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Find an interaction partner by its primary identifier, not another protein's alias - #14
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…alias InteractorsBuilder.getOrCreate looked a partner up in the container's IdentifiersMap, which also holds every interactor under its gene names and secondary identifiers. A partner whose identifier was another protein's alias was merged into that protein and never created, in an order that depended on hash iteration (#13). InteractorNodes now creates each interactor once per primary identifier, keyed as IdentifiersMap keys it (trimmed, upper-cased), and still records aliases in the map so analyses can be submitted with them. Tested; the alias test fails with the old lookup. Fixes #13 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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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>
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…s) (#929) * Spec 006 T103: research D25 and the tasks it splits into 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> * Spec 006 T103: compute the sizes from the graph; the 79 a recorded difference 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> --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
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Closed for now: the bug is tracked in #13 and will be fixed with a Reactome release. The branch is kept as a starting point. |
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Fixes #13.
Change
InteractorNodes(new, package-private): creates each interactor once per primary identifier per resource, keyed asIdentifiersMapkeys it (trimmed, upper-cased). It still records gene names and secondary identifiers ininteractorsMap(addAlias), so analyses submitted with them work as before.InteractorsBuilderuses it in place ofgetOrCreate, which looked partners up ininteractorsMap, aliases included. Itsncounter moves intoInteractorNodes.created().Effect
totalEntityAndInteractorscounts it. In release 98, 79 of 3,067 human pathways rise by one or two.Tests
InteractorNodesTesthas three tests: the alias case (Q6NSH3 / P0DMU9 from release 98), case and whitespace, and resources kept apart.mvn testpasses.Not done
The data file has not been rebuilt with this change. That needs a full build against a release graph, so the release-98 numbers above are counted from the graph, not from a rebuilt file.
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