details: http://www.bx.psu.edu/hg/galaxy/rev/d301a67eda40 changeset: 2686:d301a67eda40 user: Greg Von Kuster <greg@bx.psu.edu> date: Mon Sep 14 11:05:36 2009 -0400 description: Move the data library admin methods to a separate library_admin controller. 23 file(s) affected in this change: lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/library_admin.py templates/admin/index.mako templates/admin/library/browse_libraries.mako templates/admin/library/browse_library.mako templates/admin/library/common.mako templates/admin/library/folder_info.mako templates/admin/library/folder_permissions.mako templates/admin/library/ldda_edit_info.mako templates/admin/library/ldda_info.mako templates/admin/library/ldda_permissions.mako templates/admin/library/library_dataset_info.mako templates/admin/library/library_dataset_permissions.mako templates/admin/library/library_info.mako templates/admin/library/library_permissions.mako templates/admin/library/new_dataset.mako templates/admin/library/new_folder.mako templates/admin/library/new_library.mako templates/admin/library/select_info_template.mako templates/admin/requests/show_request.mako test/base/twilltestcase.py test/functional/test_forms_and_requests.py test/functional/test_security_and_libraries.py diffs (truncated from 3482 to 3000 lines): diff -r f2af04af3caa -r d301a67eda40 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Sep 11 16:09:02 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Sep 14 11:05:36 2009 -0400 @@ -1,15 +1,9 @@ -import shutil, StringIO, operator, urllib, gzip, tempfile, string, sys +import string, sys from datetime import datetime, timedelta from galaxy import util, datatypes from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.web.controllers.forms import get_all_forms, get_form_widgets -# Older py compatibility -try: - set() -except: - from sets import Set as set - import logging log = logging.getLogger( __name__ ) @@ -673,1188 +667,6 @@ out_groups=out_groups, msg=msg, messagetype=messagetype ) - - # Galaxy Library Stuff - @web.expose - @web.require_admin - def browse_libraries( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - return trans.fill_template( '/admin/library/browse_libraries.mako', - libraries=trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \ - .order_by( trans.app.model.Library.name ).all(), - deleted=False, - show_deleted=False, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def browse_library( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - id = params.get( 'id', None ) - deleted = util.string_as_bool( params.get( 'deleted', False ) ) - show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) - if not id: - msg = "You must specify a library id." - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_libraries', - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - library = library=trans.app.model.Library.get( id ) - if not library: - msg = "Invalid library id ( %s )." - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_libraries', - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - created_ldda_ids = params.get( 'created_ldda_ids', '' ) - return trans.fill_template( '/admin/library/browse_library.mako', - library=trans.app.model.Library.get( id ), - deleted=deleted, - created_ldda_ids=created_ldda_ids, - forms=get_all_forms( trans, filter=dict(deleted=False) ), - msg=msg, - messagetype=messagetype, - show_deleted=show_deleted ) - @web.expose - @web.require_admin - def library( self, trans, id=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'new', False ): - action = 'new' - elif params.get( 'delete', False ): - action = 'delete' - elif params.get( 'permissions', False ): - action = 'permissions' - else: - action = 'information' - if not id and not action == 'new': - msg = "You must specify a library to %s." % action - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_libraries', - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if not action == 'new': - library = trans.app.model.Library.get( int( id ) ) - if action == 'new': - if params.new == 'submitted': - library = trans.app.model.Library( name = util.restore_text( params.name ), - description = util.restore_text( params.description ) ) - root_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = "" ) - root_folder.flush() - library.root_folder = root_folder - library.flush() - msg = "The new library named '%s' has been created" % library.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library.id, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) - elif action == 'information': - # See if we have any associated templates - info_association = library.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] - if params.get( 'rename_library_button', False ): - old_name = library.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/library/library_info.mako', - library=library, - widgets=widgets, - msg=msg, - messagetype='error' ) - else: - library.name = new_name - library.description = new_description - library.flush() - # Rename the root_folder - library.root_folder.name = new_name - library.root_folder.description = new_description - library.root_folder.flush() - msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='library', - id=id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/library_info.mako', - library=library, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'delete': - def delete_folder( library_folder ): - library_folder.refresh() - for folder in library_folder.folders: - delete_folder( folder ) - for library_dataset in library_folder.datasets: - library_dataset.refresh() - ldda = library_dataset.library_dataset_dataset_association - if ldda: - ldda.refresh() - # We don't set ldda.dataset.deleted to True here because the cleanup_dataset script - # will eventually remove it from disk. The purge_library method below sets the dataset - # to deleted. This allows for the library to be undeleted ( before it is purged ), - # restoring all of its contents. - ldda.deleted = True - ldda.flush() - library_dataset.deleted = True - library_dataset.flush() - library_folder.deleted = True - library_folder.flush() - library.refresh() - delete_folder( library.root_folder ) - library.deleted = True - library.flush() - msg = "Library '%s' and all of its contents have been marked deleted" % library.name - return trans.response.send_redirect( web.url_for( action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='done' ) ) - elif action == 'permissions': - if params.get( 'update_roles_button', False ): - # The user clicked the Save button on the 'Associate With Roles' form - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( library, permissions ) - library.refresh() - # 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 - return trans.response.send_redirect( web.url_for( controller='admin', - action='library', - id=id, - permissions=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/library_permissions.mako', - library=library, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def deleted_libraries( self, trans, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - libraries=trans.app.model.Library.filter( and_( trans.app.model.Library.table.c.deleted==True, - trans.app.model.Library.table.c.purged==False ) ) \ - .order_by( trans.app.model.Library.table.c.name ).all() - return trans.fill_template( '/admin/library/browse_libraries.mako', - libraries=libraries, - deleted=True, - msg=msg, - messagetype=messagetype, - show_deleted=True ) - @web.expose - @web.require_admin - def purge_library( self, trans, **kwd ): - params = util.Params( kwd ) - library = trans.app.model.Library.get( int( params.id ) ) - def purge_folder( library_folder ): - for lf in library_folder.folders: - purge_folder( lf ) - library_folder.refresh() - for library_dataset in library_folder.datasets: - library_dataset.refresh() - ldda = library_dataset.library_dataset_dataset_association - if ldda: - ldda.refresh() - dataset = ldda.dataset - dataset.refresh() - # If the dataset is not associated with any additional undeleted folders, then we can delete it. - # We don't set dataset.purged to True here because the cleanup_datasets script will do that for - # us, as well as removing the file from disk. - #if not dataset.deleted and len( dataset.active_library_associations ) <= 1: # This is our current ldda - dataset.deleted = True - dataset.flush() - ldda.deleted = True - ldda.flush() - library_dataset.deleted = True - library_dataset.flush() - library_folder.deleted = True - library_folder.purged = True - library_folder.flush() - if not library.deleted: - msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_libraries', - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - else: - purge_folder( library.root_folder ) - library.purged = True - library.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 - return trans.response.send_redirect( web.url_for( controller='admin', - action='deleted_libraries', - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - @web.expose - @web.require_admin - def folder( self, trans, id, library_id, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'new', False ): - action = 'new' - elif params.get( 'delete', False ): - action = 'delete' - elif params.get( 'permissions', False ): - action = 'permissions' - else: - # 'information' will be the default - action = 'information' - folder = trans.app.model.LibraryFolder.get( int( id ) ) - if not folder: - msg = "Invalid folder specified, id: %s" % str( id ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if action == 'new': - if params.new == 'submitted': - new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), - description=util.restore_text( params.description ) ) - # We are associating the last used genome build with folders, so we will always - # initialize a new folder with the first dbkey in util.dbnames which is currently - # ? unspecified (?) - new_folder.genome_build = util.dbnames.default_value - folder.add_folder( new_folder ) - new_folder.flush() - # New folders default to having the same permissions as their parent folder - trans.app.security_agent.copy_library_permissions( folder, new_folder ) - msg = "New folder named '%s' has been added to the library" % new_folder.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/new_folder.mako', - library_id=library_id, - folder=folder, - msg=msg, - messagetype=messagetype ) - elif action == 'information': - # See if we have any associated templates - info_association = folder.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] - if params.get( 'rename_folder_button', False ): - old_name = folder.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/library/folder_info.mako', - folder=folder, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype='error' ) - else: - folder.name = new_name - folder.description = new_description - folder.flush() - msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='folder', - id=id, - library_id=library_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/folder_info.mako', - folder=folder, - library_id=library_id, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'delete': - folder.deleted = True - folder.flush() - msg = "Folder '%s' and all of its contents have been marked deleted" % folder.name - return trans.response.send_redirect( web.url_for( action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - elif action =='permissions': - if params.get( 'update_roles_button', False ): - # The user clicked the Save button on the 'Associate With Roles' form - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - trans.app.security_agent.set_all_library_permissions( folder, permissions ) - folder.refresh() - msg = "Permissions updated for folder '%s'" % folder.name - return trans.response.send_redirect( web.url_for( controller='admin', - action='folder', - id=id, - library_id=library_id, - permissions=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - return trans.fill_template( '/admin/library/folder_permissions.mako', - folder=folder, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def library_dataset( self, trans, id, library_id, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'permissions', False ): - action = 'permissions' - else: - action = 'information' - library_dataset = trans.app.model.LibraryDataset.get( id ) - if not library_dataset: - msg = "Invalid library dataset specified, id: %s" %str( id ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if action == 'information': - if params.get( 'edit_attributes_button', False ): - old_name = library_dataset.name - 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' - else: - library_dataset.name = new_name - library_dataset.info = new_info - library_dataset.flush() - msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name ) - messagetype = 'done' - return trans.fill_template( '/admin/library/library_dataset_info.mako', - library_dataset=library_dataset, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - elif action == 'permissions': - if params.get( 'update_roles_button', False ): - # The user clicked the Save button on the 'Edit permissions and role associations' form - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( library_dataset, permissions ) - library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions ) - library_dataset.library_dataset_dataset_association.refresh() - msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name - return trans.fill_template( '/admin/library/library_dataset_permissions.mako', - library_dataset=library_dataset, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def library_dataset_dataset_association( self, trans, library_id, folder_id, id=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', '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', None ) - if isinstance( dbkey, list ): - last_used_build = dbkey[0] - else: - last_used_build = dbkey - folder = trans.app.model.LibraryFolder.get( folder_id ) - if folder and last_used_build in [ 'None', None, '?' ]: - last_used_build = folder.genome_build - replace_id = params.get( 'replace_id', None ) - if replace_id: - replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) ) - if not last_used_build: - last_used_build = replace_dataset.library_dataset_dataset_association.dbkey - else: - replace_dataset = None - # Let's not overwrite the imported datatypes module with the variable datatypes? - # The built-in 'id' is overwritten in lots of places as well - ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] - ldatatypes.sort() - if params.get( 'new_dataset_button', False ): - upload_option = params.get( 'upload_option', 'upload_file' ) - created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, - controller='admin', - library_id=library_id, - folder_id=folder_id, - replace_dataset=replace_dataset, - **kwd ) - if created_ldda_ids: - total_added = len( created_ldda_ids.split( ',' ) ) - if replace_dataset: - msg = "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 ) - else: - msg = "Added %d datasets to the folder '%s' ( each is selected ). " % ( total_added, folder.name ) - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." - messagetype='done' - else: - msg = "Upload failed" - messagetype='error' - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - created_ldda_ids=created_ldda_ids, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) - elif not id or replace_dataset: - # See if we have any associated templates - info_association = folder.get_info_association() - if info_association: - template = info_association.template - widgets = get_form_widgets( trans, template ) - else: - widgets = [] - upload_option = params.get( 'upload_option', 'upload_file' ) - # No dataset(s) specified, so display the upload form. Send list of data formats to the form - # so the "extension" select list can be populated dynamically - file_formats = trans.app.datatypes_registry.upload_file_formats - # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically - def get_dbkey_options( last_used_build ): - for dbkey, build_name in util.dbnames: - yield build_name, dbkey, ( dbkey==last_used_build ) - dbkeys = get_dbkey_options( last_used_build ) - # Send list of roles to the form so the dataset can be associated with 1 or more of them. - roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() - # Send the current history to the form to enable importing datasets from history to library - history = trans.get_history() - history.refresh() - return trans.fill_template( '/admin/library/new_dataset.mako', - upload_option=upload_option, - library_id=library_id, - folder_id=folder_id, - replace_id=replace_id, - file_formats=file_formats, - dbkeys=dbkeys, - last_used_build=last_used_build, - roles=roles, - history=history, - widgets=widgets, - msg=msg, - messagetype=messagetype, - replace_dataset=replace_dataset ) - else: - if params.get( 'permissions', False ): - action = 'permissions' - elif params.get( 'edit_info', False ): - action = 'edit_info' - else: - action = 'info' - if id.count( ',' ): - ids = id.split( ',' ) - id = None - else: - ids = None - if id: - # ldda_id specified, display attributes form - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda: - msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # See if we have any associated templates - info_association = ldda.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] - if action == 'permissions': - if params.get( 'update_roles_button', False ): - permissions = {} - accessible = False - for k, v in trans.app.model.Dataset.permitted_actions.items(): - # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not - # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible - if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - if len( in_roles ) > 1: - # Get the set of all users that are being associated with the dataset - in_roles_set = set() - for role in in_roles: - in_roles_set.add( role ) - users_set = set() - for role in in_roles: - for ura in role.users: - users_set.add( ura.user ) - # Make sure that at least 1 user has every role being associated with the dataset - for user in users_set: - user_roles_set = set() - for ura in user.roles: - user_roles_set.add( ura.role ) - if in_roles_set.issubset( user_roles_set ): - accessible = True - break - else: - accessible = True - if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions - # TODO: keep access permissions as they originally were, rather than automatically making public - permissions[ trans.app.security_agent.get_action( v.action ) ] = [] - else: - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - if not accessible: - msg = "At least 1 user must have every role associated with accessing dataset '%s'. " % ldda.name - msg += "The roles you attempted to associate for access would make this dataset inaccessible by everyone, " - msg += "so access permissions were not set. All other permissions were updated for the dataset." - messagetype = 'error' - else: - msg = "Permissions updated for dataset '%s'" % ldda.name - return trans.fill_template( '/admin/library/ldda_permissions.mako', - ldda=ldda, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - elif action == 'info': - return trans.fill_template( '/admin/library/ldda_info.mako', - ldda=ldda, - library_id=library_id, - deleted=deleted, - show_deleted=show_deleted, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif action == 'edit_info': - if params.get( 'change', False ): - # The user clicked the Save button on the 'Change data type' form - 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.app.model.flush() - msg = "Data type changed for library dataset '%s'" % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - else: - return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) ) - elif params.get( 'save', False ): - # The user clicked the Save button on the 'Edit Attributes' form - old_name = ldda.name - new_name = util.restore_text( params.get( 'name', '' ) ) - 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' - else: - ldda.name = new_name - ldda.info = new_info - ldda.message = new_message - # The following for loop will save all metadata_spec items - for name, spec in ldda.datatype.metadata_spec.items(): - if spec.get("readonly"): - continue - optional = params.get( "is_" + name, None ) - if optional and optional == 'true': - # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) - setattr( ldda.metadata, name, None ) - else: - setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) - ldda.metadata.dbkey = dbkey - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - messagetype = 'done' - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'detect', False ): - # The user clicked the Auto-detect button on the 'Edit Attributes' form - for name, spec in ldda.datatype.metadata_spec.items(): - # We need to be careful about the attributes we are resetting - if name not in [ 'name', 'info', 'dbkey' ]: - if spec.get( 'default' ): - setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) - ldda.datatype.set_meta( ldda ) - ldda.datatype.after_edit( ldda ) - trans.app.model.flush() - msg = 'Attributes updated for library dataset %s' % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif params.get( 'delete', False ): - ldda.deleted = True - ldda.flush() - msg = 'Dataset %s has been removed from this library' % ldda.name - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - ldda.datatype.before_edit( ldda ) - if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: - # Copy dbkey into metadata, for backwards compatability - # This looks like it does nothing, but getting the dbkey - # returns the metadata dbkey unless it is None, in which - # case it resorts to the old dbkey. Setting the dbkey - # sets it properly in the metadata - ldda.metadata.dbkey = ldda.dbkey - return trans.fill_template( "/admin/library/ldda_edit_info.mako", - ldda=ldda, - library_id=library_id, - datatypes=ldatatypes, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - elif ids: - # Multiple ids specfied, display permission form, permissions will be updated for all simultaneously. - lddas = [] - for id in [ int( id ) for id in ids ]: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if ldda is None: - msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - lddas.append( ldda ) - if len( lddas ) < 2: - msg = 'You must specify at least two datasets on which to modify permissions, ids you sent: %s' % str( ids ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if action == 'permissions': - if params.get( 'update_roles_button', False ): - permissions = {} - accessible = False - for k, v in trans.app.model.Dataset.permitted_actions.items(): - # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not - # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible - if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - if len( in_roles ) > 1: - # Get the set of all users that are being associated with the dataset - in_roles_set = set() - for role in in_roles: - in_roles_set.add( role ) - users_set = set() - for role in in_roles: - for ura in role.users: - users_set.add( ura.user ) - # Make sure that at least 1 user has every role being associated with the dataset - for user in users_set: - user_roles_set = set() - for ura in user.roles: - user_roles_set.add( ura.role ) - if in_roles_set.issubset( user_roles_set ): - accessible = True - break - else: - accessible = True - if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: - # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions - # TODO: keep access permissions as they originally were, rather than automatically making public - permissions[ trans.app.security_agent.get_action( v.action ) ] = [] - else: - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - if not accessible: - msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas ) - msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, " - msg += "so access permissions were not set. All other permissions were updated for the datasets." - messagetype = 'error' - else: - msg = "Permissions have been updated on %d datasets" % len( lddas ) - return trans.fill_template( "/admin/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - # Ensure that the permissions across all library items are identical, otherwise we can't update them together. - check_list = [] - for ldda in lddas: - permissions = [] - # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation - # will always be the same as the permissions on the associated LibraryDataset, so we only need to - # check one Library object - for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): - if library_permission.action not in permissions: - permissions.append( library_permission.action ) - for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): - if dataset_permission.action not in permissions: - permissions.append( dataset_permission.action ) - permissions.sort() - 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' - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - return trans.fill_template( "/admin/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - try: - folder = trans.app.model.LibraryFolder.get( int( folder_id ) ) - except: - msg = "Invalid folder id: %s" % str( folder_id ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - replace_id = params.get( 'replace_id', None ) - if replace_id: - replace_dataset = trans.app.model.LibraryDataset.get( replace_id ) - else: - replace_dataset = None - # See if the current history is empty - history = trans.get_history() - history.refresh() - if not history.active_datasets: - msg = 'Your current history is empty' - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - if params.get( 'add_history_datasets_to_library_button', False ): - hda_ids = util.listify( hda_ids ) - if hda_ids: - dataset_names = [] - created_ldda_ids = '' - for hda_id in hda_ids: - hda = trans.app.model.HistoryDatasetAssociation.get( hda_id ) - if hda: - ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset ) - created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) ) - dataset_names.append( ldda.name ) - if not replace_dataset: - # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new - # LDDA and LibraryDataset. - trans.app.security_agent.copy_library_permissions( folder, ldda ) - trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset ) - # 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 ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='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 ) - 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 ) - else: - msg = "Added %d datasets to the folder '%s' ( each is selected ). " % ( total_added, folder.name ) - msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - created_ldda_ids=created_ldda_ids, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - else: - msg = 'Select at least one dataset from the list of active datasets in your current history' - messagetype = '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 - file_formats = trans.app.datatypes_registry.upload_file_formats - # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically - def get_dbkey_options( last_used_build ): - for dbkey, build_name in util.dbnames: - yield build_name, dbkey, ( dbkey==last_used_build ) - dbkeys = get_dbkey_options( last_used_build ) - # Send list of roles to the form so the dataset can be associated with 1 or more of them. - roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() - return trans.fill_template( "/admin/library/new_dataset.mako", - upload_option=upload_option, - library_id=library_id, - folder_id=folder_id, - replace_id=replace_id, - file_formats=file_formats, - dbkeys=dbkeys, - last_used_build=last_used_build, - roles=roles, - history=history, - widgets=widgets, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def info_template( self, trans, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if id: - library_item = trans.app.model.FormDefinition.get( int( id ) ) - library_item_desc = 'information template' - response_action = 'info_template' - response_id = id - elif folder_id: - library_item = trans.app.model.LibraryFolder.get( int( folder_id ) ) - library_item_desc = 'folder' - response_action = 'folder' - response_id = folder_id - elif ldda_id: - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) ) - library_item_desc = 'library dataset' - response_action = 'library_dataset_dataset_association' - response_id = ldda_id - else: - library_item = trans.app.model.Library.get( int( library_id ) ) - library_item_desc = 'library' - response_action = 'browse_library' - response_id = library_id - forms = get_all_forms( trans, filter=dict(deleted=False) ) - if not forms: - msg = "There are no forms on which to base the template, so create a form and " - msg += "try again to add the information template to the %s." % library_item_desc - trans.response.send_redirect( web.url_for( controller='forms', - action='new', - new=True, - msg=msg, - messagetype='done' ) ) - if params.get( 'add', False ): - if params.get( 'add_info_template_button', False ): - form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) - #fields = list( copy.deepcopy( form.fields ) ) - form_values = trans.app.model.FormValues( form, [] ) - form_values.flush() - if folder_id: - assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) - elif ldda_id: - assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) - else: - assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) - assoc.flush() - msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) - trans.response.send_redirect( web.url_for( controller='admin', - action=response_action, - id=response_id, - msg=msg, - message_type='done' ) ) - return trans.fill_template( '/admin/library/select_info_template.mako', - library_item_name=library_item.name, - library_item_desc=library_item_desc, - library_id=library_id, - folder_id=folder_id, - ldda_id=ldda_id, - forms=forms, - msg=msg, - messagetype=messagetype ) - @web.expose - @web.require_admin - def edit_template_info( self, trans, library_id, num_widgets, library_item_id=None, library_item_type=None, **kwd ): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - folder_id = None - if library_item_type == 'library': - library_item = trans.app.model.Library.get( library_item_id ) - elif library_item_type == 'library_dataset': - library_item = trans.app.model.LibraryDataset.get( library_item_id ) - elif library_item_type == 'folder': - library_item = trans.app.model.LibraryFolder.get( library_item_id ) - elif library_item_type == 'library_dataset_dataset_association': - library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) - # This response_action method requires a folder_id - folder_id = library_item.library_dataset.folder.id - else: - msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - # Save updated template field contents - field_contents = [] - for index in range( int( num_widgets ) ): - field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) - if field_contents: - # Since information templates are inherited, the template fields can be displayed on the information - # page for a folder or library dataset when it has no info_association object. If the user has added - # field contents on an inherited template via a parent's info_association, we'll need to create a new - # form_values and info_association for the current object. - info_association = library_item.get_info_association( restrict=True ) - if info_association: - template = info_association.template - info = info_association.info - form_values = trans.app.model.FormValues.get( info.id ) - # Update existing content only if it has changed - if form_values.content != field_contents: - form_values.content = field_contents - form_values.flush() - else: - # Inherit the next available info_association so we can get the template - info_association = library_item.get_info_association() - template = info_association.template - # Create a new FormValues object - form_values = trans.app.model.FormValues( template, field_contents ) - form_values.flush() - # Create a new info_association between the current library item and form_values - if library_item_type == 'folder': - info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) - info_association.flush() - elif library_item_type == 'library_dataset_dataset_association': - info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) - info_association.flush() - msg = 'The information has been updated.' - return trans.response.send_redirect( web.url_for( controller='admin', - action=library_item_type, - id=library_item.id, - library_id=library_id, - folder_id=folder_id, - edit_info=True, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - @web.expose - @web.require_admin - def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - # id must refer to a LibraryDatasetDatasetAssociation object - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) - fStat = os.stat( ldda.file_name ) - trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ldda.name - fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) - try: - return open( ldda.file_name ) - except: - msg = 'This dataset contains no content' - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - @web.expose - @web.require_admin - def datasets( self, trans, library_id, **kwd ): - # This method is used by the select list labeled "Perform action on selected datasets" - # on the admin library browser. - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - if params.get( 'action_on_datasets_button', False ): - if not params.ldda_ids: - msg = "At least one dataset must be selected for %s" % params.action - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - ldda_ids = util.listify( params.ldda_ids ) - if params.action == 'edit': - # We need the folder containing the LibraryDatasetDatasetAssociation(s) - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] ) - trans.response.send_redirect( web.url_for( controller='admin', - action='library_dataset_dataset_association', - library_id=library_id, - folder_id=ldda.library_dataset.folder.id, - id=",".join( ldda_ids ), - permissions=True, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) - elif params.action == 'delete': - for id in ldda_ids: - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) - ldda.deleted = True - ldda.flush() - msg = "The selected datasets have been removed from this library" - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - show_deleted=False, - msg=util.sanitize_text( msg ), - messagetype='done' ) ) - else: - msg = "Action %s is not yet implemented" % str( params.action ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - else: - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_library', - id=library_id, - msg=util.sanitize_text( msg ), - messagetype=messagetype ) ) - @web.expose - @web.require_admin - def delete_library_item( self, trans, library_id, library_item_id, library_item_type ): - # This action will handle deleting all types of library items. State is saved for libraries and - # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously - # deleted / purged contents will have the same state ). When a library or folder has been deleted for - # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its - # contents will be purged. The association between this method and the cleanup_datasets.py script - # enables clean maintenance of libraries and library dataset disk files. This is also why the following - # 3 objects, and not any of the associations ( the cleanup_datasets.py scipot handles everything else ). - library_item_types = { 'library': trans.app.model.Library, - 'folder': trans.app.model.LibraryFolder, - 'library_dataset': trans.app.model.LibraryDataset } - if library_item_type not in library_item_types: - msg = 'Bad library_item_type specified: %s' % str( library_item_type ) - messagetype = 'error' - else: - if library_item_type == 'library_dataset': - library_item_desc = 'Dataset' - else: - library_item_desc = library_item_type.capitalize() - library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) - library_item.deleted = True - library_item.flush() - msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) ) - messagetype = 'done' - if library_item_type == 'library': - return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) - else: - return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) - @web.expose - @web.require_admin - def undelete_library_item( self, trans, library_id, library_item_id, library_item_type ): - # This action will handle undeleting all types of library items - library_item_types = { 'library': trans.app.model.Library, - 'folder': trans.app.model.LibraryFolder, - 'library_dataset': trans.app.model.LibraryDataset } - if library_item_type not in library_item_types: - msg = 'Bad library_item_type specified: %s' % str( library_item_type ) - messagetype = 'error' - else: - if library_item_type == 'library_dataset': - library_item_desc = 'Dataset' - else: - library_item_desc = library_item_type.capitalize() - library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) - if library_item.purged: - msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_desc, library_item.name ) - messagetype = 'error' - else: - library_item.deleted = False - library_item.flush() - msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_desc, library_item.name ) ) - messagetype = 'done' - if library_item_type == 'library': - return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) - else: - return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) @web.expose @web.require_admin def memdump( self, trans, ids = 'None', sorts = 'None', pages = 'None', new_id = None, new_sort = None, **kwd ): diff -r f2af04af3caa -r d301a67eda40 lib/galaxy/web/controllers/library_admin.