Exécution de commandes ODK via Docker

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name: odk-make description: Use whenever you run a Makefile target (e.g. make travis_build, make test, make reasoned.ofn) or any one-off ROBOT / owltools / dosdp-tools / scala-cli command derived from a Makefile recipe. These must run inside the pinned ODK Docker image, not against host tools. Covers validation, reasoning, imports, and release builds in src/ontology.

The core rule

Every Makefile target and every one-off command copied from a Makefile recipe must run inside the ODK Docker image (obolibrary/odkfull). The Makefile recipes call robot, owltools, dosdp-tools, and scala-cli; the ODK image is what provides those tools at the exact versions GO's build and CI expect. Running make or robot against whatever happens to be on the host PATH is not reproducible — host tools may be missing, or be the wrong version, and you will get results that don't match CI.

The canonical console invocation is the wrapper src/ontology/run.sh, which a human editor runs from inside src/ontology:

cd src/ontology
./run.sh make test
./run.sh robot --version

run.sh is just docker run ... obolibrary/odkfull:<pinned-version> "$@", with the repo mounted at /work and the working directory set to /work/src/ontology. It mounts $PWD/../../, so it only mounts correctly when invoked from src/ontology.

How YOU (an agent) should run these commands

run.sh requests an interactive TTY (docker run -ti). That fails in a non-interactive shell — the normal case when you run commands — with:

cannot attach stdin to a TTY-enabled container because stdin is not a terminal

So do not call ./run.sh directly. Use the bundled TTY-free wrapper in this skill instead. It mirrors run.sh exactly (same image tag — read live from run.sh so it never drifts — same mount, same workdir) but omits -ti, and it works from any directory in the repo:

.claude/skills/odk-make/odk-run.sh make travis_test
.claude/skills/odk-make/odk-run.sh make reasoned.ofn
.claude/skills/odk-make/odk-run.sh robot --version

Decision rule:

• Local development / agent on a workstation (Docker available, you are NOT already inside the ODK container): always go through odk-run.sh.
• Already inside the ODK image (GitHub Actions / ai4c-agent, where the job itself runs in the ODK container; or you launched an interactive ./run.sh bash shell): the tools are already on PATH, so call make / robot directly with no wrapper. Don't nest Docker.

If you're unsure which environment you're in: robot --version succeeding on the bare PATH and a /work working directory are signs you're already inside ODK. Otherwise assume you need odk-run.sh.

Note on the project guide: it writes validation as cd src/ontology && make travis_test. That shorthand assumes the ODK environment is already active (as in CI). On a local machine, run the equivalent through the wrapper: .claude/skills/odk-make/odk-run.sh make travis_test.

Common targets

| Goal | Command (local) | | --- | --- | | Full validation (CI gate) | .claude/skills/odk-make/odk-run.sh make travis_test | | Reasoning + SPARQL only (part of the above) | .claude/skills/odk-make/odk-run.sh make travis_build | | Test suite | .claude/skills/odk-make/odk-run.sh make test | | Reason the edit file | .claude/skills/odk-make/odk-run.sh make reasoned.ofn | | Regenerate an import | .claude/skills/odk-make/odk-run.sh make imports/<name>.owl | | Regenerate all imports | .claude/skills/odk-make/odk-run.sh make all_imports | | Simulate a release build | .claude/skills/odk-make/odk-run.sh make |

make travis_test is the primary post-edit validation gate, and is exactly what CI runs. Allow at least ~10 minutes for it to run; don't kill it early. Don't substitute make travis_build: that is only the ROBOT half (pre-reasoning SPARQL, ELK reasoning, post-reasoning SPARQL) and skips all seven of its siblings -- check_taxon_constraint_idspaces, check_all_taxon_constraints_columns, the perl OBO check, qc-selftest, datalog-check, chebi_pH_7_3_check, and change-report.txt (the gate on dropped or renumbered GO ids and missing labels).

travis_test also needs network access, where travis_build does not: both GO.xrf_abbs and go-lastrelease.owl are rebuilt whenever go-edit.obo changes, so each run re-fetches the db-xrefs metadata and the released go.owl. In a sandbox without egress it fails at wget, which is not an ontology defect. If it times out, you can run the SPARQL verification checks and the ELK reasoning step on their own (see the AUTOMATED-VALIDATION section of CLAUDE.md) — those are also Makefile-derived commands, so run them through odk-run.sh too, e.g.:

.claude/skills/odk-make/odk-run.sh \
  robot reason -r ELK -i go-edit.obo -o go-edit.reasoned.obo

One-off ROBOT / owltools commands

Anything you'd lift from a Makefile recipe — a robot verify, robot explain, robot convert -vvv for a syntax stack trace, an owltools diff — goes through the same wrapper. Paths are relative to src/ontology (the container's working directory), so reference files the way the Makefile does (go-edit.obo, imports/..., ../sparql/..., ../taxon_constraints/...):

# Syntax error stack trace
.claude/skills/odk-make/odk-run.sh robot convert -vvv -i go-edit.obo -f obo -o go-edit.TMP.obo

# Explain unsatisfiable classes
.claude/skills/odk-make/odk-run.sh \
  robot explain --input go-edit.obo --reasoner ELK -M unsatisfiability \
  --unsatisfiable all explanations.md

Gotchas

• Use ELK, never a DL reasoner (HermiT) on the full ontology — GO is large and only has EL axioms; ELK is the default and is sufficient. HermiT will not scale.
• Run from the repo, not a stray subdir. odk-run.sh figures out the repo root from its own path, but the paths you pass to commands are interpreted inside /work/src/ontology. Keep the repo as your working tree.
• First run pulls the image. If the ODK image isn't cached locally, the first docker invocation downloads it (can take a while). This is expected.
• Don't commit build artifacts. Targets write many derived files (*.ofn, *.owl, reasoned.*, reports). Only commit the source files you actually edited (normally src/ontology/go-edit.obo), per CLAUDE.md.
• Don't edit run.sh to drop -ti — console editors rely on the interactive shell. Use odk-run.sh for non-interactive runs instead.