3-1.jpg">tinywga_All_3x3-1.jpg</a> (19.3 KB)</td></tr> +<tr><td><a href="tinywga_All_3x3.pdf">tinywga_All_3x3.pdf</a> (82.4 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-0.jpg">tinywga_All_Paged-0.jpg</a> (13.6 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-1.jpg">tinywga_All_Paged-1.jpg</a> (26.3 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-10.jpg">tinywga_All_Paged-10.jpg</a> (31.4 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-11.jpg">tinywga_All_Paged-11.jpg</a> (29.8 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-2.jpg">tinywga_All_Paged-2.jpg</a> (32.3 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-3.jpg">tinywga_All_Paged-3.jpg</a> (11.1 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-4.jpg">tinywga_All_Paged-4.jpg</a> (26.7 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-5.jpg">tinywga_All_Paged-5.jpg</a> (18.4 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-6.jpg">tinywga_All_Paged-6.jpg</a> (28.1 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-7.jpg">tinywga_All_Paged-7.jpg</a> (11.9 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-8.jpg">tinywga_All_Paged-8.jpg</a> (29.6 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged-9.jpg">tinywga_All_Paged-9.jpg</a> (17.9 KB)</td></tr> +<tr><td><a href="tinywga_All_Paged.pdf">tinywga_All_Paged.pdf</a> (81.9 KB)</td></tr> <tr><td><a href="tinywga_fracmiss.jpg">tinywga_fracmiss.jpg</a> (12.0 KB)</td></tr> <tr><td><a href="tinywga_fracmiss.pdf">tinywga_fracmiss.pdf</a> (6.4 KB)</td></tr> <tr><td><a href="tinywga_fracmiss_cum.jpg">tinywga_fracmiss_cum.jpg</a> (30.0 KB)</td></tr> <tr><td><a href="tinywga_fracmiss_cum.pdf">tinywga_fracmiss_cum.pdf</a> (7.0 KB)</td></tr> +<tr><td><a href="tinywga_logphweunaff.jpg">tinywga_logphweunaff.jpg</a> (13.6 KB)</td></tr> +<tr><td><a href="tinywga_logphweunaff.pdf">tinywga_logphweunaff.pdf</a> (5.7 KB)</td></tr> +<tr><td><a href="tinywga_logphweunaff_cum.jpg">tinywga_logphweunaff_cum.jpg</a> (26.8 KB)</td></tr> +<tr><td><a href="tinywga_logphweunaff_cum.pdf">tinywga_logphweunaff_cum.pdf</a> (5.8 KB)</td></tr> +<tr><td><a href="tinywga_maf.jpg">tinywga_maf.jpg</a> (18.5 KB)</td></tr> +<tr><td><a href="tinywga_maf.pdf">tinywga_maf.pdf</a> (6.4 KB)</td></tr> +<tr><td><a href="tinywga_maf_cum.jpg">tinywga_maf_cum.jpg</a> (28.5 KB)</td></tr> +<tr><td><a href="tinywga_maf_cum.pdf">tinywga_maf_cum.pdf</a> (6.0 KB)</td></tr> +<tr><td><a href="tinywga_missfrac.jpg">tinywga_missfrac.jpg</a> (11.1 KB)</td></tr> +<tr><td><a href="tinywga_missfrac.pdf">tinywga_missfrac.pdf</a> (5.9 KB)</td></tr> +<tr><td><a href="tinywga_missfrac_cum.jpg">tinywga_missfrac_cum.jpg</a> (27.3 KB)</td></tr> +<tr><td><a href="tinywga_missfrac_cum.pdf">tinywga_missfrac_cum.pdf</a> (5.9 KB)</td></tr> <tr><td><a href="tinywga_s_het.jpg">tinywga_s_het.jpg</a> (18.0 KB)</td></tr> <tr><td><a href="tinywga_s_het.pdf">tinywga_s_het.pdf</a> (6.8 KB)</td></tr> <tr><td><a href="tinywga_s_het_cum.jpg">tinywga_s_het_cum.jpg</a> (31.9 KB)</td></tr> <tr><td><a href="tinywga_s_het_cum.pdf">tinywga_s_het_cum.pdf</a> (7.3 KB)</td></tr> -</table><h4>QC run log contents</h4><pre>## subject reports starting at 25/03/2010 21:01:19 +</table><h4>QC run log contents</h4><pre>## subject reports starting at 05/04/2010 14:05:21 ## imissfile /opt/galaxy/test-data/rgtestouts/rgQC/tinywga.imiss contained 40 ids -### writing /opt/galaxy/test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls report with ['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat']## marker reports starting at 25/03/2010 21:01:19 -## error - no hwefile /opt/galaxy/test-data/rgtestouts/rgQC.hwe found -No /opt/galaxy/test-data/rgtestouts/rgQC.lmendel file - assuming not family data -## starting plotpage, newfpath=/opt/galaxy/test-data/rgtestouts/rgQC,m=[['snp', 'chrom', 'maf', 'a1', 'a2', 'missfrac', 'p_hwe_all', 'logp_hwe_all', 'p_hwe_unaff', 'logp_hwe_unaff', 'N_Mendel']],s=[['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat'], ['101', '1', '0.04', '0', '2', '0', 'PROBLEM', 'nan', '-0.03355']]/n## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner +### writing /opt/galaxy/test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls report with ['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat']## marker reports starting at 05/04/2010 14:05:21 +hwe header testpos=2,ppos=8,snppos=1 +## starting plotpage, newfpath=/opt/galaxy/test-data/rgtestouts/rgQC,m=[['snp', 'chromosome', 'offset', 'maf', 'a1', 'a2', 'missfrac', 'p_hwe_all', 'logp_hwe_all', 'p_hwe_unaff', 'logp_hwe_unaff', 'N_Mendel'], ['rs2283802', '22', '21784722', '0.2593', '4', '2', '0', '0.638', '0.195179', '0.638', '0.195179', '0']],s=[['famId', 'iId', 'FracMiss', 'Mendel_errors', 'Ped_sex', 'SNP_sex', 'Status', 'XHomEst', 'F_Stat'], ['101', '1', '0.04', '0', '2', '0', 'PROBLEM', 'nan', '-0.03355']]/n## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner @----------------------------------------------------------@ | PLINK! | v1.06 | 24/Apr/2009 | @@ -89,7 +127,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -115,7 +153,7 @@ 27 founders and 13 non-founders found Writing allele frequencies (founders-only) to [ tinywga.frq ] -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 @----------------------------------------------------------@ @@ -129,7 +167,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -168,7 +206,7 @@ After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 @----------------------------------------------------------@ @@ -182,7 +220,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -224,7 +262,7 @@ Writing per-locus Mendel summary to [ tinywga.lmendel ] 0 Mendel errors detected in total -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 @----------------------------------------------------------@ @@ -238,7 +276,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -271,7 +309,7 @@ Converting data to Individual-major format Writing X-chromosome sex check results to [ tinywga.sexcheck ] -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 ## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner @@ -299,7 +337,7 @@ Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 @@ -369,7 +407,7 @@ -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 @@ -399,7 +437,7 @@ Writing this text to log file [ ldp_tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 @@ -467,7 +505,7 @@ -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 @@ -497,7 +535,7 @@ Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 @@ -565,7 +603,7 @@ -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga.log --- a/test-data/rgtestouts/rgQC/tinywga.log Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/tinywga.log Mon Apr 05 14:14:09 2010 -0400 @@ -10,7 +10,7 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:19 2010 +Analysis started: Mon Apr 5 14:05:21 2010 Options in effect: --noweb @@ -44,5 +44,5 @@ Converting data to Individual-major format Writing individual heterozygosity information to [ tinywga.het ] -Analysis finished: Thu Mar 25 21:01:19 2010 +Analysis finished: Mon Apr 5 14:05:21 2010 diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf Binary file test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf Binary file test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf has changed diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf --- a/test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf Mon Apr 05 14:14:09 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210119) -/ModDate (D:20100325210119) +/CreationDate (D:20100405140521) +/ModDate (D:20100405140521) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf --- a/test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf Mon Apr 05 14:14:09 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210120) -/ModDate (D:20100325210120) +/CreationDate (D:20100405140521) +/ModDate (D:20100405140521) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_s_het.pdf --- a/test-data/rgtestouts/rgQC/tinywga_s_het.pdf Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/tinywga_s_het.pdf Mon Apr 05 14:14:09 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210120) -/ModDate (D:20100325210120) +/CreationDate (D:20100405140521) +/ModDate (D:20100405140521) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) diff -r f00f2d0699fa -r fabf48e747ae test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf --- a/test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf Sun Apr 04 19:41:07 2010 -0400 +++ b/test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf Mon Apr 05 14:14:09 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210120) -/ModDate (D:20100325210120) +/CreationDate (D:20100405140521) +/ModDate (D:20100405140521) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) diff -r f00f2d0699fa -r fabf48e747ae tools/data_source/upload.py --- a/tools/data_source/upload.py Sun Apr 04 19:41:07 2010 -0400 +++ b/tools/data_source/upload.py Mon Apr 05 14:14:09 2010 -0400 @@ -178,7 +178,7 @@ # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress is_gzipped, is_valid = check_gzip( dataset.path ) if is_gzipped and not is_valid: - file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_gzipped and is_valid: # We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format @@ -206,7 +206,7 @@ # See if we have a zip archive is_zipped, is_valid, test_ext = check_zip( dataset.path ) if is_zipped and not is_valid: - file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + file_err( 'The zipped uploaded file contains inappropriate content', dataset, json_file ) return elif is_zipped and is_valid: # Currently, we force specific tools to handle this case. We also require the user @@ -231,7 +231,7 @@ if len( parts ) > 1: ext = parts[1].strip().lower() if ext not in unsniffable_binary_formats: - file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file ) return elif ext in unsniffable_binary_formats and dataset.file_type != ext: err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext ) @@ -240,7 +240,7 @@ if not data_type: # We must have a text file if check_html( dataset.path ): - file_err( 'The uploaded file contains inappropriate content', dataset, json_file ) + file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file ) return if data_type != 'binary' and data_type != 'zip': # don't convert newlines on data we're only going to symlink diff -r f00f2d0699fa -r fabf48e747ae tools/rgenetics/rgManQQ.py --- a/tools/rgenetics/rgManQQ.py Sun Apr 04 19:41:07 2010 -0400 +++ b/tools/rgenetics/rgManQQ.py Mon Apr 05 14:14:09 2010 -0400 @@ -124,7 +124,14 @@ rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%d, offsetcolumn=%d, pvalscolumns=%s, title="%s",grey=%d) { -d = read.table(infile,head=T,sep='\t') +rawd = read.table(infile,head=T,sep='\t') +dn = names(rawd) +cc = dn[chromcolumn] +oc = dn[offsetcolumn] +nams = c(cc,oc) +d = rawd[do.call(order,rawd[nams]),] +# mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according… +# in case not yet ordered print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' ')) for (pvalscolumn in pvalscolumns) { if (pvalscolumn > 0) diff -r f00f2d0699fa -r fabf48e747ae tools/rgenetics/rgQC.py --- a/tools/rgenetics/rgQC.py Sun Apr 04 19:41:07 2010 -0400 +++ b/tools/rgenetics/rgQC.py Mon Apr 05 14:14:09 2010 -0400 @@ -994,7 +994,7 @@ mapdict = {} if maplist <> None: rslist = [x[1] for x in maplist] - offset = [x[3] for x in maplist] + offset = [(x[0],x[3]) for x in maplist] mapdict = dict(zip(rslist,offset)) hwefile = '%s.hwe' % froot lmissfile = '%s.lmiss' % froot @@ -1009,8 +1009,9 @@ lmenddict = {} Tops = {} Tnames = ['Ranked Marker MAF', 'Ranked Marker Missing Genotype', 'Ranked Marker HWE', 'Ranked Marker Mendel'] - Tsorts = [2,5,9,10] + Tsorts = [3,6,10,11] Treverse = [False,True,True,True] # so first values are worse(r) + #res.append([rs,chrom,offset,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend]) #rhead = ['snp','chrom','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel'] # -------------------hwe-------------------------- # hwe has SNP TEST GENO O(HET) E(HET) P_HWD @@ -1057,12 +1058,13 @@ hwedict[rs] = {} markerlist.append(rs) chromlist.append(chrom) # one place to find it? + lpvals = 0 if ps.upper() <> 'NA' and ps.upper() <> 'NAN': # worth keeping lpvals = '0' if ps <> '1': try: pval = float(ps) - lpvals = '%f6' % -math.log10(pval) + lpvals = '%f' % -math.log10(pval) except: pass hwedict[rs][test] = (ps,lpvals) @@ -1147,49 +1149,33 @@ rhead = ['snp','chromosome','offset','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel'] res = [] fres = [] - for i in xrange(len(markerlist)): # for each snp in found order - chrom = chromlist[i] - rs = markerlist[i] + for rs in markerlist: # for each snp in found order f_missing = lmissdict.get(rs,'NA') maf,a1,a2 = freqdict.get(rs,('NA','NA','NA')) hwe_all = hwedict[rs].get('ALL',('NA','NA')) # hope this doesn't change... hwe_unaff = hwedict[rs].get('UNAFF',('NA','NA')) nmend = lmenddict.get(rs,'NA') - offset=mapdict.get(rs,'0') + (chrom,offset)=mapdict.get(rs,('?','0')) res.append([rs,chrom,offset,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend]) + ntokeep = max(10,len(res)/keepfrac) + + def msortk(item=None): + """ + deal with non numeric sorting + """ try: - fmaf = '%f' % float(maf) + return float(item) except: - fmaf = 'NA' - try: - inmend = '%d' % int(nmend) - except: - inmend = 'NA' - try: - fhweall = '%f' % float(hwe_all[1]) # the log value - except: - fhweall = 'NA' - try: - fhweunaff = '%f' % float(hwe_unaff[1]) # the log value - except: - fhweunaff = 'NA' - try: - ff_missing = '%f' % float(f_missing) # the log value - except: - ff_missing = 'NA' - #fres.append([rs,chrom,fmaf,a1,a2,ff_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],fhwe,inmend]) - arow = [rs,chrom,offset,fmaf,a1,a2,ff_missing,hwe_all[0],fhweall,hwe_unaff[0],fhweunaff,inmend] - fres.append(arow) - ntokeep = max(10,len(res)/keepfrac) + return item + for i,col in enumerate(Tsorts): - fres.sort(key=operator.itemgetter(col)) + res.sort(key=msortk(lambda x:x[col])) if Treverse[i]: - fres.reverse() + res.reverse() repname = Tnames[i] - Tops[repname] = fres[0:ntokeep] - #Tops[repname] = [map(str,x) for x in Tops[repname]] + Tops[repname] = res[0:ntokeep] Tops[repname].insert(0,rhead) - res.sort() + res.sort(key=lambda x: '%s_%10d' % (x[1].ljust(4,'0'),int(x[2]))) # in chrom offset order res.insert(0,rhead) f = open(outfile,'w') f.write('\n'.join(['\t'.join(x) for x in res])) @@ -1315,10 +1301,6 @@ dat = subjectTops.get(ttitle,None) if not dat: dat = markerTops.get(ttitle,None) - if not dat: - print '## iterating plotpage - cannot find title=%s/ttitle=%s' % (title,ttitle) - else: - print '## iterating plotpage - found title=%s/ttitle=%s' % (title,ttitle) imghref = '%s.jpg' % os.path.splitext(url)[0] # removes .pdf thumbnail = os.path.join(newfpath,imghref) if not os.path.exists(thumbnail): # for multipage pdfs, mogrify makes multiple jpgs - fugly hack diff -r f00f2d0699fa -r fabf48e747ae tools/rgenetics/rgtest_one_tool.