2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2b23d8a722bb/ Changeset: 2b23d8a722bb User: dannon Date: 2014-09-17 20:05:17+00:00 Summary: Import and whitespace cleanup in lda_datasets. Affected #: 1 file diff -r 9300f9bd7ba1b791b97e91fd1db75fc88280f013 -r 2b23d8a722bb3f537edcac5902e430dcef5b5e87 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -2,31 +2,26 @@ API operations on the library datasets. """ import glob -import operator import os import os.path import string import sys -import tarfile import tempfile -import urllib -import urllib2 import zipfile +from galaxy import exceptions +from galaxy import util from galaxy import web -from galaxy import util -from galaxy import exceptions +from galaxy.exceptions import ObjectNotFound from galaxy.managers import folders, roles -from galaxy.exceptions import ObjectNotFound -from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError +from galaxy.tools.actions import upload_common +from galaxy.util.json import to_json_string +from galaxy.util.streamball import StreamBall from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous -from galaxy.security import Action -from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin +from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError from sqlalchemy.orm.exc import MultipleResultsFound from sqlalchemy.orm.exc import NoResultFound -from galaxy.tools.actions import upload_common -from galaxy.util.json import to_json_string, from_json_string import logging @@ -183,7 +178,7 @@ def _get_current_roles( self, trans, library_dataset): """ - Find all roles currently connected to relevant permissions + Find all roles currently connected to relevant permissions on the library dataset and the underlying dataset. :param library_dataset: the model object @@ -194,7 +189,7 @@ """ dataset = library_dataset.library_dataset_dataset_association.dataset - # Omit duplicated roles by converting to set + # Omit duplicated roles by converting to set access_roles = set( dataset.get_access_roles( trans ) ) modify_roles = set( trans.app.security_agent.get_roles_for_action( library_dataset, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY ) ) manage_roles = set( dataset.get_manage_permissions_roles( trans ) ) @@ -212,18 +207,18 @@ *POST /api/libraries/datasets/{encoded_dataset_id}/permissions :param encoded_dataset_id: the encoded id of the dataset to update permissions of - :type encoded_dataset_id: an encoded id string + :type encoded_dataset_id: an encoded id string :param action: (required) describes what action should be performed available actions: make_private, remove_restrictions, set_permissions - :type action: string + :type action: string :param access_ids[]: list of Role.name defining roles that should have access permission on the dataset - :type access_ids[]: string or list + :type access_ids[]: string or list :param manage_ids[]: list of Role.name defining roles that should have manage permission on the dataset - :type manage_ids[]: string or list + :type manage_ids[]: string or list :param modify_ids[]: list of Role.name defining roles that should have modify permission on the library dataset item - :type modify_ids[]: string or list + :type modify_ids[]: string or list :rtype: dictionary :returns: dict of current roles for all available permission types @@ -275,7 +270,7 @@ new_access_roles_ids = [ new_access_roles_ids ] for role_id in new_access_roles_ids: role = self._load_role( trans, role_id ) - + # Check whether role is in the set of allowed roles valid_roles, total_roles = trans.app.security_agent.get_valid_roles( trans, dataset ) if role in valid_roles: @@ -283,7 +278,7 @@ else: invalid_access_roles_names.append( role_id ) if len( invalid_access_roles_names ) > 0: - log.warning( "The following roles could not be added to the dataset access permission: " + str( invalid_access_roles_names ) ) + log.warning( "The following roles could not be added to the dataset access permission: " + str( invalid_access_roles_names ) ) access_permission = dict( access=valid_access_roles ) trans.app.security_agent.set_dataset_permission( dataset, access_permission ) @@ -292,8 +287,8 @@ valid_manage_roles = [] invalid_manage_roles_names = [] new_manage_roles_ids = util.listify( new_manage_roles_ids ) - - # Load all access roles to check + + # Load all access roles to check active_access_roles = dataset.get_access_roles( trans ) for role_id in new_manage_roles_ids: @@ -306,7 +301,7 @@ invalid_manage_roles_names.append( role_id ) if len( invalid_manage_roles_names ) > 0: - log.warning( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) + log.warning( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) manage_permission = { trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS : valid_manage_roles } trans.app.security_agent.set_dataset_permission( dataset, manage_permission ) @@ -315,8 +310,8 @@ valid_modify_roles = [] invalid_modify_roles_names = [] new_modify_roles_ids = util.listify( new_modify_roles_ids ) - - # Load all access roles to check + + # Load all access roles to check active_access_roles = dataset.get_access_roles( trans ) for role_id in new_modify_roles_ids: @@ -329,13 +324,13 @@ invalid_modify_roles_names.append( role_id ) if