Fix rhea in allbase
Koeng101 opened this issue · 5 comments
This a good issue to get @TimothyStiles up-to-date with how allbase is deployed and such. Basically, I fixed the code issue with #1 , but this code fix needs to be propagated to the main database. I need you to:
- ssh into the allbase server
- Update allbase with a new version of the rhea tables (this will require either dropping those tables in SQL or implementing incremental updates in the code itself)
I simply compiled the cmd directory into a script that I scp'd to the server. You may wish to do something different. Up to you. Please poke me with any questions.
@Koeng101 this should probably update on a cron job like system. Is this how all databases are being integrated at the moment?
this should probably update on a cron job like system
Yes
Is this how all databases are being integrated at the moment?
I ran one script and it did the thing. In the future, we want this to be on a cron job or something, redownloading the databases as needed and applying changes (in the case of rhea, it's no time at all, so dropping the tables is probably a fine solution, but uniprot we'd want incremental changes). I did not set up a cron job system just so we could get this up and running ASAP.
Aye. @Koeng101. Is this update necessary or more of a training exercise for me? 😉
Both. We can't do mapping to chebi's without it, but it'd also be nice for you to interact with the data a little bit :)
It honestly wouldn't take me very long to do it, but thought it would perhaps be a good exercise. If you're busy, however, I can go do it.
@Koeng101 if you can update it that'd be great. I'm finishing my draft for the poly refactor for everyone to review and then seeing if I can get the roadmap draft done by tonight. Hopefully will be able to look at allbase tomorrow.