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[23.1] List extra files only for terminal datasets #16705

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@mvdbeek mvdbeek commented Sep 16, 2023

Fixes:

WouldBlock: null
  File "anyio/streams/memory.py", line 98, in receive
    return self.receive_nowait()
  File "anyio/streams/memory.py", line 93, in receive_nowait
    raise WouldBlock
EndOfStream: null
  File "starlette/middleware/base.py", line 78, in call_next
    message = await recv_stream.receive()
  File "anyio/streams/memory.py", line 118, in receive
    raise EndOfStream
KeyError: None
  File "starlette/applications.py", line 122, 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_context/middleware/raw_middleware.py", line 93, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 108, 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 84, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 70, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 79, in __call__
    raise exc
  File "starlette/middleware/exceptions.py", line 68, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 20, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 17, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 718, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 276, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 66, in app
    response = await func(request)
  File "fastapi/routing.py", line 241, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 169, 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 33, in run_sync
    return await get_asynclib().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 877, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 807, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/datasets.py", line 253, in extra_files
    return self.service.extra_files(trans, history_content_id)
  File "galaxy/webapps/galaxy/services/datasets.py", line 548, in extra_files
    extra_files_path = hda.extra_files_path
  File "galaxy/model/__init__.py", line 4421, in extra_files_path
    return self.dataset.extra_files_path
  File "galaxy/model/__init__.py", line 3989, in get_extra_files_path
    return self.object_store.construct_path(
  File "galaxy/objectstore/__init__.py", line 419, in construct_path
    return self._invoke("construct_path", obj, **kwargs)
  File "galaxy/objectstore/__init__.py", line 413, in _invoke
    return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
  File "galaxy/objectstore/__init__.py", line 1157, in _construct_path
    return self.backends[obj.object_store_id].construct_path(obj, **kwargs)

(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
(For UI components, it is recommended to include screenshots or screencasts)

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

Fixes:

```
WouldBlock: null
  File "anyio/streams/memory.py", line 98, in receive
    return self.receive_nowait()
  File "anyio/streams/memory.py", line 93, in receive_nowait
    raise WouldBlock
EndOfStream: null
  File "starlette/middleware/base.py", line 78, in call_next
    message = await recv_stream.receive()
  File "anyio/streams/memory.py", line 118, in receive
    raise EndOfStream
KeyError: None
  File "starlette/applications.py", line 122, 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_context/middleware/raw_middleware.py", line 93, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 108, 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 84, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 70, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 79, in __call__
    raise exc
  File "starlette/middleware/exceptions.py", line 68, in __call__
    await self.app(scope, receive, sender)
  File "fastapi/middleware/asyncexitstack.py", line 20, in __call__
    raise e
  File "fastapi/middleware/asyncexitstack.py", line 17, in __call__
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 718, in __call__
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 276, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 66, in app
    response = await func(request)
  File "fastapi/routing.py", line 241, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 169, 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 33, in run_sync
    return await get_asynclib().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 877, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 807, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/datasets.py", line 253, in extra_files
    return self.service.extra_files(trans, history_content_id)
  File "galaxy/webapps/galaxy/services/datasets.py", line 548, in extra_files
    extra_files_path = hda.extra_files_path
  File "galaxy/model/__init__.py", line 4421, in extra_files_path
    return self.dataset.extra_files_path
  File "galaxy/model/__init__.py", line 3989, in get_extra_files_path
    return self.object_store.construct_path(
  File "galaxy/objectstore/__init__.py", line 419, in construct_path
    return self._invoke("construct_path", obj, **kwargs)
  File "galaxy/objectstore/__init__.py", line 413, in _invoke
    return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs)
  File "galaxy/objectstore/__init__.py", line 1157, in _construct_path
    return self.backends[obj.object_store_id].construct_path(obj, **kwargs)
```
@github-actions github-actions bot added this to the 23.2 milestone Sep 16, 2023
mvdbeek added a commit to mvdbeek/planemo that referenced this pull request Sep 17, 2023
Otherwise we'd attempt to download results too early.
That's how I discovered
galaxyproject/galaxy#16705.
mvdbeek added a commit to mvdbeek/planemo that referenced this pull request Sep 17, 2023
Otherwise we'd attempt to download results too early.
That's how I discovered
galaxyproject/galaxy#16705.
@bgruening bgruening merged commit 60b7d65 into galaxyproject:release_23.1 Sep 17, 2023
38 checks passed
mvdbeek added a commit to mvdbeek/planemo that referenced this pull request Sep 17, 2023
Otherwise we'd attempt to download results too early.
That's how I discovered
galaxyproject/galaxy#16705.
@dannon dannon modified the milestones: 23.2, 23.1 Sep 22, 2023
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3 participants