Unverified Commit 90c2c1fa authored by mvdbeek's avatar mvdbeek
Browse files

Fix serialization response for importing datasets from folders 

And remove `default_view` query parameter parsing. That was never meant
to be definable via the API, users were meant to set the view, and the
controller code sets the appropriate default_view.

Fixes
https://sentry.galaxyproject.org/share/issue/e26374bcf34f4ac0aed92c343c5a1fe6/:

```

App Only

Full

Raw
WouldBlock: null
  File "anyio/streams/memory.py", line 94, in receive
    return self.receive_nowait()
  File "anyio/streams/memory.py", line 89, in receive_nowait
    raise WouldBlock
EndOfStream: null
  File "starlette/middleware/base.py", line 43, in call_next
    message = await recv_stream.receive()
  File "anyio/streams/memory.py", line 114, in receive
    raise EndOfStream
TypeError: serialize_to_view() got multiple values for keyword argument 'default_view'
  File "starlette/middleware/base.py", line 68, in __call__
    response = await self.dispatch_func(request, call_next)
  File "galaxy/webapps/galaxy/fast_app.py", line 103, in add_x_frame_options
    response = await call_next(request)
  File "starlette/middleware/base.py", line 46, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/exceptions.py", line 93, in __call__
    raise exc
  File "starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 65, in app
    response = await func(request)
  File "fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 162, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
  File "starlette/concurrency.py", line 41, in run_in_threadpool
    return await anyio.to_thread.run_sync(func, *args)
  File "anyio/to_thread.py", line 31, in run_sync
    return await get_asynclib().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 937, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 867, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/history_contents.py", line 593, in create
    return self.service.create(trans, history_id, payload, serialization_params)
  File "galaxy/webapps/galaxy/services/history_contents.py", line 527, in create
    return self.__create_datasets_from_library_folder(trans, history, payload, serialization_params)
  File "galaxy/webapps/galaxy/services/history_contents.py", line 1336, in __create_datasets_from_library_folder
    hda_dict = self.hda_serializer.serialize_to_view(
```
parent 522e0c25

lib/galaxy/webapps/galaxy/api/common.py

+1 −8
Original line number Diff line number Diff line
@@ -31,12 +31,6 @@ SerializationKeysQueryParam: Optional[str] = Query( 
    description="Comma-separated list of keys to be passed to the serializer",

)



SerializationDefaultViewQueryParam: Optional[str] = Query(

    None,

    title="Default View",

    description="The item view that will be used in case no particular view was specified.",

)



FilterQueryQueryParam: Optional[List[str]] = Query(

    default=None,

    title="Filter Query",
@@ -67,9 +61,8 @@ def parse_serialization_params( 
def query_serialization_params(

    view: Optional[str] = SerializationViewQueryParam,

    keys: Optional[str] = SerializationKeysQueryParam,

    default_view: Optional[str] = SerializationDefaultViewQueryParam,

) -> SerializationParams:

    return parse_serialization_params(view=view, keys=keys, default_view=default_view, format=format)

    return parse_serialization_params(view=view, keys=keys)





def get_value_filter_query_params(

lib/galaxy/webapps/galaxy/api/history_contents.py

+1 −1
Original line number Diff line number Diff line
@@ -587,7 +587,7 @@ class FastAPIHistoryContents: 
        ),

        serialization_params: SerializationParams = Depends(query_serialization_params),

        payload: CreateHistoryContentPayload = Body(...),

    ) -> AnyHistoryContentItem:

    ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:

        """Create a new `HDA` or `HDCA` in the given History."""

        payload.type = type or payload.type

        return self.service.create(trans, history_id, payload, serialization_params)

lib/galaxy/webapps/galaxy/services/history_contents.py

+3 −4
Original line number Diff line number Diff line
@@ -511,7 +511,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 
        history_id: EncodedDatabaseIdField,

        payload: CreateHistoryContentPayload,

        serialization_params: SerializationParams,

    ) -> AnyHistoryContentItem:

    ) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:

        """

        Create a new HDA or HDCA.
@@ -520,6 +520,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 
        """

        history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)



        serialization_params.default_view = "detailed"

        history_content_type = payload.type

        if history_content_type == HistoryContentType.dataset:

            source = payload.source
@@ -1334,7 +1335,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 
                    history, add_to_history=True

                )

                hda_dict = self.hda_serializer.serialize_to_view(

                    hda, user=trans.user, trans=trans, default_view="detailed", **serialization_params.dict()

                    hda, user=trans.user, trans=trans, **serialization_params.dict()

