odk - SKILL.md Agent Skill

name: odk description: Use when running any ODK-backed command in this repo — owltools, robot, make NORM, robot verify, or any other tool that lives inside the ODK docker image

Running ODK commands in this repo

TL;DR

src/ontology/run.sh is the official wrapper, but it ends in docker run -ti so it fails silently in any non-TTY context (Claude Code, CI, non-interactive shells) with the input device is not a TTY and exits without running the command.

If you have a TTY, prefer run.sh. If you don't, call docker directly with -i only.

When you have a TTY (interactive terminal)

cd src/ontology && sh run.sh <command> <args...>

Examples:

sh run.sh make NORM
sh run.sh owltools --use-catalog mondo-edit.obo --obsolete-replace MONDO:A MONDO:B -o -f obo mondo-edit.obo
sh run.sh robot verify --catalog catalog-v001.xml -i mondo-edit.obo --queries ../sparql/qc/general/qc-foo.sparql -O reports/

When you don't have a TTY (Claude Code, CI, scripts)

Symptom: sh run.sh <anything> prints the input device is not a TTY and exits with no further output, no file changes.

Workaround — invoke docker directly using the same image and mounts as run.sh, but with -i only:

docker run --memory=8g \
  -v /ABSOLUTE/PATH/TO/REPO:/work \
  -w /work/src/ontology \
  -e ROBOT_JAVA_ARGS=-Xmx8G -e JAVA_OPTS=-Xmx8G \
  --rm -i obolibrary/odkfull:<TAG-FROM-RUN.SH> \
  <command> <args...>

Where:

/ABSOLUTE/PATH/TO/REPO = the repo root (the parent of src/).
<TAG-FROM-RUN.SH> = whatever tag is set in IMAGE= in src/ontology/run.sh. Always read run.sh first to look up the current tag — do not hardcode v1.6 or any other version.

Reading the right image tag

Don't memorize the version. The line in run.sh is the source of truth:

grep '^IMAGE=' src/ontology/run.sh
# IMAGE=${IMAGE:-odkfull:v1.6}

Common ODK commands you'll need

What	Command body (after `run.sh` or after the `docker run ... -i obolibrary/odkfull:<TAG>` prefix)
Normalize edit file	`make NORM` then `mv NORM mondo-edit.obo` (run from `src/ontology`)
Convert / syntax check	`robot convert --catalog catalog-v001.xml -i mondo-edit.obo -f obo -o mondo-edit.TMP.obo`
Run a QC query	`robot verify --catalog catalog-v001.xml -i mondo-edit.obo --queries ../sparql/qc/general/qc-X.sparql -O reports/`
Merge / obsolete with replacement	`owltools --use-catalog mondo-edit.obo --obsolete-replace MONDO:A MONDO:B -o -f obo mondo-edit.obo`

Notes

All ODK commands assume CWD is src/ontology/.
make NORM writes to a file called NORM in src/ontology/. You must mv NORM mondo-edit.obo afterward.
robot verify exits non-zero on QC failures and writes one TSV per failing query under -O reports/. Empty exit + PASS Rule ... 0 violation(s) = clean.
If run.sh reports the input device is not a TTY, do not retry the same command — it will keep failing. Switch to the docker-direct invocation.