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Merge pull request #18568 from mvdbeek/drop_unused_datasets_controller_Code
Drop unused datasets controller methods
This commit is contained in:
Marius van den Beek
@@ -42,11 +42,8 @@ from galaxy.util import (
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from galaxy.util.sanitize_html import sanitize_html
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from galaxy.util.zipstream import ZipstreamWrapper
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from galaxy.web import form_builder
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from galaxy.web.framework.helpers import iff
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from galaxy.webapps.base.controller import (
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BaseUIController,
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ERROR,
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SUCCESS,
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url_for,
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UsesExtendedMetadataMixin,
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)
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@@ -454,28 +451,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
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trans.app.security_agent.set_dataset_permission(data.dataset, permissions)
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return data, None
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@web.expose
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def imp(self, trans, dataset_id=None, **kwd):
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"""Import another user's dataset via a shared URL; dataset is added to user's current history."""
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# Set referer message.
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referer = trans.request.referer
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if referer and not referer.startswith(f"{trans.request.application_url}{url_for('/login')}"):
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referer_message = f"<a href='{escape(referer)}'>return to the previous page</a>"
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else:
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referer_message = f"<a href='{url_for('/')}'>go to Galaxy's start page</a>"
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# Error checking.
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if not dataset_id:
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return trans.show_error_message(
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f"You must specify a dataset to import. You can {referer_message}.", use_panels=True
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)
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# Do import.
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cur_history = trans.get_history(create=True)
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status, message = self._copy_datasets(trans, [dataset_id], [cur_history], imported=True)
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message = (
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f"Dataset imported. <br>You can <a href='{url_for('/')}'>start using the dataset</a> or {referer_message}."
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)
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return trans.show_message(message, type=status, use_panels=True)
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@web.expose
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def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True, **kwargs):
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"""Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""
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@@ -512,34 +487,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
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first_chunk=first_chunk,
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)
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@web.expose
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def annotate_async(self, trans, id, new_annotation=None, **kwargs):
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# TODO:?? why is this an access check only?
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decoded_id = self.decode_id(id)
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dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
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dataset = self.hda_manager.error_if_uploading(dataset)
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if not dataset:
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web.httpexceptions.HTTPNotFound()
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if dataset and new_annotation:
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# Sanitize annotation before adding it.
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new_annotation = sanitize_html(new_annotation)
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self.add_item_annotation(trans.sa_session, trans.get_user(), dataset, new_annotation)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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return new_annotation
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@web.expose
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def get_annotation_async(self, trans, id):
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decoded_id = self.decode_id(id)
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dataset = self.hda_manager.get_accessible(decoded_id, trans.user)
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dataset = self.hda_manager.error_if_uploading(dataset)
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if not dataset:
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web.httpexceptions.HTTPNotFound()
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annotation = self.get_item_annotation_str(trans.sa_session, trans.user, dataset)
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if annotation and isinstance(annotation, str):
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annotation = annotation.encode("ascii", "replace") # paste needs ascii here
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return annotation
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@web.expose
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def display_at(self, trans, dataset_id, filename=None, **kwd):
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"""Sets up a dataset permissions so it is viewable at an external site"""
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@@ -723,177 +670,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
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"You do not have permission to view this dataset at an external display application."
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)
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def _delete(self, trans, dataset_id):
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message = None
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status = "done"
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id = None
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try:
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id = self.decode_id(dataset_id)
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hda = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
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self.hda_manager.error_unless_mutable(hda.history)
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hda.mark_deleted()
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hda.clear_associated_files()
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trans.log_event(f"Dataset id {str(id)} marked as deleted")
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self.hda_manager.stop_creating_job(hda, flush=True)
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except Exception:
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msg = f"HDA deletion failed (encoded: {dataset_id}, decoded: {id})"
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log.exception(msg)
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trans.log_event(msg)
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message = "Dataset deletion failed"
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status = "error"
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return (message, status)
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def _undelete(self, trans, dataset_id):
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message = None
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status = "done"
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id = None
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try:
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id = self.decode_id(dataset_id)
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item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
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self.hda_manager.error_unless_mutable(item.history)
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self.hda_manager.undelete(item)
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trans.log_event(f"Dataset id {str(id)} has been undeleted")
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except Exception:
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msg = f"HDA undeletion failed (encoded: {dataset_id}, decoded: {id})"
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log.exception(msg)
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trans.log_event(msg)
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message = "Dataset undeletion failed"
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status = "error"
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return (message, status)
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def _unhide(self, trans, dataset_id):
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try:
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id = self.decode_id(dataset_id)
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item = self.hda_manager.get_owned(id, trans.user, current_history=trans.history)
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self.hda_manager.error_unless_mutable(item.history)
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item.mark_unhidden()
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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trans.log_event(f"Dataset id {str(id)} has been unhidden")
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return True
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except Exception:
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return False
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def _purge(self, trans, dataset_id):
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message = None
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status = "done"
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try:
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id = self.decode_id(dataset_id)
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user = trans.get_user()
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hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get(id)
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# Invalid HDA
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assert hda, "Invalid history dataset ID"
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# If the user is anonymous, make sure the HDA is owned by the current session.
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if not user:
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current_history_id = trans.galaxy_session.current_history_id
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assert hda.history.id == current_history_id, "Data does not belong to current user"
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# If the user is known, make sure the HDA is owned by the current user.
