Unverified Commit 4ac6a1e4 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` 

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)
```
parent 06590c92

lib/galaxy/tool_util/biotools/source.py

+6 −5
Original line number Diff line number Diff line
@@ -54,12 +54,13 @@ class ApiBiotoolsMetadataSource(BiotoolsMetadataSource): 


    def _raw_get_metadata(self, biotools_reference) -> Optional[str]:

        api_url = f"https://bio.tools/api/tool/{biotools_reference}?format=json"

        try:

            req = requests.get(api_url, timeout=DEFAULT_SOCKET_TIMEOUT)

            req.raise_for_status()

            req.encoding = req.apparent_encoding

        if req.status_code == 404:

            return None

        else:

            return req.text

        except Exception:

            return None



    def get_biotools_metadata(self, biotools_reference: str) -> Optional[BiotoolsEntry]:

        createfunc = functools.partial(self._raw_get_metadata, biotools_reference)