From 0b9bac096c67ba3ffe5a76409e20e76a9e350ae2 Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Sat, 24 Oct 2026 11:58:25 +0000 Subject: [PATCH] Spec 015: the reference harness fixes five defects, not four (R9) Co-Authored-By: Claude Opus 5.5 --- specs/015-graph-exports/reference-harness.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/specs/015-graph-exports/reference-harness.md b/specs/015-graph-exports/reference-harness.md index 150808af..977f44f9 100644 --- a/specs/015-graph-exports/reference-harness.md +++ b/specs/015-graph-exports/reference-harness.md @@ -1,6 +1,6 @@ # The SBML reference harness (T003) -How spec 015's SBML references are made: sbml-exporter's graph-only converter, with four defects fixed, run against a private copy of the release's graph. The harness and its output stay outside the repository; the output holds people's names (SBML creators). Host-specific paths below are placeholders. +How spec 015's SBML references are made: sbml-exporter's graph-only converter, with its five defects fixed, run against a private copy of the release's graph. The harness and its output stay outside the repository; the output holds people's names (SBML creators). Host-specific paths below are placeholders. ## What runs @@ -12,7 +12,9 @@ How spec 015's SBML references are made: sbml-exporter's graph-only converter, w - **Harness.java** initialises graph-core with `(bolt-uri, user, password, database, GraphNeo4jConfig.class)` and turns on `Helper.setUseIdentifierURL(true)`, as it is inside ContentService. For each id it runs `findById`, then `new SbmlConverter(event, version, ads).convert()`, and writes `toString()` as UTF-8 to `{stId}.sbml`. - **The runtime** is JDK 11, with `-Duser.timezone=UTC -Duser.language=en -Duser.country=US -Dfile.encoding=UTF-8`. The classes are compiled with JDK 17's `javac --release 11`. -## The four fixes (research R1) +## The five fixes (research R1, R9) + +The first three are in `DataFactory` (catalysts, negative regulators and positive regulators all taken from the right column), the fourth is the reused `Participant`, and the fifth is `ReactionBaseResult.build` never reading `catalysts`. In `org/reactome/server/tools/sbml/data/DataFactory.java`: