Skip to content

Spec 015: the reference harness fixes five defects, not four #654

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
adamjohnwright merged 1 commit into from
Oct 24, 2026
Merged

Spec 015: the reference harness fixes five defects, not four #654

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions specs/015-graph-exports/reference-harness.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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`:

Expand Down
Loading