1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/d3e72ceda152/ Changeset: d3e72ceda152 User: martenson Date: 2014-09-02 16:37:14 Summary: next chunk of API managers - libs, folders, roles Affected #: 5 files

diff -r 188aa379bd9b25322e8532da73fae6dcece47231 -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a lib/galaxy/managers/folders.py --- a/lib/galaxy/managers/folders.py +++ b/lib/galaxy/managers/folders.py @@ -38,9 +38,7 @@ raise exceptions.RequestParameterInvalidException( 'No folder found with the id provided.' ) except Exception, e: raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) - folder = self.secure( trans, folder, check_ownership, check_accessible ) - return folder

def secure( self, trans, folder, check_ownership=True, check_accessible=True ): @@ -94,7 +92,7 @@ :param folder: folder item :type folder: LibraryFolder

- :returns: dict with data about the new folder + :returns: dict with data about the folder :rtype: dictionary

""" @@ -153,8 +151,33 @@ manage_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) add_roles = set( trans.app.security_agent.get_roles_for_action( folder, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) )

- modify_folder_role_list = [ modify_role.name for modify_role in modify_roles ] - manage_folder_role_list = [ manage_role.name for manage_role in manage_roles ] - add_library_item_role_list = [ add_role.name for add_role in add_roles ] + modify_folder_role_list = [ ( modify_role.name, trans.security.encode_id( modify_role.id ) ) for modify_role in modify_roles ] + manage_folder_role_list = [ ( manage_role.name, trans.security.encode_id( manage_role.id ) ) for manage_role in manage_roles ] + add_library_item_role_list = [ ( add_role.name, trans.security.encode_id( add_role.id ) ) for add_role in add_roles ] + return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list )

- return dict( modify_folder_role_list=modify_folder_role_list, manage_folder_role_list=manage_folder_role_list, add_library_item_role_list=add_library_item_role_list ) + def cut_the_prefix( self, encoded_folder_id ): + """ + Remove the prefix from the encoded folder id. + """ + if ( ( len( encoded_folder_id ) % 16 == 1 ) and encoded_folder_id.startswith( 'F' ) ): + cut_id = encoded_folder_id[ 1: ] + else: + raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) + return cut_id + + def decode_folder_id( self, trans, encoded_folder_id ): + """ + Decode the folder id given that it has already lost the prefixed 'F'. + """ + try: + decoded_id = trans.security.decode_id( encoded_folder_id ) + except ValueError: + raise exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_folder_id ) ) ) + return decoded_id + + def cut_and_decode( self, trans, encoded_folder_id ): + """ + Cuts the folder prefix (the prepended 'F') and returns the decoded id. + """ + return self.decode_folder_id( trans, self.cut_the_prefix( encoded_folder_id ) )

