From b68ae080705c554a5b54a7439776b5152df2250d Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Thu, 29 Oct 2026 17:27:12 +0000 Subject: [PATCH] Spec 001, from #94's review: the authors' claim limited to the files' authors The published files name only the people who author cited literature, so the first-name form is said to be these 62's alone among those authors, not among every Person in the relational database. The one Person whose display name the importer does not rebuild is the interaction import's user, which the importer makes itself (TrackingObjects.createGraphImporterUserNode). Co-Authored-By: Claude Opus 5.5 --- specs/001-biopax-from-graph/differences.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specs/001-biopax-from-graph/differences.md b/specs/001-biopax-from-graph/differences.md index 9802014..3cdab92 100644 --- a/specs/001-biopax-from-graph/differences.md +++ b/specs/001-biopax-from-graph/differences.md @@ -197,7 +197,7 @@ Measured 29 Oct 2026 on all 15 species, from a private copy of release 98's grap - **Why they differ:** the two writers take a Person's name from different rules. - The release's converter wrote the relational `_displayName`. The curator tool's rule for it (`InstanceDisplayNameGenerator.generatePersonName`) puts the first name first, and the initials only when there is none. - The graph importer does not copy a Person's `_displayName`, as it does every other class's: `ReactomeBatchImporter` rebuilds it as `surname, initial`, the first name only when there is no initial, "to fix different styles in Person display name". It has done so since its first commit (2016), so whichever commit built release 98's graph. - - So every Person in the graph has the initials form (all but one, a script's, whose display name is its own), whatever the relational database holds; it says nothing of the data. The published files do: there, every other author has the initials form too, so in release 98's relational database these 62 alone held the curator tool's first-name form. + - So every Person in the graph that came from the relational database has the initials form, whatever that database holds; it says nothing of the data. (One more Person, the interaction import's user, is made by the importer itself with its display name set as it is, `TrackingObjects.createGraphImporterUserNode`, and is not rebuilt.) The published files say something of the data, but only of the authors they name: of those, every other one has the initials form too, so among the authors in release 98's files these 62 alone held the curator tool's first-name form. People the files do not name (curators, or authors of literature no event cites) were not compared. - **Which form is meant:** the importer normalises on purpose, and the exporter writes the graph's display name, as it should; neither is a fault here. Whether a Person's display name is meant to be the importer's `surname, initial` or the curator tool's `surname, firstname` is a question for those two tools' owners (T022). Until it is settled, the files written from the graph give these authors their initials. ## Paxtools 6, Kotlin 2.4, JUnit 6 (#66)