Merge branch 'release_24.1' into release_24.2 (cd11d221) · Commits · NDIP / Galaxy

lib/galaxy/model/init.py

+11 −6

Original line number	Diff line number	Diff line
		@@ -230,9 +230,12 @@ from galaxy.util.json import safe_loads
		from galaxy.util.sanitize_html import sanitize_html

		if TYPE_CHECKING:
		from sqlalchemy.sql.expression import BindParameter

		from galaxy.objectstore import (
		BaseObjectStore,
		ObjectStorePopulator,
		QuotaSourceMap,
		)
		from galaxy.schema.invocation import InvocationMessageUnion

		@@ -674,9 +677,9 @@ WHERE dataset.id IN (SELECT dataset_id FROM per_hist_hdas)
		"""


		def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=False):
		def calculate_user_disk_usage_statements(user_id: int, quota_source_map: "QuotaSourceMap", for_sqlite: bool = False):
		"""Standalone function so can be reused for postgres directly in pgcleanup.py."""
		statements = []
		statements: List[Tuple[str, Dict[str, Any]]] = []
		default_quota_enabled = quota_source_map.default_quota_enabled
		default_exclude_ids = quota_source_map.default_usage_excluded_ids()
		default_cond = "dataset.object_store_id IS NULL" if default_quota_enabled and default_exclude_ids else ""
		@@ -692,7 +695,7 @@ def calculate_user_disk_usage_statements(user_id, quota_source_map, for_sqlite=F
		UPDATE galaxy_user SET disk_usage = ({default_usage})
		WHERE id = :id
		"""
		params = {"id": user_id}
		params: Dict[str, Any] = {"id": user_id}
		if default_exclude_ids:
		params["exclude_object_store_ids"] = default_exclude_ids
		statements.append((default_usage, params))
		@@ -1161,13 +1164,13 @@ ON CONFLICT
		usage = sa_session.scalar(sql_calc, params)
		return usage

		def calculate_and_set_disk_usage(self, object_store):
		def calculate_and_set_disk_usage(self, object_store: "BaseObjectStore"):
		"""
		Calculates and sets user disk usage.
		"""
		self._calculate_or_set_disk_usage(object_store=object_store)

		def _calculate_or_set_disk_usage(self, object_store):
		def _calculate_or_set_disk_usage(self, object_store: "BaseObjectStore"):
		"""
		Utility to calculate and return the disk usage. If dryrun is False,
		the new value is set immediately.
		@@ -1175,11 +1178,13 @@ ON CONFLICT
		assert object_store is not None
		quota_source_map = object_store.get_quota_source_map()
		sa_session = object_session(self)
		assert sa_session
		assert sa_session.bind
		for_sqlite = "sqlite" in sa_session.bind.dialect.name
		statements = calculate_user_disk_usage_statements(self.id, quota_source_map, for_sqlite)
		for sql, args in statements:
		statement = text(sql)
		binds = []
		binds: List[BindParameter] = []
		for key, _ in args.items():
		expand_binding = key.endswith("s")
		binds.append(bindparam(key, expanding=expand_binding))

lib/galaxy/objectstore/init.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -403,7 +403,7 @@ class ObjectStore(metaclass=abc.ABCMeta):
		raise NotImplementedError()

		@abc.abstractmethod
		def get_quota_source_map(self):
		def get_quota_source_map(self) -> "QuotaSourceMap":
		"""Return QuotaSourceMap describing mapping of object store IDs to quota sources."""

		@abc.abstractmethod
		@@ -715,7 +715,7 @@ class BaseObjectStore(ObjectStore):
		badges.append({"type": type, "message": message})
		return badges

		def get_quota_source_map(self):
		def get_quota_source_map(self) -> "QuotaSourceMap":
		# I'd rather keep this abstract... but register_singleton wants it to be instantiable...
		raise NotImplementedError()

scripts/cleanup_datasets/pgcleanup.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -401,7 +401,8 @@ class RequiresDiskUsageRecalculation:
		statements = calculate_user_disk_usage_statements(user_id, quota_source_map)

		for sql, args in statements:
		sql, _ = re.subn(r"\:([\w]+)", r"%(\1)s", sql)
		sql = sql.replace("%", "%%")
		sql = re.sub(r"\:([\w]+)", r"%(\1)s", sql)
		new_args = {}
		for key, val in args.items():
		if isinstance(val, list):