[arog-bioinfo]

Problem

Hi! While I was using UPIMAPI to annotate metagenomic bins I occasionally encountered a UniProt server-side error that caused the annotation to stall in the UPIMAPI job.

When UniProt marks an asynchronous ID-mapping job as failed, its status endpoint can return HTTP 400 with jobStatus: "ERROR" and error code 50. Because requests.get() returns this as a response rather than raising an exception, get_url() did not increment its retry counter or leave the loop. It consequently kept requesting the status of the same failed job, which could never recover.

Solution

This change identifies server-side failures from general HTTP 5xx responses and terminal UniProt responses containing jobStatus: "ERROR" with error code 50.

These responses raise a dedicated UniProtServerError. To prevent a UniProt-side failure from stopping the entire UPIMAPI run, the ID-mapping batch functions catch this error and submit the same chunk again, producing a new job ID instead of continuing to poll the failed job. Fresh submissions are limited by the existing --max-tries setting, preventing another infinite retry loop. Other HTTP errors continue to propagate normally and do not trigger a new submission.

I performed local tests covering the observed code-50 response and the fix appears to work as intended.

[iquasere]

Very nice