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pvanheus
@pvanheus
@karinlag that file has long been slated for retirement.
Aaron Petkau
@apetkau
@karinlag this is the Java class that uses that file. But @pvanheus is right that this is quite old code
Karin Lagesen
@karinlag
so, this is where we go to look if we want to add species to the system?
in the dropdown menu to avoid butter fingers?
pvanheus
@pvanheus
in theory yes, in practice no, because basically there is no good procedure for adding to that file apparently.
Karin Lagesen
@karinlag
gah
and we have like 20 species to add
otherwise people will get creative
seems like maybe we just need to find a fix, and maybe do a PR :)
@ajkarloss sorry notsorry for giving you work to do :D
Aaron Petkau
@apetkau
Unfortunately, I do not recall right now who originally created the NCBItax.owl file for us
pvanheus
@pvanheus
and a while ago I tried editing the OWL but... it broke things.
I seem to recall the OWL being a bit over-kill-ish
pvanheus
@pvanheus
image.png
seems we have a problem :)
Jeevan Karloss
@ajkarloss
@karinlag 😀😣😆
Karin Lagesen
@karinlag
apologies if this is a faq somewhere, but is there an api to get metadata into the system, and to get results out of it?
Aaron Petkau
@apetkau
@karinlag there should be an HTTP GET command for getting metadata from a project: https://phac-nml.github.io/irida-documentation/swagger-ui/index.html#/projects/getProjectSampleMetadata
There are some POST and PUT commands in there too for putting metadata into the system
Though I don't know exactly how complete they are right now for e.g., batch upload of metadata to an entire project
Though we do that periodically, so I'd have to check how it's done currently (there has been discussion on how to make this more efficient for all the SARS-CoV-2 genomes we have)
Karin Lagesen
@karinlag
thanks, @apetkau !
Aaron Petkau
@apetkau
:smile:
Jeff Thiessen
@JeffreyThiessen
@karinlag Here is some code we have been using metadata uploads using the python api for irida from the irida uploader codebase. https://github.com/phac-nml/ncov2019-artic-nf/blob/update/sample_naming/bin/upload.py
You'll probably have to modify it heavily to fit your use case but it should give you a good idea of the code flow
Karin Lagesen
@karinlag
thanks so much @JeffreyThiessen !
this is exactly what we need :)
Eric Enns
@ericenns
Hi everyone. Thanks to @apetkau we created a 21.09.2 release to fix some old dependencies that had Critical|High issues as reported by Grype. Note the only one which would have been the easiest to exploit was excel parsing used by the metadata importer. (https://github.com/phac-nml/irida/releases/tag/21.09.2)
More information can be found here (https://github.com/phac-nml/irida/blob/master/UPGRADING.md).
Aaron Petkau
@apetkau
Thanks @ericenns . The specific changes we made are in the PR: phac-nml/irida#1149
George Marselis @NVI
@georgemarselis-nvi
I miss IRC...
hi guys
George Marselis @NVI
@georgemarselis-nvi
irida latest 21.0.1 i think: war deploys, page reports 404 when navigated to
this is on tomcat 10
George Marselis @NVI
@georgemarselis-nvi
i know the app is configured right, cuz i made a copy of the original app started right away
anyways, happy holidies get back to me when you can
pvanheus
@pvanheus
@georgemarselis-nvi can you past the log somewhere? and how did you start up the IRIDA server?
George Marselis @NVI
@georgemarselis-nvi
@pvanheus sure, but the log is squeaky clean
@pvanheus the irida server? you mean tomcat?
George Marselis @NVI
@georgemarselis-nvi
last link is better cuz it autodownloads
middle link will open the remote file in the dropbox site
Eric Enns
@ericenns
@georgemarselis-nvi Java 11 or higher is required for IRIDA and from looking at your logs specifically line 35353 in catalina.out it shows that java 8 is being used.
pvanheus
@pvanheus
and btw Tomcat must be version below 10