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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
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docker composition should load all VFs during install #227

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago

Namely, using VFs from https://github.com/phac-nml/ecoli_vf/blob/master/data/repaired_ecoli_vfs_shortnames.ffn

This is related to https://github.com/superphy/backend/issues/202, to ensure that all Stx1, Stx2 and Eae markers are in the DB. e.g. so someone doing a fresh install can still use phylotyper w/o running any of the ECTyper tasks.

kevinkle commented 6 years ago

Needs to be addressed to complete https://github.com/superphy/backend/issues/202

kevinkle commented 6 years ago

I'm going to embed this into superphy_subtyping.ttl in phylotyper (on backend)

kevinkle commented 6 years ago

This should also resolve phylotyper's dependence on submitting an ECTyper task before running

kevinkle commented 6 years ago

https://github.com/superphy/backend/commit/6b6e3ad97e99e7297aff8f309d1083fe9817d94e shows how we addressed this. When phylotyper does its check for ontology definitions in the db., it will also upload a graph of all the VFs if the definition isnt found.

This is different from the title of this issue: the problem is resolved within the phylotyper module instead of the docker composition.

Closing issue. https://github.com/superphy/backend/issues/228 will cover the removal of the ectyper job enqueu from phylotyper

kevinkle commented 6 years ago

There were a number of fixes that were needed and added in https://github.com/superphy/backend/tree/rc-4.4.1