                )

                rval.append(hda_dict)

        else:
@@ -1368,7 +1369,6 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 
            return None



        trans.sa_session.flush()

        serialization_params.default_view = "detailed"

        return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())



    def __create_hda_from_ldda(self, trans, history: History, ldda_id: EncodedDatabaseIdField):
@@ -1465,7 +1465,6 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 


        # if the consumer specified keys or view, use the secondary serializer

        if serialization_params.view or serialization_params.keys:

            serialization_params.default_view = "detailed"

            return self.hdca_serializer.serialize_to_view(

                dataset_collection_instance, user=trans.user, trans=trans, **serialization_params.dict()

            )

lib/galaxy_test/api/test_folders.py

+16 −1
Original line number Diff line number Diff line 
from galaxy_test.base.populators import LibraryPopulator

from galaxy_test.base.populators import (

    DatasetPopulator,

    LibraryPopulator,

)

from ._framework import ApiTestCase





class FoldersApiTestCase(ApiTestCase):

    def setUp(self):

        super().setUp()

        self.dataset_populator = DatasetPopulator(self.galaxy_interactor)

        self.library_populator = LibraryPopulator(self.galaxy_interactor)

        self.library = self.library_populator.new_library("FolderTestsLibrary")
@@ -78,6 +82,17 @@ class FoldersApiTestCase(ApiTestCase): 
        undeleted_folder = undelete_response.json()

        assert undeleted_folder["deleted"] is False



    def test_import_folder_to_history(self):

        library, response = self.library_populator.fetch_single_url_to_folder()

        dataset = self.library_populator.get_library_contents_with_path(library["id"], "/4.bed")

        with self.dataset_populator.test_history() as history_id:

            create_data = {"source": "library_folder", "content": dataset["folder_id"]}

            create_response = self._post(f"histories/{history_id}/contents", create_data, json=True)

            create_response.raise_for_status()

            datasets = create_response.json()

            assert len(datasets) == 1

            assert datasets[0]["name"] == "4.bed"



    def test_update_deleted_raise_403(self):

        folder = self._create_folder("Test Update Deleted Folder")

        folder_id = folder["id"]

lib/galaxy_test/api/test_libraries.py

+3 −28
Original line number Diff line number Diff line
@@ -10,15 +10,13 @@ from galaxy.model.unittest_utils.store_fixtures import ( 
from galaxy_test.base.populators import (

    DatasetCollectionPopulator,

    DatasetPopulator,

    FILE_URL,

    LibraryPopulator,

    skip_if_github_down,

    skip_without_asgi,

)

from ._framework import ApiTestCase



FILE_URL = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed"

FILE_MD5 = "37b59762b59fff860460522d271bc111"





class LibrariesApiTestCase(ApiTestCase):

    def setUp(self):
@@ -268,38 +266,15 @@ class LibrariesApiTestCase(ApiTestCase): 
        assert dataset["file_size"] == 61, dataset



    def test_fetch_single_url_to_folder(self):

        library, response = self._fetch_single_url_to_folder()

        library, response = self.library_populator.fetch_single_url_to_folder()

        dataset = self.library_populator.get_library_contents_with_path(library["id"], "/4.bed")

        assert dataset["file_size"] == 61, dataset



    def test_fetch_single_url_with_invalid_datatype(self):

        _, response = self._fetch_single_url_to_folder("xxx", assert_ok=False)

        _, response = self.library_populator.fetch_single_url_to_folder("xxx", assert_ok=False)

        self._assert_status_code_is(response, 400)

        assert response.json()["err_msg"] == "Requested extension 'xxx' unknown, cannot upload dataset."



    def _fetch_single_url_to_folder(self, file_type="auto", assert_ok=True):

        history_id, library, destination = self._setup_fetch_to_folder("single_url")

        items = [

            {

                "src": "url",

                "url": FILE_URL,

                "MD5": FILE_MD5,

                "ext": file_type,

            }

        ]

        targets = [

            {

                "destination": destination,

                "items": items,

            }

        ]

        payload = {

            "history_id": history_id,  # TODO: Shouldn't be needed :(

            "targets": targets,

            "validate_hashes": True,

        }

        return library, self.dataset_populator.fetch(payload, assert_ok=assert_ok)



    def test_legacy_upload_unknown_datatype(self):

        library = self.library_populator.new_private_library("ForLegacyUpload")

        folder_response = self._create_folder(library)