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/controllers/library_admin.py Mon Sep 14 11:05:36 2009 -0400 @@ -0,0 +1,1195 @@ +import sys +from galaxy import util +from galaxy.web.base.controller import * +from galaxy.model.orm import * +from galaxy.web.controllers.forms import get_all_forms, get_form_widgets +# Older py compatibility +try: + set() +except: + from sets import Set as set + +import logging +log = logging.getLogger( __name__ ) + +class LibraryAdmin( BaseController ): + @web.expose + @web.require_admin + def browse_libraries( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + return trans.fill_template( '/admin/library/browse_libraries.mako', + libraries=trans.app.model.Library.filter( trans.app.model.Library.table.c.deleted==False ) \ + .order_by( trans.app.model.Library.name ).all(), + deleted=False, + show_deleted=False, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def browse_library( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + id = params.get( 'id', None ) + deleted = util.string_as_bool( params.get( 'deleted', False ) ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + if not id: + msg = "You must specify a library id." + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_libraries', + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + library = library=trans.app.model.Library.get( id ) + if not library: + msg = "Invalid library id ( %s )." + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_libraries', + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + created_ldda_ids = params.get( 'created_ldda_ids', '' ) + return trans.fill_template( '/admin/library/browse_library.mako', + library=trans.app.model.Library.get( id ), + deleted=deleted, + created_ldda_ids=created_ldda_ids, + forms=get_all_forms( trans, filter=dict(deleted=False) ), + msg=msg, + messagetype=messagetype, + show_deleted=show_deleted ) + @web.expose + @web.require_admin + def library( self, trans, id=None, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'new', False ): + action = 'new' + elif params.get( 'delete', False ): + action = 'delete' + elif params.get( 'permissions', False ): + action = 'permissions' + else: + action = 'information' + if not id and not action == 'new': + msg = "You must specify a library to %s." % action + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_libraries', + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + if not action == 'new': + library = trans.app.model.Library.get( int( id ) ) + if action == 'new': + if params.new == 'submitted': + library = trans.app.model.Library( name = util.restore_text( params.name ), + description = util.restore_text( params.description ) ) + root_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = "" ) + root_folder.flush() + library.root_folder = root_folder + library.flush() + msg = "The new library named '%s' has been created" % library.name + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library.id, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) + elif action == 'information': + # See if we have any associated templates + info_association = library.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + widgets = get_form_widgets( trans, template, info.content ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] + if params.get( 'rename_library_button', False ): + old_name = library.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/library/library_info.mako', + library=library, + widgets=widgets, + msg=msg, + messagetype='error' ) + else: + library.name = new_name + library.description = new_description + library.flush() + # Rename the root_folder + library.root_folder.name = new_name + library.root_folder.description = new_description + library.root_folder.flush() + msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='library', + id=id, + edit_info=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/library_info.mako', + library=library, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif action == 'delete': + def delete_folder( library_folder ): + library_folder.refresh() + for folder in library_folder.folders: + delete_folder( folder ) + for library_dataset in library_folder.datasets: + library_dataset.refresh() + ldda = library_dataset.library_dataset_dataset_association + if ldda: + ldda.refresh() + # We don't set ldda.dataset.deleted to True here because the cleanup_dataset script + # will eventually remove it from disk. The purge_library method below sets the dataset + # to deleted. This allows for the library to be undeleted ( before it is purged ), + # restoring all of its contents. + ldda.deleted = True + ldda.flush() + library_dataset.deleted = True + library_dataset.flush() + library_folder.deleted = True + library_folder.flush() + library.refresh() + delete_folder( library.root_folder ) + library.deleted = True + library.flush() + msg = "Library '%s' and all of its contents have been marked deleted" % library.name + return trans.response.send_redirect( web.url_for( action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='done' ) ) + elif action == 'permissions': + if params.get( 'update_roles_button', False ): + # The user clicked the Save button on the 'Associate With Roles' form + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + trans.app.security_agent.set_all_library_permissions( library, permissions ) + library.refresh() + # 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 + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='library', + id=id, + permissions=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/library_permissions.mako', + library=library, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def deleted_libraries( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + libraries=trans.app.model.Library.filter( and_( trans.app.model.Library.table.c.deleted==True, + trans.app.model.Library.table.c.purged==False ) ) \ + .order_by( trans.app.model.Library.table.c.name ).all() + return trans.fill_template( '/admin/library/browse_libraries.mako', + libraries=libraries, + deleted=True, + msg=msg, + messagetype=messagetype, + show_deleted=True ) + @web.expose + @web.require_admin + def purge_library( self, trans, **kwd ): + params = util.Params( kwd ) + library = trans.app.model.Library.get( int( params.id ) ) + def purge_folder( library_folder ): + for lf in library_folder.folders: + purge_folder( lf ) + library_folder.refresh() + for library_dataset in library_folder.datasets: + library_dataset.refresh() + ldda = library_dataset.library_dataset_dataset_association + if ldda: + ldda.refresh() + dataset = ldda.dataset + dataset.refresh() + # If the dataset is not associated with any additional undeleted folders, then we can delete it. + # We don't set dataset.purged to True here because the cleanup_datasets script will do that for + # us, as well as removing the file from disk. + #if not dataset.deleted and len( dataset.active_library_associations ) <= 1: # This is our current ldda + dataset.deleted = True + dataset.flush() + ldda.deleted = True + ldda.flush() + library_dataset.deleted = True + library_dataset.flush() + library_folder.deleted = True + library_folder.purged = True + library_folder.flush() + if not library.deleted: + msg = "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', + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + else: + purge_folder( library.root_folder ) + library.purged = True + library.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 + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='deleted_libraries', + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + @web.expose + @web.require_admin + def folder( self, trans, id, library_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'new', False ): + action = 'new' + elif params.get( 'delete', False ): + action = 'delete' + elif params.get( 'permissions', False ): + action = 'permissions' + else: + # 'information' will be the default + action = 'information' + folder = trans.app.model.LibraryFolder.get( int( id ) ) + if not folder: + msg = "Invalid folder specified, id: %s" % str( id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + if action == 'new': + if params.new == 'submitted': + new_folder = trans.app.model.LibraryFolder( name=util.restore_text( params.name ), + description=util.restore_text( params.description ) ) + # We are associating the last used genome build with folders, so we will always + # initialize a new folder with the first dbkey in util.dbnames which is currently + # ? unspecified (?) + new_folder.genome_build = util.dbnames.default_value + folder.add_folder( new_folder ) + new_folder.flush() + # New folders default to having the same permissions as their parent folder + trans.app.security_agent.copy_library_permissions( folder, new_folder ) + msg = "New folder named '%s' has been added to the library" % new_folder.name + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/new_folder.mako', + library_id=library_id, + folder=folder, + msg=msg, + messagetype=messagetype ) + elif action == 'information': + # See if we have any associated templates + info_association = folder.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + widgets = get_form_widgets( trans, template, info.content ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] + if params.get( 'rename_folder_button', False ): + old_name = folder.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/library/folder_info.mako', + folder=folder, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype='error' ) + else: + folder.name = new_name + folder.description = new_description + folder.flush() + msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='folder', + id=id, + library_id=library_id, + edit_info=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/folder_info.mako', + folder=folder, + library_id=library_id, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif action == 'delete': + folder.deleted = True + folder.flush() + msg = "Folder '%s' and all of its contents have been marked deleted" % folder.name + return trans.response.send_redirect( web.url_for( action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + elif action =='permissions': + if params.get( 'update_roles_button', False ): + # The user clicked the Save button on the 'Associate With Roles' form + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( int( x ) ) for x in util.listify( params.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + trans.app.security_agent.set_all_library_permissions( folder, permissions ) + folder.refresh() + msg = "Permissions updated for folder '%s'" % folder.name + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='folder', + id=id, + library_id=library_id, + permissions=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + return trans.fill_template( '/admin/library/folder_permissions.mako', + folder=folder, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def library_dataset( self, trans, id, library_id, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'permissions', False ): + action = 'permissions' + else: + action = 'information' + library_dataset = trans.app.model.LibraryDataset.get( id ) + if not library_dataset: + msg = "Invalid library dataset specified, id: %s" %str( id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + if action == 'information': + if params.get( 'edit_attributes_button', False ): + old_name = library_dataset.name + 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' + else: + library_dataset.name = new_name + library_dataset.info = new_info + library_dataset.flush() + msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name ) + messagetype = 'done' + return trans.fill_template( '/admin/library/library_dataset_info.mako', + library_dataset=library_dataset, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + elif action == 'permissions': + if params.get( 'update_roles_button', False ): + # The user clicked the Save button on the 'Edit permissions and role associations' form + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( library_dataset, permissions ) + library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( library_dataset.library_dataset_dataset_association, permissions ) + library_dataset.library_dataset_dataset_association.refresh() + msg = 'Permissions and roles have been updated for library dataset %s' % library_dataset.name + return trans.fill_template( '/admin/library/library_dataset_permissions.mako', + library_dataset=library_dataset, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def library_dataset_dataset_association( self, trans, library_id, folder_id, id=None, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', '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', None ) + if isinstance( dbkey, list ): + last_used_build = dbkey[0] + else: + last_used_build = dbkey + folder = trans.app.model.LibraryFolder.get( folder_id ) + if folder and last_used_build in [ 'None', None, '?' ]: + last_used_build = folder.genome_build + replace_id = params.get( 'replace_id', None ) + if replace_id: + replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) ) + if not last_used_build: + last_used_build = replace_dataset.library_dataset_dataset_association.dbkey + else: + replace_dataset = None + # Let's not overwrite the imported datatypes module with the variable datatypes? + # The built-in 'id' is overwritten in lots of places as well + ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ] + ldatatypes.sort() + if params.get( 'new_dataset_button', False ): + upload_option = params.get( 'upload_option', 'upload_file' ) + created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans, + controller='library_admin', + library_id=library_id, + folder_id=folder_id, + replace_dataset=replace_dataset, + **kwd ) + if created_ldda_ids: + total_added = len( created_ldda_ids.split( ',' ) ) + if replace_dataset: + msg = "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 ) + else: + msg = "Added %d datasets to the folder '%s' ( each is selected ). " % ( total_added, folder.name ) + msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + messagetype='done' + else: + msg = "Upload failed" + messagetype='error' + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + created_ldda_ids=created_ldda_ids, + msg=util.sanitize_text( msg ), + messagetype=messagetype ) ) + elif not id or replace_dataset: + # See if we have any associated templates + info_association = folder.get_info_association() + if info_association: + template = info_association.template + widgets = get_form_widgets( trans, template ) + else: + widgets = [] + upload_option = params.get( 'upload_option', 'upload_file' ) + # No dataset(s) specified, so display the upload form. Send list of data formats to the form + # so the "extension" select list can be populated dynamically + file_formats = trans.app.datatypes_registry.upload_file_formats + # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically + def get_dbkey_options( last_used_build ): + for dbkey, build_name in util.dbnames: + yield build_name, dbkey, ( dbkey==last_used_build ) + dbkeys = get_dbkey_options( last_used_build ) + # Send list of roles to the form so the dataset can be associated with 1 or more of them. + roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() + # Send the current history to the form to enable importing datasets from history to library + history = trans.get_history() + history.refresh() + return trans.fill_template( '/admin/library/new_dataset.mako', + upload_option=upload_option, + library_id=library_id, + folder_id=folder_id, + replace_id=replace_id, + file_formats=file_formats, + dbkeys=dbkeys, + last_used_build=last_used_build, + roles=roles, + history=history, + widgets=widgets, + msg=msg, + messagetype=messagetype, + replace_dataset=replace_dataset ) + else: + if params.get( 'permissions', False ): + action = 'permissions' + elif params.get( 'edit_info', False ): + action = 'edit_info' + else: + action = 'info' + if id.count( ',' ): + ids = id.split( ',' ) + id = None + else: + ids = None + if id: + # ldda_id specified, display attributes form + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) + if not ldda: + msg = "Invalid LibraryDatasetDatasetAssociation specified, id: %s" % str( id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + # See if we have any associated templates + info_association = ldda.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents + info = info_association.info + if info: + widgets = get_form_widgets( trans, template, info.content ) + else: + widgets = get_form_widgets( trans, template ) + else: + widgets = [] + if action == 'permissions': + if params.get( 'update_roles_button', False ): + permissions = {} + accessible = False + for k, v in trans.app.model.Dataset.permitted_actions.items(): + # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not + # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] + # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible + if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + if len( in_roles ) > 1: + # Get the set of all users that are being associated with the dataset + in_roles_set = set() + for role in in_roles: + in_roles_set.add( role ) + users_set = set() + for role in in_roles: + for ura in role.users: + users_set.add( ura.user ) + # Make sure that at least 1 user has every role being associated with the dataset + for user in users_set: + user_roles_set = set() + for ura in user.roles: + user_roles_set.add( ura.role ) + if in_roles_set.issubset( user_roles_set ): + accessible = True + break + else: + accessible = True + if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions + # TODO: keep access permissions as they originally were, rather than automatically making public + permissions[ trans.app.security_agent.get_action( v.action ) ] = [] + else: + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + # Set the DATASET permissions on the Dataset + trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) + ldda.dataset.refresh() + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) + ldda.library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( ldda, permissions ) + ldda.refresh() + if not accessible: + msg = "At least 1 user must have every role associated with accessing dataset '%s'. " % ldda.name + msg += "The roles you attempted to associate for access would make this dataset inaccessible by everyone, " + msg += "so access permissions were not set. All other permissions were updated for the dataset." + messagetype = 'error' + else: + msg = "Permissions updated for dataset '%s'" % ldda.name + return trans.fill_template( '/admin/library/ldda_permissions.mako', + ldda=ldda, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + elif action == 'info': + return trans.fill_template( '/admin/library/ldda_info.mako', + ldda=ldda, + library_id=library_id, + deleted=deleted, + show_deleted=show_deleted, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif action == 'edit_info': + if params.get( 'change', False ): + # The user clicked the Save button on the 'Change data type' form + 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.app.model.flush() + msg = "Data type changed for library dataset '%s'" % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + datatypes=ldatatypes, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + else: + return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( ldda.extension, params.datatype ) ) + elif params.get( 'save', False ): + # The user clicked the Save button on the 'Edit Attributes' form + old_name = ldda.name + new_name = util.restore_text( params.get( 'name', '' ) ) + 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' + else: + ldda.name = new_name + ldda.info = new_info + ldda.message = new_message + # The following for loop will save all metadata_spec items + for name, spec in ldda.datatype.metadata_spec.items(): + if spec.get("readonly"): + continue + optional = params.get( "is_" + name, None ) + if optional and optional == 'true': + # optional element... == 'true' actually means it is NOT checked (and therefore ommitted) + setattr( ldda.metadata, name, None ) + else: + setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) + ldda.metadata.dbkey = dbkey + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + messagetype = 'done' + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + datatypes=ldatatypes, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'detect', False ): + # The user clicked the Auto-detect button on the 'Edit Attributes' form + for name, spec in ldda.datatype.metadata_spec.items(): + # We need to be careful about the attributes we are resetting + if name not in [ 'name', 'info', 'dbkey' ]: + if spec.get( 'default' ): + setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) + ldda.datatype.set_meta( ldda ) + ldda.datatype.after_edit( ldda ) + trans.app.model.flush() + msg = 'Attributes updated for library dataset %s' % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + datatypes=ldatatypes, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif params.get( 'delete', False ): + ldda.deleted = True + ldda.flush() + msg = 'Dataset %s has been removed from this library' % ldda.name + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + datatypes=ldatatypes, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + ldda.datatype.before_edit( ldda ) + if "dbkey" in ldda.datatype.metadata_spec and not ldda.metadata.dbkey: + # Copy dbkey into metadata, for backwards compatability + # This looks like it does nothing, but getting the dbkey + # returns the metadata dbkey unless it is None, in which + # case it resorts to the old dbkey. Setting the dbkey + # sets it properly in the metadata + ldda.metadata.dbkey = ldda.dbkey + return trans.fill_template( "/admin/library/ldda_edit_info.mako", + ldda=ldda, + library_id=library_id, + datatypes=ldatatypes, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + elif ids: + # Multiple ids specfied, display permission form, permissions will be updated for all simultaneously. + lddas = [] + for id in [ int( id ) for id in ids ]: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) + if ldda is None: + msg = 'You specified an invalid LibraryDatasetDatasetAssociation id: %s' %str( id ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + lddas.append( ldda ) + if len( lddas ) < 2: + msg = 'You must specify at least two datasets on which to modify permissions, ids you sent: %s' % str( ids ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + if action == 'permissions': + if params.get( 'update_roles_button', False ): + permissions = {} + accessible = False + for k, v in trans.app.model.Dataset.permitted_actions.items(): + # TODO: need to handle case where a user has the DATASET_MANAGE_PERMISSIONS permission, but not + # the DATASET_ACCESS permission, making the former useless. Need to display a warning message. + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] + # At least 1 user must have every role associated with this dataset, or the dataset is inaccessible + if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + if len( in_roles ) > 1: + # Get the set of all users that are being associated with the dataset + in_roles_set = set() + for role in in_roles: + in_roles_set.add( role ) + users_set = set() + for role in in_roles: + for ura in role.users: + users_set.add( ura.user ) + # Make sure that at least 1 user has every role being associated with the dataset + for user in users_set: + user_roles_set = set() + for ura in user.roles: + user_roles_set.add( ura.role ) + if in_roles_set.issubset( user_roles_set ): + accessible = True + break + else: + accessible = True + if not accessible and v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: + # Don't set the permissions for DATASET_ACCESS if inaccessbile, but set all other permissions + # TODO: keep access permissions as they originally were, rather than automatically making public + permissions[ trans.app.security_agent.get_action( v.action ) ] = [] + else: + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the DATASET permissions on the Dataset + trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) + ldda.dataset.refresh() + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) + ldda.library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( ldda, permissions ) + ldda.refresh() + if not accessible: + msg = "At least 1 user must have every role associated with accessing these %d datasets. " % len( lddas ) + msg += "The roles you attempted to associate for access would make these datasets inaccessible by everyone, " + msg += "so access permissions were not set. All other permissions were updated for the datasets." + messagetype = 'error' + else: + msg = "Permissions have been updated on %d datasets" % len( lddas ) + return trans.fill_template( "/admin/library/ldda_permissions.mako", + ldda=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + # Ensure that the permissions across all library items are identical, otherwise we can't update them together. + check_list = [] + for ldda in lddas: + permissions = [] + # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation + # will always be the same as the permissions on the associated LibraryDataset, so we only need to + # check one Library object + for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): + if library_permission.action not in permissions: + permissions.append( library_permission.action ) + for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): + if dataset_permission.action not in permissions: + permissions.append( dataset_permission.action ) + permissions.sort() + 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' + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + