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ga4gh / vrs-python

GA4GH Variation Representation Python Implementation
https://github.com/ga4gh/vrs
Apache License 2.0
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Passing an invalid variant description to AlleleTranslator.translate_from() throws TypeError #400

Closed ehclark closed 7 months ago

ehclark commented 7 months ago

If a variant description that does not match any of the supported formats is passed in to AlleleTranslator.translate_from(), a TypeError is thrown.

>>> tlr.translate_from('BRAF amplification')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/workspaces/gdh/vrs-python/src/ga4gh/vrs/extras/translator.py", line 98, in translate_from
    o = t(var, **kwargs)
  File "/workspaces/gdh/vrs-python/src/ga4gh/vrs/extras/translator.py", line 305, in _from_hgvs
    return self._create_allele(allele_values, **kwargs)
  File "/workspaces/gdh/vrs-python/src/ga4gh/vrs/extras/translator.py", line 167, in _create_allele
    seq_ref = models.SequenceReference(refgetAccession=values["refget_accession"])
TypeError: 'NoneType' object is not subscriptable

This is because the hgvs_tools.extract_allele_values can return None when the description is not HGVS syntax. And there is no null defense in AlleleTranslator._create_allele.

Invoking AlleleTranslator.translate_from() with an invalid description should instead raise a ValueError with the message: "Unable to parse data as beacon, gnomad, hgvs, spdi, vrs"