len( invalid_modify_roles_names ) > 0: - log.warning( "The following roles could not be added to the dataset modify permission: " + str( invalid_modify_roles_names ) ) + log.warning( "The following roles could not be added to the dataset modify permission: " + str( invalid_modify_roles_names ) ) modify_permission = { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } trans.app.security_agent.set_library_item_permission( library_dataset, modify_permission ) else: - raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' 'Allowed values are: "remove_restrictions", "make_private", "set_permissions"' ) return self._get_current_roles( trans, library_dataset ) @@ -345,7 +340,7 @@ 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 + :type role_name: string :rtype: Role :returns: the loaded Role object @@ -368,12 +363,12 @@ delete( self, trans, encoded_dataset_id, **kwd ): * DELETE /api/libraries/datasets/{encoded_dataset_id} Marks the dataset deleted or undeleted based on the value - of the undelete flag. + of the undelete flag. If the flag is not present it is considered False and the item is marked deleted. :param encoded_dataset_id: the encoded id of the dataset to change - :type encoded_dataset_id: an encoded id string + :type encoded_dataset_id: an encoded id string :rtype: dictionary :returns: dict containing information about the dataset @@ -482,7 +477,7 @@ # import_folder_root = [next(part for part in path.split(os.path.sep) if part) for path in [os.path.splitdrive(path_to_root_import_folder)[1]]] # new_folder = self.folder_manager.create( trans, folder_id, import_folder_root[0] ) - uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( + uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) uploaded_datasets = uploaded_datasets_bunch[0] if uploaded_datasets is None: @@ -493,7 +488,7 @@ # user wants to import from path (admins only) if source == "admin_path": # validate the path is within root - uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( + uploaded_datasets_bunch = trans.webapp.controllers[ 'library_common' ].get_path_paste_uploaded_datasets( trans, 'api', params, library_bunch, 200, '' ) uploaded_datasets = uploaded_datasets_bunch[0] if uploaded_datasets is None: https://bitbucket.org/galaxy/galaxy-central/commits/e43bbc51534f/ Changeset: e43bbc51534f User: dannon Date: 2014-09-17 20:14:45+00:00 Summary: More pep8, remove unused variables. The only complaints left are needed refactoring to reduce method complexity, and the assigned lambda should be a proper function. Affected #: 1 file diff -r 2b23d8a722bb3f537edcac5902e430dcef5b5e87 -r e43bbc51534f807cc8a6966433af9531c36964a4 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -303,7 +303,7 @@ if len( invalid_manage_roles_names ) > 0: log.warning( "The following roles could not be added to the dataset manage permission: " + str( invalid_manage_roles_names ) ) - manage_permission = { trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS : valid_manage_roles } + manage_permission = { trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: valid_manage_roles } trans.app.security_agent.set_dataset_permission( dataset, manage_permission ) # MODIFY LIBRARY ITEM ROLES @@ -326,12 +326,12 @@ if len( invalid_modify_roles_names ) > 0: log.warning( "The following roles could not be added to the dataset modify permission: " + str( invalid_modify_roles_names ) ) - modify_permission = { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY : valid_modify_roles } + modify_permission = { trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles } trans.app.security_agent.set_library_item_permission( library_dataset, modify_permission ) else: - raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value.' - 'Allowed values are: "remove_restrictions", "make_private", "set_permissions"' ) + raise exceptions.RequestParameterInvalidException( 'The mandatory parameter "action" has an invalid value. ' + 'Allowed values are: "remove_restrictions", "make_private", "set_permissions"' ) return self._get_current_roles( trans, library_dataset ) @@ -427,7 +427,6 @@ if path is None: raise exceptions.RequestParameterMissingException( 'The required atribute path is missing.' ) folder = self.folder_manager.get( trans, folder_id ) - link_data = util.string_as_bool( kwd.get( 'link_data', False ) ) source = kwd.get( 'source', None ) if source not in [ 'userdir_file', 'userdir_folder', 'admin_path' ]: @@ -457,7 +456,7 @@ tool_id = 'upload1' tool = trans.app.toolbox.get_tool( tool_id ) state = tool.new_state( trans ) - errors = tool.update_state( trans, tool.inputs_by_page[ 0 ], state.inputs, kwd ) + tool.update_state( trans, tool.inputs_by_page[ 0 ], state.inputs, kwd ) tool_params = state.inputs dataset_upload_inputs = [] for input_name, input in tool.inputs.iteritems(): @@ -708,7 +707,7 @@ if folder.parent_id is None: path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) else: - # We add the current folder and traverse up one folder. + # We add the current folder and traverse up one folder. path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( self._build_path( trans, upper_folder ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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