Source code for galaxy.webapps.galaxy.api.extended_metadata
"""
API operations on annotations.
"""
import logging
from galaxy import web
from galaxy import managers
from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems, UsesStoredWorkflowMixin, UsesExtendedMetadataMixin, HTTPNotImplemented
log = logging.getLogger( __name__ )
[docs]class BaseExtendedMetadataController( BaseAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin ):
@web.expose_api
[docs] def index( self, trans, **kwd ):
idnum = kwd[self.exmeta_item_id]
item = self._get_item_from_id(trans, idnum, check_writable=False)
if item is not None:
ex_meta = self.get_item_extended_metadata_obj( trans, item )
if ex_meta is not None:
return ex_meta.data
@web.expose_api
[docs] def create( self, trans, payload, **kwd ):
idnum = kwd[self.exmeta_item_id]
item = self._get_item_from_id(trans, idnum, check_writable=True)
if item is not None:
ex_obj = self.get_item_extended_metadata_obj(trans, item)
if ex_obj is not None:
self.unset_item_extended_metadata_obj(trans, item)
self.delete_extended_metadata(trans, ex_obj)
ex_obj = self.create_extended_metadata(trans, payload)
self.set_item_extended_metadata_obj(trans, item, ex_obj)
@web.expose_api
[docs] def delete( self, trans, **kwd ):
idnum = kwd[self.tagged_item_id]
item = self._get_item_from_id(trans, idnum, check_writable=True)
if item is not None:
ex_obj = self.get_item_extended_metadata_obj(trans, item)
if ex_obj is not None:
self.unset_item_extended_metadata_obj(trans, item)
self.delete_extended_metadata(trans, ex_obj)
@web.expose_api
[docs]class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController):
controller_name = "library_dataset_extended_metadata"
exmeta_item_id = "library_content_id"
def _get_item_from_id(self, trans, idstr, check_writable=True):
if check_writable:
item = self.get_library_dataset_dataset_association( trans, idstr)
if trans.app.security_agent.can_modify_library_item( trans.get_current_user_roles(), item ):
return item
else:
item = self.get_library_dataset_dataset_association( trans, idstr)
if trans.app.security_agent.can_access_library_item( trans.get_current_user_roles(), item, trans.user ):
return item
return None
[docs]class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController):
controller_name = "history_dataset_extended_metadata"
exmeta_item_id = "history_content_id"
def __init__( self, app ):
super( HistoryDatasetExtendMetadataController, self ).__init__( app )
self.hda_manager = managers.hdas.HDAManager( app )
def _get_item_from_id(self, trans, idstr, check_writable=True):
decoded_idstr = self.decode_id( idstr )
if check_writable:
return self.hda_manager.get_owned( decoded_idstr, trans.user, current_history=trans.history )
else:
hda = self.hda_manager.get_accessible( decoded_idstr, trans.user )
return self.hda_manager.error_if_uploading( hda )