Add operational observations addendum from MAC FDT v2 cleanup pass#2
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Five operational observations surfaced during the MAC FDT v2 catalogue cleanup work (Erik Schultes, May-June 2026), offered as input to the nanopub-skill maintenance work and companion to the earlier PR knowledgepixels#1 addition on the publisher-facing vs admin-derived retraction distinction. Sections: 1. npx:retracts subject convention. Manually constructed retraction nanopubs using this: npx:retracts <target> are registry-rejected; the nanopub-java retract subcommand emits the publisher-ORCID-as- subject form, which is accepted. 2. Content negotiation for registry GET. Without Accept: application/trig, registries return an HTML viewer wrapper; HTTP status alone is not a liveness indicator (registries return 200 with an HTML 404 page for non-existent nanopubs). 3. SELECT DISTINCT on /repo/full. The endpoint indexes the same triple across multiple graph views; raw COUNT(*) over-reports. Verification queries must use DISTINCT to get the actual count. 4. Publish-to-GET propagation lag. Immediate HTTP GET on a freshly published Trusty URI can return 404 from the read-side resolver; a 5s wait + optional 10s retry resolved all cases across a 38-instance batch. 5. Future-dated dct:created rejection. All three registries reject nanopubs whose dct:created is in the future relative to the registry's wall clock, with the misleading error "Nanopublication not supported" (same wording used by other policy-side rejections, e.g., Section 1's npx:retracts subject-form gate). Diagnosed live by Tobias Kuhn during the KP Office Hours 2026-06-03 incubator meeting; reproduced empirically with three timestamped attempts. Includes a suggested fix (date -u injection at sign time, not template-write time) and a suggested registry-side improvement (disambiguate the 400 error message for this case). Each section carries an Origin: PROMPT footer for traceability back to the specific phase of the cleanup pass where the observation was captured. Operationally validated against nanopub-java 1.88.0, registry.petapico.org, registry.knowledgepixels.com, w3id.org/np/<Trusty>, JDK 21, and the registry timestamp policy observed during KP Office Hours 2026-06-03. Source file authored in mac-fdt-staging at commit 3ca806b on branch paper-v06-consolidation (https://github.com/easchultes/mac-fdt-staging/tree/paper-v06-consolidation). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Five operational observations surfaced during the MAC FDT v2 catalogue cleanup work (Erik Schultes, May-June 2026), offered as input to the nanopub-skill maintenance work and companion to the earlier PR #1 addition on the publisher-facing vs admin-derived retraction distinction.
Sections:
npx:retracts subject convention. Manually constructed retraction nanopubs using this: npx:retracts are registry-rejected; the nanopub-java retract subcommand emits the publisher-ORCID-as- subject form, which is accepted.
Content negotiation for registry GET. Without Accept: application/trig, registries return an HTML viewer wrapper; HTTP status alone is not a liveness indicator (registries return 200 with an HTML 404 page for non-existent nanopubs).
SELECT DISTINCT on /repo/full. The endpoint indexes the same triple across multiple graph views; raw COUNT(*) over-reports. Verification queries must use DISTINCT to get the actual count.
Publish-to-GET propagation lag. Immediate HTTP GET on a freshly published Trusty URI can return 404 from the read-side resolver; a 5s wait + optional 10s retry resolved all cases across a 38-instance batch.
Future-dated dct:created rejection. All three registries reject nanopubs whose dct:created is in the future relative to the registry's wall clock, with the misleading error "Nanopublication not supported" (same wording used by other policy-side rejections, e.g., Section 1's npx:retracts subject-form gate). Diagnosed live by Tobias Kuhn during the KP Office Hours 2026-06-03 incubator meeting; reproduced empirically with three timestamped attempts. Includes a suggested fix (date -u injection at sign time, not template-write time) and a suggested registry-side improvement (disambiguate the 400 error message for this case).
Each section carries an Origin: PROMPT footer for traceability back to the specific phase of the cleanup pass where the observation was captured.
Operationally validated against nanopub-java 1.88.0, registry.petapico.org, registry.knowledgepixels.com, w3id.org/np/, JDK 21, and the registry timestamp policy observed during KP Office Hours 2026-06-03.
Source file authored in mac-fdt-staging at commit 3ca806b on branch paper-v06-consolidation
(https://github.com/easchultes/mac-fdt-staging/tree/paper-v06-consolidation).