Ruby - unknown keyword: :permitted_classes (ArgumentError)

[KunathBJ]

Hi,

I've tried to run Unipept Cli on a centos server.
The Ruby and Unipept Installation worked well, Unipept --version or --help returned the expected outputs and a typical
"unipept pept2lca AALTER" also worked... at first.

I then tried to give a list of peptide from a file as input and to print the results in an output file and I received this error:
Traceback (most recent call last):
13: from /home/users/bkunath/.gem/ruby/2.7.0/bin/unipept:23:in main
12: from /home/users/bkunath/.gem/ruby/2.7.0/bin/unipept:23:in load
11: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/bin/unipept:8:in <top (required)>
10: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/lib/commands/unipept.rb:373:in run
9: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/lib/commands/unipept.rb:43:in run
8: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/cri-2.15.11/lib/cri/command.rb:316:in run
7: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/cri-2.15.11/lib/cri/command.rb:298:in run
6: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/cri-2.15.11/lib/cri/command.rb:362:in run_this
5: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/cri-2.15.11/lib/cri/command_dsl.rb:294:in block in runner
4: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/cri-2.15.11/lib/cri/command_dsl.rb:294:in new
3: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/lib/commands/unipept/api_runner.rb:9:in initialize
2: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/lib/commands/unipept/api_runner.rb:9:in new
1: from /mnt/irisgpfs/users/bkunath/.gem/ruby/2.7.0/gems/unipept-3.0.0/lib/configuration.rb:17:in initialize
/mnt/irisgpfs/apps/resif/aion/2020b/epyc/software/Ruby/2.7.2-GCCcore-10.2.0/lib/ruby/2.7.0/psych.rb:576:in load_file: unknown keyword: :permitted_classes (ArgumentError)

And from now on, even running the command "unipept pept2lca AALTER" returns the same issue.
Do you guys have any idea why I have that? I guess it's due to ruby but I don't know enough about it to try to fix it.

Thanks a lot for any support you may bring.

Ben

[bmesuere]

Hi Ben, thanks for your report. I can't seem to reproduce the issue here, but I'll try again later today using Ruby 2.7.

Can you check if the two previous versions of the cli run ok? You can install them using gem install unipept -v 2.2.2 and gem install unipept -v 2.2.1

Between 2.2.1 and 2.2.2 the psych dependency was updated (which might have caused this issue) and support for old ruby versions was dropped (but ruby 2.7 should still be supported).

[bmesuere]

After some digging, I have found the potential issue. Ruby comes with a default version of the psych gem which in your case doesn't yet support the permitted_classes. I have added a newer version of psych as an explicit dependency which hopefully solves the problem and released a new gem version as 3.0.1.

I was unable to test/reproduce this because both my mac and the Ubuntu version of GitHub Actions seem to include a compatible psych version by default.

Your feedback is thus most welcome!

[KunathBJ]

Hi Bart,

Thanks for the quick answer. So quick I didn't even had time to try your first solution ^^
I used the version 3.0.1 and it now works.
I do have a slurm file with multiple instance of the message: API request failed! log can be found in /home/users/bkunath/.unipept/unipept-2022-04-27-16:45:57.log

but the expected output is produced so for me it works ;)

Thanks a lot,
Ben

[bmesuere]

Hmm, the message means that one or more requests failed which shouldn't happen. This is probably an issue on our side, maybe @pverscha can figure out what happens by checking the server logs around that time.

[KunathBJ]

I've rerun more today and I had the same bunch of messages.
The different times were:
API request failed! log can be found in /home/users/bkunath/.unipept/unipept-2022-04-28-15:05:20.log
API request failed! log can be found in /home/users/bkunath/.unipept/unipept-2022-04-28-15:05:27.log
API request failed! log can be found in /home/users/bkunath/.unipept/unipept-2022-04-28-15:05:46.log

Ben

[pverscha]

Hi @KunathBJ,

I was able to reproduce your issue and I have made a change to our server configuration, can you please let me know if the issue still persists for you?

[bmesuere]

Hi Ben,

Has this resolved your problem so I can close this issue?