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[23.2] Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata #18510

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nsoranzo
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@nsoranzo nsoranzo commented Jul 8, 2024

Fix the following traceback when running planemo lint if bio.tools is down:

File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/galaxy/tool\_util/biotools/source.py", line 69, in get\_biotools\_metadata
return BiotoolsEntry.from\_json(json.loads(content))
^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/**init**.py", line 346, in loads
return \_default\_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw\_decode(s, idx=\_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/decoder.py", line 355, in raw\_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

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.

…adata``

Fix the following traceback when running `planemo lint` if bio.tools is down:

```
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/galaxy/tool\_util/biotools/source.py", line 69, in get\_biotools\_metadata
return BiotoolsEntry.from\_json(json.loads(content))
^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/**init**.py", line 346, in loads
return \_default\_decoder.decode(s)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/decoder.py", line 337, in decode
obj, end = self.raw\_decode(s, idx=\_w(s, 0).end())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/json/decoder.py", line 355, in raw\_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
```
@nsoranzo nsoranzo added this to the 24.2 milestone Jul 8, 2024
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nsoranzo commented Jul 8, 2024

Test failures unrelated.

@nsoranzo nsoranzo merged commit 1b0b82f into galaxyproject:release_23.2 Jul 8, 2024
36 of 47 checks passed
@nsoranzo nsoranzo deleted the release_23.2_fix_ApiBiotoolsMetadataSource._raw_get_metadata branch July 8, 2024 18:26
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2 participants