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Spec 015: BioPAX's exporter work ticked; the website's BioPAX planned (4) - #753
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BioPAX3Exporter's own spec 001 has done T045-T048 and T051, and the species half of T049 and T050; each is ticked with its pull requests, and T031 is withdrawn for its ci/compare.py, as T030 was for SBML. T049 and T050 keep the website's part: the library's per-event files against the legacy service's. T052 becomes T069-T072, on SBML's terms: the operation in the library service, node's endpoint, the route, and the check on beta. Research R10 is amended: BioPAX joins the service here, with node as its client. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…easured T069's pom sets kotlin.version to the library's (Boot 2.7 would bring Kotlin's standard library down to 1.6.21), and its jar check covers the BioPAX library, kotlin-stdlib and paxtools-core. Its memory is measured at the worst case the shares allow, two BioPAX and two SBML conversions at once, and the largest's cold time against node's 290 s. T072 checks R6's headers rather than the legacy service's; T049 compares with T004's answers at the graph's release and sends what is left to BioPAX3Exporter. T020 merged as BioPAX3Exporter#79, not #78. T035 is withdrawn, the citations of T047 and T048 corrected, and the dependencies, strategy, spec, plan and checks no longer say SBML alone or T052 alone. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ne release The legacy service reads the relational database at release 97 while beta's graph is at 98, so T049 runs the library on a private graph copy at the legacy database's release, and T072 checks beta's bodies by containment in the graph's release's species file instead. The plan's order of work, the data model's ontology comment, spec.md's citation and T035's releases follow. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…own species file T032 now agrees with T049: the copy is at the legacy database's release, which beta no longer keeps, so release 97's image is pulled with the disk checked first, or the relational database moves to 98 and T004 is retaken. T072 checks containment in the library's own species file at beta's release, not the published zip. T049 and T050 run T069's image against the copy; R8 and the plan's comparison tools follow. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Spec 015 (specs/015-graph-exports). This replaces #752 (and #751, #750), carrying their commits. What they change is described in #751 and #752.
From #752's review:
biopax.zip, which differs by the recorded differences.🤖 Generated with Claude Code