diff -r 188aa379bd9b25322e8532da73fae6dcece47231 -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a lib/galaxy/managers/libraries.py --- /dev/null +++ b/lib/galaxy/managers/libraries.py @@ -0,0 +1,244 @@ +""" +Manager and Serializer for libraries. +""" + +import galaxy.web +from galaxy import exceptions +from galaxy.model import orm +from galaxy.managers import base as manager_base +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound + +import logging +log = logging.getLogger( __name__ ) + + +# ============================================================================= +class LibraryManager( object ): + """ + Interface/service object for interacting with libraries. + """ + + def __init__( self, *args, **kwargs ): + super( LibraryManager, self ).__init__( *args, **kwargs ) + + def get( self, trans, decoded_library_id, check_accessible=True ): + """ + Get the library from the DB. + + :param decoded_library_id: decoded library id + :type decoded_library_id: int + :param check_accessible: flag whether to check that user can access item + :type check_accessible: bool + + :returns: the requested library + :rtype: Library + """ + try: + library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.id == decoded_library_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple libraries found with the same id.' ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str( e ) ) + library = self.secure( trans, library, check_accessible) + return library + + def create( self, trans, name, description='', synopsis=''): + """ + Create a new library. + """ + if not trans.user_is_admin: + raise exceptions.ItemAccessibilityException( 'Only administrators can create libraries.' ) + else: + library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) + root_folder = trans.app.model.LibraryFolder( name=name, description='' ) + library.root_folder = root_folder + trans.sa_session.add_all( ( library, root_folder ) ) + trans.sa_session.flush() + return library + + def update( self, trans, library, name=None, description=None, synopsis=None ): + """ + Update the given library + """ + changed = False + if not trans.user_is_admin(): + raise exceptions.ItemAccessibilityException( 'Only administrators can update libraries.' ) + if library.deleted: + raise exceptions.RequestParameterInvalidException( 'You cannot modify a deleted library. Undelete it first.' ) + if name is not None: + library.name = name + changed = True + if description is not None: + library.description = description + changed = True + if synopsis is not None: + library.synopsis = synopsis + changed = True + if changed: + trans.sa_session.add( library ) + trans.sa_session.flush() + return library + + def delete( self, trans, library, undelete=False ): + """ + Mark given library deleted/undeleted based on the flag. + """ + if not trans.user_is_admin(): + raise exceptions.ItemAccessibilityException( 'Only administrators can delete and undelete libraries.' ) + if undelete: + library.deleted = False + else: + library.deleted = True + trans.sa_session.add( library ) + trans.sa_session.flush() + return library + + def list( self, trans, deleted=False ): + """ + Return a list of libraries from the DB. + + :param deleted: if True, show only ``deleted`` libraries, if False show only ``non-deleted`` + :type deleted: boolean (optional) + """ + is_admin = trans.user_is_admin() + query = trans.sa_session.query( trans.app.model.Library ) + + if is_admin: + if deleted is None: + # Flag is not specified, do not filter on it. + pass + elif deleted: + query = query.filter( trans.app.model.Library.table.c.deleted == True ) + else: + query = query.filter( trans.app.model.Library.table.c.deleted == False ) + else: + # Nonadmins can't see deleted libraries + current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] + library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action + restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) + .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) + .distinct() ) ] + accessible_restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) + .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, + trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ) ] + query = query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) + return query + + def secure( self, trans, library, check_accessible=True ): + """ + Check if library is accessible to user. + + :param folder: library + :type folder: Library + :param check_accessible: flag whether to check that user can access library + :type check_accessible: bool + + :returns: the original folder + :rtype: LibraryFolder + """ + # all libraries are accessible to an admin + if trans.user_is_admin(): + return library + if check_accessible: + library = self.check_accessible( trans, library ) + return library + + def check_accessible( self, trans, library ): + """ + Check whether the library is accessible to current user. + """ + if not trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ): + raise exceptions.ObjectNotFound( 'Library with the id provided was not found.' ) + elif library.deleted: + raise exceptions.ObjectNotFound( 'Library with the id provided is deleted.' ) + else: + return library + + def get_library_dict( self, trans, library ): + """ + Return library data in the form of a dictionary. + + :param library: library + :type library: Library + + :returns: dict with data about the library + :rtype: dictionary + """ + library_dict = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + if trans.app.security_agent.library_is_public( library, contents=False ): + library_dict[ 'public' ] = True + current_user_roles = trans.get_current_user_roles() + if not trans.user_is_admin(): + library_dict[ 'can_user_add' ] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) + library_dict[ 'can_user_modify' ] = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) + library_dict[ 'can_user_manage' ] = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) + else: + library_dict[ 'can_user_add' ] = True + library_dict[ 'can_user_modify' ] = True + library_dict[ 'can_user_manage' ] = True + return library_dict + + def get_current_roles( self, trans, library ): + """ + Load all permissions currently related to the given library. + + :param library: the model object + :type library: Library + + :rtype: dictionary + :returns: dict of current roles for all available permission types + """ + access_library_role_list = [ ( access_role.name, trans.security.encode_id( access_role.id ) ) for access_role in self.get_access_roles( trans, library ) ] + modify_library_role_list = [ ( modify_role.name, trans.security.encode_id( modify_role.id ) ) for modify_role in self.get_modify_roles( trans, library ) ] + manage_library_role_list = [ ( manage_role.name, trans.security.encode_id( manage_role.id ) ) for manage_role in self.get_manage_roles( trans, library ) ] + add_library_item_role_list = [ ( add_role.name, trans.security.encode_id( add_role.id ) ) for add_role in self.get_add_roles( trans, library ) ] + return dict( access_library_role_list=access_library_role_list, + modify_library_role_list=modify_library_role_list, + manage_library_role_list=manage_library_role_list, + add_library_item_role_list=add_library_item_role_list ) + + def get_access_roles( self, trans, library ): + """ + Load access roles for all library permissions + """ + return set( library.get_access_roles( trans ) ) + + def get_modify_roles( self, trans, library ): + """ + Load modify roles for all library permissions + """ + return set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) + + def get_manage_roles( self, trans, library ): + """ + Load manage roles for all library permissions + """ + return set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) + + def get_add_roles( self, trans, library ): + """ + Load add roles for all library permissions + """ + return set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) + + def set_permission_roles( self, trans, library, access_roles, modify_roles, manage_roles, add_roles ): + """ + Set permissions on the given library. + """ + + def make_public( self, trans, library ): + """ + Makes the given library public (removes all access roles) + """ + trans.app.security_agent.make_library_public( library ) + return self.is_public( trans, library ) + + def is_public( self, trans, library ): + """ + Return true if lib is public. + """ + return trans.app.security_agent.library_is_public( library ) +

