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OpenTreeOfLife / reference-taxonomy

Open Tree Reference Taxonomy (OTT) tools
BSD 2-Clause "Simplified" License
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Help using new patch system #369

Closed kcranston closed 5 years ago

kcranston commented 5 years ago

I am trying to fix feedback issue#397 using the new patch system. Put some notes in feedback.md on branch ott3.1 and did an initial attempt at a fix in amedments.py. (I thought this was similar to Joseph's Quiscalus error). The fix doesn't work, and I get this warning in the logs:

** Ambiguous taxon name: Placopecten (ott)
**   Placopecten (genus in Bilateria) = (Placopecten =worms:156971+1) in Mollusca
**   Placopecten (genus in phylum Cnidaria) = (Placopecten =gbif:2285951+4) in Cnidaria

I see that the proclaim directive doesn't work as is, but I am not sure how to fix this. I'd like there to no longer be 'Placopecten (genus in Bilateria)' and 'Placopecten (genus in phylum Cnidaria)' but just 'Placopecten' and for it to be in Bilateria. Synonymizing the two name strings seems insufficient, because that would not solve the placement problem.

kcranston commented 5 years ago

Figured it out - I needed this in adjustments.py for gbif, not in amendments.py for ott. Ended up just pruning the misplaced GBIF taxon, but in a way that should reinstate it once we have a new version.