return trans.fill_template( "/admin/library/ldda_permissions.mako", + ldda=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def add_history_datasets_to_library( self, trans, library_id, folder_id, hda_ids='', **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + folder = trans.app.model.LibraryFolder.get( int( folder_id ) ) + except: + msg = "Invalid folder id: %s" % str( folder_id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + replace_id = params.get( 'replace_id', None ) + if replace_id: + replace_dataset = trans.app.model.LibraryDataset.get( replace_id ) + else: + replace_dataset = None + # See if the current history is empty + history = trans.get_history() + history.refresh() + if not history.active_datasets: + msg = 'Your current history is empty' + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + if params.get( 'add_history_datasets_to_library_button', False ): + hda_ids = util.listify( hda_ids ) + if hda_ids: + dataset_names = [] + created_ldda_ids = '' + for hda_id in hda_ids: + hda = trans.app.model.HistoryDatasetAssociation.get( hda_id ) + if hda: + ldda = hda.to_library_dataset_dataset_association( target_folder=folder, replace_dataset=replace_dataset ) + created_ldda_ids = '%s,%s' % ( created_ldda_ids, str( ldda.id ) ) + dataset_names.append( ldda.name ) + if not replace_dataset: + # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new + # LDDA and LibraryDataset. + trans.app.security_agent.copy_library_permissions( folder, ldda ) + trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset ) + # 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 ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='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 ) + 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 ) + else: + msg = "Added %d datasets to the folder '%s' ( each is selected ). " % ( total_added, folder.name ) + msg += "Click the Go button at the bottom of this page to edit the permissions on these datasets if necessary." + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + created_ldda_ids=created_ldda_ids, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + else: + msg = 'Select at least one dataset from the list of active datasets in your current history' + messagetype = '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 + file_formats = trans.app.datatypes_registry.upload_file_formats + # Send list of genome builds to the form so the "dbkey" select list can be populated dynamically + def get_dbkey_options( last_used_build ): + for dbkey, build_name in util.dbnames: + yield build_name, dbkey, ( dbkey==last_used_build ) + dbkeys = get_dbkey_options( last_used_build ) + # Send list of roles to the form so the dataset can be associated with 1 or more of them. + roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.c.name ).all() + return trans.fill_template( "/admin/library/new_dataset.mako", + upload_option=upload_option, + library_id=library_id, + folder_id=folder_id, + replace_id=replace_id, + file_formats=file_formats, + dbkeys=dbkeys, + last_used_build=last_used_build, + roles=roles, + history=history, + widgets=widgets, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def info_template( self, trans, library_id, id=None, folder_id=None, ldda_id=None, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if id: + library_item = trans.app.model.FormDefinition.get( int( id ) ) + library_item_desc = 'information template' + response_action = 'info_template' + response_id = id + elif folder_id: + library_item = trans.app.model.LibraryFolder.get( int( folder_id ) ) + library_item_desc = 'folder' + response_action = 'folder' + response_id = folder_id + elif ldda_id: + library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( int( ldda_id ) ) + library_item_desc = 'library dataset' + response_action = 'library_dataset_dataset_association' + response_id = ldda_id + else: + library_item = trans.app.model.Library.get( int( library_id ) ) + library_item_desc = 'library' + response_action = 'browse_library' + response_id = library_id + forms = get_all_forms( trans, filter=dict(deleted=False) ) + if not forms: + msg = "There are no forms on which to base the template, so create a form and " + msg += "try again to add the information template to the %s." % library_item_desc + trans.response.send_redirect( web.url_for( controller='forms', + action='new', + new=True, + msg=msg, + messagetype='done' ) ) + if params.get( 'add', False ): + if params.get( 'add_info_template_button', False ): + form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) ) + #fields = list( copy.deepcopy( form.fields ) ) + form_values = trans.app.model.FormValues( form, [] ) + form_values.flush() + if folder_id: + assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) + elif ldda_id: + assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) + else: + assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) + assoc.flush() + msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action=response_action, + id=response_id, + msg=msg, + message_type='done' ) ) + return trans.fill_template( '/admin/library/select_info_template.mako', + library_item_name=library_item.name, + library_item_desc=library_item_desc, + library_id=library_id, + folder_id=folder_id, + ldda_id=ldda_id, + forms=forms, + msg=msg, + messagetype=messagetype ) + @web.expose + @web.require_admin + def edit_template_info( self, trans, library_id, num_widgets, library_item_id=None, library_item_type=None, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + folder_id = None + if library_item_type == 'library': + library_item = trans.app.model.Library.get( library_item_id ) + elif library_item_type == 'library_dataset': + library_item = trans.app.model.LibraryDataset.get( library_item_id ) + elif library_item_type == 'folder': + library_item = trans.app.model.LibraryFolder.get( library_item_id ) + elif library_item_type == 'library_dataset_dataset_association': + library_item = trans.app.model.LibraryDatasetDatasetAssociation.get( library_item_id ) + # This response_action method requires a folder_id + folder_id = library_item.library_dataset.folder.id + else: + msg = "Invalid library item type ( %s ) specified, id ( %s )" % ( str( library_item_type ), str( library_item_id ) ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + # Save updated template field contents + field_contents = [] + for index in range( int( num_widgets ) ): + field_contents.append( util.restore_text( params.get( 'field_%i' % ( index ), '' ) ) ) + if field_contents: + # Since information templates are inherited, the template fields can be displayed on the information + # page for a folder or library dataset when it has no info_association object. If the user has added + # field contents on an inherited template via a parent's info_association, we'll need to create a new + # form_values and info_association for the current object. + info_association = library_item.get_info_association( restrict=True ) + if info_association: + template = info_association.template + info = info_association.info + form_values = trans.app.model.FormValues.get( info.id ) + # Update existing content only if it has changed + if form_values.content != field_contents: + form_values.content = field_contents + form_values.flush() + else: + # Inherit the next available info_association so we can get the template + info_association = library_item.get_info_association() + template = info_association.template + # Create a new FormValues object + form_values = trans.app.model.FormValues( template, field_contents ) + form_values.flush() + # Create a new info_association between the current library item and form_values + if library_item_type == 'folder': + info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) + info_association.flush() + elif library_item_type == 'library_dataset_dataset_association': + info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) + info_association.flush() + msg = 'The information has been updated.' + return trans.response.send_redirect( web.url_for( controller='library_admin', + action=library_item_type, + id=library_item.id, + library_id=library_id, + folder_id=folder_id, + edit_info=True, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + @web.expose + @web.require_admin + def download_dataset_from_folder(self, trans, id, library_id=None, **kwd): + """Catches the dataset id and displays file contents as directed""" + # id must refer to a LibraryDatasetDatasetAssociation object + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) + if not ldda.dataset: + msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( id ) + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) + trans.response.set_content_type( mime ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( id ), fname ) + try: + return open( ldda.file_name ) + except: + msg = 'This dataset contains no content' + return trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + @web.expose + @web.require_admin + def datasets( self, trans, library_id, **kwd ): + # This method is used by the select list labeled "Perform action on selected datasets" + # on the admin library browser. + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if params.get( 'action_on_datasets_button', False ): + if not params.ldda_ids: + msg = "At least one dataset must be selected for %s" % params.action + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + ldda_ids = util.listify( params.ldda_ids ) + if params.action == 'edit': + # We need the folder containing the LibraryDatasetDatasetAssociation(s) + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( ldda_ids[0] ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action='library_dataset_dataset_association', + library_id=library_id, + folder_id=ldda.library_dataset.folder.id, + id=",".join( ldda_ids ), + permissions=True, + msg=util.sanitize_text( msg ), + messagetype=messagetype ) ) + elif params.action == 'delete': + for id in ldda_ids: + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( id ) + ldda.deleted = True + ldda.flush() + msg = "The selected datasets have been removed from this library" + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + show_deleted=False, + msg=util.sanitize_text( msg ), + messagetype='done' ) ) + else: + msg = "Action %s is not yet implemented" % str( params.action ) + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + else: + trans.response.send_redirect( web.url_for( controller='library_admin', + action='browse_library', + id=library_id, + msg=util.sanitize_text( msg ), + messagetype=messagetype ) ) + @web.expose + @web.require_admin + def delete_library_item( self, trans, library_id, library_item_id, library_item_type ): + # This action will handle deleting all types of library items. State is saved for libraries and + # folders ( i.e., if undeleted, the state of contents of the library or folder will remain, so previously + # deleted / purged contents will have the same state ). When a library or folder has been deleted for + # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its + # contents will be purged. The association between this method and the cleanup_datasets.py script + # enables clean maintenance of libraries and library dataset disk files. This is also why the following + # 3 objects, and not any of the associations ( the cleanup_datasets.py scipot handles everything else ). + library_item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } + if library_item_type not in library_item_types: + msg = 'Bad library_item_type specified: %s' % str( library_item_type ) + messagetype = 'error' + else: + if library_item_type == 'library_dataset': + library_item_desc = 'Dataset' + else: + library_item_desc = library_item_type.capitalize() + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + library_item.deleted = True + library_item.flush() + msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) ) + messagetype = 'done' + if library_item_type == 'library': + return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) + else: + return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) + @web.expose + @web.require_admin + def undelete_library_item( self, trans, library_id, library_item_id, library_item_type ): + # This action will handle undeleting all types of library items + library_item_types = { 'library': trans.app.model.Library, + 'folder': trans.app.model.LibraryFolder, + 'library_dataset': trans.app.model.LibraryDataset } + if library_item_type not in library_item_types: + msg = 'Bad library_item_type specified: %s' % str( library_item_type ) + messagetype = 'error' + else: + if library_item_type == 'library_dataset': + library_item_desc = 'Dataset' + else: + library_item_desc = library_item_type.capitalize() + library_item = library_item_types[ library_item_type ].get( int( library_item_id ) ) + if library_item.purged: + msg = '%s %s has been purged, so it cannot be undeleted' % ( library_item_desc, library_item.name ) + messagetype = 'error' + else: + library_item.deleted = False + library_item.flush() + msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_desc, library_item.name ) ) + messagetype = 'done' + if library_item_type == 'library': + return self.browse_libraries( trans, msg=msg, messagetype=messagetype ) + else: + return self.browse_library( trans, id=library_id , msg=msg, messagetype=messagetype ) diff -r f2af04af3caa -r d301a67eda40 templates/admin/index.mako --- a/templates/admin/index.