search

mountetna / timur

Data browser for biologists
GNU General Public License v2.0
3 stars 6 forks source link

Cs remove magma client #261

Closed coleshaw closed 4 years ago

coleshaw commented 4 years ago

This removes the dependency on the Magma gem and instead uses the Etna::Client to talk to Magma. This will hopefully make CI and monoetna easier to use, since the etna gem is published to RubyGems and we will not have to build magma gem manually.

NOTE: This change requires a new HMAC entry for archimedes in both Magma's and Timur's config.yml files, that need to have matching values.

@graft , is there a way to test that the various Archimedes methods work? question still seems to work since Timur can query and fetch data from Magma, but how do I know if the table method works? In the Timur UI, is there a specific set of Manifest commands that I can run to verify it still works? The "manifest tutorial" one in the VM seems to work okay, if that is an indicator.

graft commented 4 years ago

The plots on the ipi front page will all make table() calls via a manifest; if you goto https://timur/ipi/, the redirect to https://timur/ipi/browse/project/UCSF%20Immunoprofiler will require a call to question(). If both of these work, the client is doing its thing.