Raise ``ParameterValueError`` if input collection elements deleted (3b65665b) · Commits · NDIP / Galaxy

lib/galaxy/model/init.py

+8 −0

Original line number	Diff line number	Diff line
		@@ -6499,6 +6499,14 @@ class DatasetCollection(Base, Dictifiable, UsesAnnotations, Serializable):
		q = q.order_by(*order_by_columns)
		return q

		@property
		def elements_deleted(self):
		stmt = self._build_nested_collection_attributes_stmt(
		hda_attributes=("deleted",), dataset_attributes=("deleted",)
		)
		stmt = exists(stmt).where(or_(HistoryDatasetAssociation.deleted == true(), Dataset.deleted == true()))
		return object_session(self).execute(select(stmt)).scalar()

		@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
		@@ -2188,19 +2188,37 @@ 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)
		@@ -2497,10 +2515,19 @@ 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):

Admin message