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nextstrain / fauna

RethinkDB database to support real-time virus analysis
GNU Affero General Public License v3.0
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Citation not updating #25

Closed trvrb closed 8 years ago

trvrb commented 8 years ago

The previous RuntimeError: Search Backend failed: Database is not supported: nuccore error has resolved itself on NCBI's end. I was update to add citations to most strains via python vdb/update.py -db vdb -v zika. However, some aren't taking. Trying for example:

python vdb/update.py -db vdb -v zika --accessions KX087102

The Genbank entry is lacking a title, but does have authors. The running update is not revising authors however.

There are a number of other accessions that behave the same way. Checkout new_server.vdb.zika and look for strains that have null for authors.

chacalle commented 8 years ago

Update wasn't finding the correct strain name, it now uses zika_upload.fix_name() to parse the correct strain name. I believe zika_update now works.

trvrb commented 8 years ago

This is working as intended now. Thanks!