Unverified Commit ebc74c7a authored by mvdbeek's avatar mvdbeek
Browse files

Use _check_dataset in display_username_by_slug in dataset controller 

Fixes
https://sentry.galaxyproject.org/share/issue/77cd5728ab4e4911a62db7a08a09dbee/:
```
FileNotFoundError: [Errno 2] No such file or directory: ''
  File "uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    raise app_exc
  File "starlette/middleware/base.py", line 36, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "starlette/middleware/base.py", line 69, in __call__
    await response(scope, receive, send)
  File "starlette/responses.py", line 260, in __call__
    await wrap(partial(self.listen_for_disconnect, receive))
  File "anyio/_backends/_asyncio.py", line 662, in __aexit__
    raise exceptions[0]
  File "starlette/responses.py", line 256, in wrap
    await func()
  File "starlette/responses.py", line 245, in stream_response
    async for chunk in self.body_iterator:
  File "starlette/middleware/base.py", line 58, in body_stream
    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 418, in handle
    await self.app(scope, receive, send)
  File "a2wsgi/wsgi.py", line 140, in __call__
    return await responder(scope, receive, send)
  File "a2wsgi/wsgi.py", line 179, in __call__
    raise self.exc_info[0].with_traceback(
  File "galaxy/web/framework/middleware/error.py", line 165, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/recursive.py", line 85, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__
    req = self.application(environ, start_response)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/paste/httpexceptions.py", line 640, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 159, in __call__
    return self.handle_request(environ, start_response)
  File "galaxy/web/framework/base.py", line 244, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/webapps/galaxy/controllers/dataset.py", line 592, in display_by_username_and_slug
    first_chunk = dataset.datatype.get_chunk(trans, dataset, 0)
  File "galaxy/datatypes/tabular.py", line 105, in get_chunk
    with compression_utils.get_fileobj(dataset.file_name) as f:
  File "galaxy/util/compression_utils.py", line 66, in get_fileobj
    return get_fileobj_raw(filename, mode, compressed_formats)[1]
  File "galaxy/util/compression_utils.py", line 126, in get_fileobj_raw
    return compressed_format, open(filename, mode, encoding="utf-8")
```
parent aebc4968

lib/galaxy/webapps/galaxy/controllers/dataset.py

+42 −46
Original line number Diff line number Diff line
@@ -148,7 +148,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
            except Exception:

                data = None

        if not data:

            raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable(f"Invalid reference dataset id: {str(hda_id)}.")

            raise web.httpexceptions.HTTPNotFound(f"Invalid reference dataset id: {str(hda_id)}.")

        if not self._can_access_dataset(trans, data):

            return trans.show_error_message("You are not allowed to access this dataset")

        if data.purged:
@@ -570,11 +570,9 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
    @web.expose

    def display_by_username_and_slug(self, trans, username, slug, filename=None, preview=True):

        """Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset's id."""

        id = slug

        decoded_id = self.decode_id(id)

        dataset = self.hda_manager.get_accessible(decoded_id, trans.user)

        dataset = self.hda_manager.error_if_uploading(dataset)

        if dataset:

        dataset = self._check_dataset(trans, slug)

        if not isinstance(dataset, trans.app.model.DatasetInstance):

            return dataset

        # Filename used for composite types.

        if filename:

            return self.display(trans, dataset_id=slug, filename=filename)
@@ -617,8 +615,6 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
                num_ratings=num_ratings,

                first_chunk=first_chunk,

            )

        else:

            raise web.httpexceptions.HTTPNotFound()



    @web.expose

    def get_item_content_async(self, trans, id):