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rgenetics/rgtest_one_tool.sh Mon Apr 05 14:14:09 2010 -0400 @@ -0,0 +1,218 @@ +#!/bin/sh +# script to generate all functional test outputs for each rgenetics tool +# could be run at installation to ensure all dependencies are in place? +case $# in 0) echo "USAGE: ${0##*/} TooltoTest"; exit 1;; + [2-10]*) echo "Too many arguments - name of tool only"; exit 2;; + *) +esac +GALAXYROOT=`pwd` +echo "using $GALAXYROOT" +# change this as needed for your local install +INPATH="${GALAXYROOT}/test-data" +BINPATH="${GALAXYROOT}/tool-data/rg/bin" +TOOLPATH="${GALAXYROOT}/tools/rgenetics" +OROOT="${GALAXYROOT}/test-data/rgtestouts" +NORMALOROOT="${GALAXYROOT}/test-data" +case "$1" in +'rgManQQ') + +TOOL="rgManQQ" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0" +# rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' +# '$pval_col' +#python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1 +#/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7 +echo "Testing $TOOL using $CL" +python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0 +;; + +'rgfakePhe') +TOOL="rgfakePhe" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +PSSCRIPT="$OUTPATH/script_file" +echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT +echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT +echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT +echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT +echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT +echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT +echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT +echo "now doing $TOOL" +python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT +# <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name' +# "$title1" '$ppheout' '$ppheout.files_path' '$script_file' +# +;; +'rgQC') + +TOOL="rgQC" +NPRE=${TOOL}test1 +echo "now doing $TOOL" +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH +# rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix" +# -s '$html_file' -p '$html_file.files_path' +# +;; + +'rgGRR') +TOOL="rgGRR" +NPRE=${TOOL}test1 +echo "now doing $TOOL" +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6' +# rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name" +#'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z' +;; +'rgLDIndep') +TOOL="rgLDIndep" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1 +#rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' +# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' +#'$out_file1.files_path' '$window' '$step' '$r2' +;; + +'rgPedSub') +TOOL="rgPedSub" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +PSSCRIPT="$OUTPATH/pedsub.script" +echo "title~~~~$NPRE" > $PSSCRIPT +echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT +echo "outformat~~~~lped" >> $PSSCRIPT +echo "basename~~~~tinywga" >> $PSSCRIPT +echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT +echo "outdir~~~~$OUTPATH" >> $PSSCRIPT +echo "region~~~~" >> $PSSCRIPT +echo "relfilter~~~~all" >> $PSSCRIPT +echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT +echo "now doing $TOOL" +python $TOOLPATH/$TOOL.py $PSSCRIPT +rm -rf $PSSCRIPT +;; + +'rgfakePhe') + +TOOL="rgfakePhe" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +PSSCRIPT="$OUTPATH/script_file" +echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT +echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT +echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT +echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT +echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT +echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT +echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT +echo "now doing $TOOL" +python $TOOLPATH/$TOOL.py $PSSCRIPT +;; + +'rgClean') +TOOL="rgClean" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0 +# rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind' +# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path' +# '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff' +# +;; + +'rgEigPCA') + +TOOL="rgEigPCA" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt +# rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1" +# "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca" +# +;; + +'rgfakePed') +TOOL="rgfakePed" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +echo "now doing $TOOL" +python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0" +#rgfakePed.py --title '$title1' +# -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal' +# -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat' +# -d '$mafdist' -m '$missingRate' -M '$mendelRate' +;; + +'rgHaploView') + +TOOL="rgHaploView" +NPRE=${TOOL}test1 +OUTPATH="$OROOT/$TOOL" +rm -rf $OUTPATH/* +python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \ +"$NPRE" $OUTPATH/${NPRE}.html "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" \ +"YRI" $BINPATH/haploview.jar +# rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1" +# "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name" +# "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path" +# "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar +# note these statistical tools do NOT generate composite outputs +;; + +'rgGLM') +TOOL="rgGLM" +NPRE=${TOOL}test1 +OUTPATH=$NORMALOROOT +python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \ +$OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff +## rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name' +## "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name' +## '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout' +;; + +'rgTDT') +TOOL="rgTDT" +NPRE=${TOOL}test1 +OUTPATH=$NORMALOROOT +python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \ +-l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff +## rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title' +## -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' +## -g '$gffout' +;; + +'rgCaCo') +TOOL="rgCaCo" +NPRE=${TOOL}test1 +OUTPATH=$NORMALOROOT +echo "now doing $TOOL" +python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff +# echo tp=$TOOLPATH t=$TOOL op=$OUTPATH b=$BINPATH +# rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" '$out_file1' '$logf' '$logf.files_path' '$gffout' +;; + +'rgQQ') +TOOL="rgQQ" +echo "now doing $TOOL" +NPRE=${TOOL}test1 +OUTPATH=$NORMALOROOT +CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH" +echo "running $TOOL using $CL" +python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH +# rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__ +;; +esac

1 0

[hg] galaxy 3610: Add offset to marker reports so can use manhat...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f00f2d0699fa changeset: 3610:f00f2d0699fa user: fubar: ross Lazarus at gmail period com date: Sun Apr 04 19:41:07 2010 -0400 description: Add offset to marker reports so can use manhattan plots Fix spelling of manhattan diffstat: tools/rgenetics/rgManQQ.xml | 4 ++-- tools/rgenetics/rgQC.py | 26 +++++++++++++++++++++----- 2 files changed, 23 insertions(+), 7 deletions(-) diffs (98 lines): diff -r b95a24c9187e -r f00f2d0699fa tools/rgenetics/rgManQQ.xml --- a/tools/rgenetics/rgManQQ.xml Fri Apr 02 14:23:55 2010 -0400 +++ b/tools/rgenetics/rgManQQ.xml Sun Apr 04 19:41:07 2010 -0400 @@ -24,7 +24,7 @@ help='Select "None" if offset not available or no Manhattan plot required' dynamic_options="get_phecols(i,True,'offs')" /> <param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false" - label="Grey scale for Manhatten plot (default is colour"/> + label="Grey scale for Manhattan plot (default is colour"/> </page> </inputs> @@ -76,7 +76,7 @@ **Summary** This tool will create a qq plot and a Manhattan plot for one or more GWA P value columns from a tabular -dataset. For Manhatten plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and +dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot can be created. diff -r b95a24c9187e -r f00f2d0699fa tools/rgenetics/rgQC.py --- a/tools/rgenetics/rgQC.py Fri Apr 02 14:23:55 2010 -0400 +++ b/tools/rgenetics/rgQC.py Sun Apr 04 19:41:07 2010 -0400 @@ -984,13 +984,18 @@ f.close() return res,Tops -def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None ): +def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None,maplist=None ): """by marker (hwe = .hwe, missingness=.lmiss, freq = .frq) keep a list of marker order but keep all stats in dicts write out a fake xls file for R or SAS etc kinda clunky, but.. TODO: ensure stable if any file not found? """ + mapdict = {} + if maplist <> None: + rslist = [x[1] for x in maplist] + offset = [x[3] for x in maplist] + mapdict = dict(zip(rslist,offset)) hwefile = '%s.hwe' % froot lmissfile = '%s.lmiss' % froot freqfile = '%s.frq' % froot @@ -1139,7 +1144,7 @@ else: logf.write('No %s file - assuming not family data\n' % lmendfile) # now assemble result list - rhead = ['snp','chrom','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel'] + rhead = ['snp','chromosome','offset','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel'] res = [] fres = [] for i in xrange(len(markerlist)): # for each snp in found order @@ -1150,7 +1155,8 @@ hwe_all = hwedict[rs].get('ALL',('NA','NA')) # hope this doesn't change... hwe_unaff = hwedict[rs].get('UNAFF',('NA','NA')) nmend = lmenddict.get(rs,'NA') - res.append([rs,chrom,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend]) + offset=mapdict.get(rs,'0') + res.append([rs,chrom,offset,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend]) try: fmaf = '%f' % float(maf) except: @@ -1172,7 +1178,7 @@ except: ff_missing = 'NA' #fres.append([rs,chrom,fmaf,a1,a2,ff_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],fhwe,inmend]) - arow = [rs,chrom,fmaf,a1,a2,ff_missing,hwe_all[0],fhweall,hwe_unaff[0],fhweunaff,inmend] + arow = [rs,chrom,offset,fmaf,a1,a2,ff_missing,hwe_all[0],fhweall,hwe_unaff[0],fhweunaff,inmend] fres.append(arow) ntokeep = max(10,len(res)/keepfrac) for i,col in enumerate(Tsorts): @@ -1256,6 +1262,16 @@ pass ofn = basename bfn = options.infile + try: + mapf = '%s.bim' % bfn + maplist = file(mapf,'r').readlines() + maplist = [x.split() for x in maplist] + except: + maplist = None + alogf.write('## error - cannot open %s to read map - no offsets will be available for output files') + #rerla@beast galaxy]$ head test-data/tinywga.bim + #22 rs2283802 0 21784722 4 2 + #22 rs2267000 0 21785366 4 2 rgbin = os.path.split(rexe)[0] # get our rg bin path #plinktasks = [' --freq',' --missing',' --mendel',' --hardy',' --check-sex'] # plink v1 fixes that bug! # if we could, do all at once? Nope. Probably never. @@ -1276,7 +1292,7 @@ subjects,subjectTops = subjectRep(froot=repout,outfname=asubjf,newfpath=newfpath, logf=alogf) # writes the subject_froot.xls file markers,markerTops = markerRep(froot=repout,outfname=amarkf,newfpath=newfpath, - logf=alogf) # marker_froot.xls + logf=alogf,maplist=maplist) # marker_froot.xls nbreaks = 100 s = '## starting plotpage, newfpath=%s,m=%s,s=%s/n' % (newfpath,markers[:2],subjects[:2]) alogf.write(s)

1 0