diff -r 188aa379bd9b25322e8532da73fae6dcece47231 -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a lib/galaxy/managers/roles.py --- /dev/null +++ b/lib/galaxy/managers/roles.py @@ -0,0 +1,41 @@ +""" +Manager and Serializer for Roles. +""" + +import galaxy.web +from galaxy import exceptions +from galaxy.model import orm +from sqlalchemy.orm.exc import MultipleResultsFound +from sqlalchemy.orm.exc import NoResultFound + +import logging +log = logging.getLogger( __name__ ) + + +# ============================================================================= +class RoleManager( object ): + """ + Interface/service object for interacting with folders. + """ + + def get( self, trans, decoded_role_id): + """ + Method loads the role from the DB based on the given role id. + + :param decoded_role_id: id of the role to load from the DB + :type decoded_role_id: int + + :returns: the loaded Role object + :rtype: Role + + :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError + """ + try: + role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.id == decoded_role_id ).one() + except MultipleResultsFound: + raise exceptions.InconsistentDatabase( 'Multiple roles found with the same id.' ) + except NoResultFound: + raise exceptions.RequestParameterInvalidException( 'No role found with the id provided.' ) + except Exception, e: + raise exceptions.InternalServerError( 'Error loading from the database.' + str(e) ) + return role

diff -r 188aa379bd9b25322e8532da73fae6dcece47231 -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -1,5 +1,5 @@ """ -API operations on library folders +API operations on library folders. """ from galaxy import util from galaxy import web @@ -43,7 +43,8 @@ :returns: dictionary including details of the folder :rtype: dict """ - folder = self.folder_manager.get( trans, self.__cut_and_decode( trans, id ), check_ownership=False, check_accessible=True ) + folder_id = self.folder_manager.cut_and_decode( trans, id ) + folder = self.folder_manager.get( trans, folder_id, check_ownership=False, check_accessible=True ) return_dict = self.folder_manager.get_folder_dict( trans, folder ) return return_dict

@@ -77,7 +78,7 @@ if name is None: raise exceptions.RequestParameterMissingException( "Missing required parameter 'name'." ) description = payload.get( 'description', '' ) - decoded_parent_folder_id = self.__cut_and_decode( trans, encoded_parent_folder_id ) + decoded_parent_folder_id = self.folder_manager.cut_and_decode( trans, encoded_parent_folder_id ) parent_folder = self.folder_manager.get( trans, decoded_parent_folder_id ) new_folder = self.folder_manager.create( trans, parent_folder.id, name, description ) return self.folder_manager.get_folder_dict( trans, new_folder ) @@ -102,8 +103,7 @@ """ current_user_roles = trans.get_current_user_roles() is_admin = trans.user_is_admin() - encoded_folder_id = self.__cut_the_prefix( encoded_folder_id ) - decoded_folder_id = self.__decode_folder_id( trans, encoded_folder_id ) + decoded_folder_id = self.folder_manager.cut_and_decode( trans, encoded_folder_id ) folder = self.folder_manager.get( trans, decoded_folder_id )

if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) ): @@ -128,7 +128,8 @@ roles, total_roles = trans.app.security_agent.get_valid_roles( trans, folder, query, page, page_limit ) return_roles = [] for role in roles: - return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) + role_id = trans.security.encode_id( role.id ) + return_roles.append( dict( id=role_id, name=role.name, type=role.type ) ) return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) else: raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" ) @@ -146,15 +147,15 @@ available actions: set_permissions :type action: string

