Fix UniProt alias error handling - #296
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pablosanchezizquierdo wants to merge 3 commits into
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mtiberti
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Jul 30, 2026
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this is fine, but I think we should also handle this case in the calling function.
What happens if the conversion fails and this is None?
I think we should check and raise an Exception in the calling function e.g. for ValueError unless we have a way around it
| if t_keyword is not None: | ||
| self.log.info('using extracted keyword %s to parse results' % t_keyword) | ||
| out[t] = results['to'][t_keyword] | ||
| out[t] = results['to'].get(t_keyword) |
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it was to avoid KeyError but if we handle the error in get_sequence I can revert it
mtiberti
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Jul 30, 2026
| if upid is None: | ||
| this_upid = self._get_aliases(this_upac, ['UniProtKB_uniProtkbId'])['UniProtKB_uniProtkbId'] | ||
| if this_upid is None: | ||
| raise ValueError(f"Could not resolve UniProt primary accession for {this_upac}") |
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is this still primary accession?
this is different from the other two calls
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fix #294
This PR improves the error handling in
UniProt._get_aliases().Changes
Nonewhen an alias cannot be resolvedNonefor unresolved aliases while continuing to process the remaining requested aliases