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/index.mako Mon Sep 14 11:05:36 2009 -0400 @@ -89,7 +89,7 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='library_admin', action='browse_libraries' )}" target="galaxy_main">Manage data libraries</a></div> </div> </div> <div class="toolSectionPad"></div> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/browse_libraries.mako --- a/templates/admin/library/browse_libraries.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/browse_libraries.mako Mon Sep 14 11:05:36 2009 -0400 @@ -13,10 +13,10 @@ <ul class="manage-table-actions"> %if not deleted: <li> - <a class="action-button" href="${h.url_for( controller='admin', action='library', new=True )}"><span>Create a new data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library', new=True )}"><span>Create a new data library</span></a> </li> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='deleted_libraries' )}"><span>Manage deleted libraries</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='deleted_libraries' )}"><span>Manage deleted libraries</span></a> </li> %endif </ul> @@ -42,7 +42,7 @@ <tbody> %for library in libraries: <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><a href="${h.url_for( controller='admin', action='browse_library', id=library.id, deleted=deleted, show_deleted=show_deleted )}">${library.name}</a></td> + <td><a href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, deleted=deleted, show_deleted=show_deleted )}">${library.name}</a></td> <td><i>${library.description}</i></td> </tr> %endfor diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/browse_library.mako Mon Sep 14 11:05:36 2009 -0400 @@ -97,26 +97,26 @@ <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> %endif <span class="libraryItemDeleted-${ldda.deleted}"> - <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> + <a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> </span> <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> %if not library.deleted and not folder.deleted and not library_dataset.deleted: <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use - ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + ##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> %if current_version: - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> %endif %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> %endif - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> </div> %elif not library.deleted and not folder.deleted and library_dataset.deleted: <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> </div> %endif </td> @@ -156,23 +156,23 @@ %endif %if not folder.deleted: <div popupmenu="folder-${folder.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> ## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition ##%if folder.info_association: ## <% form_id = folder.info_association[0].template.id %> ## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this folder's information template</a> ##%else: %if not folder.info_association: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, folder_id=folder.id, add=True )}">Add an information template to this folder</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, folder_id=folder.id, add=True )}">Add an information template to this folder</a> %endif - <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> - <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> + <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a> </div> %elif not deleted and folder.deleted and not folder.purged: <div popupmenu="folder-${folder.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Undelete this folder</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Undelete this folder</a> </div> %endif </li> @@ -216,10 +216,10 @@ <ul class="manage-table-actions"> %if not deleted: <li> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a> </li> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this data library</a> </li> %endif </ul> @@ -228,7 +228,7 @@ ${render_msg( msg, messagetype )} %endif -<form name="update_multiple_datasets" action="${h.url_for( controller='admin', action='datasets', library_id=library.id )}" onSubmit="javascript:return checkForm();" method="post"> +<form name="update_multiple_datasets" action="${h.url_for( controller='library_admin', action='datasets', library_id=library.id )}" onSubmit="javascript:return checkForm();" method="post"> <ul> <li class="libraryRow libraryOrFolderRow" id="libraryRow"> <div class="rowTitle"> @@ -244,24 +244,24 @@ <a id="library-${library.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="library-${library.id}-popup"> %if not deleted: - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this data library's information</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library', id=library.id, information=True )}">Edit this data library's information</a> ## Editing templates disabled until we determine optimal approach to re-linking library item to new version of form definition ##%if library.info_association: ## <% form_id = library.info_association[0].template.id %> ## <a class="action-button" href="${h.url_for( controller='forms', action='edit', form_id=form_id, show_form=True )}">Edit this data library's information template</a> ##%else: %if not library.info_association: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a> %endif - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this data library's permissions</a> - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this data library and its contents</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library', id=library.id, permissions=True )}">Edit this data library's permissions</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this data library and its contents</a> %if show_deleted: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted data library items</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted data library items</a> %else: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted data library items</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted data library items</a> %endif %elif not library.purged: - <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this data library</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this data library</a> %endif </div> </th> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/common.mako --- a/templates/admin/library/common.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/common.mako Mon Sep 14 11:05:36 2009 -0400 @@ -22,7 +22,7 @@ <div class="toolFormTitle">Other information about ${library_item_desc} ${library_item.name}</div> <div class="toolFormBody"> %if editable: - <form name="edit_info" action="${h.url_for( controller='admin', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post"> + <form name="edit_info" action="${h.url_for( controller='library_admin', action='edit_template_info', library_id=library_id, num_widgets=len( widgets ) )}" method="post"> <input type="hidden" name="library_item_id" value="${library_item.id}"/> <input type="hidden" name="library_item_type" value="${library_item_type}"/> %for i, field in enumerate( widgets ): diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/folder_info.mako --- a/templates/admin/library/folder_info.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/folder_info.mako Mon Sep 14 11:05:36 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -16,7 +16,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit folder name and description</div> <div class="toolFormBody"> - <form name="folder" action="${h.url_for( controller='admin', action='folder', information=True, id=folder.id, library_id=library_id )}" method="post" > + <form name="folder" action="${h.url_for( controller='library_admin', action='folder', information=True, id=folder.id, library_id=library_id )}" method="post" > <div class="form-row"> <label>Name:</label> <input type="text" name="name" value="${folder.name}" size="40"/> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/folder_permissions.mako --- a/templates/admin/library/folder_permissions.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/folder_permissions.mako Mon Sep 14 11:05:36 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -17,4 +17,4 @@ roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all() %> -${render_permission_form( folder, folder.name, h.url_for( controller='admin', action='folder', id=folder.id, library_id=library_id, permissions=True ), roles )} +${render_permission_form( folder, folder.name, h.url_for( controller='library_admin', action='folder', id=folder.id, library_id=library_id, permissions=True ), roles )} diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/ldda_edit_info.mako --- a/templates/admin/library/ldda_edit_info.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/ldda_edit_info.mako Mon Sep 14 11:05:36 2009 -0400 @@ -12,7 +12,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -35,7 +35,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit attributes of ${ldda.name}</div> <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> + <form name="edit_attributes" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> <input type="hidden" name="id" value="${ldda.id}"/> <br/> <div class="form-row"> @@ -73,7 +73,7 @@ <input type="submit" name="save" value="Save"/> </div> </form> - <form name="auto_detect" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> + <form name="auto_detect" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> <div class="form-row"> <input type="hidden" name="id" value="${ldda.id}"/> <input type="submit" name="detect" value="Auto-detect"/> @@ -89,7 +89,7 @@ <div class="toolFormTitle">Change data type of ${ldda.name}</div> <div class="toolFormBody"> %if ldda.datatype.allow_datatype_change: - <form name="change_datatype" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> + <form name="change_datatype" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, edit_info=True )}" method="post"> <input type="hidden" name="id" value="${ldda.id}"/> <div class="form-row"> <label>New Type:</label> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Mon Sep 14 11:05:36 2009 -0400 @@ -20,7 +20,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id, deleted=library.deleted, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -41,18 +41,18 @@ %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use - ##<a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + ##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library_id, library_dataset_id=ldda.library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> %if current_version: - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> %endif %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library_id )}">Download this dataset</a> %endif %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.deleted: - <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Delete this dataset</a> + <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=ldda.library_dataset.folder.id, id=ldda.id, delete=True )}">Delete this dataset</a> %endif </div> %endif @@ -104,7 +104,7 @@ <div class="toolFormTitle">Expired versions of ${ldda.name}</div> %for expired_ldda in expired_lddas: <div class="form-row"> - <a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a> + <a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=expired_ldda.library_dataset.folder.id, id=expired_ldda.id, info=True )}">${expired_ldda.name}</a> </div> %endfor %endif diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/ldda_permissions.mako --- a/templates/admin/library/ldda_permissions.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/ldda_permissions.mako Mon Sep 14 11:05:36 2009 -0400 @@ -15,7 +15,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -35,7 +35,7 @@ <a id="ldda-${ldd_assoc.id}-popup" class="popup-arrow" style="display: none;">▼</a> </div> <div popupmenu="ldd_assoc-${ldd_assoc.