- :param add_ids[]: list of Role.name defining roles that should have add item permission on the folder + :param add_ids[]: list of Role.id defining roles that should have add item permission on the folder :type add_ids[]: string or list - :param manage_ids[]: list of Role.name defining roles that should have manage permission on the folder + :param manage_ids[]: list of Role.id defining roles that should have manage permission on the folder :type manage_ids[]: string or list - :param modify_ids[]: list of Role.name defining roles that should have modify permission on the folder + :param modify_ids[]: list of Role.id defining roles that should have modify permission on the folder :type modify_ids[]: string or list

:rtype: dictionary - :returns: dict of current roles for all available permission types + :returns: dict of current roles for all available permission types.

:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError RequestParameterMissingException @@ -162,7 +163,7 @@ is_admin = trans.user_is_admin() current_user_roles = trans.get_current_user_roles()

- decoded_folder_id = self.__decode_folder_id( trans, self.__cut_the_prefix( encoded_folder_id ) ) + decoded_folder_id = self.folder_manager.decode_folder_id( trans, self.folder_manager.cut_the_prefix( encoded_folder_id ) ) folder = self.folder_manager.get( trans, decoded_folder_id ) if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, folder ) ): raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to modify permissions of this folder.' ) @@ -236,32 +237,7 @@ """ raise exceptions.NotImplemented( 'Updating folder through this endpoint is not implemented yet.' )

- def __cut_the_prefix( self, encoded_id ): - """ - Remove the prefix from the encoded folder id. - """ - if ( ( len( encoded_id ) % 16 == 1 ) and encoded_id.startswith( 'F' ) ): - cut_id = encoded_id[ 1: ] - else: - raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_id ) ) - return cut_id - - def __decode_folder_id( self, trans, encoded_id ): - """ - Decode the folder id given that it has already lost the prefixed 'F'. - """ - try: - decoded_id = trans.security.decode_id( encoded_id ) - except ValueError: - raise exceptions.MalformedId( "Malformed folder id ( %s ) specified, unable to decode" % ( str( encoded_id ) ) ) - return decoded_id - - def __cut_and_decode( self, trans, encoded_folder_id ): - """ - Cuts the prefix (the prepended 'F') and returns the decoded id. - """ - return self.__decode_folder_id( trans, self.__cut_the_prefix( encoded_folder_id ) ) - + # TODO move to Role manager def _load_role( self, trans, role_name ): """ Method loads the role from the DB based on the given role name.

diff -r 188aa379bd9b25322e8532da73fae6dcece47231 -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -3,6 +3,7 @@ """ from galaxy import util from galaxy import exceptions +from galaxy.managers import libraries, folders, roles from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous from galaxy.model.orm import and_, not_, or_ @@ -16,6 +17,12 @@

class LibrariesController( BaseAPIController ):

+ def __init__( self, app ): + super( LibrariesController, self ).__init__( app ) + self.folder_manager = folders.FolderManager() + self.library_manager = libraries.LibraryManager() + self.role_manager = roles.RoleManager() + @expose_api_anonymous def index( self, trans, **kwd ): """ @@ -32,51 +39,25 @@ .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys`

