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Latest docker image, e1513f80a4f3, fails to start due to ModuleNotFoundError #1336

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kkaris opened this issue Dec 22, 2024 · 0 comments · May be fixed by #1337
Open

Latest docker image, e1513f80a4f3, fails to start due to ModuleNotFoundError #1336

kkaris opened this issue Dec 22, 2024 · 0 comments · May be fixed by #1337

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@kkaris
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kkaris commented Dec 22, 2024

Pulling the latest docker images, e1513f80a4f3, and starting it using

docker run -i --detach --name bioregistry -p 8766:8766 biopragmatics/bioregistry:latest

Gives the following error on startup:

Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/local/lib/python3.11/site-packages/bioregistry/__main__.py", line 8, in <module>
    main()
  File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.11/site-packages/bioregistry/app/cli.py", line 53, in web
    from .impl import get_app
  File "/usr/local/lib/python3.11/site-packages/bioregistry/app/impl.py", line 9, in <module>
    from curies.mapping_service import MappingServiceGraph, MappingServiceSPARQLProcessor
  File "/usr/local/lib/python3.11/site-packages/curies/mapping_service/__init__.py", line 104, in <module>
    from .api import (
  File "/usr/local/lib/python3.11/site-packages/curies/mapping_service/api.py", line 13, in <module>
    from .utils import CONTENT_TYPE_TO_RDFLIB_FORMAT, handle_header
  File "/usr/local/lib/python3.11/site-packages/curies/mapping_service/utils.py", line 11, in <module>
    from defusedxml import ElementTree
ModuleNotFoundError: No module named 'defusedxml'
@kkaris kkaris changed the title Latest docker image e1513f80a4f3 fails to start due to ModuleNotFoundError Latest docker image, e1513f80a4f3, fails to start due to ModuleNotFoundError Dec 22, 2024
@kkaris kkaris linked a pull request Dec 22, 2024 that will close this issue
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