[hg] galaxy 3609: Fix a bug where using repeat grouping construc...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/23fb19105d96 changeset: 3609:23fb19105d96 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 05 13:57:19 2010 -0400 description: Fix a bug where using repeat grouping constructs and change_format tags or output data label templates in a tool would cause a JSON server error. Lists were not being properly psuedo-deepcopied before being wrapped for usage. diffstat: lib/galaxy/tools/actions/__init__.py | 13 +++++++++++++ 1 files changed, 13 insertions(+), 0 deletions(-) diffs (31 lines): diff -r 59645595001f -r 23fb19105d96 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Fri Apr 02 17:29:15 2010 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Mon Apr 05 13:57:19 2010 -0400 @@ -107,14 +107,27 @@ Makes a copy of input dictionary from_dict such that all values that are dictionaries result in creation of a new dictionary ( a sort of deepcopy ). We may need to handle other complex types ( e.g., lists, etc ), but not sure... + Yes, we need to handle lists (and now are)... """ copy_from_dict = {} for key, value in from_dict.items(): if type( value ).__name__ == 'dict': copy_from_dict[ key ] = make_dict_copy( value ) + elif isinstance( value, list ): + copy_from_dict[ key ] = make_list_copy( value ) else: copy_from_dict[ key ] = value return copy_from_dict + def make_list_copy( from_list ): + new_list = [] + for value in from_list: + if isinstance( value, dict ): + new_list.append( make_dict_copy( value ) ) + elif isinstance( value, list ): + new_list.append( make_list_copy( value ) ) + else: + new_list.append( value ) + return new_list def wrap_values( inputs, input_values ): # Wrap tool inputs as necessary for input in inputs.itervalues():

1 0

[hg] galaxy 3608: Generalize the dbkey text + autocomplete featu...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/59645595001f changeset: 3608:59645595001f user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 02 17:29:15 2010 -0400 description: Generalize the dbkey text + autocomplete feature to work with any select box and replace all select boxes with >20 options--mostly the dbkey and dataset format selects--with text + autocomplete inputs. Also add icon to text + autocomplete inputs so that it's clearer that they're text + autocomplete, not just text. diffstat: static/images/fugue/plus-white.png | 0 static/june_2007_style/base.css.tmpl | 6 + static/june_2007_style/blue/base.css | 2 +- static/scripts/galaxy.base.js | 87 +++++++++++++++----------- static/scripts/packed/galaxy.base.js | 2 +- templates/dataset/edit_attributes.mako | 6 - templates/library/common/common.mako | 2 +- templates/library/common/ldda_edit_info.mako | 7 -- templates/tool_form.mako | 5 +- 9 files changed, 60 insertions(+), 57 deletions(-) diffs (227 lines): diff -r 2b6910fd7d93 -r 59645595001f static/images/fugue/plus-white.png Binary file static/images/fugue/plus-white.png has changed diff -r 2b6910fd7d93 -r 59645595001f static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Apr 02 16:48:35 2010 -0400 +++ b/static/june_2007_style/base.css.tmpl Fri Apr 02 17:29:15 2010 -0400 @@ -838,4 +838,10 @@ .editable-text:hover { cursor: text; border: dotted #999999 1px; +} + +.text-and-autocomplete-select { + background-image:url(/static/images/fugue/plus-white.png); + background-repeat: no-repeat; + background-position:top right; } \ No newline at end of file diff -r 2b6910fd7d93 -r 59645595001f static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Apr 02 16:48:35 2010 -0400 +++ b/static/june_2007_style/blue/base.css Fri Apr 02 17:29:15 2010 -0400 @@ -146,4 +146,4 @@ .tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor: text;border: dotted #999999 1px;} - +.text-and-autocomplete-select{background-image:url(/static/images/fugue/plus-white.png);background-repeat: no-repeat;background-position:top right;} diff -r 2b6910fd7d93 -r 59645595001f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Apr 02 16:48:35 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri Apr 02 17:29:15 2010 -0400 @@ -1,3 +1,7 @@ +$(document).ready(function() { + replace_big_select_inputs(); +}); + $.fn.makeAbsolute = function(rebase) { return this.each(function() { var el = $(this); @@ -115,13 +119,21 @@ return count; } -// Replace dbkey select box with text input box & autocomplete. -function replace_dbkey_select() { - var select_elt = $('select[name=dbkey]'); - var start_value = select_elt.attr('value'); - if (select_elt.length !== 0) { +// Replace any select box with 20+ options with a text input box + autocomplete. +// TODO: make this work _well_ on pages with multiple forms; currently, value is reverted when any form is submitted - +// value should be reverted when only the form that element is in is submitted. +function replace_big_select_inputs() { + $('select').each( function() { + var select_elt = $(this); + // Skip if there are < 20 options. + if (select_elt.find('option').length < 20) + return; + + // Replace select with text + autocomplete. + var start_value = select_elt.attr('value'); + // Set up text input + autocomplete element. - var text_input_elt = $("<input id='dbkey-input' type='text'></input>"); + var text_input_elt = $("<input type='text' class='text-and-autocomplete-select'></input>"); text_input_elt.attr('size', 40); text_input_elt.attr('name', select_elt.attr('name')); text_input_elt.click( function() { @@ -133,61 +145,62 @@ $(this).select(); }); - // Get options for dbkey for autocomplete. - var dbkey_options = []; - var dbkey_mapping = {}; + // Get options for select for autocomplete. + var select_options = []; + var select_mapping = {}; select_elt.children('option').each( function() { // Get text, value for option. var text = $(this).text(); var value = $(this).attr('value'); - + // Ignore values that are '?' if (value == '?') { return; } - + // Set options and mapping. Mapping is (i) [from text to value] AND (ii) [from value to value]. This // enables a user to type the value directly rather than select the text that represents the value. - dbkey_options.push( text ); - dbkey_mapping[ text ] = value; - dbkey_mapping[ value ] = value; - + select_options.push( text ); + select_mapping[ text ] = value; + select_mapping[ value ] = value; + // If this is the start value, set value of input element. if ( value == start_value ) { text_input_elt.attr('value', text); } }); + + // Set initial text if it's empty. if ( text_input_elt.attr('value') == '' ) { - text_input_elt.attr('value', 'Click to Search or Select Build'); + text_input_elt.attr('value', 'Click to Search or Select'); } - + // Do autocomplete. var autocomplete_options = { selectFirst: false, autoFill: false, mustMatch: false, matchContains: true, max: 1000, minChars : 0, hideForLessThanMinChars : false }; - text_input_elt.autocomplete(dbkey_options, autocomplete_options); + text_input_elt.autocomplete(select_options, autocomplete_options); + + // Replace select with text input. + select_elt.replaceWith(text_input_elt); - // Replace select with text input. - select_elt.replaceWith(text_input_elt); - - // When form is submitted, change the text entered into the input to the corresponding value. If text doesn't correspond to value, remove it. - $('form').submit( function() { - var dbkey_text_input = $('#dbkey-input'); - if (dbkey_text_input.length !== 0) { - // Try to convert text to value. - var cur_value = dbkey_text_input.attr('value'); - var new_value = dbkey_mapping[cur_value]; - if (new_value !== null && new_value !== undefined) { - dbkey_text_input.attr('value', new_value); + // Set trigger to replace text with value when element's form is submitted. If text doesn't correspond to value, default to start value. + text_input_elt.parents('form').submit( function() { + // Try to convert text to value. + var cur_value = text_input_elt.attr('value'); + var new_value = select_mapping[cur_value]; + if (new_value !== null && new_value !== undefined) { + text_input_elt.attr('value', new_value); + } + else { + // If there is a non-empty start value, use that; otherwise unknown. + if (start_value != "") { + text_input_elt.attr('value', start_value); } else { - // If there is a non-empty start value, use that; otherwise unknown. - if (start_value != "") { - dbkey_text_input.attr('value', start_value); - } else { - dbkey_text_input.attr('value', '?'); - } + // This is needed to make the DB key work. + text_input_elt.attr('value', '?'); } } }); - } + }); } // Edit and save text asynchronously. diff -r 2b6910fd7d93 -r 59645595001f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Apr 02 16:48:35 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Apr 02 17:29:15 2010 -0400 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmenu(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id"! )+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function replace_dbkey_select(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!==0){var e=$("<input id='dbkey-input' type='text'></input>! ");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){ var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=[];var a={};c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;a[g]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!==0){var h=i.attr("value");var g=a[h];if(g!==null&&g!==undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i.attr("value","?")}}}})}}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({! rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); \ No newline at end of file +$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function replace_big_select_inputs(){$("select").each(function(){var a=$(this);if(a.find("optio! n").length<20){return}var b=a.attr("value");var c=$("<input type='text ' class='text-and-autocomplete-select'></input>");c.attr("size",40);c.attr("name",a.attr("name"));c.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var f=[];var e={};a.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}f.push(h);e[h]=g;e[g]=g;if(g==b){c.attr("value",h)}});if(c.attr("value")==""){c.attr("value","Click to Search or Select")}var d={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};c.autocomplete(f,d);a.replaceWith(c);c.parents("form").submit(function(){var h=c.attr("value");var g=e[h];if(g!==null&&g!==undefined){c.attr("value",g)}else{if(b!=""){c.attr("value",b)}else{c.attr("value","?")}}})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0! ){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}$(document).ready(function(){$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus()}); \ No newline at end of file diff -r 2b6910fd7d93 -r 59645595001f templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Fri Apr 02 16:48:35 2010 -0400 +++ b/templates/dataset/edit_attributes.mako Fri Apr 02 17:29:15 2010 -0400 @@ -10,12 +10,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "galaxy.base", "jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - $(document).ready(function() - { - replace_dbkey_select('${data.dbkey}'); - }); - </script> </%def> <%def name="datatype( dataset, datatypes )"> diff -r 2b6910fd7d93 -r 59645595001f templates/library/common/common.mako --- a/templates/library/common/common.mako Fri Apr 02 16:48:35 2010 -0400 +++ b/templates/library/common/common.mako Fri Apr 02 17:29:15 2010 -0400 @@ -321,7 +321,7 @@ <script type="text/javascript"> // Replace dbkey select with search+select. jQuery(document).ready( function() { - replace_dbkey_select(); + replace_big_select_inputs(); }); </script> %elif upload_option == 'import_from_history': diff -r 2b6910fd7d93 -r 59645595001f templates/library/common/ldda_edit_info.mako --- a/templates/library/common/ldda_edit_info.mako Fri Apr 02 16:48:35 2010 -0400 +++ b/templates/library/common/ldda_edit_info.mako Fri Apr 02 17:29:15 2010 -0400 @@ -6,13 +6,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - ## Script to replace dbkey select with select+search. - <script type="text/javascript"> - // Replace dbkey select with search+select. - jQuery(document).ready( function() { - replace_dbkey_select(); - }); - </script> </%def> <%def name="stylesheets()"> diff -r 2b6910fd7d93 -r 59645595001f templates/tool_form.mako --- a/templates/tool_form.mako Fri Apr 02 16:48:35 2010 -0400 +++ b/templates/tool_form.mako Fri Apr 02 17:29:15 2010 -0400 @@ -48,10 +48,7 @@ } ); $( "#tool_form" ).submit(); } - }); - - // Replace dbkey select with search+select. - replace_dbkey_select(); + }); }); %if not add_frame.debug: if( window.name != "galaxy_main" ) {

1 0

[hg] galaxy 3607: Only preview for non-binary files. Closes #283
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2b6910fd7d93 changeset: 3607:2b6910fd7d93 user: Kanwei Li <kanwei(a)gmail.com> date: Fri Apr 02 16:48:35 2010 -0400 description: Only preview for non-binary files. Closes #283 diffstat: lib/galaxy/web/controllers/dataset.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r f2b6d4f3189c -r 2b6910fd7d93 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Apr 02 16:06:43 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Apr 02 16:48:35 2010 -0400 @@ -352,7 +352,7 @@ return open( data.file_name ) if os.path.exists( data.file_name ): max_peek_size = 1000000 # 1 MB - if preview and os.stat( data.file_name ).st_size > max_peek_size: + if preview and (not isinstance(data.datatype, datatypes.binary.Binary)) and os.stat( data.file_name ).st_size > max_peek_size: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", truncated_data = open( data.file_name ).read(max_peek_size),

1 0

[hg] galaxy 3606: Move toward standardizing the way messages are...