""" - is_admin = trans.user_is_admin() - query = trans.sa_session.query( trans.app.model.Library ) - deleted = kwd.get( 'deleted', 'missing' ) - try: - if not is_admin: - # non-admins can't see deleted libraries - deleted = False - else: - deleted = util.asbool( deleted ) - if deleted: - query = query.filter( trans.app.model.Library.table.c.deleted == True ) - else: - query = query.filter( trans.app.model.Library.table.c.deleted == False ) - except ValueError: - # given value wasn't true/false but the user is admin so we don't filter on this parameter at all - pass - - if not is_admin: - # non-admins can see only allowed and public libraries - current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ] - library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action - restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) - .filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) - .distinct() ) ] - accessible_restricted_library_ids = [ lp.library_id for lp in ( trans.sa_session.query( trans.model.LibraryPermissions ) - .filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action, - trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ) ] - query = query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ), trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) + deleted = kwd.get( 'deleted', None ) + query = self.library_manager.list( trans, deleted ) libraries = [] for library in query: - item = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) - if trans.app.security_agent.library_is_public( library, contents=False ): - item[ 'public' ] = True - current_user_roles = trans.get_current_user_roles() - if not trans.user_is_admin(): - item['can_user_add'] = trans.app.security_agent.can_add_library_item( current_user_roles, library ) - item['can_user_modify'] = trans.app.security_agent.can_modify_library_item( current_user_roles, library ) - item['can_user_manage'] = trans.app.security_agent.can_manage_library_item( current_user_roles, library ) - else: - item['can_user_add'] = True - item['can_user_modify'] = True - item['can_user_manage'] = True - libraries.append( item ) + libraries.append( self.library_manager.get_library_dict( trans, library ) ) return libraries

+ def __decode_id( self, trans, encoded_id, object_name=None ): + """ + Try to decode the id. + + :param object_name: Name of the object the id belongs to. (optional) + :type object_name: str + """ + try: + return trans.security.decode_id( encoded_id ) + except TypeError: + raise exceptions.MalformedId( 'Malformed %s id specified, unable to decode.' % object_name if object_name is not None else '' ) + @expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): """ @@ -98,24 +79,9 @@

:raises: MalformedId, ObjectNotFound """ - library_id = id - deleted = util.string_as_bool( deleted ) - library = self._load_library( trans, library_id, deleted ) - if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( trans.get_current_user_roles(), library ) ): - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) - return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) - - def _load_library( self, trans, encoded_library_id, deleted=False ): - try: - decoded_library_id = trans.security.decode_id( encoded_library_id ) - except TypeError: - raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) - try: - library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) - assert library.deleted == deleted - except Exception: - library = None - return library + library = self.library_manager.get( trans, self.__decode_id( trans, id, 'library' ) ) + library_dict = self.library_manager.get_library_dict( trans, library ) + return library_dict

@expose_api def create( self, trans, payload, **kwd ): @@ -137,8 +103,6 @@

:raises: ItemAccessibilityException, RequestParameterMissingException """ - if not trans.user_is_admin(): - raise exceptions.ItemAccessibilityException( 'Only administrators can create libraries.' ) params = util.Params( payload ) name = util.restore_text( params.get( 'name', None ) ) if not name: @@ -147,19 +111,9 @@ synopsis = util.restore_text( params.get( 'synopsis', '' ) ) if synopsis in [ 'None', None ]: synopsis = '' - library = trans.app.model.Library( name=name, description=description, synopsis=synopsis ) - root_folder = trans.app.model.LibraryFolder( name=name, description='' ) - library.root_folder = root_folder - trans.sa_session.add_all( ( library, root_folder ) ) - trans.sa_session.flush() - - item = library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) - item['can_user_add'] = True - item['can_user_modify'] = True - item['can_user_manage'] = True - if trans.app.security_agent.library_is_public( library, contents=False ): - item[ 'public' ] = True - return item + library = self.library_manager.create( trans, name, description, synopsis ) + library_dict = self.library_manager.get_library_dict( trans, library ) + return library_dict

@expose_api def update( self, trans, id, **kwd ): @@ -183,37 +137,21 @@

:raises: ItemAccessibilityException, MalformedId, ObjectNotFound, RequestParameterInvalidException, RequestParameterMissingException """ - if not trans.user_is_admin(): - raise exceptions.ItemAccessibilityException( 'Only administrators can update libraries.' ) - - try: - decoded_id = trans.security.decode_id( id ) - except Exception: - raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) - library = None - try: - library = trans.sa_session.query( trans.app.model.Library ).get( decoded_id ) - except Exception: - library = None - if not library: - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) - if library.deleted: - raise exceptions.RequestParameterInvalidException( 'You cannot modify a deleted library. Undelete it first.' ) + library = self.library_manager.get( trans, self.__decode_id( trans, id, 'library' ) ) payload = kwd.get( 'payload', None ) if payload: name = payload.get( 'name', None ) if name == '': raise exceptions.RequestParameterMissingException( "Parameter 'name' of library is required. You cannot remove it." ) - library.name = name if payload.get( 'description', None ) or payload.get( 'description', None ) == '': - library.description = payload.get( 'description', None ) + description = payload.get( 'description', None ) if payload.get( 'synopsis', None ) or payload.get( 'synopsis', None ) == '': - library.synopsis = payload.get( 'synopsis', None ) + synopsis = payload.get( 'synopsis', None ) else: raise exceptions.RequestParameterMissingException( "You did not specify any payload." ) - trans.sa_session.add( library ) - trans.sa_session.flush() - return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + updated_library = self.library_manager.update( trans, library, name, description, synopsis ) + library_dict = self.library_manager.get_library_dict( trans, updated_library ) + return library_dict

