Merge pull request #18517 from mvdbeek/fix_deleted_ipnut_submission_collection (ba3c58d8) · Commits · NDIP / Galaxy

lib/galaxy/model/init.py

+17 −0

Original line number	Diff line number	Diff line
		@@ -6499,6 +6499,23 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
		q = q.order_by(*order_by_columns)
		return q

		@property
		def elements_deleted(self):
		if not hasattr(self, "_elements_deleted"):
		if session := object_session(self):
		stmt = self._build_nested_collection_attributes_stmt(
		hda_attributes=("deleted",), dataset_attributes=("deleted",)
		)
		stmt = stmt.exists().where(or_(HistoryDatasetAssociation.deleted == true(), Dataset.deleted == true()))
		self._elements_deleted = session.execute(select(stmt)).scalar()
		else:
		self._elements_deleted = False
		for dataset_instance in self.dataset_instances:
		if dataset_instance.deleted or dataset_instance.dataset.deleted:
		self._elements_deleted = True
		break
		return self._elements_deleted

		@property
		def dataset_states_and_extensions_summary(self):
		if not hasattr(self, "_dataset_states_and_extensions_summary"):

lib/galaxy/tools/parameters/basic.py

+40 −13

Original line number	Diff line number	Diff line
		@@ -2189,19 +2189,37 @@ class DataToolParameter(BaseDataToolParameter):
		dataset_matcher_factory = get_dataset_matcher_factory(trans)
		dataset_matcher = dataset_matcher_factory.dataset_matcher(self, other_values)
		for v in rval:
		if v:
		if hasattr(v, "deleted") and v.deleted:
		if isinstance(v, DatasetCollectionElement):
		if hda := v.hda:
		v = hda
		elif ldda := v.ldda:
		v = ldda
		elif collection := v.child_collection:
		v = collection
		elif not v.collection and v.collection.populated_optimized:
		raise ParameterValueError("the selected collection has not been populated.", self.name)
		else:
		raise ParameterValueError("Collection element in unexpected state", self.name)
		if isinstance(v, DatasetInstance):
		if v.deleted:
		raise ParameterValueError("the previously selected dataset has been deleted.", self.name)
		elif hasattr(v, "dataset") and v.dataset.state in [Dataset.states.ERROR, Dataset.states.DISCARDED]:
		elif v.dataset and v.dataset.state in [Dataset.states.ERROR, Dataset.states.DISCARDED]:
		raise ParameterValueError(
		"the previously selected dataset has entered an unusable state", self.name
		)
		elif hasattr(v, "dataset"):
		if isinstance(v, DatasetCollectionElement):
		v = v.hda
		match = dataset_matcher.hda_match(v)
		if match and match.implicit_conversion:
		v.implicit_conversion = True # type:ignore[union-attr]
		elif isinstance(v, HistoryDatasetCollectionAssociation):
		if v.deleted:
		raise ParameterValueError("the previously selected dataset collection has been deleted.", self.name)
		v = v.collection
		if isinstance(v, DatasetCollection):
		if v.elements_deleted:
		raise ParameterValueError(
		"the previously selected dataset collection has elements that are deleted.", self.name
		)

		if not self.multiple:
		if len(rval) > 1:
		raise ParameterValueError("more than one dataset supplied to single input dataset parameter", self.name)
		@@ -2498,10 +2516,19 @@ class DataCollectionToolParameter(BaseDataToolParameter):
		rval = session.get(HistoryDatasetCollectionAssociation, int(value[len("hdca:") :]))
		else:
		rval = session.get(HistoryDatasetCollectionAssociation, int(value))
		if rval and isinstance(rval, HistoryDatasetCollectionAssociation):
		if rval:
		if isinstance(rval, HistoryDatasetCollectionAssociation):
		if rval.deleted:
		raise ParameterValueError("the previously selected dataset collection has been deleted", self.name)
		# TODO: Handle error states, implement error states ...
		if rval.collection.elements_deleted:
		raise ParameterValueError(
		"the previously selected dataset collection has elements that are deleted.", self.name
		)
		if isinstance(rval, DatasetCollectionElement):
		if (child_collection := rval.child_collection) and child_collection.elements_deleted:
		raise ParameterValueError(
		"the previously selected dataset collection has elements that are deleted.", self.name
		)
		return rval

		def to_text(self, value):

lib/galaxy_test/api/test_jobs.py

+17 −0

Original line number	Diff line number	Diff line
		@@ -576,6 +576,23 @@ steps:
		if output_dataset_paths_exist:
		wait_on(paths_deleted, "path deletion")

		def test_submission_on_collection_with_deleted_element(self, history_id):
		hdca = self.dataset_collection_populator.create_list_of_list_in_history(history_id=history_id, wait=True).json()
		hda_id = hdca["elements"][0]["object"]["elements"][0]["object"]["id"]
		self.dataset_populator.delete_dataset(history_id=history_id, content_id=hda_id)
		response = self.dataset_populator.run_tool_raw(
		"is_of_type",
		inputs={
		"collection": {"batch": True, "values": [{"src": "hdca", "id": hdca["id"], "map_over_type": "list"}]},
		},
		history_id=history_id,
		)
		assert response.status_code == 400
		assert (
		response.json()["err_msg"]
		== "parameter 'collection': the previously selected dataset collection has elements that are deleted."
		)

		@pytest.mark.require_new_history
		@skip_without_tool("create_2")
		def test_purging_output_cleaned_after_ok_run(self, history_id):

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