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else:
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assert hda.history.user == user, "Data does not belong to current user"
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# Ensure HDA is deleted
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hda.deleted = True
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# HDA is purgeable
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# Decrease disk usage first
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hda.purge_usage_from_quota(user, hda.dataset.quota_source_info)
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# Mark purged
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hda.purged = True
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trans.sa_session.add(hda)
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trans.log_event(f"HDA id {hda.id} has been purged")
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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# Don't delete anything if there are active HDAs or any LDDAs, even if
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# the LDDAs are deleted. Let the cleanup scripts get it in the latter
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# case.
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if hda.dataset.user_can_purge:
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try:
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hda.dataset.full_delete()
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trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the purge of HDA id {hda.id}")
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trans.sa_session.add(hda.dataset)
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except Exception:
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log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):")
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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except Exception:
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msg = f"HDA purge failed (encoded: {dataset_id}, decoded: {id})"
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log.exception(msg)
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trans.log_event(msg)
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message = "Dataset removal from disk failed"
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status = "error"
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return (message, status)
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@web.expose
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def delete(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
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message, status = self._delete(trans, dataset_id)
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return trans.response.send_redirect(
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web.url_for(
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controller="root",
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action="history",
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show_deleted=show_deleted_on_refresh,
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message=message,
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status=status,
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)
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)
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@web.expose
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def delete_async(self, trans, dataset_id, filename):
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message, status = self._delete(trans, dataset_id)
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if status == "done":
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return "OK"
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else:
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raise Exception(message)
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@web.expose
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def undelete(self, trans, dataset_id, filename):
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message, status = self._undelete(trans, dataset_id)
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return trans.response.send_redirect(
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web.url_for(controller="root", action="history", show_deleted=True, message=message, status=status)
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)
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@web.expose
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def undelete_async(self, trans, dataset_id, filename):
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message, status = self._undelete(trans, dataset_id)
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if status == "done":
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return "OK"
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else:
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raise Exception(message)
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@web.expose
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def unhide(self, trans, dataset_id, filename):
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if self._unhide(trans, dataset_id):
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return trans.response.send_redirect(web.url_for(controller="root", action="history", show_hidden=True))
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raise Exception("Error unhiding")
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@web.expose
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def purge(self, trans, dataset_id, filename, show_deleted_on_refresh=False):
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if trans.app.config.allow_user_dataset_purge:
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message, status = self._purge(trans, dataset_id)
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else:
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message = "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator."
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status = "error"
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return trans.response.send_redirect(
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web.url_for(
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controller="root",
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action="history",
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show_deleted=show_deleted_on_refresh,
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message=message,
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status=status,
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)
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)
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@web.expose
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def purge_async(self, trans, dataset_id, filename):
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if trans.app.config.allow_user_dataset_purge:
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message, status = self._purge(trans, dataset_id)
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else:
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message = "Removal of datasets by users is not allowed in this Galaxy instance. Please contact your Galaxy administrator."
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status = "error"
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if status == "done":
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return "OK"
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else:
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raise Exception(message)
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@web.expose
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def copy_datasets(
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self,
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@@ -1039,53 +815,3 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
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error_msg=error_msg,
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refresh_frames=refresh_frames,
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)
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def _copy_datasets(self, trans, dataset_ids, target_histories, imported=False):
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"""Helper method for copying datasets."""
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user = trans.get_user()
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done_msg = error_msg = ""
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invalid_datasets = 0
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if not dataset_ids or not target_histories:
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error_msg = "You must provide both source datasets and target histories."
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else:
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# User must own target histories to copy datasets to them.
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for history in target_histories:
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if user != history.user:
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error_msg = (
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error_msg
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+ "You do not have permission to add datasets to %i requested histories. "
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% (len(target_histories))
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)
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for dataset_id in dataset_ids:
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decoded_id = self.decode_id(dataset_id)
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data = self.hda_manager.get_accessible(decoded_id, trans.user)
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data = self.hda_manager.error_if_uploading(data)
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if data is None:
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error_msg = f"{error_msg}You tried to copy a dataset that does not exist or that you do not have access to. "
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invalid_datasets += 1
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else:
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for hist in target_histories:
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dataset_copy = data.copy()
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if imported:
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dataset_copy.name = f"imported: {dataset_copy.name}"
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hist.add_dataset(dataset_copy)
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with transaction(trans.sa_session):
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trans.sa_session.commit()
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num_datasets_copied = len(dataset_ids) - invalid_datasets
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done_msg = "%i dataset%s copied to %i histor%s." % (
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num_datasets_copied,
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iff(num_datasets_copied == 1, "", "s"),
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len(target_histories),
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iff(len(target_histories) == 1, "y", "ies"),
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)
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trans.sa_session.refresh(history)
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if error_msg != "":
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status = ERROR
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message = error_msg
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else:
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status = SUCCESS
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message = done_msg
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return status, message
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@@ -82,10 +82,6 @@
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%if data.deleted:
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<div class="errormessagelarge" id="deleted-data-message">
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You are viewing a deleted dataset.
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%if data.history and data.history.user == trans.get_user():
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<br />
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<a href="javascript:void(0)" role="button" onclick="$.ajax( {type: 'GET', cache: false, url: '${h.url_for( controller='dataset', action='undelete_async', dataset_id=trans.security.encode_id( data.id ) )}', dataType: 'text', contentType: 'text/html', success: function( data, textStatus, jqXHR ){ if (data == 'OK' ){ $( '#deleted-data-message' ).slideUp( 'slow' ) } else { alert( 'Undelete failed.' ) } }, error: function( data, textStatus, jqXHR ){ alert( 'Undelete failed.' ); } } );">Undelete</a>
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%endif
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</div>
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%endif
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</%def>
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