Fix AttributeError when AMRFinderPlus subclass is not in CARD conversion table - #35
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…ion table Fixes AMRverse#28 _assign_drug_from_amrfp() called card_amrfp_conversion.get(self.amrfp_subclass) and then immediately chained .get('drug', '-') / .get('class', '-') onto the result. When the AMRFinderPlus subclass has no entry in the hand-maintained amrfp_to_card_drugs_classes.txt table, the outer .get() returns None and the chained .get() raises AttributeError: 'NoneType' object has no attribute 'get', crashing the whole run instead of falling through to the existing "unassigned markers" fallback path a few lines below. This now defaults the lookup to an empty dict when the subclass is missing (matching the .get('drug class', '-') fallback pattern already used in _assign_drug_from_rule), and emits a warnings.warn() so a gap in the conversion table is visible instead of silent.
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Fixes #28.
Genotype._assign_drug_from_amrfp()chained.get('drug', '-')/.get('class', '-')directly ontocard_amrfp_conversion.get(self.amrfp_subclass). Theamrfp_to_card_drugs_classes.txtconversion table is maintained by hand and can lag behind whatever AMRFinderPlus/NCBI database is in use. When a subclass isn't in the table (e.g.FUSIDIC_ACIDvs a table only carryingFUSIDIC ACID), the outer.get()returnsNone, and.get('drug', '-')onNoneraisesAttributeError: 'NoneType' object has no attribute 'get', crashing the whole run.Found via a real production failure: 19 pipeline runs hit exactly this for an unmapped
FUSIDIC_ACIDsubclass on S. aureus samples.Fix: fall back to
{}when the lookup misses, so it flows into the existingif self.drug_class == '-': self.drug_class = 'unassigned markers'path instead of crashing, and emit awarnings.warn()so an unmapped subclass is at least visible rather than silent.(Re-opened from #34 under a different account — same commit, no code changes.)