by Greg Von Kuster 16 Apr '10

16 Apr '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f2b6d4f3189c changeset: 3606:f2b6d4f3189c user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 02 16:06:43 2010 -0400 description: Move toward standardizing the way messages are displayed on Galaxy forms by using params 'message' and 'status' instead of 'msg' and 'messagetype'. diffstat: lib/galaxy/web/controllers/admin.py | 140 +- lib/galaxy/web/controllers/forms.py | 76 +- lib/galaxy/web/controllers/history.py | 7 +- lib/galaxy/web/controllers/library.py | 16 +- lib/galaxy/web/controllers/library_admin.py | 46 +- lib/galaxy/web/controllers/library_common.py | 548 +++++++------- lib/galaxy/web/controllers/requests.py | 164 ++-- lib/galaxy/web/controllers/requests_admin.py | 298 +++--- lib/galaxy/web/controllers/root.py | 32 +- lib/galaxy/web/controllers/user.py | 200 ++-- templates/admin/dataset_security/group/group.mako | 4 +- templates/admin/dataset_security/group/group_create.mako | 4 +- templates/admin/dataset_security/group/group_rename.mako | 4 +- templates/admin/dataset_security/role/role.mako | 4 +- templates/admin/dataset_security/role/role_create.mako | 4 +- templates/admin/dataset_security/role/role_rename.mako | 4 +- templates/admin/forms/create_form.mako | 4 +- templates/admin/forms/edit_form.mako | 4 +- templates/admin/forms/show_form_read_only.mako | 4 +- templates/admin/jobs.mako | 4 +- templates/admin/library/new_library.mako | 4 +- templates/admin/memdump.mako | 4 +- templates/admin/reload_tool.mako | 4 +- templates/admin/requests/add_states.mako | 4 +- templates/admin/requests/create_request_type.mako | 4 +- templates/admin/requests/edit_request.mako | 4 +- templates/admin/requests/edit_request_type.mako | 4 +- templates/admin/requests/events.mako | 4 +- templates/admin/requests/get_data.mako | 4 +- templates/admin/requests/new_request.mako | 4 +- templates/admin/requests/reject.mako | 4 +- templates/admin/requests/show_request.mako | 4 +- templates/admin/requests/view_request_type.mako | 4 +- templates/admin/samples/bar_codes.mako | 4 +- templates/admin/samples/events.mako | 4 +- templates/admin/user/reset_password.mako | 4 +- templates/admin/user/user.mako | 4 +- templates/dataset/edit_attributes.mako | 4 +- templates/history/sharing.mako | 4 +- templates/library/browse_libraries.mako | 4 +- templates/library/common/browse_library.mako | 4 +- templates/library/common/edit_template.mako | 4 +- templates/library/common/folder_info.mako | 4 +- templates/library/common/folder_permissions.mako | 4 +- templates/library/common/ldda_edit_info.mako | 4 +- templates/library/common/ldda_info.mako | 4 +- templates/library/common/ldda_permissions.mako | 4 +- templates/library/common/library_dataset_info.mako | 4 +- templates/library/common/library_dataset_permissions.mako | 4 +- templates/library/common/library_info.mako | 4 +- templates/library/common/library_permissions.mako | 4 +- templates/library/common/new_folder.mako | 4 +- templates/library/common/select_template.mako | 4 +- templates/library/common/upload.mako | 4 +- templates/mobile/manage_library.mako | 4 +- templates/requests/edit_request.mako | 4 +- templates/requests/events.mako | 4 +- templates/requests/new_request.mako | 4 +- templates/requests/show_data.mako | 4 +- templates/requests/show_request.mako | 4 +- templates/sample/sample_events.mako | 4 +- templates/user/edit_address.mako | 4 +- templates/user/index.mako | 4 +- templates/user/info.mako | 4 +- templates/user/login.mako | 4 +- templates/user/logout.mako | 4 +- templates/user/new_address.mako | 4 +- templates/user/register.mako | 4 +- templates/user/reset_password.mako | 4 +- 69 files changed, 883 insertions(+), 880 deletions(-) diffs (truncated from 4762 to 3000 lines): diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Apr 02 16:06:43 2010 -0400 @@ -263,9 +263,9 @@ @web.require_admin def index( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - return trans.fill_template( '/admin/index.mako', msg=msg, messagetype=messagetype ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/admin/index.mako', message=message, status=status ) @web.expose @web.require_admin def center( self, trans, **kwd ): @@ -274,17 +274,17 @@ @web.require_admin def reload_tool( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, msg=msg, messagetype=messagetype ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, message=message, status=status ) @web.expose @web.require_admin def tool_reload( self, trans, tool_version=None, **kwd ): params = util.Params( kwd ) tool_id = params.tool_id self.app.toolbox.reload( tool_id ) - msg = 'Reloaded tool: ' + tool_id - return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, msg=msg, messagetype='done' ) + message = 'Reloaded tool: ' + tool_id + return trans.fill_template( '/admin/reload_tool.mako', toolbox=self.app.toolbox, message=message, status='done' ) # Galaxy Role Stuff @web.expose @@ -312,8 +312,8 @@ @web.require_admin def create_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_role_button', False ): name = util.restore_text( params.name ) description = util.restore_text( params.description ) @@ -321,9 +321,9 @@ in_groups = util.listify( params.get( 'in_groups', [] ) ) create_group_for_role = params.get( 'create_group_for_role', 'no' ) if not name or not description: - msg = "Enter a valid name and a description" + message = "Enter a valid name and a description" elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first(): - msg = "A role with that name already exists" + message = "A role with that name already exists" else: # Create the role role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN ) @@ -340,13 +340,13 @@ # Create the group group = trans.app.model.Group( name=name ) trans.sa_session.add( group ) - msg = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ + message = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ ( 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 ) ) + message = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) trans.sa_session.flush() - 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' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='roles', message=util.sanitize_text( message ), status='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='create_role', message=util.sanitize_text( message ), status='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ .filter( trans.app.model.User.table.c.deleted==False ) \ @@ -362,39 +362,39 @@ out_users=out_users, in_groups=[], out_groups=out_groups, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def rename_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) role = get_role( trans, params.id ) if params.get( 'rename_role_button', False ): old_name = role.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) if not new_name: - msg = 'Enter a valid name' - return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype='error' ) + message = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status='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/role_rename.mako', role=role, msg=msg, messagetype='error' ) + message = 'A role with that name already exists' + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status='error' ) else: role.name = new_name role.description = new_description trans.sa_session.add( role ) trans.sa_session.flush() - msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) - 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 ) + message = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, message=message, status=status ) @web.expose @web.require_admin def manage_users_and_groups_for_role( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) 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 ) ] @@ -414,8 +414,8 @@ in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] 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', message=util.sanitize_text( msg ), status=messagetype ) ) + message = "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', message=util.sanitize_text( message ), status=status ) ) in_users = [] out_users = [] in_groups = [] @@ -467,8 +467,8 @@ in_groups=in_groups, out_groups=out_groups, library_dataset_actions=library_dataset_actions, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def mark_role_deleted( self, trans, **kwd ): @@ -554,39 +554,39 @@ @web.require_admin def rename_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) group = get_group( trans, params.id ) if params.get( 'rename_group_button', False ): 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/group_rename.mako', group=group, msg=msg, messagetype='error' ) + message = 'Enter a valid name' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status='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/group_rename.mako', group=group, msg=msg, messagetype='error' ) + message = 'A group with that name already exists' + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status='error' ) else: group.name = new_name trans.sa_session.add( group ) trans.sa_session.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/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) + message = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) + return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, message=message, status=status ) @web.expose @web.require_admin def manage_users_and_roles_for_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) 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', message=util.sanitize_text( msg ), status=messagetype ) ) + message += "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', message=util.sanitize_text( message ), status=status ) ) in_roles = [] out_roles = [] in_users = [] @@ -605,29 +605,29 @@ in_users.append( ( user.id, user.email ) ) 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 ) ) + message += '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/group.mako', group=group, in_roles=in_roles, out_roles=out_roles, in_users=in_users, out_users=out_users, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def create_group( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_group_button', False ): name = util.restore_text( params.name ) in_users = util.listify( params.get( 'in_users', [] ) ) in_roles = util.listify( params.get( 'in_roles', [] ) ) if not name: - msg = "Enter a valid name" + message = "Enter a valid name" elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): - msg = "A group with that name already exists" + message = "A group with that name already exists" else: # Create the group group = trans.app.model.Group( name=name ) @@ -643,9 +643,9 @@ gra = trans.app.model.GroupRoleAssociation( group, role ) trans.sa_session.add( gra ) trans.sa_session.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', 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' ) ) + message = "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', message=util.sanitize_text( message ), status='done' ) ) + trans.response.send_redirect( web.url_for( controller='admin', action='create_group', message=util.sanitize_text( message ), status='error' ) ) out_users = [] for user in trans.sa_session.query( trans.app.model.User ) \ .filter( trans.app.model.User.table.c.deleted==False ) \ @@ -661,8 +661,8 @@ out_users=out_users, in_roles=[], out_roles=out_roles, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose @web.require_admin def mark_group_deleted( self, trans, **kwd ): @@ -671,8 +671,8 @@ group.deleted = True trans.sa_session.add( group ) trans.sa_session.flush() - msg = "Group '%s' has been marked as deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) + message = "Group '%s' has been marked as deleted." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def undelete_group( self, trans, **kwd ): @@ -681,8 +681,8 @@ group.deleted = False trans.sa_session.add( group ) trans.sa_session.flush() - msg = "Group '%s' has been marked as not deleted." % group.name - trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) + message = "Group '%s' has been marked as not deleted." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin def purge_group( self, trans, **kwd ): @@ -692,8 +692,8 @@ 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', message=util.sanitize_text( msg ), status='error' ) ) + message = "Group '%s' has not been deleted, so it cannot be purged." % group.name + trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='error' ) ) # Delete UserGroupAssociations for uga in group.users: trans.sa_session.delete( uga ) @@ -972,8 +972,8 @@ out_roles=out_roles, in_groups=in_groups, out_groups=out_groups, - msg=message, - messagetype=status ) + message=message, + status=status ) @web.expose @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): @@ -1020,11 +1020,11 @@ def jobs( self, trans, stop = [], stop_msg = None, cutoff = 180, **kwd ): deleted = [] msg = None - messagetype = None + status = None job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' - messagetype = 'error' + status = 'error' elif job_ids: if stop_msg[-1] not in string.punctuation: stop_msg += '.' @@ -1037,7 +1037,7 @@ msg += 's' msg += ' for deletion: ' msg += ', '.join( deleted ) - messagetype = 'done' + status = 'done' cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, @@ -1053,7 +1053,7 @@ last_updated[job.id] = '%s hours' % int( delta.seconds / 60 / 60 ) else: last_updated[job.id] = '%s minutes' % int( delta.seconds / 60 ) - return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, messagetype = messagetype ) + return trans.fill_template( '/admin/jobs.mako', jobs = jobs, last_updated = last_updated, cutoff = cutoff, msg = msg, status = status ) ## ---- Utility methods ------------------------------------------------------- diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Fri Apr 02 16:06:43 2010 -0400 @@ -102,8 +102,8 @@ except: return trans.response.send_redirect( web.url_for( controller='forms', action='manage', - msg='Invalid form', - messagetype='error' ) ) + message='Invalid form', + status='error' ) ) return trans.fill_template( '/admin/forms/show_form_read_only.mako', form=fdc.latest_form ) def __form_types_widget(self, trans, selected='none'): @@ -127,16 +127,16 @@ @web.require_admin def new( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) self.__imported_from_file = False if params.get( 'create_form_button', False ): - fd, msg = self.__save_form( trans, fdc_id=None, **kwd ) + fd, message = self.__save_form( trans, fdc_id=None, **kwd ) if not fd: return trans.response.send_redirect( web.url_for( controller='forms', action='new', - msg=msg, - messagetype='error', + message=message, + status='error', name=util.restore_text( params.get( 'name', '' ) ), description=util.restore_text( params.get( 'description', '' ) ) )) self.__get_saved_form( fd ) @@ -158,8 +158,8 @@ ( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ] return trans.fill_template( '/admin/forms/create_form.mako', inputs=inputs, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) def __delete( self, trans, **kwd ): id_list = util.listify( kwd['id'] ) delete_failed = [] @@ -205,8 +205,8 @@ edit_template() method in the library_common controller. ''' params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: fdc = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( trans.security.decode_id(kwd['id']) ) except: @@ -219,22 +219,22 @@ # Save changes # if params.get( 'save_changes_button', False ): - fd_new, msg = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd ) + fd_new, message = self.__save_form( trans, fdc_id=fd.form_definition_current.id, **kwd ) # if validation error encountered while saving the form, show the # unsaved form, with the error message if not fd_new: current_form = self.__get_form( trans, **kwd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype='error', response_redirect=response_redirect, **kwd ) + message=message, status='error', response_redirect=response_redirect, **kwd ) # everything went fine. form saved successfully. Show the saved form or redirect # to response_redirect if appropriate. if response_redirect: return trans.response.send_redirect( response_redirect ) fd = fd_new current_form = self.__get_saved_form( fd ) - msg = "The form '%s' has been updated with the changes." % fd.name + message = "The form '%s' has been updated with the changes." % fd.name return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add a layout grid # @@ -243,7 +243,7 @@ current_form['layout'].append('') # show the form again return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Delete a layout grid # @@ -252,7 +252,7 @@ index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1 del current_form['layout'][index] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add a field # @@ -261,7 +261,7 @@ current_form['fields'].append( self.empty_field ) # show the form again with one empty field return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Delete a field # @@ -271,33 +271,33 @@ index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1 del current_form['fields'][index] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Add SelectField option # elif 'Add' in kwd.values(): - return self.