Bot identity, pubinfo tags, and migrate-pipeline fixes (v0.2.0) - #4
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A published nanopub is immutable, so baking in a reference to a term that does not exist (a dangling foreign key, e.g. left behind when a duplicate compound was deduplicated upstream) is worse than omitting it: the link can never resolve. Previously such references were kept with their old ids and logged as a warning. Now split_references drops dangling references from the minted graph, and _resolve_all does the same in the superseding pass so a superseding nanopub never reintroduces a broken link. The term still mints with its remaining triples. migrate.py logs each dropped reference at ERROR (with the offending target) plus a batch summary telling the curator to fix the source and re-run; the run still completes (non-fatal), so a known-bad source link does not block publishing the rest. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
serialize_nanopub now binds a curated set of vocabulary prefixes (schema, pehterms, biochementity, obo, skos, prov, dcterms) before serializing, so namespaces render as meaningful prefixes instead of rdflib's auto-numbered ns1:/ns2:. The header is ordered with this: and sub: first (the nanopub and its sub-graphs anchor every file), then the rest alphabetically, so the .trig reads top-down. Callers can extend or override via a new `prefixes` argument. Purely a rendering change: binding happens at write time, after signing, so trusty artifact codes and signatures are unaffected (verified is_valid). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
Add a generic, identity-agnostic way to bootstrap a publishing bot's cryptographic identity, mirroring the nanopub-community declaredBy pattern: - introduction.py: build_introduction() builds the self-signed key-declaration nanopub. The agent is a fresh URI minted inside the introduction itself, typed npx:Bot/npx:SoftwareAgent, frbr:owner-ed by a human ORCID, with its RSA public key declared. The agent self-URI only exists post-sign, so it (and npx:signedBy) use the ~~~ARTIFACTCODE~~~ placeholder, resolved at sign time like scheme A. Tagged nt:wasCreatedFromTemplate so Nanodash renders it nicely. - cli/bootstrap_identity.py: pubmate-bootstrap-identity. Generates (or reuses) an RSA keypair and writes the signed introduction to --output-dir. Signs offline by default: does NOT publish and never touches a secret store, so the private key (the bot's identity) can be generated locally and reviewed before anything goes out. Refuses to overwrite an existing key; chmod 600 on the private key. - utils.py: bind foaf/frbr/nt prefixes so introductions render readably. Tests cover validity, self-signing, agent typing/ownership, the key declaration, owner attribution, and the template tag (incl. opt-out). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
A term often carries an untagged label plus localized variants (e.g. "Lead" and "Lood"@NL-BE). The nanopub's own rdfs:label (pubinfo) was taken from the first rdfs:label rdflib happened to yield, so it sometimes picked a localized one. Add preferred_label() (untagged > English > any, ties broken by text for determinism) and use it for both the defining (term_input_from_assertion) and superseding (migrate._label) labels. The assertion keeps every label variant — only the nanopub's headline label changes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
Source assertions use anonymous blank nodes ([ a pehterms:ContextAlias; … ]), whose rdflib ids are long (e.g. ndf301ab1d67…b1) and regenerated each parse. nanopub-py skolemizes each blank node to a sub:_<id> URI, so those long, non-reproducible ids leaked into the published nanopub (sub:_ndf301ab1d67…b1). Add relabel_blank_nodes(): rename blank nodes to short, content-ordered labels (b1, b2, …) before each builder wraps the assertion, so they serialize as sub:_b1. Wired into the defining and superseding builders. Pure relabeling (the graph stays isomorphic; nanopub-py already skolemized these), and the labels are assigned by a content key rather than the source's random ids, so the same input always yields the same labels — and therefore reproducible artifact codes. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
Add pubmate-migrate --default-suggester <orcid>, attributing prov:wasAttributedTo on every term that carries none — the case when migrating an existing batch all contributed by one person. Threads through to both the defining nanopubs (via the minter's existing default_suggester_orcid) and the superseding ones. The suggester goes in provenance, distinct from the bot signer; per-term wasAttributedTo (when present) still wins. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
resolve_signing passed the CLI key-file path strings straight to nanopub.Profile, which only reads a key file when given a pathlib.Path — a str is taken as the raw key material, so signing crashed with "RSA key format is not supported". This hit every real-key signing path (pubmate-migrate and pubmate-mint-publish); only the testsuite-key path was exercised before. Pass Path objects so the files are read. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01NnygThDJDwSVZg3kYujJKz
…omTemplate Add generic support for two Nanodash pubinfo hints on the defining and supersession builders: npx:hasNanopubType (repeatable, the kind of thing the nanopub asserts) and nt:wasCreatedFromTemplate (the assertion template it follows, so Nanodash renders it with the matching form). Shared via a new add_pubinfo_tags() helper; threaded through pubmate-migrate as --nanopub-type/--template. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
New features since v0.1.1: bootstrap-identity / introduction CLIs, pubinfo hasNanopubType + wasCreatedFromTemplate tags, readable prefixes, and the dangling-reference / blank-node / label fixes in the migrate pipeline. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
GertjanBisschop
approved these changes
Jun 25, 2026
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Brings the fork's
mainup to v0.2.0. Clean fast-forward overeu-parc/main(9 commits ahead, 0 behind), tests included and passing (96 passed).Features
feat(introduction): a self-signed agent-introduction (key-declaration) nanopub builder +pubmate-bootstrap-identityCLI. Generates a bot keypair offline and declares the publishing agent, binding it to its signing key (mirrors the communitydeclaredBypattern).feat(pubinfo): defining and supersession builders can tag every nanopub withnpx:hasNanopubType(repeatable) andnt:wasCreatedFromTemplate, threaded throughpubmate-migrateas--nanopub-type/--template(so Nanodash renders minted nanopubs with the matching assertion-template form).feat(migrate):--default-suggesterattributes any term lacking its own suggester viaprov:wasAttributedTo.feat(utils): bind well-known prefixes and lead withthis:/sub:.Fixes
fix(migrate): drop dangling references and report them as errors (a clean migration expects zero).fix(bnode): short, deterministic blank-node labels (sub:_b1) instead of long random hashes.fix(label): prefer the untagged literal for a nanopub'srdfs:label(e.g. "Lead" over "Lood"@NL-BE).fix(signing): read key material from--private-key/--public-keyas file paths.Follow-up
After merge + a
v0.2.0release tag, thebiochementity-vocabularypubmatepin bumps fromv0.1.0tov0.2.0(itsmake migratetarget now uses--nanopub-type/--template).🤖 Generated with Claude Code