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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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Refactor Phylotyper Integration #311

Open kevinkle opened 6 years ago

kevinkle commented 6 years ago

@mwhitesi raised some good points about https://github.com/superphy/spfy/pull/309 We've currently hotfixed it for now, but here are Matt's points for a future refactor.

Does order matter? i.e. the phylotyper ontology graph is created before linking it to the results graph and its also created before checking if the loci exist. Not sure if building edges during the phylotyper ontology graph construction will add empty `:stx2a`, `:stx2b` nodes. I would check for the existence of the marker loci before creating the MarkerSequences object and going to the trouble of building the phylotyper ontology