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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):
[docs] @web.expose_api 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
[docs] @web.expose_api 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)
[docs] @web.expose_api 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)
[docs] @web.expose_api def undelete(self, trans, **kwd): raise HTTPNotImplemented()
[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"
[docs] 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)