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Remove phyloreference status tracking (pso:holdsStatusInTime) from PhylorefWrapper - #198
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getCurrentStatus(), getStatusChanges(), setStatus() and getStatusCURIEsInEnglish() recorded a history of Publishing Status Ontology states under pso:holdsStatusInTime. We now track where a phyloreference stands outside the Phyx file (for example, on GitHub), so the methods and their tests go. Klados does not call them. The pso, tvc and timeinterval prefixes stay in every published JSON-LD context, including the development one, because older Phyx files (two in clade-ontology, and test/examples/incorrect/otl-resolution-errors.json) still carry pso:holdsStatusInTime entries, which must keep expanding to full IRIs. The remaining half of #135, a single owl:deprecated marker, is a separate change. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
getStatusChanges() was its only caller. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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Master (#198) removed PhylorefWrapper's status methods, which this branch had fixed (single pso:holdsStatusInTime entries, entries with no status). The conflicts are resolved in master's favour: the status methods, their tests and the getStatusesInTime()/getStatusCURIE() helpers this branch added are gone, and the #196 changelog entry no longer mentions them. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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PhylorefWrappercarried a small publishing workflow:getCurrentStatus(),getStatusChanges(),setStatus()and the staticgetStatusCURIEsInEnglish()recorded a history of Publishing Status Ontology states (draft, final draft, under review, tested, published, retracted) underpso:holdsStatusInTimeon each phyloreference. We have since decided that was more machinery than the problem needed: curators can track where a phyloreference stands in curator notes, or by filing Phyx files in a directory per status, and the one case with real semantics, deprecation, belongs in standard OWL asowl:deprecated. Klados has already dropped its status editor and does not call these methods. This PR removes the four methods, their tests, and themomentdependency they were the only user of. It is the first half of #135.Hilmar's review of #196 prompted this: that PR adds fixes to these same methods, which is why the leftover code came up. The two PRs conflict in
src/wrappers/PhylorefWrapper.js. If this one merges first, #196 should drop its status-method fixes, their tests, and the matching sentence in its changelog line, since there is nothing left to fix. If #196 merges first, this branch needs a rebase that deletes the fixed code as well.What this deliberately does not do
owl:deprecatedmarker in place ofpso:retracted-from-publication(klados#81), is a separate PR stacked on this one, so Remove status tracking code from PhylorefWrapper #135 stays open.pso,tvcandtimeintervalprefixes stay in every JSON-LD context undercontext/, includingdevelopment. Older Phyx files still carrypso:holdsStatusInTimeentries (two papers in clade-ontology, and our owntest/examples/incorrect/otl-resolution-errors.json), and those keep expanding to full IRIs rather than becoming undefined terms. The library still reads such files; it just no longer interprets that property.Verification
npm testpasses on 0d28b7d: all 210-odd tests, lint clean.🤖 Generated with Claude Code