Unverified Commit b731dde2 authored by John Davis's avatar John Davis Committed by GitHub
Browse files

Merge pull request #19925 from jdavcs/24.1_19880 

[24.1] Handle special charater in raw SQL
parents 953a9723 1bf72997

lib/galaxy/model/__init__.py

+14 −6
Original line number Diff line number Diff line
@@ -225,6 +225,12 @@ 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,

        QuotaSourceMap,

    )

    from galaxy.schema.invocation import InvocationMessageUnion



log = logging.getLogger(__name__)
@@ -652,9 +658,9 @@ 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 ""
@@ -670,7 +676,7 @@ 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))
@@ -1147,13 +1153,13 @@ 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.
@@ -1161,11 +1167,13 @@ 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
@@ -368,7 +368,7 @@ 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
@@ -523,7 +523,7 @@ 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):