IRIDA/Lobby

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

Aaron Petkau

@apetkau

Or, maybe it's contacting the IRIDA web UI and not the API

Jeff Thiessen

@JeffreyThiessen

That resource error usually indicates trying to access a project your user does not have permissions to.

Jeevan Karloss

@ajkarloss

@apetkau this is the first time I am using it. The user has created the project which has id 25. Client "test_client_2" is created by the addmin

Is the API url correct?

Jeevan Karloss

@ajkarloss

The client "Write and Auto approve?" was not selected. Now, I have selected it and getting this errors. The sample names have been addded to the project. But the fastq files are not

2021-12-13 19:44:20 INFO looking for run in /Users/xxxx/S_Enterica_FastQ
2021-12-13 19:44:22 INFO looking for run in /Users/xxxx/S_Enterica_FastQ
2021-12-13 19:44:22 INFO Beginning Parsing
2021-12-13 19:44:22 INFO Looking for sample sheet in /Users/xxxx/S_Enterica_FastQ
2021-12-13 19:44:22 INFO Reading data from sample sheet /Users/xxxx/S_Enterica_FastQ/SampleList.csv
2021-12-13 19:44:22 INFO Validating sequencing run
2021-12-13 19:44:22 INFO Parsing Done
{'_sample_name': 'sample-1', '_description': '', '_sample_number': 1, '_sample_dict': {'File_Forward': 'xxxxxxxxxxx_R1_001.fastq', 'File_Reverse': 'XXXXXXXX_R2_001.fastq', 'sample_project': '25'}, '_sequence_file': <iridauploader.model.sequence_file.SequenceFile object at 0x7f9ce81e5c50>, '_skip': False}
{'_sample_name': 'sample-2', '_description': '', '_sample_number': 2, '_sample_dict': {'File_Forward': 'YYYYYYY_R1_001.fastq', 'File_Reverse': 'YYYYYYYYYYY_R2_001.fastq', 'sample_project': '25'}, '_sequence_file': <iridauploader.model.sequence_file.SequenceFile object at 0x7f9ce81e5208>, '_skip': False}
2021-12-13 19:44:24 INFO looking for run in /Users/xxxxx/S_Enterica_FastQ
2021-12-13 19:44:24 INFO Run with status error is being force uploaded
2021-12-13 19:44:24 INFO Adding log file to /Users/xxxx/S_Enterica_FastQ
2021-12-13 19:44:24 INFO ==================================================
2021-12-13 19:44:24 INFO ---------------STARTING UPLOAD RUN----------------
2021-12-13 19:44:24 INFO Uploader Version 0.6.2
2021-12-13 19:44:24 INFO Logging to file in: /Users/xxxx/Library/Logs/irida-uploader
2021-12-13 19:44:24 INFO ==================================================
2021-12-13 19:44:24 INFO Starting upload for '/Users/xxxx/S_Enterica_FastQ' with continue partial upload = 'False'
2021-12-13 19:44:24 INFO Beginning Parsing
2021-12-13 19:44:24 INFO Looking for sample sheet in /Users/xxxx/S_Enterica_FastQ
2021-12-13 19:44:24 INFO Reading data from sample sheet /Users/xxxx/S_Enterica_FastQ/SampleList.csv
2021-12-13 19:44:24 INFO Validating sequencing run
2021-12-13 19:44:24 INFO Parsing Done
2021-12-13 19:44:25 INFO Connected
2021-12-13 19:44:25 INFO Verifying run (online validation)
2021-12-13 19:44:25 INFO Loading projects.
2021-12-13 19:44:25 INFO Getting samples from project '25'
2021-12-13 19:44:26 INFO Creating sample 'sample-1' for project '25' on IRIDA.
2021-12-13 19:44:27 INFO Getting samples from project '25'
2021-12-13 19:44:27 INFO Getting samples from project '25'
2021-12-13 19:44:27 INFO Creating sample 'sample-2' for project '25' on IRIDA.
2021-12-13 19:44:28 INFO Getting samples from project '25'
2021-12-13 19:44:28 INFO Run Verified
2021-12-13 19:44:28 INFO Starting Upload
2021-12-13 19:44:29 ERROR Encountered error while creating sequence run: 405
2021-12-13 19:44:29 ERROR Lost connection to Irida
2021-12-13 19:44:29 ERROR Errors: ('Error encountered while communicating with IRIDA: 405: \n',)
2021-12-13 19:44:29 INFO ==================================================
2021-12-13 19:44:29 INFO ----------------ENDING UPLOAD RUN-----------------
2021-12-13 19:44:29 INFO ==================================================
2021-12-13 19:44:29 INFO Stopped active logging to run directory

Aaron Petkau

@apetkau

@ajkarloss it sounds like the uploader lost connection to IRIDA in the middle of uploading. You should be able to re-run it and I believe it will pick up where it left off

Jeevan Karloss

@ajkarloss

Ok, thanks

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?

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