Closed ftzohra22 closed 1 year ago
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.
The issue is on the NCBI API side. We created a workaround. It should be OK moving forward.
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
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.
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 😅
@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.