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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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Should separate concepts of 'table' and 'virus' in vdb #26

Closed trvrb closed 8 years ago

trvrb commented 8 years ago

For the ZIBRA project, it will be easiest to have a separate table within vdb. I'm setting this up now as vdb/zibra. However, this should still have a virus field that says zika. We can be merging vdb/zibra into vdb/zika based on shared fields.

I'd suggest changing -v zibra / -v flu to -t zibra / -t flu. So swapping "virus" for "table". You could have a command that looks like:

python vdb/zibra_upload.py -db vdb -t zibra --fname seq.fasta --source zibra --virus zika

that uploads sequences to the vdb/zibra table, but still labels each virus field as zika.

I suspect this will be a generally useful semantic separation as well.

chacalle commented 8 years ago

Made branch table_field. Added -tb --table argument, -v --virus is still an argument. Basically changed all the lines that were using the rethink module, now they talk to self.table instead of self.virus.

trvrb commented 8 years ago

Great! I merged this into master. Consider it resolved.