Merge pull request #14330 from nsoranzo/release_22.01_dataset_API_fix_extension_list_filter (ce0d3a75) · Commits · NDIP / Galaxy

lib/galaxy/managers/base.py

+23 −17

Original line number	Diff line number	Diff line
		@@ -977,15 +977,17 @@ class ModelFilterParser(HasAModelManager):
		Set up, extend, or alter `orm_filter_parsers` and `fn_filter_parsers`.
		"""
		# note: these are the default filters for all models
		self.orm_filter_parsers.update({
		self.orm_filter_parsers.update(
		{
		# (prob.) applicable to all models
		'id': {'op': ('in')},
		'encoded_id': {'column': 'id', 'op': ('in'), 'val': self.parse_id_list},
		"id": {"op": ("in")},
		"encoded_id": {"column": "id", "op": ("in"), "val": self.parse_id_list},
		# dates can be directly passed through the orm into a filter (no need to parse into datetime object)
		'extension': {'op': ('eq', 'like', 'in')},
		'create_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
		'update_time': {'op': ('le', 'ge', 'lt', 'gt'), 'val': self.parse_date},
		})
		"extension": {"op": ("eq", "like", "in"), "val": {"in": lambda v: v.split(",")}},
		"create_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
		"update_time": {"op": ("le", "ge", "lt", "gt"), "val": self.parse_date},
		}
		)

		def build_filter_params(
		self,
		@@ -1075,7 +1077,7 @@ class ModelFilterParser(HasAModelManager):
		"""
		Attempt to parse a non-ORM filter function.
		"""
		# fn_filter_list is a dict: fn_filter_list[ attr ] = { 'opname1' : opfn1, 'opname2' : opfn2, etc. }
		# fn_filter_parsers is a dict: fn_filter_parsers[attr] = {"opname1": opfn1, "opname2": opfn2, etc. }

		# attr, op is a nested dictionary pointing to the filter fn
		attr_map = self.fn_filter_parsers.get(attr, None)
		@@ -1095,13 +1097,13 @@ class ModelFilterParser(HasAModelManager):
		return self.parsed_filter(filter_type="function", filter=lambda i: filter_fn(i, val))

		# ---- ORM filters
		def _parse_orm_filter(self, attr, op, val):
		def _parse_orm_filter(self, attr, op, val) -> Optional[ParsedFilter]:
		"""
		Attempt to parse a ORM-based filter.

		Using SQLAlchemy, this would yield a sql.elements.BinaryExpression.
		"""
		# orm_filter_list is a dict: orm_filter_list[ attr ] = <list of allowed ops>
		# orm_filter_parsers is a dict: orm_filter_parsers[attr] = <column map>
		column_map = self.orm_filter_parsers.get(attr, None)
		if not column_map:
		# no column mapping (not allowlisted)
		@@ -1124,16 +1126,20 @@ class ModelFilterParser(HasAModelManager):
		allowed_ops = column_map['op']
		if op not in allowed_ops:
		return None
		op = self._convert_op_string_to_fn(column, op)
		if not op:
		converted_op = self._convert_op_string_to_fn(column, op)
		if not converted_op:
		return None

		# parse the val from string using the 'val' parser if present (otherwise, leave as string)
		val_parser = column_map.get('val', None)
		val_parser = column_map.get("val")
		# val_parser can be a dictionary indexed by the operations, in case different functions
		# need to be called depending on the operation
		if isinstance(val_parser, dict):
		val_parser = val_parser.get(op)
		if val_parser:
		val = val_parser(val)

		orm_filter = op(val)
		orm_filter = converted_op(val)
		return self.parsed_filter(filter_type="orm", filter=orm_filter)

		#: these are the easier/shorter string equivalents to the python operator fn names that need '__' around them
		@@ -1171,7 +1177,7 @@ class ModelFilterParser(HasAModelManager):
		# TODO: These should go somewhere central - we've got ~6 parser modules/sections now
		def parse_id_list(self, id_list_string, sep=','):
		"""
		Split `id_list_string` at `sep`.
		Split `id_list_string` at `sep` and decode as ids.
		"""
		# TODO: move id decoding out
		id_list = [self.app.security.decode_id(id_) for id_ in id_list_string.split(sep)]

lib/galaxy_test/api/test_datasets.py

+33 −0

Original line number	Diff line number	Diff line
		@@ -86,6 +86,39 @@ class DatasetsApiTestCase(ApiTestCase):
		result = self._get("datasets", payload).json()
		assert len(result) == 0

		def test_search_by_extension(self):
		self.dataset_populator.new_dataset(self.history_id, wait=True)
		payload = {
		"q": ["extension"],
		"qv": ["txt"],
		"history_id": self.history_id,
		}
		assert len(self._get("datasets", payload).json()) == 1
		payload = {
		"q": ["extension"],
		"qv": ["bam"],
		"history_id": self.history_id,
		}
		assert len(self._get("datasets", payload).json()) == 0
		payload = {
		"q": ["extension-in"],
		"qv": ["bam,txt"],
		"history_id": self.history_id,
		}
		assert len(self._get("datasets", payload).json()) == 1
		payload = {
		"q": ["extension-like"],
		"qv": ["t%t"],
		"history_id": self.history_id,
		}
		assert len(self._get("datasets", payload).json()) == 1
		payload = {
		"q": ["extension-like"],
		"qv": ["b%m"],
		"history_id": self.history_id,
		}
		assert len(self._get("datasets", payload).json()) == 0

		def test_invalid_search(self):
		payload = {'limit': 10, 'offset': 0, 'q': ['history_content_type', 'tag-invalid_op'], 'qv': ['dataset', 'notag']}
		index_response = self._get("datasets", payload)