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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.base import transaction
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] if (item := self._get_item_from_id(trans, idnum)) 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] if (item := self._get_item_from_id(trans, idnum)) 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) with transaction(trans.sa_session): trans.sa_session.commit() return new_annotation return ""
[docs] @expose_api def delete(self, trans: ProvidesHistoryContext, **kwd): idnum = kwd[self.tagged_item_id] if (item := self._get_item_from_id(trans, idnum)) 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