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Data provider doesn't check for empty files #18277

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galaxyproject-sentryintegration bot opened this issue May 31, 2024 · 0 comments
Closed

Data provider doesn't check for empty files #18277

galaxyproject-sentryintegration bot opened this issue May 31, 2024 · 0 comments

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@galaxyproject-sentryintegration

To fix this check that converted dataset is in OK state and raise appropriate exception if file has not data.

Sentry Issue: GALAXY-MAIN-YQT

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(

ValueError: invalid literal for int() with base 10: ''
(26 additional frame(s) were not displayed)
...
  File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options
    response = await call_next(request)
  File "galaxy/webapps/galaxy/api/datasets.py", line 446, in show
    return self.service.show(trans, dataset_id, hda_ldda, serialization_params, data_type, **extra_params)
  File "galaxy/webapps/galaxy/services/datasets.py", line 393, in show
    rval = self._search_features(trans, dataset, query=extra_params.get("query", None))
  File "galaxy/webapps/galaxy/services/datasets.py", line 873, in _search_features
    return data_provider.get_data(query)
  File "galaxy/visualization/data_providers/genome.py", line 111, in get_data
    line_len = int(textloc_file.readline())
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