IRIDA/Lobby

General discussion related to the IRIDA project - http://www.irida.ca

Jeevan Karloss

@ajkarloss

@apetkau can the command line version irida-uploader be used to upload the samples to IRIDA? Its asking for SampleShseet file

Jeff Thiessen

@JeffreyThiessen

@ajkarloss Yes, you can either change your config file manually to use directory parser (I'm not sure where this file exists on mac), or use --config=/path/to/file.conf to define a config file you want to use.

we have documentation here https://irida-uploader.readthedocs.io/en/stable/ and specific documentation for the directory uploads here https://irida-uploader.readthedocs.io/en/stable/parsers/directory.html

Jeevan Karloss

@ajkarloss

@JeffreyThiessen Thanks a lot :)

Jeevan Karloss

@ajkarloss

Few more questions regarding Irida-uploader:

Does the uploader communicate usernname, password and client secret communicated to Irida by HTTPS or ?
Is it possible to prompt for the username and password when we run the Irida uploader?

Thanks

Jeff Thiessen

@JeffreyThiessen

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

Jeevan Karloss

@ajkarloss

Excellent @JeffreyThiessen . Thanks a lot

Jeff Thiessen

@JeffreyThiessen

No problem :)

Jeevan Karloss

@ajkarloss

Is there a ER diagram for the IRIDA MySQL db? Thanks

Also, If we add a new species in IRIDA using the gui, will that be stored in the database?

When we use upload the data using IRIDA-Uploader, will the client id be stored in the DB for that data/transfer?

Aaron Petkau

@apetkau

@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there's a very old document here https://phac-nml.github.io/irida-documentation/developer/data-model/ but it's quite out-of-date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

Aaron Petkau

@apetkau

The organism entry is stored in the database as a string, so it will be stored in the database. But the list you get presented with is stored someplace else so you'd likely have to type in the same name over again.

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.

Karin Lagesen

@karinlag

@apetkau do you recall where the species are stored?

I. E

That is, the stuff in the gui species drop down menu?

Aaron Petkau

@apetkau

@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

Karin Lagesen

@karinlag

thanks @apetkau !

any info anywhere on how this file interacts with the rest of the system?

(or the logic in it for that matter :))

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

https://github.com/phac-nml/irida/blob/development/src/main/java/ca/corefacility/bioinformatics/irida/service/impl/InMemoryTaxonomyService.java

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

This might be useful https://github.com/obophenotype/ncbitaxon

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

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

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