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Jeevan Karloss
@ajkarloss
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:

  1. Does the uploader communicate usernname, password and client secret communicated to Irida by HTTPS or ?

  2. Is it possible to prompt for the username and password when we run the Irida uploader?

Thanks

Jeff Thiessen
@JeffreyThiessen
  1. Yes using https (your irida instance needs to be configured with https not http) with oauth
  2. 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?
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
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)