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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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Entrez email bug #22

Closed trvrb closed 8 years ago

trvrb commented 8 years ago

In 5e6ffd52ca0fd52084c50eee8ba4940942863349, running python vdb/update.py -db test_vdb -v zika --accessions KX101066,KX101060 results in:

/usr/local/lib/python2.7/site-packages/Bio/Entrez/__init__.py:451: UserWarning: 
Email address is not specified.

I figured out that this is due to neither Entrez.email nor self.email being set when get_GIs is called here: https://github.com/blab/nextstrain-db/blob/master/vdb/update.py#L17. The function Entrez.esearch within get_GIs needs Entrez.email to be set and it's not.

trvrb commented 8 years ago

This fixes the email bug, but I'm now getting RuntimeError: Search Backend failed: Database is not supported: nuccore. Internet tells me this may just be a transient issue with NCBI. @chacalle: has this happened to you before?

trvrb commented 8 years ago

I'm going to call this resolved after 606d5f642b2b132f09554ad839a4912b39d30b83. I'm pretty sure the RuntimeError: Search Backend failed: Database is not supported: nuccore will fix itself on NCBI's end.