Regarding ODK Release of Ontology - Issue with ODK/tools - Broken ODK Image

[karanthpallavi]

Hi, have tried to pull ODK image, download is successful, but its unable to find /tools/odk:
docker run --rm -ti obolibrary/odkfull /bin/bash
root@f48c0ab3ee2e:/tools# ls -l /tools/odk
ls: cannot access '/tools/odk': No such file or directory

Have tried resolving this, but in vain, Can I get some help on this? Thanks

[gouttegd]

Err, there is no /tools/odk directory in the ODK image; never has been for at least as long as I have used the ODK.

What were you trying to to? What were you looking for in that non-existing /tools/odk directory?

[karanthpallavi]

Tried to run ODK library run make script to release an Ontology which was seeded using ODK toolkit, but ran into errors...

[karanthpallavi]

Here are the steps I have followed: first to prepare a release, within ontology directory, ran :

sh run.sh make prepare_release_fast,

Got:
robot --catalog catalog-v001.xml report -i tmp/merged-rosettastmtont-edit.ofn -l true --profile profile.txt --fail-on ERROR --print 5 -o reports/rosettastmtont-edit.owl-obo-report.tsv
Violations: 67

ERROR: 0
WARN: 63
INFO: 4

First 5 violations:
WARN missing_definition description IAO:0000115
WARN missing_definition license IAO:0000115
WARN missing_definition title IAO:0000115
WARN missing_definition root node IAO:0000115
WARN missing_definition assertion IAO:0000115
reports/rosettastmtont-edit.owl-obo-report.tsv (Permission denied)
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
make[1]: *** [Makefile:246: reports/rosettastmtont-edit.owl-obo-report.tsv] Error 1
make[1]: Leaving directory '/work/src/ontology'
make: *** [Makefile:311: prepare_release_fast] Error 2

Next, tried running make update_repo:
sh ../scripts/update_repo.sh
This (experimental) update script will create a new repo according to your config file. It will:
(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh).
(2) and add missing files, if any.
../scripts/update_repo.sh: 14: /tools/odk.py: not

make: *** [Makefile:611: update_repo] Error 127

Got: make: *** No rule to make target 'update-repo'. Stop.

Unable to release ontology, Can I get some help to resolve this issue?

Am I doing something wrong here?

[gouttegd]

This is what caused the entire release pipeline to fail:

reports/rosettastmtont-edit.owl-obo-report.tsv (Permission denied)

Here, ROBOT is complaining that it could not write one of its reports into the src/ontology/reports directory because of a permission issue.

Am I correct to assume you are running under a GNU/Linux system? (Please state which system you are using otherwise.)

Can you check the permissions in your src/ontology directory?

[karanthpallavi]

Am running on Ubuntu (WSL) , have given permissions to src/ontology, trying to run now, looks like prepare_release_fast has been running for hours now, shall update, thanks!

[karanthpallavi]

Able to run successfully after resolving docker and make issues, thanks for support, closing this thread.