- Yes using https (your irida instance needs to be configured with https not http) with oauth
- When using the command line uploader, using any of the config arguments without defining a value (ex: iridauploader --password --username) will then prompt the user to enter those values
When we use upload the data using IRIDA-Uploader, will the client id be stored in the DB for that data/transfer?
@ajkarloss there's a very old document here https://phac-nml.github.io/irida-documentation/developer/data-model/ but it's quite out-of-date
The best solution is probably to auto-generate an ER diagram from the existing IRIDA database, though I forget which software can do this right now
describe project;
+---------------------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+---------------------------+--------------+------+-----+---------+----------------+
| id | bigint(20) | NO | PRI | NULL | auto_increment |
...
| organism | varchar(255) | YES | | NULL | |
...
+---------------------------+--------------+------+-----+---------+----------------+I'm not quite sure what you mean by client id stored in the database, since the client information is associated with a particular IRIDA instance (and so must already be in the database before upload of data)?
For resuming uploads though, I believe the IRIDA uploader writes a JSON file in the upload directory with information on what files were uploaded/when it was completed.
I. E
That is, the stuff in the gui species drop down menu?
@karinlag I believe it's this file: https://github.com/phac-nml/irida/blob/development/src/main/resources/ca/corefacility/bioinformatics/irida/ontology/NCBItax.owl
It likely hasn't been updated in a long time, but I actually don't recall how it was first generated/where it was downloaded from
any info anywhere on how this file interacts with the rest of the system?
(or the logic in it for that matter :))
in the dropdown menu to avoid butter fingers?
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
Unfortunately, I do not recall right now who originally created the NCBItax.owl file for us
I seem to recall the OWL being a bit over-kill-ish
seems we have a problem :)
@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)
@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
this is exactly what we need :)
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).