LinkML SQL DDL regression blocks upgrade past 1.9.x

[cmungall]

ChemROF currently cannot move cleanly to linkml==1.10.0 or linkml==1.11.0rc3 because SQL DDL generation fails in LinkML.

Upstream LinkML issue: linkml/linkml#3501

Symptom

Running ChemROF generation with newer LinkML fails during gen-project / gen-sqlddl:

sqlalchemy.exc.NoReferencedColumnError: Could not initialize target column for ForeignKey 'AtomOccurrence.id' on table 'AtomicBond': table 'AtomOccurrence' has no column named 'id'

The relevant ChemROF shape is:

• ChemicalRelationship is an abstract parent with no authored identifier.
• AtomOccurrence extends it and declares name as its identifier.
• AtomicBond.subject and AtomicBond.object range over AtomOccurrence.

The expected SQL FKs are:

FOREIGN KEY(subject) REFERENCES "AtomOccurrence" (name)
FOREIGN KEY(object) REFERENCES "AtomOccurrence" (name)

Version boundary

A reduced LinkML reproducer shows this is not newly introduced by the 1.11.0rc3 release candidate:

linkml==1.8.7 + linkml-runtime==1.8.3: passes
linkml==1.9.6 + linkml-runtime==1.9.5: passes
linkml==1.10.0: fails
linkml==1.11.0rc3: fails

So this appears to be a LinkML 1.10.0 regression that ChemROF encounters when upgrading beyond the 1.9.x-era behavior.

Local verification

With linkml==1.11.0rc3, make test fails at project generation with the AtomOccurrence.id FK error.

With a local LinkML patch for linkml/linkml#3501, ChemROF make test completes successfully in a throwaway worktree, and generated SQL uses AtomOccurrence.name for AtomicBond.subject and AtomicBond.object.

Suggested action

Track linkml/linkml#3501 and retest ChemROF once a LinkML release or patch release includes the SQL DDL fix.