@expose_api def delete( self, trans, id, **kwd ): @@ -237,28 +175,11 @@

:raises: ItemAccessibilityException, MalformedId, ObjectNotFound """ + library = self.library_manager.get( trans, self.__decode_id( trans, id, 'library' )) undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) - if not trans.user_is_admin(): - raise exceptions.ItemAccessibilityException( 'Only administrators can delete and undelete libraries.' ) - try: - decoded_id = trans.security.decode_id( id ) - except Exception: - raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % id ) - try: - library = trans.sa_session.query( trans.app.model.Library ).get( decoded_id ) - except Exception: - library = None - if not library: - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) - - if undelete: - library.deleted = False - else: - library.deleted = True - - trans.sa_session.add( library ) - trans.sa_session.flush() - return library.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id } ) + library = self.library_manager.delete( trans, library, undelete ) + library_dict = self.library_manager.get_library_dict( trans, library ) + return library_dict

@expose_api def get_permissions( self, trans, encoded_library_id, **kwd ): @@ -283,9 +204,7 @@ """ current_user_roles = trans.get_current_user_roles() is_admin = trans.user_is_admin() - library = self._load_library( trans, encoded_library_id ) - if not library or not ( is_admin or trans.app.security_agent.can_access_library( current_user_roles, library ) ): - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) + library = self.library_manager.get( trans, self.__decode_id( trans, encoded_library_id, 'library' ) ) if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, library ) ): raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to access permissions of this library.' )

@@ -293,7 +212,8 @@ is_library_access = util.string_as_bool( kwd.get( 'is_library_access', False ) )

if scope == 'current' or scope is None: - return self._get_current_roles( trans, library ) + roles = self.library_manager.get_current_roles( trans, library ) + return roles

# Return roles that are available to select. elif scope == 'available': @@ -315,34 +235,12 @@

return_roles = [] for role in roles: - return_roles.append( dict( id=role.name, name=role.name, type=role.type ) ) + role_id = trans.security.encode_id ( role.id ) + return_roles.append( dict( id=role_id, name=role.name, type=role.type ) ) return dict( roles=return_roles, page=page, page_limit=page_limit, total=total_roles ) else: raise exceptions.RequestParameterInvalidException( "The value of 'scope' parameter is invalid. Alllowed values: current, available" )

- def _load_role( self, trans, role_name ): - """ - Method loads the role from the DB based on the given role name. - - :param role_name: name of the role to load from the DB - :type role_name: string - - :rtype: Role - :returns: the loaded Role object - - :raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError - """ - try: - role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.name == role_name ).one() - except MultipleResultsFound: - raise exceptions.InconsistentDatabase( 'Multiple roles found with the same name. Name: ' + str( role_name ) ) - except NoResultFound: - raise exceptions.RequestParameterInvalidException( 'No role found with the name provided. Name: ' + str( role_name ) ) - except Exception, e: - raise exceptions.InternalServerError( 'Error loading from the database.' + str(e)) - return role - - @expose_api def set_permissions( self, trans, encoded_library_id, **kwd ): """ @@ -356,13 +254,13 @@ available actions: remove_restrictions, set_permissions :type action: string

