Upgrade ODK 1.5.4 → 1.6.1 (make update_repo currently fails on version skew)

[turbomam]

The repo's generated ODK scaffold (src/ontology/Makefile, src/scripts/*) is ODK v1.5.4, but the local/CI ODK image is v1.6.1. Because of that skew, sh run.sh make update_repo fails:

cp: cannot stat 'target/metpo/src/scripts/update_repo.sh': No such file or directory
make: *** [Makefile:603: update_repo] Error 1

The v1.5.4 update_repo.sh generates a v1.6.1 seed into target/ then copies files back, but the newer seed lays scripts out differently, so the copy-back aborts. It changes no tracked files (clean abort), but it means update_repo cannot be used until the repo is upgraded to 1.6.1 via the proper ODK upgrade procedure (re-seed), not a one-liner. The build's recurring Your ODK configuration has changed… run 'make update_repo' warning is a side effect of this and is otherwise cosmetic.

Why this matters / what to preserve on upgrade. Several IRI-scheme values are currently maintained as hand-edits to the generated Makefile because update_repo can't apply them:

• URIBASE=https://w3id.org, ONTBASE=https://w3id.org/metpo (Version IRI has duplicated metpo/ path segment #436, Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435) #462)
• base-artifact filter --base-iri $(URIBASE)/metpo (metpo-base.* release artifacts contain no METPO terms (base-IRI filter mismatch) #463, Populate empty -base release artifacts; clarify README IRI wording (#463) #464) — the ODK default is $(URIBASE)/METPO, which does not match METPO's lowercase w3id term IRIs and silently empties the -base products.

A working update_repo after upgrade will regenerate the Makefile and revert these unless the values are made configurable in metpo-odk.yaml (or re-applied). The upgrade task must verify the version/product IRIs stay single-metpo/ and that metpo-base.* still contains METPO terms.

Related: #436, #463, #464, #433.

[turbomam]

The w3id IRI-scheme correctness belongs to this upgrade (via odk.yaml regen, not Makefile edits)

This ODK upgrade is the right (and only sanctioned) place to fix METPO's IRI scheme. src/ontology/Makefile must not be hand-edited (update_repo regenerates it), so the values below have to come from metpo-odk.yaml and/or a metpo.Makefile override, then be regenerated.

Root cause: ODK's IRI machinery is OBO-PURL-centric and doesn't fit METPO's w3id per-namespace delegation. w3id only resolves under https://w3id.org/metpo/, so the main ontology IRI, version IRI, products, and the base-IRI filter must all sit under /metpo/. ODK's standard URIBASE + ONTBASE = $(URIBASE)/$(ONT) derivation cannot produce that from a single uribase value.

Concrete defects to fix and verify after the upgrade:

1. Main ontology IRI is a dead 404. Released metpo.owl declares https://w3id.org/metpo.owl, which is outside the /metpo/ delegation: curl returns 404. It must be https://w3id.org/metpo/metpo.owl (resolves 200, and matches the edit file, satisfying Edit-file ontology IRI inconsistent with released OWL #434). Introduced by Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435) #462's URIBASE change.
2. /METPO_ vestige in the report recipe (Makefile:245,248): --base-iri $(URIBASE)/METPO_ is ODK's OBO-underscore assumption and matches no METPO term (terms are .../metpo/<id>, not .../METPO_<id>). Should be the w3id term base https://w3id.org/metpo.
3. Base-artifact filter (Makefile:542) base-IRI must be https://w3id.org/metpo, or metpo-base.* ships with zero terms (metpo-base.* release artifacts contain no METPO terms (base-IRI filter mismatch) #463/Populate empty -base release artifacts; clarify README IRI wording (#463) #464).

Proven-correct values (verified by rebuild; achieve via config, not hand-edit): URIBASE=https://w3id.org/metpo, ONTBASE=https://w3id.org/metpo, base-IRI $(URIBASE). Note ONTBASE != $(URIBASE)/$(ONT), so confirm whether odk.yaml alone can express this or a metpo.Makefile override is required.

Acceptance: curl https://w3id.org/metpo/metpo.owl → 200; versionIRI https://w3id.org/metpo/releases/<date>/metpo.owl; products under /metpo/; no /METPO_; metpo-base.* carries all terms; edit-file IRI == released IRI.

Related: #434 (auto-satisfied by the fix), #462, #463, #464, #436.

[turbomam]

Upgrade complete on branch upgrade-odk-1.6.1 (commit deb7e00). Summary of what was done and what is now in metpo.Makefile instead of as hand-edits to the generated Makefile.

Completed

• ODK image pinned to v1.6.1 in qc.yml and run.sh.conf (local).
• Generated Makefile, run.sh, SPARQL queries regenerated for v1.6.1.
• All tests pass: make test and make prepare_release both clean.

Overrides in metpo.Makefile (survive future update_repo runs)

1. $(ONT).owl and $(ONT).json recipes: change $(URIBASE)/$@ → $(ONTBASE)/$@ so the main product IRI is https://w3id.org/metpo/metpo.owl, not https://w3id.org/metpo.owl. Root cause: uribase: https://w3id.org in metpo-odk.yaml is intentional (keeps ONTBASE single-segment per Version IRI has duplicated metpo/ path segment #436/Finalize w3id IRI scheme: collapse version-IRI doubling (#436), declare w3id canonical (#435) #462); the generated recipe's use of URIBASE for the main product is a design tension in ODK, not a bug to fix upstream.

2. $(ONT)-base.owl recipe: change --base-iri $(URIBASE)/METPO → --base-iri $(URIBASE)/metpo (lowercase). Re-applies the fix from metpo-base.* release artifacts contain no METPO terms (base-IRI filter mismatch) #463/Populate empty -base release artifacts; clarify README IRI wording (#463) #464 which the Makefile regeneration reverted.

Still open on this branch

• The w3id .htaccess only has a specific raw-GitHub rule for metpo.owl; metpo-full.owl and metpo-base.owl fall through to the BioPortal catch-all. A separate draft PR to perma-id/w3id.org will add explicit rules for those files.
• PR to merge this branch is next.

[turbomam]

Done. ODK upgraded 1.5.4 → 1.6.1 and merged via #487. make update_repo now works (the version-skew failure is gone); I have run it successfully several times since. The SPARQL-regeneration footgun it exposed is also fixed permanently: namespaces: [https://w3id.org/metpo/] in metpo-odk.yaml (commit 3b0e642) so update_repo regenerates the term-namespace filters correctly instead of falling back to the wrong https://w3id.org/METPO_ pattern.