Study 722: Taxon "Bacteria" exported as empty string

[ftzohra22]

@tosfos https://bugsigdb.org/Study_722 is not displaying one of the bacteria names. To specify its the kingdom bacteria, the first name on the list under signature 1 and 2. Please see attached screenshot.

[tosfos]

This is a repeat of #160. Since this is the second time this happened, we'll investigate the cause further. Chances are the immediate issue will fix itself soon.

[tosfos]

The issue is on the NCBI API side. We created a workaround. It should be OK moving forward.

[lgeistlinger]

It seems there is a hiccup in the export here. The taxon "Bacteria" (NCBI ID: 2) is exported as an empty string in both the MetaPhlAn taxon names as well as the NCBI Taxonomy IDs column. See the leading comma / semicolon in these columns (this is an excerpt from the exported signatures.csv file).

This causes some hiccups downstream as well. https://github.com/waldronlab/bugsigdbr/issues/43

[tosfos]

This should be resolved. It is possible that some of the old blank values have been cached and that was the cause. We can't purge the caches until we do a container restart, which we plan in a couple of weeks or so.

[lwaldron]

It's displaying correctly for me now. It's pretty odd that the authors reported "Bacteria" as both increased and decreased in cases and we were probably doing them a favor by not displaying that 😅