Unverified Commit d23186b6 authored by mvdbeek's avatar mvdbeek
Browse files

Use pydantic UUID4 type to validate UUID strings 

This works fine for prasing strings:
```
In [9]: UserConcreteObjectStoreModel(uuid=uuid.uuid4().hex, private=False, quota={"enabled": False}, badges=[])
Out[9]: UserConcreteObjectStoreModel(object_store_id=None, private=False, name=None, description=None, quota=QuotaModel(source=None, enabled=False), badges=[], device=None, uuid=UUID('c7a6751b-4d78-4d7f-b3b1-b2baf0a50d90'))
```

Fixes https://github.com/galaxyproject/galaxy/issues/18684#event-13846279733
parent 2d149f6e

client/src/api/schema/schema.ts

+8 −2
Original line number Diff line number Diff line
@@ -12848,7 +12848,10 @@ export interface components { 
             * @enum {string}

             */

            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";

            /** Uuid */

            /**

             * Uuid

             * Format: uuid4

             */

            uuid: string;

            /** Variables */

            variables: {
@@ -12922,7 +12925,10 @@ export interface components { 
            type: "ftp" | "posix" | "s3fs" | "azure";

            /** Uri Root */

            uri_root: string;

            /** Uuid */

            /**

             * Uuid

             * Format: uuid4

             */

            uuid: string;

            /** Variables */

            variables: {

lib/galaxy/managers/file_source_instances.py

+10 −9
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ from uuid import uuid4 


from pydantic import (

    BaseModel,

    UUID4,

    ValidationError,

)
@@ -87,7 +88,7 @@ USER_FILE_SOURCES_SCHEME = "gxuserfiles" 




class UserFileSourceModel(BaseModel):

    uuid: str

    uuid: UUID4

    uri_root: str

    name: str

    description: Optional[str]
@@ -142,16 +143,16 @@ class FileSourceInstancesManager: 
        stores = self._sa_session.query(UserFileSource).filter(UserFileSource.user_id == trans.user.id).all()

        return [self._to_model(trans, s) for s in stores]



    def show(self, trans: ProvidesUserContext, uuid: str) -> UserFileSourceModel:

    def show(self, trans: ProvidesUserContext, uuid: UUID4) -> UserFileSourceModel:

        user_file_source = self._get(trans, uuid)

        return self._to_model(trans, user_file_source)



    def purge_instance(self, trans: ProvidesUserContext, uuid: str) -> None:

    def purge_instance(self, trans: ProvidesUserContext, uuid: UUID4) -> None:

        persisted_file_source = self._get(trans, uuid)

        purge_template_instance(trans, persisted_file_source, self._app_config)



    def modify_instance(

        self, trans: ProvidesUserContext, id: str, payload: ModifyInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: ModifyInstancePayload

    ) -> UserFileSourceModel:

        if isinstance(payload, UpgradeInstancePayload):

            return self._upgrade_instance(trans, id, payload)
@@ -162,7 +163,7 @@ class FileSourceInstancesManager: 
            return self._update_instance(trans, id, payload)



    def _upgrade_instance(

        self, trans: ProvidesUserContext, id: str, payload: UpgradeInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload

    ) -> UserFileSourceModel:

        persisted_file_source = self._get(trans, id)

        template = self._get_template(persisted_file_source, payload.template_version)
@@ -181,7 +182,7 @@ class FileSourceInstancesManager: 
        return self._to_model(trans, persisted_file_source)



    def _update_instance(

        self, trans: ProvidesUserContext, id: str, payload: UpdateInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload

    ) -> UserFileSourceModel:

        persisted_file_source = self._get(trans, id)

        template = self._get_template(persisted_file_source)
@@ -189,7 +190,7 @@ class FileSourceInstancesManager: 
        return self._to_model(trans, persisted_file_source)



    def _update_instance_secret(

        self, trans: ProvidesUserContext, id: str, payload: UpdateInstanceSecretPayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstanceSecretPayload

