Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.galaxy.api.annotations

"""
API operations on annotations.
"""
import logging
from abc import abstractmethod

from galaxy import (
    exceptions,
    managers
)
from galaxy.managers.context import ProvidesHistoryContext
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import expose_api
from galaxy.webapps.base.controller import (
    UsesStoredWorkflowMixin
)
from . import BaseGalaxyAPIController, depends

log = logging.getLogger(__name__)


[docs]class BaseAnnotationsController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, UsesAnnotations): tagged_item_id: str
[docs] @expose_api def index(self, trans: ProvidesHistoryContext, **kwd): idnum = kwd[self.tagged_item_id] item = self._get_item_from_id(trans, idnum) if item is not None: return self.get_item_annotation_str(trans.sa_session, trans.user, item)
[docs] @expose_api def create(self, trans: ProvidesHistoryContext, payload: dict, **kwd): if "text" not in payload: return "" idnum = kwd[self.tagged_item_id] item = self._get_item_from_id(trans, idnum) if item is not None: new_annotation = payload.get("text") # TODO: sanitize on display not entry new_annotation = sanitize_html(new_annotation) self.add_item_annotation(trans.sa_session, trans.user, item, new_annotation) trans.sa_session.flush() return new_annotation return ""
[docs] @expose_api def delete(self, trans: ProvidesHistoryContext, **kwd): idnum = kwd[self.tagged_item_id] item = self._get_item_from_id(trans, idnum) if item is not None: return self.delete_item_annotation(trans.sa_session, trans.user, item)
[docs] @expose_api def undelete(self, trans: ProvidesHistoryContext, **kwd): raise exceptions.NotImplemented()
@abstractmethod def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr): """Return item with annotation association."""
[docs]class HistoryAnnotationsController(BaseAnnotationsController): controller_name = "history_annotations" tagged_item_id = "history_id" history_manager: managers.histories.HistoryManager = depends(managers.histories.HistoryManager) def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr): decoded_idstr = self.decode_id(idstr) history = self.history_manager.get_accessible(decoded_idstr, trans.user, current_history=trans.history) return history
[docs]class HistoryContentAnnotationsController(BaseAnnotationsController): controller_name = "history_content_annotations" tagged_item_id = "history_content_id" hda_manager: managers.hdas.HDAManager = depends(managers.hdas.HDAManager) def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr): decoded_idstr = self.decode_id(idstr) hda = self.hda_manager.get_accessible(decoded_idstr, trans.user) hda = self.hda_manager.error_if_uploading(hda) return hda
[docs]class WorkflowAnnotationsController(BaseAnnotationsController): controller_name = "workflow_annotations" tagged_item_id = "workflow_id" def _get_item_from_id(self, trans: ProvidesHistoryContext, idstr): hda = self.get_stored_workflow(trans, idstr) return hda