seed-via-docker.sh doesnt do anything (windows/ubuntu)

[AsaphHall]

I tried to follow this tutorial and i am currently stuck at generating the repo with 'sh seed-via-docker.sh -c -C cato-odk.yaml'. I keep getting this message
"This script only works with ODK 1.3.2 and later. For ODK 1.3.1 or earlier, use https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh"
but nothing happens afterwards. Im running the latest release version of odkfull.
There was a similar issue and i followed the proposals but still ended up with the same problem.

Im running ubuntu 22.04.05 lts as a vm on windows 10

[gouttegd]

It’s weird that you don’t even get an error message.

If you run sh seed-via-docker.sh --help, do you get the help message from the seeding script? Something that looks like the following:

Usage: odk.py seed [OPTIONS] [REPO]...

  Seeds an ontology project

Options:
  -C, --config PATH         path to a YAML configuration. See examples folder
                            for examples. This is optional, configuration can
                            also be passed by command line, but an explicit
                            config file is preferred.
  -c, --clean / --no-clean
  -T, --templatedir TEXT
  -D, --outdir TEXT
  -d, --dependencies TEXT
  -t, --title TEXT
  -u, --user TEXT
  -s, --source TEXT         path to existing source for ontology edit file.
                            Optional. If not passed, a stub ontology will be
                            created.
  -v, --verbose
  -g, --skipgit
  -n, --gitname TEXT
  -e, --gitemail TEXT
  --help

?

[AsaphHall]

Thank you for your reply. Upon entering sh seed-via-docker.sh --help i get the same message as above.

Edit. I tried it on a different machine and ran into the same message.

[AsaphHall]

After using the commands on https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh it created a folder target but it only contains a folder none which contains 3 Files: CODE_OF_CONDUCT, CONTRIBUTING and issues_template

[matentzn]

I was using this and it worked for me:

 sh -c "$(curl -fsSL https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/seed-via-docker.sh)" -C oba-odk.yaml 

(replace oba-odk.yaml with whatever your config file is called)

Also remember to run docker pull obolibrary/odkfull.

Many of us have recently switched to https://github.com/gouttegd/odkrunner which is a much more sane way to interact with ODK then these shell scripts - but you will have to check if it supports seeding

[gouttegd]

Many of us have recently switched to https://github.com/gouttegd/odkrunner which is a much more sane way to interact with ODK then these shell scripts - but you will have to check if it supports seeding

It does. Just call it with odkrun seed [your seeding options...].

But I doubt the seed-via-docker.sh script is the problem here (and so, that replacing it with odkrun would change anything). It seems to be doing its job, since we can see that it is effectively invoking Docker (calling it with --help produces the error message from the odk.py script, which means the container had indeed been started and that the odk.py script had correctly been called).

[AsaphHall]

I was using this and it worked for me:

 sh -c "$(curl -fsSL https://raw.githubusercontent.com/INCATools/ontology-development-kit/master/seed-via-docker.sh)" -C oba-odk.yaml 

(replace oba-odk.yaml with whatever your config file is called)

Also remember to run docker pull obolibrary/odkfull.

Many of us have recently switched to https://github.com/gouttegd/odkrunner which is a much more sane way to interact with ODK then these shell scripts - but you will have to check if it supports seeding

Thank you for your reply. Unfortunately, this runs into the same error message. (I did replace 'oba-odk.yaml' with 'cato-odk.yaml' (my file) and pulled the image again to be sure)

[matentzn]

@AsaphHall in this case unfortunately its difficult to assist as I cant replicate the error. Sorry about that! Will you try ODK runner and report if that worked for you?

[AsaphHall]

No worries. Thank you for trying. I´ll give it a try with the ODK Runner.

[AsaphHall]

Hi,
just a quick update.
I managed to finish the tutorial with the odkrunner. I had to use a mix of sh and the odkrun commands tho.

[matentzn]

Awesome, thanks @AsaphHall for following up! Much appreciated!

can you tell us for which cases you need to use sh?

[AsaphHall]

Hi, i cannot recall which commands made me use the sh commands. After wrapping my head around the odkrunner and the make commands i eventually did figure out how to use odkrun for all cases.

[matentzn]

Can we close the issue?