    ) -> UserFileSourceModel:

        persisted_file_source = self._get(trans, id)

        template = self._get_template(persisted_file_source)
@@ -300,10 +301,10 @@ class FileSourceInstancesManager: 
            exception = e

        return file_source, connection_exception_to_status("file source", exception)



    def _index_filter(self, uuid: str):

    def _index_filter(self, uuid: UUID4):

        return UserFileSource.__table__.c.uuid == uuid



    def _get(self, trans: ProvidesUserContext, uuid: str) -> UserFileSource:

    def _get(self, trans: ProvidesUserContext, uuid: UUID4) -> UserFileSource:

        filter = self._index_filter(uuid)

        user_file_source = self._sa_session.query(UserFileSource).filter(filter).one_or_none()

        if user_file_source is None:

lib/galaxy/managers/object_store_instances.py

+11 −9
Original line number Diff line number Diff line
@@ -16,6 +16,8 @@ from typing import ( 
)

from uuid import uuid4



from pydantic import UUID4



from galaxy.exceptions import (

    ItemOwnershipException,

    RequestParameterInvalidException,
@@ -73,7 +75,7 @@ log = logging.getLogger(__name__) 




class UserConcreteObjectStoreModel(ConcreteObjectStoreModel):

    uuid: str

    uuid: UUID4

    type: ObjectStoreTemplateType

    template_id: str

    template_version: int
@@ -106,7 +108,7 @@ class ObjectStoreInstancesManager: 
        return self._catalog.summaries



    def modify_instance(

        self, trans: ProvidesUserContext, id: str, payload: ModifyInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: ModifyInstancePayload

    ) -> UserConcreteObjectStoreModel:

        if isinstance(payload, UpgradeInstancePayload):

            return self._upgrade_instance(trans, id, payload)
@@ -116,12 +118,12 @@ class ObjectStoreInstancesManager: 
            assert isinstance(payload, UpdateInstancePayload)

            return self._update_instance(trans, id, payload)



    def purge_instance(self, trans: ProvidesUserContext, id: str) -> None:

    def purge_instance(self, trans: ProvidesUserContext, id: UUID4) -> None:

        persisted_object_store = self._get(trans, id)

        purge_template_instance(trans, persisted_object_store, self._app_config)



    def _upgrade_instance(

        self, trans: ProvidesUserContext, id: str, payload: UpgradeInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpgradeInstancePayload

    ) -> UserConcreteObjectStoreModel:

        persisted_object_store = self._get(trans, id)

        template = self._get_template(persisted_object_store, payload.template_version)
@@ -140,7 +142,7 @@ class ObjectStoreInstancesManager: 
        return self._to_model(trans, persisted_object_store)



    def _update_instance(

        self, trans: ProvidesUserContext, id: str, payload: UpdateInstancePayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstancePayload

    ) -> UserConcreteObjectStoreModel:

        persisted_object_store = self._get(trans, id)

        template = self._get_template(persisted_object_store)
@@ -148,7 +150,7 @@ class ObjectStoreInstancesManager: 
        return self._to_model(trans, persisted_object_store)



    def _update_instance_secret(

        self, trans: ProvidesUserContext, id: str, payload: UpdateInstanceSecretPayload

        self, trans: ProvidesUserContext, id: UUID4, payload: UpdateInstanceSecretPayload

    ) -> UserConcreteObjectStoreModel:

        persisted_object_store = self._get(trans, id)

        template = self._get_template(persisted_object_store)
@@ -200,14 +202,14 @@ class ObjectStoreInstancesManager: 
        stores = self._sa_session.query(UserObjectStore).filter(UserObjectStore.user_id == trans.user.id).all()

        return [self._to_model(trans, s) for s in stores]



    def show(self, trans: ProvidesUserContext, id: str) -> UserConcreteObjectStoreModel:

    def show(self, trans: ProvidesUserContext, id: UUID4) -> UserConcreteObjectStoreModel:

        user_object_store = self._get(trans, id)

        return self._to_model(trans, user_object_store)



    def _save(self, persisted_object_store: UserObjectStore) -> None:

        save_template_instance(self._sa_session, persisted_object_store)



    def _get(self, trans: ProvidesUserContext, id: str) -> UserObjectStore:

    def _get(self, trans: ProvidesUserContext, id: UUID4) -> UserObjectStore:

        filter = self._index_filter(id)