__add_selectbox_option(trans, fd, msg, messagetype, response_redirect=response_redirect, **kwd) + return self.__add_selectbox_option(trans, fd, message, status, response_redirect=response_redirect, **kwd) # # Remove SelectField option # elif 'Remove' in kwd.values(): - return self.__remove_selectbox_option(trans, fd, msg, messagetype, response_redirect=response_redirect, **kwd) + return self.__remove_selectbox_option(trans, fd, message, status, response_redirect=response_redirect, **kwd) # # Refresh page # elif params.get( 'refresh', False ): current_form = self.__get_form( trans, **kwd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) # # Show the form for editing # else: current_form = self.__get_saved_form( fd ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) - def __add_selectbox_option( self, trans, fd, msg, messagetype, response_redirect=None, **kwd ): + def __add_selectbox_option( self, trans, fd, message, status, response_redirect=None, **kwd ): ''' This method adds a selectbox option. The kwd dict searched for the field index which needs to be removed @@ -313,13 +313,13 @@ if index == -1: # something wrong happened return self.__show( trans=trans, form=fd, current_form=current_form, - msg='Error in adding selectfield option', - messagetype='error', response_redirect=response_redirect, **kwd ) + message='Error in adding selectfield option', + status='error', response_redirect=response_redirect, **kwd ) # add an empty option current_form[ 'fields' ][ index ][ 'selectlist' ].append( '' ) return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) - def __remove_selectbox_option( self, trans, fd, msg, messagetype, response_redirect=None, **kwd ): + message=message, status=status, response_redirect=response_redirect, **kwd ) + def __remove_selectbox_option( self, trans, fd, message, status, response_redirect=None, **kwd ): ''' This method removes a selectbox option. The kwd dict searched for the field index and option index which needs to be removed @@ -336,12 +336,12 @@ if option == -1: # something wrong happened return self.__show( trans=trans, form=fd, current_form=current_form, - msg='Error in removing selectfield option', - messagetype='error', response_redirect=response_redirect, **kwd ) + message='Error in removing selectfield option', + status='error', response_redirect=response_redirect, **kwd ) # remove the option del current_form[ 'fields' ][ index ][ 'selectlist' ][ option ] return self.__show( trans=trans, form=fd, current_form=current_form, - msg=msg, messagetype=messagetype, response_redirect=response_redirect, **kwd ) + message=message, status=status, response_redirect=response_redirect, **kwd ) def __get_field(self, index, **kwd): @@ -497,9 +497,9 @@ This method saves the current form ''' # check the form for invalid inputs - flag, msg = self.__validate_form(**kwd) + flag, message = self.__validate_form(**kwd) if not flag: - return None, msg + return None, message current_form = self.__get_form( trans, **kwd ) # validate fields for field in current_form[ 'fields' ]: @@ -523,8 +523,8 @@ fdc.latest_form = fd trans.sa_session.add( fdc ) trans.sa_session.flush() - msg = "The new form named '%s' has been created. " % (fd.name) - return fd, msg + message = "The new form named '%s' has been created. " % (fd.name) + return fd, message class FieldUI(object): def __init__(self, trans, layout_grids, index, field=None, field_type=None, form_type=None): @@ -631,7 +631,7 @@ def label(self): return str(self.index)+'.'+self.label - def __show( self, trans, form, current_form, msg='', messagetype='done', response_redirect=None, **kwd ): + def __show( self, trans, form, current_form, message='', status='done', response_redirect=None, **kwd ): ''' This method displays the form and any of the changes made to it, The empty_form param allows for this method to simulate clicking @@ -662,8 +662,8 @@ field_details=field_details, form=form, field_types=BaseField.form_field_types(), - msg=msg, - messagetype=messagetype, + message=message, + status=status, current_form_type=current_form[ 'type' ], layout_grids=form_layout, response_redirect=response_redirect ) diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Apr 02 16:06:43 2010 -0400 @@ -648,8 +648,11 @@ elif 'unshare_user' in kwargs: user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwargs[ 'unshare_user' ] ) ) if not user: - msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) - return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' ) + message = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) + return trans.fill_template( 'history/sharing.mako', + histories=histories, + message=message, + status='error' ) husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=user, history=history ).all() if husas: for husa in husas: diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/library.py Fri Apr 02 16:06:43 2010 -0400 @@ -10,17 +10,17 @@ @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) return trans.fill_template( "/library/index.mako", default_action=params.get( 'default_action', None ), - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def browse_libraries( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) current_user_roles = trans.get_current_user_roles() all_libraries = trans.sa_session.query( trans.app.model.Library ) \ .filter( trans.app.model.Library.table.c.deleted==False ) \ @@ -32,5 +32,5 @@ return trans.fill_template( '/library/browse_libraries.mako', libraries=authorized_libraries, default_action=params.get( 'default_action', None ), - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Fri Apr 02 16:06:43 2010 -0400 @@ -92,8 +92,8 @@ @web.require_admin def create_library( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get( 'create_library_button', False ): name = util.restore_text( params.get( 'name', 'No name' ) ) description = util.restore_text( params.get( 'description', '' ) ) @@ -105,14 +105,14 @@ library.root_folder = root_folder trans.sa_session.add_all( ( library, root_folder ) ) trans.sa_session.flush() - msg = "The new library named '%s' has been created" % library.name + message = "The new library named '%s' has been created" % library.name return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=trans.security.encode_id( library.id ), - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) + message=util.sanitize_text( message ), + status='done' ) ) + return trans.fill_template( '/admin/library/new_library.mako', message=message, status=status ) @web.expose @web.require_admin def purge_library( self, trans, **kwd ): @@ -146,20 +146,20 @@ trans.sa_session.add( library_folder ) trans.sa_session.flush() if not library.deleted: - msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) + message = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', - message=util.sanitize_text( msg ), + message=util.sanitize_text( message ), status='error' ) ) else: purge_folder( library.root_folder ) library.purged = True trans.sa_session.add( library ) trans.sa_session.flush() - msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name + message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_libraries', - message=util.sanitize_text( msg ), + message=util.sanitize_text( message ), status='done' ) ) @web.expose @web.require_admin @@ -176,8 +176,8 @@ 'folder': trans.app.model.LibraryFolder, 'library_dataset': trans.app.model.LibraryDataset } if item_type not in item_types: - msg = 'Bad item_type specified: %s' % str( item_type ) - messagetype = 'error' + message = 'Bad item_type specified: %s' % str( item_type ) + status = 'error' else: if item_type == 'library_dataset': item_desc = 'Dataset' @@ -187,18 +187,18 @@ library_item.deleted = True trans.sa_session.add( library_item ) trans.sa_session.flush() - msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) - messagetype = 'done' + message = util.sanitize_text( "%s '%s' has been marked deleted" % ( item_desc, library_item.name ) ) + status = 'done' if item_type == 'library': - return self.browse_libraries( trans, message=msg, status=messagetype ) + return self.browse_libraries( trans, message=message, status=status ) else: return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=library_id, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) ) + message=message, + status=status ) ) @web.expose @web.require_admin def undelete_library_item( self, trans, library_id, item_id, item_type, **kwd ): @@ -208,7 +208,7 @@ 'folder': trans.app.model.LibraryFolder, 'library_dataset': trans.app.model.LibraryDataset } if item_type not in item_types: - msg = 'Bad item_type specified: %s' % str( item_type ) + message = 'Bad item_type specified: %s' % str( item_type ) status = ERROR else: if item_type == 'library_dataset': @@ -217,21 +217,21 @@ item_desc = item_type.capitalize() library_item = trans.sa_session.query( item_types[ item_type ] ).get( trans.security.decode_id( item_id ) ) if library_item.purged: - msg = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) + message = '%s %s has been purged, so it cannot be undeleted' % ( item_desc, library_item.name ) status = ERROR else: library_item.deleted = False trans.sa_session.add( library_item ) trans.sa_session.flush() - msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) + message = util.sanitize_text( "%s '%s' has been marked undeleted" % ( item_desc, library_item.name ) ) status = SUCCESS if item_type == 'library': - return self.browse_libraries( trans, message=msg, status=status ) + return self.browse_libraries( trans, message=message, status=status ) else: return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller='library_admin', id=library_id, show_deleted=show_deleted, - msg=msg, - messagetype=status ) ) + message=message, + status=status ) ) diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Fri Apr 02 16:06:43 2010 -0400 @@ -79,18 +79,18 @@ @web.expose def browse_library( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) library_id = params.get( 'id', None ) if not library_id: # To handle bots - msg = "You must specify a library id." - messagetype = 'error' + message = "You must specify a library id." + status = 'error' library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) if not library: # To handle bots - msg = "Invalid library id ( %s )." % str( library_id ) - messagetype = 'error' + message = "Invalid library id ( %s )." % str( library_id ) + status = 'error' else: # If use_panels is True, the library is being accessed via an external link # which did not originate from within the Galaxy instance, and the library will @@ -100,12 +100,12 @@ created_ldda_ids = params.get( 'created_ldda_ids', '' ) hidden_folder_ids = util.listify( params.get( 'hidden_folder_ids', '' ) ) current_user_roles = trans.get_current_user_roles() - if created_ldda_ids and not msg: - msg = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \ + if created_ldda_ids and not message: + message = "%d datasets are uploading in the background to the library '%s' (each is selected). " % \ ( len( created_ldda_ids.split( ',' ) ), library.name ) - msg += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the " - msg += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." - messagetype = "info" + message += "Don't navigate away from Galaxy or use the browser's \"stop\" or \"reload\" buttons (on this tab) until the " + message += "message \"This job is running\" is cleared from the \"Information\" column below for each selected dataset." + status = "info" return trans.fill_template( '/library/common/browse_library.mako', cntrller=cntrller, use_panels=use_panels, @@ -115,19 +115,19 @@ show_deleted=show_deleted, comptypes=comptypes, current_user_roles=current_user_roles, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) return trans.response.send_redirect( web.url_for( use_panels=use_panels, controller=cntrller, action='browse_libraries', default_action=params.get( 'default_action', None ), - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) @web.expose def library_info( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -140,8 +140,8 @@ old_name = library.name new_name = util.restore_text( params.get( 'name', 'No name' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype='error' + message = 'Enter a valid name' + status='error' else: new_description = util.restore_text( params.get( 'description', '' ) ) new_synopsis = util.restore_text( params.get( 'synopsis', '' ) ) @@ -155,15 +155,15 @@ library.root_folder.description = new_description trans.sa_session.add_all( ( library, library.root_folder ) ) trans.sa_session.flush() - msg = "The information has been updated." + message = "The information has been updated." return trans.response.send_redirect( web.url_for( controller='library_common', action='library_info', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) return trans.fill_template( '/library/common/library_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -173,13 +173,13 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def library_permissions( self, trans, cntrller, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_id = params.get( 'id', None ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -195,15 +195,15 @@ trans.sa_session.refresh( library ) # Copy the permissions to the root folder trans.app.security_agent.copy_library_permissions( library, library.root_folder ) - msg = "Permissions updated for library '%s'" % library.name + message = "Permissions updated for library '%s'" % library.name return trans.response.send_redirect( web.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, use_panels=use_panels, id=trans.security.encode_id( library.id ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_permissions.mako', cntrller=cntrller, @@ -212,26 +212,26 @@ current_user_roles=current_user_roles, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def create_folder( self, trans, cntrller, parent_id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) parent_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( parent_id ) ) if not parent_folder: - msg = "Invalid parent folder id (%s) specified" % str( parent_id ) + message = "Invalid parent folder id (%s) specified" % str( parent_id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if params.get( 'new_folder_button', False ): new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), description=util.restore_text( params.description ) ) @@ -252,8 +252,8 @@ widgets = new_folder.get_template_widgets( trans ) if info_association: current_user_roles = trans.get_current_user_roles() - msg = "The new folder named '%s' has been added to the data library. " % new_folder.name - msg += "Additional information about this folder may be added using the inherited template." + message = "The new folder named '%s' has been added to the data library. " % new_folder.name + message += "Additional information about this folder may be added using the inherited template." return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -264,18 +264,18 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype='done' ) + message=message, + status='done' ) # If not inheritable info_association, redirect to the library. - msg = "The new folder named '%s' has been added to the data library." % new_folder.name + message = "The new folder named '%s' has been added to the data library." % new_folder.name return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) # We do not render any template widgets on creation pages since saving the info_association # cannot occur before the associated item is saved. return trans.fill_template( '/library/common/new_folder.mako', @@ -284,13 +284,13 @@ library_id=library_id, folder=parent_folder, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def folder_info( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) @@ -306,18 +306,18 @@ new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) if not new_name: - msg = 'Enter a valid name' - messagetype='error' + message = 'Enter a valid name' + status='error' else: folder.name = new_name folder.description = new_description trans.sa_session.add( folder ) trans.sa_session.flush() - msg = "The information has been updated." - messagetype='done' + message = "The information has been updated." + status='done' else: - msg = "You are not authorized to edit this folder" - messagetype='error' + message = "You are not authorized to edit this folder" + status='error' return trans.fill_template( '/library/common/folder_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -328,26 +328,26 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def folder_permissions( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( id ) ) if not folder: - msg = "Invalid folder specified, id: %s" % str( id ) + message = "Invalid folder specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() if params.get( 'update_roles_button', False ): # The user clicked the Save button on the 'Associate With Roles' form @@ -361,11 +361,11 @@ permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles trans.app.security_agent.set_all_library_permissions( folder, permissions ) trans.sa_session.refresh( folder ) - msg = 'Permissions updated for folder %s' % folder.name - messagetype='done' + message = 'Permissions updated for folder %s' % folder.name + status='done' else: - msg = "You are not authorized to manage permissions on this folder" - messagetype = "error" + message = "You are not authorized to manage permissions on this folder" + status = "error" return trans.response.send_redirect( web.url_for( controller='library_common', action='folder_permissions', cntrller=cntrller, @@ -373,8 +373,8 @@ id=trans.security.encode_id( folder.id ), library_id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # If the library is public all roles are legitimate, but if the library is restricted, only those # roles associated with the LIBRARY_ACCESS permission are legitimate. library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) @@ -387,26 +387,26 @@ current_user_roles=current_user_roles, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_edit_info( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) + message = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): dbkey = dbkey[0] @@ -424,14 +424,14 @@ if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) trans.sa_session.flush() - msg = "Data type changed for library dataset '%s'" % ldda.name - messagetype = 'done' + message = "Data type changed for library dataset '%s'" % ldda.name + status = 'done' else: - msg = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) - messagetype = 'error' + message = "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) + status = 'error' else: - msg = "You are not authorized to change the data type of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to change the data type of dataset '%s'" % ldda.name + status = 'error' elif params.get( 'save', False ): # The user clicked the Save button on the 'Edit Attributes' form if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): @@ -440,8 +440,8 @@ new_info = util.restore_text( params.get( 'info', '' ) ) new_message = util.restore_text( params.get( 'message', '' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' + message = 'Enter a valid name' + status = 'error' else: ldda.name = new_name ldda.info = new_info @@ -459,11 +459,11 @@ ldda.metadata.dbkey = dbkey ldda.datatype.after_setting_metadata( ldda ) trans.sa_session.