feat(migrate): id migration with inline cross-reference resolution - #2
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Add the one-time migration from old self-referential ids to nanopub-based ids, the np-sign-"-r" pattern reimplemented for nanopub-py: - references.py: detect inter-term references, cycle-aware topological ordering (order_terms), and split_references classifying each reference as resolve- inline / defer (in-batch back-edge) / dangling (unknown target, kept + warned). - migrate.py: orchestrator that mints defining nanopubs in dependency order with acyclic references resolved to new thing URIs inline, then publishes superseding nanopubs for the deferred cyclic links (e.g. symmetric isIsomerOf). - cli/migrate.py: pubmate-migrate CLI (resumable via the id-map). - cli/_signing.py: shared signing-material resolution; mint-publish reuses it. Tests cover ordering (acyclic, 2-/3-cycles, self-ref, determinism), splitting (resolve/defer/dangling), the orchestrator (inline resolution, cycle-> supersede, idempotent re-run), and the CLI. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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What
Adds the one-time identifier migration: turn an existing vocabulary whose terms reference each other by their old ids into trusty-artifact-code defining nanopubs, rewriting the inter-term references to the new thing URIs.
This is nanopub-java's
np sign -r("resolve cross-nanopub references") pattern, reimplemented for nanopub-py: aResource→IRIrewrite over each assertion, plus the ordering that makes it sound.How
references.py— detect inter-term references; cycle-aware topological ordering (order_terms);split_referencesclassifies each reference as resolve-inline / defer (in-batch back-edge) / dangling (target neither minted nor in the batch — kept with its old id and reported).migrate.py(migrate_terms) — mint each term's defining nanopub in dependency order with acyclic references resolved to new thing URIs inline; then publish a superseding nanopub for each held-back cyclic link (e.g. symmetricisIsomerOf). Resumable via the id-map.cli/migrate.py—pubmate-migrate.cli/_signing.py— shared signing-material resolution;mint-publishrefactored onto it.A reference can be baked into a defining nanopub only if its target is already minted (fixed artifact code), which topological order guarantees for all acyclic edges; genuine cycles have no single-pass fixed point, so they go through superseding.
Tests & validation
isIsomerOfcycles, and every other inter-term link resolved to a newRA…URI. (It also flagged 7 danglingisMetaboliteOfreferences to 3 absent terms — a source-data issue, handled gracefully.)