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[24.0] Never fail dataset serialization if display_peek fails #17937

Merged
merged 4 commits into from
Apr 8, 2024
Merged

[24.0] Never fail dataset serialization if display_peek fails #17937

merged 4 commits into from
Apr 8, 2024

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mvdbeek
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@mvdbeek mvdbeek commented Apr 8, 2024

Also fix qiime2 specifically and don't set_peek in display_peek method.

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.

mvdbeek added 3 commits April 8, 2024 16:03
@mvdbeek
Never fail on display_peek wrapper
7eee169
@mvdbeek
Don't set peek in display_peek method
031d59f
@mvdbeek
Fix Qiime2 display_peek method
b971e33 
Fixes:
```
ExceptionGroup: unhandled errors in a TaskGroup
  File "starlette/_utils.py", line 87, in collapse_excgroups
    yield
  File "starlette/middleware/base.py", line 190, in __call__
    async with anyio.create_task_group() as task_group:
  File "anyio/_backends/_asyncio.py", line 678, in __aexit__
    raise BaseExceptionGroup(
AttributeError: 'NoneType' object has no attribute 'replace'
  File "starlette/applications.py", line 123, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/middleware/errors.py", line 186, in __call__
    raise exc
  File "starlette/middleware/errors.py", line 164, in __call__
    await self.app(scope, receive, _send)
  File "starlette_context/middleware/raw_middleware.py", line 92, in __call__
    await self.app(scope, receive, send_wrapper)
  File "starlette/middleware/base.py", line 189, in __call__
    with collapse_excgroups():
  File "contextlib.py", line 155, in __exit__
    self.gen.throw(typ, value, traceback)
  File "starlette/_utils.py", line 93, in collapse_excgroups
    raise exc
  File "starlette/middleware/base.py", line 191, in __call__
    response = await self.dispatch_func(request, call_next)
  File "galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
    response = await call_next(request)
  File "starlette/middleware/base.py", line 165, in call_next
    raise app_exc
  File "starlette/middleware/base.py", line 151, in coro
    await self.app(scope, receive_or_disconnect, send_no_error)
  File "starlette/middleware/exceptions.py", line 62, in __call__
    await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 758, in __call__
    await self.middleware_stack(scope, receive, send)
  File "starlette/routing.py", line 778, in app
    await route.handle(scope, receive, send)
  File "starlette/routing.py", line 299, in handle
    await self.app(scope, receive, send)
  File "starlette/routing.py", line 79, in app
    await wrap_app_handling_exceptions(app, request)(scope, receive, send)
  File "starlette/_exception_handler.py", line 64, in wrapped_app
    raise exc
  File "starlette/_exception_handler.py", line 53, in wrapped_app
    await app(scope, receive, sender)
  File "starlette/routing.py", line 74, in app
    response = await func(request)
  File "fastapi/routing.py", line 278, in app
    raw_response = await run_endpoint_function(
  File "fastapi/routing.py", line 193, in run_endpoint_function
    return await run_in_threadpool(dependant.call, **values)
  File "starlette/concurrency.py", line 42, in run_in_threadpool
    return await anyio.to_thread.run_sync(func, *args)
  File "anyio/to_thread.py", line 56, in run_sync
    return await get_async_backend().run_sync_in_worker_thread(
  File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread
    return await future
  File "anyio/_backends/_asyncio.py", line 851, in run
    result = context.run(func, *args)
  File "galaxy/webapps/galaxy/api/history_contents.py", line 465, in index
    items = self.service.index(
  File "galaxy/webapps/galaxy/services/history_contents.py", line 312, in index
    return self.__index_v2(trans, history_id, params, serialization_params, filter_query_params, accept)
  File "galaxy/webapps/galaxy/services/history_contents.py", line 992, in __index_v2
    items = [
  File "galaxy/webapps/galaxy/services/history_contents.py", line 993, in <listcomp>
    self._serialize_content_item(
  File "galaxy/webapps/galaxy/services/history_contents.py", line 1064, in _serialize_content_item
    rval = serializer.serialize_to_view(
  File "galaxy/managers/base.py", line 785, in serialize_to_view
    return self.serialize(item, all_keys, **context)
  File "galaxy/managers/hdas.py", line 614, in serialize
    return super().serialize(hda, keys, user=user, **context)
  File "galaxy/managers/datasets.py", line 770, in serialize
    serialized = super().serialize(dataset_assoc, keys, **context)
  File "galaxy/managers/base.py", line 698, in serialize
    returned[key] = self.serializers[key](item, key, **context)
  File "galaxy/managers/datasets.py", line 633, in <lambda>
    "peek": lambda item, key, **context: item.display_peek() if item.peek and item.peek != "no peek" else None,
  File "galaxy/model/__init__.py", line 4669, in display_peek
    return self.datatype.display_peek(self)
  File "galaxy/datatypes/qiime2.py", line 57, in display_peek
    table += [make_row(pair) for pair in self._peek(dataset, simple=True)]
  File "galaxy/datatypes/qiime2.py", line 57, in <listcomp>
    table += [make_row(pair) for pair in self._peek(dataset, simple=True)]
  File "galaxy/datatypes/qiime2.py", line 54, in make_row
    return f"<tr><th>{pair[0]}</th><td>{html.escape(pair[1])}</td></tr>"
  File "__init__.py", line 19, in escape
    s = s.replace("&", "&amp;") # Must be done first!
```
@github-actions github-actions bot added this to the 24.1 milestone Apr 8, 2024
@mvdbeek @nsoranzo
Fix peek typo
456f33f 
Co-authored-by: Nicola Soranzo <[email protected]>
@mvdbeek mvdbeek merged commit dda6133 into galaxyproject:release_24.0 Apr 8, 2024
49 of 50 checks passed
@martenson martenson deleted the fix_peek_display branch April 8, 2024 16:20
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@nsoranzo nsoranzo nsoranzo left review comments

@martenson martenson martenson approved these changes

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@mvdbeek @martenson @nsoranzo