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' + message = 'Attributes updated for library dataset %s' % ldda.name + status = 'done' else: - msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name + status = 'error' elif params.get( 'detect', False ): # The user clicked the Auto-detect button on the 'Edit Attributes' form if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): @@ -475,11 +475,11 @@ ldda.datatype.set_meta( ldda ) ldda.datatype.after_setting_metadata( ldda ) trans.sa_session.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' + message = 'Attributes updated for library dataset %s' % ldda.name + status = 'done' else: - msg = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to edit the attributes of dataset '%s'" % ldda.name + status = 'error' if cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: # Copy dbkey into metadata, for backwards compatability @@ -499,26 +499,26 @@ show_deleted=show_deleted, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_info( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) + message = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) # See if we have any associated templates widgets = [] @@ -536,13 +536,13 @@ current_user_roles=current_user_roles, info_association=info_association, inherited=inherited, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def ldda_permissions( self, trans, cntrller, library_id, folder_id, id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ids = util.listify( id ) @@ -550,15 +550,15 @@ for id in [ trans.security.decode_id( id ) for id in ids ]: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( id ) if ldda is None: - msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) + message = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) lddas.append( ldda ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) # If access to the dataset is restricted, then use the roles associated with the DATASET_ACCESS permission to @@ -577,7 +577,7 @@ if cntrller=='library_admin' or ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \ trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ): a = trans.app.security_agent.get_action( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action ) - permissions, in_roles, error, msg = \ + permissions, in_roles, error, message = \ trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **kwd ) for ldda in lddas: # Set the DATASET permissions on the Dataset. @@ -601,13 +601,13 @@ trans.app.security_agent.set_all_library_permissions( ldda, permissions ) trans.sa_session.refresh( ldda ) if error: - messagetype = 'error' + status = 'error' else: - msg = 'Permissions have been updated on %d datasets.' % len( lddas ) - messagetype= 'done' + message = 'Permissions have been updated on %d datasets.' % len( lddas ) + status= 'done' else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' + message = "You are not authorized to change the permissions of dataset '%s'" % ldda.name + status = 'error' return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, use_panels=use_panels, @@ -615,8 +615,8 @@ library_id=library_id, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) if len( ids ) > 1: # Ensure that the permissions across all library items are identical, otherwise we can't update them together. check_list = [] @@ -634,15 +634,15 @@ if not check_list: check_list = permissions if permissions != check_list: - msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' + message = 'The datasets you selected do not have identical permissions, so they can not be updated together' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) # Display permission form, permissions will be updated for all lddas simultaneously. return trans.fill_template( "/library/common/ldda_permissions.mako", cntrller=cntrller, @@ -651,13 +651,13 @@ library_id=library_id, roles=roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def upload_library_dataset( self, trans, cntrller, library_id, folder_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) deleted = util.string_as_bool( params.get( 'deleted', False ) ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) dbkey = params.get( 'dbkey', '?' ) @@ -694,10 +694,10 @@ error = None if roles: vars = dict( DATASET_ACCESS_in=roles ) - permissions, in_roles, error, msg = \ + permissions, in_roles, error, message = \ trans.app.security_agent.derive_roles_from_access( trans, trans.app.security.decode_id( library_id ), cntrller, library=True, **vars ) if error: - messagetype = 'error' + status = 'error' trans.response.send_redirect( web.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, @@ -706,8 +706,8 @@ replace_id=replace_id, upload_option=upload_option, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) else: # See if we have any inherited templates, but do not inherit contents. @@ -731,16 +731,16 @@ ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] created_ldda_ids=",".join( ldda_id_list ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder - msg = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) else: - msg = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) if cntrller == 'library_admin': - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." - messagetype='done' + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + status='done' else: # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need # to check one of them to see if the current user can manage permissions on them. @@ -749,7 +749,7 @@ if replace_dataset: default_action = '' else: - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: default_action = 'add' @@ -760,21 +760,21 @@ default_action=default_action, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) else: created_ldda_ids = '' - msg = "Upload failed" - messagetype='error' + message = "Upload failed" + status='error' trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) if info_association and info_association.inheritable: @@ -819,8 +819,8 @@ history=history, widgets=widgets, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ): # Set up the traditional tool state/params tool_id = 'upload1' @@ -836,8 +836,8 @@ params = util.Params( kwd ) # is this filetoolparam safe? show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) server_dir = util.restore_text( params.get( 'server_dir', '' ) ) if replace_dataset not in [ None, 'None' ]: replace_id = trans.security.encode_id( replace_dataset.id ) @@ -860,21 +860,21 @@ else: full_dir = os.path.join( import_dir, trans.user.email, server_dir ) if import_dir: - msg = 'Select a directory' + message = 'Select a directory' else: - msg = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc + message = '"%s" is not defined in the Galaxy configuration file' % import_dir_desc # Proceed with (mostly) regular upload processing precreated_datasets = upload_common.get_precreated_datasets( trans, tool_params, trans.app.model.LibraryDatasetDatasetAssociation, controller=cntrller ) if upload_option == 'upload_file': tool_params = upload_common.persist_uploads( tool_params ) uploaded_datasets = upload_common.get_uploaded_datasets( trans, cntrller, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) elif upload_option == 'upload_directory': - uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, message = self.get_server_dir_uploaded_datasets( trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, message ) elif upload_option == 'upload_paths': - uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, message = self.get_path_paste_uploaded_datasets( trans, cntrller, params, library_bunch, err_redirect, message ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if upload_option == 'upload_file' and not uploaded_datasets: - msg = 'Select a file, enter a URL or enter text' + message = 'Select a file, enter a URL or enter text' err_redirect = True if err_redirect: trans.response.send_redirect( web.url_for( controller='library_common', @@ -885,8 +885,8 @@ replace_id=replace_id, upload_option=upload_option, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) @@ -909,7 +909,7 @@ trans.sa_session.add( uploaded_dataset.data ) trans.sa_session.flush() return uploaded_dataset - def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): + def get_server_dir_uploaded_datasets( self, trans, cntrller, params, full_dir, import_dir_desc, library_bunch, err_redirect, message ): files = [] try: for entry in os.listdir( full_dir ): @@ -925,23 +925,23 @@ if os.path.isfile( path ): files.append( path ) except Exception, e: - msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) + message = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message if not files: - msg = "The directory '%s' contains no valid files" % full_dir + message = "The directory '%s' contains no valid files" % full_dir err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message uploaded_datasets = [] for file in files: name = os.path.basename( file ) uploaded_datasets.append( self.make_library_uploaded_dataset( trans, cntrller, params, name, file, 'server_dir', library_bunch ) ) return uploaded_datasets, None, None - def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, err_redirect, msg ): + def get_path_paste_uploaded_datasets( self, trans, cntrller, params, library_bunch, err_redirect, message ): if params.get( 'filesystem_paths', '' ) == '': - msg = "No paths entered in the upload form" + message = "No paths entered in the upload form" err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message preserve_dirs = True if params.get( 'dont_preserve_dirs', False ): preserve_dirs = False @@ -974,16 +974,16 @@ library_bunch, in_folder ) ) if bad_paths: - msg = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) + message = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) err_redirect = True - return None, err_redirect, msg + return None, err_redirect, message return uploaded_datasets, None, None @web.expose def add_history_datasets_to_library( self, trans, cntrller, library_id, folder_id, hda_ids='', **kwd ): params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) ) replace_id = params.get( 'replace_id', None ) if replace_id: @@ -994,14 +994,14 @@ history = trans.get_history() trans.sa_session.refresh( history ) if not history.active_datasets: - msg = 'Your current history is empty' + message = 'Your current history is empty' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if params.get( 'add_history_datasets_to_library_button', False ): hda_ids = util.listify( hda_ids ) if hda_ids: @@ -1021,28 +1021,28 @@ # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda ) else: - msg = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) + message = "The requested HistoryDatasetAssociation id %s is invalid" % str( hda_id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) if created_ldda_ids: created_ldda_ids = created_ldda_ids.lstrip( ',' ) ldda_id_list = created_ldda_ids.split( ',' ) total_added = len( ldda_id_list ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + message = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder - msg = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the library '%s' (each is selected). " % ( total_added, folder.name ) else: - msg = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) + message = "Added %d datasets to the folder '%s' (each is selected). " % ( total_added, folder.name ) if cntrller == 'library_admin': - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." else: # Since permissions on all LibraryDatasetDatasetAssociations must be the same at this point, we only need # to check one of them to see if the current user can manage permissions on them. @@ -1052,7 +1052,7 @@ if replace_dataset: default_action = '' else: - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + message += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." default_action = 'manage_permissions' else: default_action = 'add' @@ -1062,11 +1062,11 @@ id=library_id, created_ldda_ids=created_ldda_ids, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) else: - msg = 'Select at least one dataset from the list of active datasets in your current history' - messagetype = 'error' + message = 'Select at least one dataset from the list of active datasets in your current history' + status = 'error' last_used_build = folder.genome_build upload_option = params.get( 'upload_option', 'import_from_history' ) # Send list of data formats to the form so the "extension" select list can be populated dynamically @@ -1091,8 +1091,8 @@ history=history, widgets=[], show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ): """Catches the dataset id and displays file contents as directed""" @@ -1101,8 +1101,8 @@ use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) - messagetype = 'error' + message = 'Invalid LibraryDatasetDatasetAssociation id %s received for file download' % str( id ) + status = 'error' else: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) ext = ldda.extension @@ -1123,33 +1123,33 @@ try: return open( ldda.file_name ) except: - msg = 'This dataset contains no content' + message = 'This dataset contains no content' return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) @web.expose def library_dataset_info( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( id ) ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + message = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() # See if we have any associated templates widgets = [] @@ -1163,18 +1163,18 @@ new_name = util.restore_text( params.get( 'name', '' ) ) new_info = util.restore_text( params.get( 'info', '' ) ) if not new_name: - msg = 'Enter a valid name' - messagetype = 'error' + message = 'Enter a valid name' + status = 'error' else: library_dataset.name = new_name library_dataset.info = new_info trans.sa_session.add( library_dataset ) trans.sa_session.flush() - msg = "The information has been updated." - messagetype = 'done' + message = "The information has been updated." + status = 'done' else: - msg = "You are not authorized to change the attributes of this dataset" - messagetype = "error" + message = "You are not authorized to change the attributes of this dataset" + status = "error" return trans.fill_template( '/library/common/library_dataset_info.mako', cntrller=cntrller, use_panels=use_panels, @@ -1185,26 +1185,26 @@ inherited=inherited, widgets=widgets, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def library_dataset_permissions( self, trans, cntrller, id, library_id, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) library_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( id ) if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) + message = "Invalid library dataset specified, id: %s" %str( id ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) current_user_roles = trans.get_current_user_roles() if params.get( 'update_roles_button', False ): if cntrller == 'library_admin' or trans.app.security_agent.can_manage_library_item( current_user_roles, library_dataset ): @@ -1223,11 +1223,11 @@ # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions ) trans.sa_session.refresh( library_dataset.library_dataset_dataset_association ) - msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name - messagetype = 'done' + message = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name + status = 'done' else: - msg = "You are not authorized to managed the permissions of this dataset" - messagetype = "error" + message = "You are not authorized to managed the permissions of this dataset" + status = "error" library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( '/library/common/library_dataset_permissions.mako', @@ -1238,53 +1238,53 @@ roles=roles, current_user_roles=current_user_roles, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ): # Perform an action on a list of library datasets. params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) action = params.get( 'do_action', None ) if not ldda_ids: - msg = "You must select at least one dataset" - messagetype = 'error' + message = "You must select at least one dataset" + status = 'error' elif not action: - msg = "You must select an action to perform on selected datasets" - messagetype = 'error' + message = "You must select an action to perform on selected datasets" + status = 'error' else: ldda_ids = util.listify( ldda_ids ) if action == 'import_to_history' or action == 'add': history = trans.get_history() if history is None: # Must be a bot sending a request without having a history. - msg = "You do not have a current history" + message = "You do not have a current history" return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) total_imported_lddas = 0 - msg = '' - messagetype = 'done' + message = '' + status = 'done' for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - msg += "Cannot import dataset (%s) since it's state is (%s). " % ( ldda.name, ldda.dataset.state ) - messagetype = 'error' + message += "Cannot import dataset (%s) since it's state is (%s). " % ( ldda.name, ldda.dataset.state ) + status = 'error' elif ldda.dataset.state in [ 'ok', 'error' ]: hda = ldda.to_history_dataset_association( target_history=history, add_to_history=True ) total_imported_lddas += 1 if total_imported_lddas: trans.sa_session.add( history ) trans.sa_session.flush() - msg += "%i dataset(s) have been imported into your history. " % total_imported_lddas + message += "%i dataset(s) have been imported into your history. " % total_imported_lddas elif action == 'manage_permissions': # We need the folder containing the LibraryDatasetDatasetAssociation(s) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_ids[0] ) ) @@ -1296,8 +1296,8 @@ folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), id=",".join( ldda_ids ), show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) elif action == 'delete': for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) @@ -1307,7 +1307,7 @@ ld.deleted = True trans.sa_session.add( ld ) trans.sa_session.flush() - msg = "The selected datasets have been removed from this data library" + message = "The selected datasets have been removed from this data library" elif action in ['zip','tgz','tbz']: error = False killme = string.punctuation + string.whitespace @@ -1332,13 +1332,13 @@ except (OSError, zipfile.BadZipFile): error = True log.exception( "Unable to create archive for download" ) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' except: error = True log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0]) - msg = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - messagetype = 'error' + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' if not error: composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) seen = [] @@ -1374,8 +1374,8 @@ except IOError: error = True log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' continue flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths for fpath in flist: @@ -1387,8 +1387,8 @@ except IOError: error = True log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' continue else: # simple case try: @@ -1396,8 +1396,8 @@ except IOError: error = True log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' if not error: if action == 'zip': archive.close() @@ -1409,8 +1409,8 @@ except OSError: error = True log.exception( "Unable to remove temporary library download archive and directory" ) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' + message = "Unable to create archive for download, please report this error" + status = 'error' if not error: trans.response.set_content_type( "application/x-zip-compressed" ) trans.response.headers[ "Content-Disposition" ] = "attachment; filename=%s.%s" % (outfname,outext) @@ -1422,7 +1422,7 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream else: # unknown action - msg = '### unknown action = %s in act_on_multiple_datasets' % action + message = '### unknown action = %s in act_on_multiple_datasets' % action return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', @@ -1430,8 +1430,8 @@ use_panels=use_panels, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) def get_item_and_stuff( self, trans, item_type, library_id, folder_id, ldda_id ): # Return an item, description, action and an id based on the item_type. if item_type == 'library': @@ -1450,14 +1450,14 @@ action = 'ldda_edit_info' id = ldda_id else: - msg = "Invalid library item type ( %s )" % str( item_type ) + message = "Invalid library item type ( %s )" % str( item_type ) return trans.response.send_redirect( web.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + message=util.sanitize_text( message ), + status='error' ) ) return item, item_desc, action, id @web.expose def add_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): @@ -1466,19 +1466,19 @@ filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) if not forms: - msg = "There are no forms on which to base the template, so create a form and then add the template." + message = "There are no forms on which to base the template, so create a form and then add the template." trans.response.send_redirect( web.url_for( controller='forms', action='new', - msg=msg, - messagetype='done', + message=message, + status='done', form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ) ) else: params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) + message = util.restore_text( params.get( 'message', '' ) ) action = '' - messagetype = params.get( 'messagetype', 'done' ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # If the inheritable checkbox is checked, the param will be in the request inheritable = CheckboxField.is_checked( params.get( 'inheritable', '' ) ) @@ -1497,7 +1497,7 @@ assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, form, form_values ) trans.sa_session.add( assoc ) trans.sa_session.flush() - msg = 'A template based on the form "%s" has been added to this %s.' % ( form.name, item_desc ) + message = 'A template based on the form "%s" has been added to this %s.' % ( form.name, item_desc ) trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1506,11 +1506,11 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=msg, - messagetype='done' ) ) + message=message, + status='done' ) ) else: - msg = "Select a form on which to base the template." - messagetype = "error" + message = "Select a form on which to base the template." + status = "error" def generate_template_stuff( trans, forms, form_id ): # Returns the following: # - a list of template ids @@ -1555,22 +1555,22 @@ template_select_list=template_select_list, inheritable_checked=inheritable, show_deleted=show_deleted, - msg=msg, - messagetype=messagetype ) + message=message, + status=status ) @web.expose def manage_template_inheritance( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd ): params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) info_association, inherited = item.get_info_association( restrict=True ) if info_association: if info_association.inheritable: - msg = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will no longer be inherited to contained folders and datasets." % item_desc else: - msg = "The template for this %s will now be inherited to contained folders and datasets." % item_desc + message = "The template for this %s will now be inherited to contained folders and datasets." % item_desc info_association.inheritable = not( info_association.inheritable ) trans.sa_session.add( info_association ) trans.sa_session.flush() @@ -1582,16 +1582,16 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) @web.expose def edit_template( self, trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, edited=False, **kwd ): # Edit the template itself, keeping existing field contents, if any. params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # An info_association must exist at this point info_association, inherited = item.get_info_association( restrict=True ) @@ -1605,7 +1605,7 @@ info_association.template = fdc.latest_form trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = "The template for this %s has been updated with your changes." % item_desc + message = "The template for this %s has been updated with your changes." % item_desc return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1614,8 +1614,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) # "template" is a FormDefinition, so since we're changing it, we need to use the latest version of it. vars = dict( id=trans.security.encode_id( template.form_definition_current_id ), response_redirect=web.url_for( controller='library_common', @@ -1634,8 +1634,8 @@ params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) # Save updated template field contents field_contents = [] @@ -1681,7 +1681,7 @@ info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( item, template, form_values ) trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = 'The information has been updated.' + message = 'The information has been updated.' return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1690,8 +1690,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) + message=util.sanitize_text( message ), + status='done' ) ) @web.expose def delete_template( self, trans, cntrller, item_type, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): # Only adding a new template to a library or folder is currently allowed. Editing an existing template is @@ -1699,19 +1699,19 @@ params = util.Params( kwd ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) item, item_desc, action, id = self.get_item_and_stuff( trans, item_type, library_id, folder_id, ldda_id ) info_association, inherited = item.get_info_association() if not info_association: - msg = "There is no template for this %s" % item_type - messagetype = 'error' + message = "There is no template for this %s" % item_type + status = 'error' else: info_association.deleted = True trans.sa_session.add( info_association ) trans.sa_session.flush() - msg = 'The template for this %s has been deleted.' % item_type - messagetype = 'done' + message = 'The template for this %s has been deleted.' % item_type + status = 'done' return trans.response.send_redirect( web.url_for( controller='library_common', action=action, cntrller=cntrller, @@ -1720,8 +1720,8 @@ folder_id=folder_id, id=id, show_deleted=show_deleted, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) + message=util.sanitize_text( message ), + status=status ) ) # ---- Utility methods ------------------------------------------------------- diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Fri Apr 02 16:06:43 2010 -0400 @@ -164,7 +164,7 @@ elif operation == "events": return self.__request_events( trans, **kwd ) # if there are one or more requests that has been rejected by the admin - # recently, then show a msg as a reminder to the user + # recently, then show a message as a reminder to the user rlist = trans.sa_session.query( trans.app.model.Request ) \ .filter( trans.app.model.Request.table.c.deleted==False ) \ .filter( trans.app.model.Request.table.c.user_id==trans.user.id ) @@ -182,12 +182,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = request.events @@ -238,8 +238,8 @@ return request_details def __show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) add_sample = params.get('add_sample', False) try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) @@ -279,7 +279,7 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False' ) ), - msg=msg, messagetype=messagetype ) + message=message, status=status ) def __library_widgets(self, trans, user, sample_index, libraries, sample=None, **kwd): ''' This method creates the data library & folder selectbox for creating & @@ -424,8 +424,8 @@ @web.require_login( "create/submit sequencing requests" ) def show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -503,28 +503,28 @@ edit_mode=edit_mode) elif params.get('save_samples_button', False) == 'Save': # check for duplicate sample names - msg = '' + message = '' for index in range(len(current_samples)-len(request.samples)): sample_index = index + len(request.samples) sample_name = current_samples[sample_index]['name'] if not sample_name.strip(): - msg = 'Please enter the name of sample number %i' % sample_index + message = 'Please enter the name of sample number %i' % sample_index break count = 0 for i in range(len(current_samples)): if sample_name == current_samples[i]['name']: count = count + 1 if count > 1: - msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) break - if msg: + if message: return trans.fill_template( '/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), current_samples = current_samples, sample_copy=self.__copy_sample(current_samples), details=details, edit_mode=edit_mode, - messagetype='error', msg=msg) + status='error', message=message) # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): @@ -542,18 +542,18 @@ trans.sa_session.add( s ) trans.sa_session.flush() else: - messagetype = 'done' - msg = 'Changes made to the sample(s) are saved. ' + status = 'done' + message = 'Changes made to the sample(s) are saved. ' for sample_index in range(len(current_samples)): sample = request.samples[sample_index] sample.name = current_samples[sample_index]['name'] sample.library = current_samples[sample_index]['library'] sample.folder = current_samples[sample_index]['folder'] if request.submitted(): - bc_msg = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) - if bc_msg: - messagetype = 'error' - msg += bc_msg + bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) + if bc_message: + status = 'error' + message += bc_message else: sample.bar_code = current_samples[sample_index]['barcode'] trans.sa_session.add( sample ) @@ -566,8 +566,8 @@ action='list', operation='show_request', id=trans.security.encode_id(request.id), - messagetype=messagetype, - msg=msg )) + status=status, + message=message )) elif params.get('edit_samples_button', False) == 'Edit samples': edit_mode = 'True' return trans.fill_template( '/requests/show_request.mako', @@ -589,15 +589,15 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details=details, libraries=libraries, - edit_mode=edit_mode, messagetype=messagetype, msg=msg) + edit_mode=edit_mode, status=status, message=message) @web.expose @web.require_login( "create/submit sequencing requests" ) def delete_sample(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) ) current_samples, details, edit_mode = self.__update_samples( request, **kwd ) sample_index = int(params.get('sample_id', 0)) @@ -639,34 +639,34 @@ @web.require_login( "create/submit sequencing requests" ) def new(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get('select_request_type', False) == 'True': return trans.fill_template( '/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) elif params.get('create', False) == 'True': if params.get('create_request_button', False) == 'Save' \ or params.get('create_request_samples_button', False) == 'Add samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' + message = 'Please enter the <b>Name</b> of the request' kwd['create'] = 'True' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + kwd['status'] = 'error' + kwd['message'] = message kwd['create_request_button'] = None kwd['create_request_samples_button'] = None return trans.response.send_redirect( web.url_for( controller='requests', action='new', **kwd) ) request = self.__save_request(trans, None, **kwd) - msg = 'The new request named <b>%s</b> has been created' % request.name + message = 'The new request named <b>%s</b> has been created' % request.name if params.get('create_request_button', False) == 'Save': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - message=msg , + message=message , status='done') ) elif params.get('create_request_samples_button', False) == 'Add samples': new_kwd = {} @@ -675,8 +675,8 @@ new_kwd['add_sample'] = True return trans.response.send_redirect( web.url_for( controller='requests', action='list', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) else: return self.