        user_object_store = self._sa_session.query(UserObjectStore).filter(filter).one_or_none()

        if user_object_store is None:
@@ -274,7 +276,7 @@ class ObjectStoreInstancesManager: 
            exception = e

        return object_store, connection_exception_to_status("storage location", exception)



    def _index_filter(self, uuid: str):

    def _index_filter(self, uuid: UUID4):

        return UserObjectStore.__table__.c.uuid == uuid



    def _get_template(

lib/galaxy/webapps/galaxy/api/file_sources.py

+5 −4
Original line number Diff line number Diff line
@@ -7,6 +7,7 @@ from fastapi import ( 
    Response,

    status,

)

from pydantic import UUID4



from galaxy.files.templates import FileSourceTemplateSummaries

from galaxy.managers.context import ProvidesUserContext
@@ -30,7 +31,7 @@ log = logging.getLogger(__name__) 
router = Router(tags=["file_sources"])





UserFileSourceIdPathParam: str = Path(

UserFileSourceIdPathParam: UUID4 = Path(

    ..., title="User File Source UUID", description="The UUID index for a persisted UserFileSourceStore object."

)
@@ -95,7 +96,7 @@ class FastAPIFileSources: 
    def instances_show(

        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user_file_source_id: str = UserFileSourceIdPathParam,

        user_file_source_id: UUID4 = UserFileSourceIdPathParam,

    ) -> UserFileSourceModel:

        return self.file_source_instances_manager.show(trans, user_file_source_id)
@@ -107,7 +108,7 @@ class FastAPIFileSources: 
    def update_instance(

        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user_file_source_id: str = UserFileSourceIdPathParam,

        user_file_source_id: UUID4 = UserFileSourceIdPathParam,

        payload: ModifyInstancePayload = Body(...),

    ) -> UserFileSourceModel:

        return self.file_source_instances_manager.modify_instance(trans, user_file_source_id, payload)
@@ -121,7 +122,7 @@ class FastAPIFileSources: 
    def purge_instance(

        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user_file_source_id: str = UserFileSourceIdPathParam,

        user_file_source_id: UUID4 = UserFileSourceIdPathParam,

    ):

        self.file_source_instances_manager.purge_instance(trans, user_file_source_id)

        return Response(status_code=status.HTTP_204_NO_CONTENT)

lib/galaxy/webapps/galaxy/api/object_store.py

+5 −4
Original line number Diff line number Diff line
@@ -15,6 +15,7 @@ from fastapi import ( 
    Response,

    status,

)

from pydantic import UUID4



from galaxy.exceptions import (

    ObjectNotFound,
@@ -49,7 +50,7 @@ ConcreteObjectStoreIdPathParam: str = Path( 
    ..., title="Concrete Object Store ID", description="The concrete object store ID."

)



UserObjectStoreIdPathParam: str = Path(

UserObjectStoreIdPathParam: UUID4 = Path(

    ...,

    title="User Object Store UUID",

    description="The UUID used to identify a persisted UserObjectStore object.",
@@ -136,7 +137,7 @@ class FastAPIObjectStore: 
        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user: User = DependsOnUser,

        user_object_store_id: str = UserObjectStoreIdPathParam,

        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,

    ) -> UserConcreteObjectStoreModel:

        return self.object_store_instance_manager.show(trans, user_object_store_id)
@@ -160,7 +161,7 @@ class FastAPIObjectStore: 
        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user: User = DependsOnUser,

        user_object_store_id: str = UserObjectStoreIdPathParam,

        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,

        payload: ModifyInstancePayload = Body(...),

    ) -> UserConcreteObjectStoreModel:

        return self.object_store_instance_manager.modify_instance(trans, user_object_store_id, payload)
@@ -175,7 +176,7 @@ class FastAPIObjectStore: 
        self,

        trans: ProvidesUserContext = DependsOnTrans,

        user: User = DependsOnUser,

        user_object_store_id: str = UserObjectStoreIdPathParam,

        user_object_store_id: UUID4 = UserObjectStoreIdPathParam,

    ):

        self.object_store_instance_manager.purge_instance(trans, user_object_store_id)

        return Response(status_code=status.HTTP_204_NO_CONTENT)