- :param access_ids[]: list of Role.name defining roles that should have access permission on the library + :param access_ids[]: list of Role.id defining roles that should have access permission on the library :type access_ids[]: string or list - :param add_ids[]: list of Role.name defining roles that should have add item permission on the library + :param add_ids[]: list of Role.id defining roles that should have add item permission on the library :type add_ids[]: string or list - :param manage_ids[]: list of Role.name defining roles that should have manage permission on the library + :param manage_ids[]: list of Role.id defining roles that should have manage permission on the library :type manage_ids[]: string or list - :param modify_ids[]: list of Role.name defining roles that should have modify permission on the library + :param modify_ids[]: list of Role.id defining roles that should have modify permission on the library :type modify_ids[]: string or list

:rtype: dictionary @@ -373,9 +271,8 @@ """ is_admin = trans.user_is_admin() current_user_roles = trans.get_current_user_roles() - library = self._load_library( trans, encoded_library_id ) - if not library or not ( is_admin or trans.app.security_agent.can_access_library( current_user_roles, library ) ): - raise exceptions.ObjectNotFound( 'Library with the id provided ( %s ) was not found' % id ) + library = self.library_manager.get( trans, self.__decode_id( trans, encoded_library_id, 'library' ) ) + if not ( is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, library ) ): raise exceptions.InsufficientPermissionsException( 'You do not have proper permission to modify permissions of this library.' )

@@ -392,8 +289,8 @@ else: raise exceptions.RequestParameterMissingException( 'The mandatory parameter "action" is missing.' ) elif action == 'remove_restrictions': - trans.app.security_agent.make_library_public( library ) - if not trans.app.security_agent.library_is_public( library ): + is_public = self.library_manager.make_public( trans, library ) + if not is_public: raise exceptions.InternalServerError( 'An error occured while making library public.' ) elif action == 'set_permissions':

@@ -401,7 +298,7 @@ valid_access_roles = [] invalid_access_roles_names = [] for role_id in new_access_roles_ids: - role = self._load_role( trans, role_id ) + role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) ) valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library, is_library_access=True ) if role in valid_roles: valid_access_roles.append( role ) @@ -414,7 +311,7 @@ valid_add_roles = [] invalid_add_roles_names = [] for role_id in new_add_roles_ids: - role = self._load_role( trans, role_id ) + role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) ) valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) if role in valid_roles: valid_add_roles.append( role ) @@ -427,7 +324,7 @@ valid_manage_roles = [] invalid_manage_roles_names = [] for role_id in new_manage_roles_ids: - role = self._load_role( trans, role_id ) + role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) ) valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) if role in valid_roles: valid_manage_roles.append( role ) @@ -440,7 +337,7 @@ valid_modify_roles = [] invalid_modify_roles_names = [] for role_id in new_modify_roles_ids: - role = self._load_role( trans, role_id ) + role = self.role_manager.get( trans, self.__decode_id( trans, role_id, 'role' ) ) valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, library ) if role in valid_roles: valid_modify_roles.append( role ) @@ -461,34 +358,8 @@ else: raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "remove_restrictions", set_permissions"' ) - - return self._get_current_roles( trans, library ) - - - def _get_current_roles( self, trans, library): - """ - Find all roles currently connected to relevant permissions - on the library. - - :param library: the model object - :type library: Library - - :rtype: dictionary - :returns: dict of current roles for all available permission types - """ - # Omit duplicated roles by converting to set - access_roles = set( library.get_access_roles( trans ) ) - modify_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) - manage_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE ) ) - add_roles = set( trans.app.security_agent.get_roles_for_action( library, trans.app.security_agent.permitted_actions.LIBRARY_ADD ) ) - - access_library_role_list = [ access_role.name for access_role in access_roles ] - modify_library_role_list = [ modify_role.name for modify_role in modify_roles ] - manage_library_role_list = [ manage_role.name for manage_role in manage_roles ] - add_library_item_role_list = [ add_role.name for add_role in add_roles ] - - return dict( access_library_role_list=access_library_role_list, modify_library_role_list=modify_library_role_list, manage_library_role_list=manage_library_role_list, add_library_item_role_list=add_library_item_role_list ) - + roles = self.library_manager.get_current_roles( trans, library ) + return roles

def set_permissions_old( self, trans, library, payload, **kwd ): """ @@ -508,7 +379,6 @@ # Copy the permissions to the root folder trans.app.security_agent.copy_library_permissions( trans, library, library.root_folder ) message = "Permissions updated for library '%s'." % library.name - item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } ) return item

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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