__show_request_form(trans, **kwd) @@ -684,16 +684,16 @@ return self.__show_request_form(trans, **kwd) def __show_request_form(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) except: return trans.fill_template( '/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) form_values = None select_request_type = self.__select_request_type(trans, request_type.id) # list of widgets to be rendered on the request form @@ -711,8 +711,8 @@ select_request_type=select_request_type, request_type=request_type, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) def __validate(self, trans, request): ''' Validates the request entered by the user @@ -723,14 +723,14 @@ if field['required'] == 'required' and request.values.content[index] in ['', None]: empty_fields.append(field['label']) if empty_fields: - msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name for ef in empty_fields: - msg = msg + '<b>' +ef + '</b><br/>' + message = message + '<b>' +ef + '</b><br/>' return trans.response.send_redirect( web.url_for( controller='requests', action='list', operation='edit', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) )) # now check the required fields of all the samples of this request for s in request.samples: @@ -738,14 +738,14 @@ if field['required'] == 'required' and s.values.content[index] in ['', None]: empty_fields.append((s.name, field['label'])) if empty_fields: - msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name for sname, ef in empty_fields: - msg = msg + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname) + message = message + '<b>%s</b> field of sample <b>%s</b><br/>' % (ef, sname) return trans.response.send_redirect( web.url_for( controller='requests', action='list', operation='show_request', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) )) def __save_request(self, trans, request=None, **kwd): ''' @@ -823,8 +823,8 @@ @web.require_login( "create/submit sequencing requests" ) def edit(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -839,19 +839,19 @@ or params.get('edit_samples_button', False) == 'Edit samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + message = 'Please enter the <b>Name</b> of the request' + kwd['status'] = 'error' + kwd['message'] = message kwd['show'] = 'True' return trans.response.send_redirect( web.url_for( controller='requests', action='edit', **kwd) ) request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name + message = 'The changes made to the request named %s has been saved' % request.name if params.get('save_changes_request_button', False) == 'Save changes': return trans.response.send_redirect( web.url_for( controller='requests', action='list', - message=msg , + message=message , status='done') ) elif params.get('edit_samples_button', False) == 'Edit samples': new_kwd = {} @@ -859,8 +859,8 @@ new_kwd['edit_samples_button'] = 'Edit samples' return trans.response.send_redirect( web.url_for( controller='requests', action='show_request', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) elif params.get('refresh', False) == 'true': return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) @@ -869,15 +869,15 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg) ) + message=message) ) params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) select_request_type = self.__select_request_type(trans, request.type.id) # list of widgets to be rendered on the request form widgets = [] @@ -901,8 +901,8 @@ request_type=request.type, request=request, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) return self.__show_request_form(trans) def __delete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) @@ -911,12 +911,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) # a request cannot be deleted once its submitted if not request.new(): @@ -926,28 +926,28 @@ trans.sa_session.add( request ) trans.sa_session.flush() if not len(delete_failed): - msg = '%i request(s) has been deleted.' % len(id_list) + message = '%i request(s) has been deleted.' % len(id_list) status = 'done' else: - msg = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed), + message = '%i request(s) has been deleted. %i request %s could not be deleted as they have been submitted.' % (len(id_list)-len(delete_failed), len(delete_failed), str(delete_failed)) status = 'warning' return trans.response.send_redirect( web.url_for( controller='requests', action='list', status=status, - message=msg) ) + message=message) ) def __undelete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) for id in id_list: try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = False trans.sa_session.add( request ) @@ -960,12 +960,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) # check if all the required request and its sample fields have been filled self.__validate(trans, request) @@ -994,11 +994,11 @@ sample_id = int(params.get('sample_id', False)) sample = trans.sa_session.query( trans.app.model.Sample ).get( sample_id ) except: - msg = "Invalid sample ID" + message = "Invalid sample ID" return trans.response.send_redirect( web.url_for( controller='requests', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = sample.events @@ -1015,8 +1015,8 @@ @web.require_login( "create/submit sequencing requests" ) def show_datatx_page( self, trans, **kwd ): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: sample = trans.sa_session.query( trans.app.model.Sample ).get( trans.security.decode_id( kwd['sample_id'] ) ) except: diff -r 43b7a7f4bff5 -r f2b6d4f3189c lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Fri Apr 02 15:09:29 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Apr 02 16:06:43 2010 -0400 @@ -289,8 +289,8 @@ @web.require_admin def edit(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -305,19 +305,19 @@ or params.get('edit_samples_button', False) == 'Edit samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + message = 'Please enter the <b>Name</b> of the request' + kwd['status'] = 'error' + kwd['message'] = message kwd['show'] = 'True' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='edit', **kwd) ) request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name + message = 'The changes made to the request named %s has been saved' % request.name if params.get('save_changes_request_button', False) == 'Save changes': return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', - message=msg , + message=message , status='done') ) elif params.get('edit_samples_button', False) == 'Edit samples': new_kwd = {} @@ -325,8 +325,8 @@ new_kwd['edit_samples_button'] = 'Edit samples' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_request', - msg=msg , - messagetype='done', + message=message , + status='done', **new_kwd) ) elif params.get('refresh', False) == 'true': return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) @@ -335,15 +335,15 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg) ) + message=message) ) params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) select_request_type = self.__select_request_type(trans, request.type.id) # list of widgets to be rendered on the request form widgets = [] @@ -367,8 +367,8 @@ request_type=request.type, request=request, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) return self.__show_request_form(trans) def __delete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) @@ -376,34 +376,34 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = True trans.sa_session.add( request ) trans.sa_session.flush() - msg = '%i request(s) has been deleted.' % len(id_list) + message = '%i request(s) has been deleted.' % len(id_list) status = 'done' return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status=status, - message=msg) ) + message=message) ) def __undelete_request(self, trans, **kwd): id_list = util.listify( kwd['id'] ) for id in id_list: try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(id) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) request.deleted = False trans.sa_session.add( request ) @@ -416,20 +416,20 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) - msg = self.__validate(trans, request) - if msg: + message = self.__validate(trans, request) + if message: return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', operation='edit', - messagetype = 'error', - msg=msg, + status = 'error', + message=message, id=trans.security.encode_id(request.id) ) ) # change the request state to 'Submitted' if request.user.email is not trans.user: @@ -456,12 +456,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) return trans.fill_template( '/admin/requests/reject.mako', request=request) @@ -477,18 +477,18 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) # validate if not params.get('comment', ''): return trans.fill_template( '/admin/requests/reject.mako', - request=request, messagetype='error', - msg='A comment is required for rejecting a request.') + request=request, status='error', + message='A comment is required for rejecting a request.') # create an event with state 'Rejected' for this request comments = util.restore_text( params.comment ) event = trans.app.model.RequestEvent(request, request.states.REJECTED, comments) @@ -503,12 +503,12 @@ try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) except: - msg = "Invalid request ID" - log.warn( msg ) + message = "Invalid request ID" + log.warn( message ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='error', - message=msg, + message=message, **kwd) ) events_list = [] all_events = request.events @@ -547,35 +547,35 @@ @web.require_admin def new(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) if params.get('select_request_type', False) == 'True': return trans.fill_template( '/admin/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) elif params.get('create', False) == 'True': if params.get('create_request_button', False) == 'Save' \ or params.get('create_request_samples_button', False) == 'Add samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) if not util.restore_text(params.get('name', '')) \ or util.restore_text(params.get('select_user', '')) == unicode('none'): - msg = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request' + message = 'Please enter the <b>Name</b> of the request and the <b>user</b> on behalf of whom this request will be submitted before saving this request' kwd['create'] = 'True' - kwd['messagetype'] = 'error' - kwd['msg'] = msg + kwd['status'] = 'error' + kwd['message'] = message kwd['create_request_button'] = None kwd['create_request_samples_button'] = None return trans.response.send_redirect( web.url_for( controller='requests_admin', action='new', **kwd) ) request = self.__save_request(trans, None, **kwd) - msg = 'The new request named %s has been created' % request.name + message = 'The new request named %s has been created' % request.name if params.get('create_request_button', False) == 'Save': return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', - message=msg , + message=message , status='done') ) elif params.get('create_request_samples_button', False) == 'Add samples': new_kwd = {} @@ -584,7 +584,7 @@ new_kwd['add_sample'] = True return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', - message=msg , + message=message , status='done', **new_kwd) ) else: @@ -593,16 +593,16 @@ return self.__show_request_form(trans, **kwd) def __show_request_form(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) except: return trans.fill_template( '/admin/requests/new_request.mako', select_request_type=self.__select_request_type(trans, 'none'), widgets=[], - msg=msg, - messagetype=messagetype) + message=message, + status=status) form_values = None select_request_type = self.__select_request_type(trans, request_type.id) # user @@ -629,8 +629,8 @@ select_request_type=select_request_type, request_type=request_type, widgets=widgets, - msg=msg, - messagetype=messagetype) + message=message, + status=status) def __select_user(self, trans, userid): user_list = trans.sa_session.query( trans.app.model.User )\ .order_by( trans.app.model.User.email.asc() ) @@ -669,10 +669,10 @@ if field['required'] == 'required' and request.values.content[index] in ['', None]: empty_fields.append(field['label']) if empty_fields: - msg = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name + message = 'Fill the following fields of the request <b>%s</b> before submitting<br/>' % request.name for ef in empty_fields: - msg = msg + '<b>' +ef + '</b><br/>' - return msg + message = message + '<b>' +ef + '</b><br/>' + return message return None def __save_request(self, trans, request=None, **kwd): ''' @@ -746,8 +746,8 @@ # def __show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) add_sample = params.get('add_sample', False) try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) @@ -787,7 +787,7 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details='hide', edit_mode=util.restore_text( params.get( 'edit_mode', 'False' ) ), - msg=msg, messagetype=messagetype ) + message=message, status=status ) def __library_widgets(self, trans, user, sample_index, libraries, sample=None, **kwd): ''' This method creates the data library & folder selectbox for creating & @@ -932,8 +932,8 @@ @web.require_login( "create/submit sequencing requests" ) def show_request(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) try: request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) except: @@ -1010,28 +1010,28 @@ edit_mode=edit_mode) elif params.get('save_samples_button', False) == 'Save': # check for duplicate sample names - msg = '' + message = '' for index in range(len(current_samples)-len(request.samples)): sample_index = index + len(request.samples) sample_name = current_samples[sample_index]['name'] if not sample_name.strip(): - msg = 'Please enter the name of sample number %i' % sample_index + message = 'Please enter the name of sample number %i' % sample_index break count = 0 for i in range(len(current_samples)): if sample_name == current_samples[i]['name']: count = count + 1 if count > 1: - msg = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) + message = "This request has <b>%i</b> samples with the name <b>%s</b>.\nSamples belonging to a request must have unique names." % (count, sample_name) break - if msg: + if message: return trans.fill_template( '/admin/requests/show_request.mako', request=request, request_details=self.request_details(trans, request.id), current_samples = current_samples, sample_copy=self.__copy_sample(current_samples), details=details, edit_mode=edit_mode, - messagetype='error', msg=msg) + status='error', message=message) # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): @@ -1050,18 +1050,18 @@ trans.sa_session.flush() else: - messagetype = 'done' - msg = 'Changes made to the sample(s) are saved. ' + status = 'done' + message = 'Changes made to the sample(s) are saved. ' for sample_index in range(len(current_samples)): sample = request.samples[sample_index] sample.name = current_samples[sample_index]['name'] sample.library = current_samples[sample_index]['library'] sample.folder = current_samples[sample_index]['folder'] if request.submitted(): - bc_msg = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) - if bc_msg: - messagetype = 'error' - msg += bc_msg + bc_message = self.__validate_barcode(trans, sample, current_samples[sample_index]['barcode']) + if bc_message: + status = 'error' + message += bc_message else: if not sample.bar_code: # if this is a 'new' (still in its first state) sample @@ -1083,8 +1083,8 @@ action='list', operation='show_request', id=trans.security.encode_id(request.id), - messagetype=messagetype, - msg=msg )) + status=status, + message=message )) elif params.get('edit_samples_button', False) == 'Edit samples': edit_mode = 'True' return trans.fill_template( '/admin/requests/show_request.mako', @@ -1106,15 +1106,15 @@ current_samples=current_samples, sample_copy=self.__copy_sample(current_samples), details=details, libraries=libraries, - edit_mode=edit_mode, messagetype=messagetype, msg=msg) + edit_mode=edit_mode, status=status, message=message) @web.expose @web.require_login( "create/submit sequencing requests" ) def delete_sample(self, trans, **kwd): params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', 0 ) ) ) current_samples, details, edit_mode, libraries = self.__update_samples( trans, request, **kwd ) sample_index = int(params.get('sample_id', 0)) @@ -1182,11 +1182,11 @@ the given sample is gobally unique. That is, barcodes must be unique across requests in Galaxy LIMS ''' - msg = '' + message = '' for index in range(len(sample.request.samples)): # check for empty bar code if not barcode.strip(): - msg = 'Please fill the barcode for sample <b>%s</b>.' % sample.name + message = 'Please fill the barcode for sample <b>%s</b>.' % sample.name break # check all the saved bar codes all_samples = trans.sa_session.query( trans.app.model.Sample ) @@ -1195,20 +1195,20 @@

1 0