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Spec 006 T103: how the events hierarchy is ported (research D25, tasks) - #929
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Java's /data/eventsHierarchy sizes come from analysis-core's in-memory hierarchy, loaded from the AnalysisService's data file. From the graph, totalEntity matches every pathway of five species, but totalEntityAndInteractors misses 79 of 3,067 human pathways by one or two: analysis-core merges an interaction partner into another's alias in hash-map order. So the sizes, and the pathwaysOnly tree, are snapshotted from the data file at each release with analysis-core itself (T103a), and node answers from the snapshot (T103b-e). The token overlay comes through the analysis gateway; Java's own order below a hit node is random. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
adamjohnwright
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November 11, 2026 22:35
adamjohnwright
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…fference A gap of one or two entities on 79 human pathways is not visible in the Reacfoam, and a release-time Java step reading the data file would be a library build the project is not set up to keep current. The cause is reported to analysis-core (reactome/analysis-core#13, fix in reactome/analysis-core#14). T103 is now four tasks, with no release step. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
adamjohnwright
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November 11, 2026 23:16
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Plans T103,
GET /data/eventsHierarchy/{species}, the tree the Pathway Browser's Reacfoam draws. Docs only:specs/006-content-service-to-node/research.md(D25) andtasks.md.Finding: Java's sizes come from analysis-core's in-memory hierarchy, loaded from the AnalysisService's data file. Computed from the graph:
totalEntitymatches every pathway of five species (3,067 human).totalEntityAndInteractorsmatches four species exactly, but 79 of 3,067 human pathways come out one or two higher.The cause is a bug in analysis-core: a partner whose identifier is another protein's alias is merged into it, in hash-map order. It is reported as reactome/analysis-core#13, with a fix in reactome/analysis-core#14.
Decision: node computes the sizes from the graph, once per release, and the 79 are a recorded difference. The comparison with Java expects exactly them and fails on any other. The gap is too small to see in the Reacfoam, and a release-time Java step would be a library build the project is not set up to keep current. Once the fix is released, Java's numbers become node's.
Tasks: T103 splits into four PRs:
pathwaysOnlywithout a token.🤖 Generated with Claude Code