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset', id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset', id=ldd_assoc.library_dataset_id, library_id=library_id )}">Manage this dataset's versions</a> </div> </td> <td> @@ -59,4 +59,4 @@ %endif <% ldda_ids = ",".join( [ str( d.id ) for d in lddas ] ) %> -${render_permission_form( lddas[0], name_str, h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, id=ldda_ids, permissions=True ), roles )} +${render_permission_form( lddas[0], name_str, h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=lddas[0].library_dataset.folder.id, id=ldda_ids, permissions=True ), roles )} diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/library_dataset_info.mako --- a/templates/admin/library/library_dataset_info.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/library_dataset_info.mako Mon Sep 14 11:05:36 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -22,7 +22,7 @@ <div class="toolForm"> <div class="toolFormTitle">Edit attributes of ${library_dataset.name}</div> <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for( controller='admin', action='library_dataset' )}" method="post"> + <form name="edit_attributes" action="${h.url_for( controller='library_admin', action='library_dataset' )}" method="post"> <input type="hidden" name="id" value="${library_dataset.id}"/> <div class="form-row"> <label>Name:</label> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/library_dataset_permissions.mako --- a/templates/admin/library/library_dataset_permissions.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/library_dataset_permissions.mako Mon Sep 14 11:05:36 2009 -0400 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -23,4 +23,4 @@ roles = trans.app.model.Role.filter( trans.app.model.Role.table.c.deleted==False ).order_by( trans.app.model.Role.table.c.name ).all() %> -${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='admin', action='library_dataset', id=library_dataset.id, library_id=library_id, permissions=True ), roles )} +${render_permission_form( library_dataset, library_dataset.name, h.url_for( controller='library_admin', action='library_dataset', id=library_dataset.id, library_id=library_id, permissions=True ), roles )} diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/library_info.mako --- a/templates/admin/library/library_info.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/library_info.mako Mon Sep 14 11:05:36 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> @@ -16,7 +16,7 @@ <div class="toolForm"> <div class="toolFormTitle">Change library name and description</div> <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='library', information=True, id=library.id )}" method="post" > + <form name="library" action="${h.url_for( controller='library_admin', action='library', information=True, id=library.id )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/library_permissions.mako --- a/templates/admin/library/library_permissions.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/library_permissions.mako Mon Sep 14 11:05:36 2009 -0400 @@ -5,7 +5,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library.id )}"><span>Browse this data library</span></a> </li> </ul> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/new_dataset.mako --- a/templates/admin/library/new_dataset.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/new_dataset.mako Mon Sep 14 11:05:36 2009 -0400 @@ -7,16 +7,16 @@ <b>Create new data library datasets</b> <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="upload-librarydataset--popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> %endif - <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> </div> <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -32,13 +32,13 @@ <div class="toolFormTitle">Upload a directory of files</div> %endif <div class="toolFormBody"> - <form name="tool_form" action="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post"> + <form name="tool_form" action="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id )}" enctype="multipart/form-data" method="post"> <input type="hidden" name="folder_id" value="${folder_id}"/> <input type="hidden" name="upload_option" value="${upload_option}"/> %if replace_dataset: <input type="hidden" name="replace_id" value="${replace_dataset.id}"/> <div class="form-row"> - You are currently selecting a new file to replace '<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'. + You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'. <div style="clear: both"></div> </div> %endif @@ -184,13 +184,13 @@ <div class="toolFormTitle">Active datasets in your current history (${history.name})</div> <div class="toolFormBody"> %if history and history.active_datasets: - <form name="add_history_datasets_to_library" action="${h.url_for( controller='admin', action='add_history_datasets_to_library', library_id=library_id )}" enctype="multipart/form-data" method="post"> + <form name="add_history_datasets_to_library" action="${h.url_for( controller='library_admin', action='add_history_datasets_to_library', library_id=library_id )}" enctype="multipart/form-data" method="post"> <input type="hidden" name="folder_id" value="${folder_id}"/> <input type="hidden" name="upload_option" value="${upload_option}"/> %if replace_dataset: <input type="hidden" name="replace_id" value="${replace_dataset.id}"/> <div class="form-row"> - You are currently selecting a new file to replace '<a href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'. + You are currently selecting a new file to replace '<a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder_id, id=replace_dataset.library_dataset_dataset_association.id )}">${replace_dataset.name}</a>'. <div style="clear: both"></div> </div> %endif diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/new_folder.mako --- a/templates/admin/library/new_folder.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/new_folder.mako Mon Sep 14 11:05:36 2009 -0400 @@ -4,7 +4,7 @@ <br/<br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -15,7 +15,7 @@ <div class="toolForm"> <div class="toolFormTitle">Create a new folder</div> <div class="toolFormBody"> - <form name="folder" action="${h.url_for( controller='admin', action='folder', id=folder.id, library_id=library_id )}" method="post" > + <form name="folder" action="${h.url_for( controller='library_admin', action='folder', id=folder.id, library_id=library_id )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/new_library.mako --- a/templates/admin/library/new_library.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/new_library.mako Mon Sep 14 11:05:36 2009 -0400 @@ -8,7 +8,7 @@ <div class="toolForm"> <div class="toolFormTitle">Create a new data library</div> <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='library' )}" method="post" > + <form name="library" action="${h.url_for( controller='library_admin', action='library' )}" method="post" > <div class="form-row"> <label>Name:</label> <div style="float: left; width: 250px; margin-right: 10px;"> diff -r f2af04af3caa -r d301a67eda40 templates/admin/library/select_info_template.mako --- a/templates/admin/library/select_info_template.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/library/select_info_template.mako Mon Sep 14 11:05:36 2009 -0400 @@ -4,7 +4,7 @@ <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='browse_library', id=library_id )}"><span>Browse this data library</span></a> </li> </ul> @@ -14,7 +14,7 @@ <div class="toolForm"> <div class="toolFormTitle">Select a form on which to base the template for the ${library_item_desc} '${library_item_name}'</div> - <form name="new_info_template" action="${h.url_for( controller='admin', action='info_template', add=True )}" method="post" > + <form name="new_info_template" action="${h.url_for( controller='library_admin', action='info_template', add=True )}" method="post" > <div class="toolFormBody"> <div class="form-row"> <input type="hidden" name="library_id" value="${library_id}"/> diff -r f2af04af3caa -r d301a67eda40 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Fri Sep 11 16:09:02 2009 -0400 +++ b/templates/admin/requests/show_request.mako Mon Sep 14 11:05:36 2009 -0400 @@ -80,7 +80,7 @@ <i>None</i> %else: %if rd['label'] == 'Data library': - <a href="${h.url_for( controller='admin', action='browse_library', id=request.library.id )}">${rd['value']}</a> + <a href="${h.url_for( controller='library_admin', action='browse_library', id=request.library.id )}">${rd['value']}</a> %else: ${rd['value']} %endif diff -r f2af04af3caa -r d301a67eda40 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Sep 11 16:09:02 2009 -0400 +++ b/test/base/twilltestcase.py Mon Sep 14 11:05:36 2009 -0400 @@ -1139,14 +1139,14 @@ def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" self.home() - self.visit_url( "%s/admin/library?new=True" % self.url ) + self.visit_url( "%s/library_admin/library?new=True" % self.url ) self.check_page_for_string( 'Create a new data library' ) tc.fv( "1", "1", name ) # form field 1 is the field named name... tc.fv( "1", "2", description ) # form field 1 is the field named name... tc.submit( "create_library_button" ) self.home() def set_library_permissions( self, library_id, library_name, role_id, permissions_in, permissions_out ): - url = "admin/library?id=%s&permissions=True&update_roles_button=Save" % ( library_id ) + url = "library_admin/library?id=%s&permissions=True&update_roles_button=Save" % ( library_id ) for po in permissions_out: key = '%s_out' % po url ="%s&%s=%s" % ( url, key, str( role_id ) ) @@ -1161,10 +1161,10 @@ def rename_library( self, library_id, old_name, name='Library One Renamed', description='This is Library One Re-described' ): """Rename a library""" self.home() - self.visit_url( "%s/admin/library?information=True&id=%s" % ( self.url, library_id ) ) + self.visit_url( "%s/library_admin/library?information=True&id=%s" % ( self.url, library_id ) ) self.check_page_for_string( 'Change library name and description' ) # Since twill barfs on the form submisson, we ar forced to simulate it - url = "%s/admin/library?information=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \ + url = "%s/library_admin/library?information=True&id=%s&rename_library_button=Save&description=%s&name=%s" % \ ( self.url, library_id, description.replace( ' ', '+' ), name.replace( ' ', '+' ) ) self.home() self.visit_url( url ) @@ -1174,7 +1174,7 @@ def add_library_info_template( self, library_id, library_name, form_id, form_name ): """Add a new info template to a library""" self.home() - url = "%s/admin/info_template?library_id=%s&add=True" % ( self.url, library_id ) + url = "%s/library_admin/info_template?library_id=%s&add=True" % ( self.url, library_id ) self.visit_url( url ) self.check_page_for_string ( "Select a form on which to base the template" ) tc.fv( '1', 'library_id', library_id ) @@ -1184,7 +1184,7 @@ def edit_library_info( self, library_id, library_name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents ): """Add information to a library using an existing template with 2 elements""" self.home() - self.visit_url( "%s/admin/library?information=True&id=%s" % ( self.url, library_id ) ) + self.visit_url( "%s/library_admin/library?information=True&id=%s" % ( self.url, library_id ) ) check_str = 'Other information about library %s' % library_name self.check_page_for_string( check_str ) tc.fv( '2', ele_1_field_name, ele_1_contents ) @@ -1195,7 +1195,7 @@ ele_desc_1, desc_1, ele_name_2, name_2, ele_desc_2, desc_2 ): """Edit an existing library info template""" self.home() - url = "%s/admin/info_template?library_id=%s&id=%s&edit_template=True" % ( self.url, library_id, id ) + url = "%s/library_admin/info_template?library_id=%s&id=%s&edit_template=True" % ( self.url, library_id, id ) self.visit_url( url ) self.check_page_for_string ( 'Edit template' ) tc.fv( '1', 'id', id ) @@ -1213,7 +1213,7 @@ name='Folder Template 1', ele_name_0='Fu', ele_help_0='', ele_name_1='Bar', ele_help_1='' ): """Add a new info template to a folder""" self.home() - url = "%s/admin/info_template?library_id=%s&folder_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % \ + url = "%s/library_admin/info_template?library_id=%s&folder_id=%s&new_template=True&num_fields=2&create_info_template_button=Go" % \ ( self.url, library_id, folder_id ) self.home() self.visit_url( url ) @@ -1232,7 +1232,7 @@ def add_folder( self, library_id, folder_id, name='Folder One', description='This is Folder One' ): """Create a new folder""" self.home() - self.visit_url( "%s/admin/folder?library_id=%s&id=%s&new=True" % ( self.url, library_id, folder_id ) ) + self.visit_url( "%s/library_admin/folder?library_id=%s&id=%s&new=True" % ( self.url, library_id, folder_id ) )