From bb11bf8f19f7bd590e5daf8880a7e0234937a193 Mon Sep 17 00:00:00 2001
From: Bindu Gajria <37914059+bgajria@users.noreply.github.com>
Date: Tue, 18 Aug 2026 21:44:58 -0400
Subject: [PATCH] Restore JBrowse link in References table for ChIP-seq
 datasets

ChIPSeq.getDefaultLinkCategory now returns CHIP Seq, wiring it to the
datasetLinks.xml category link template of the same name. This
requires the companion EbrcModelCommon fix (getDefaultLinkCategory
hook plus load-time macro substitution in DatasetPresenterSetLoader)
to actually take effect and produce a working, fully-substituted URL.

Root cause: this mechanism worked in 2020 (ref 42010) via a
type/subtype selector on the link template plus dedicated tuning-table
substitution logic. A 2025 migration converted the whole
datasetLinks.xml selector scheme to category-based matching, but
nothing ever set the corresponding categoryOverride on any of the 58
ChIPSeq-injected presenters across all 8 sites, so the category
template has sat unused since. Fixes the missing View/Download this
Data Set in the Genome Browser link, e.g. on
ncraOR74A_Ncrassa_Klocko_2023_chipSeq_RSRC (DS_5ff37d322c).
---
 .../org/apidb/apicommon/model/datasetInjector/ChIPSeq.java   | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/ChIPSeq.java b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/ChIPSeq.java
index a94387df6c..244f920779 100644
--- a/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/ChIPSeq.java
+++ b/Model/src/main/java/org/apidb/apicommon/model/datasetInjector/ChIPSeq.java
@@ -28,6 +28,11 @@ public void injectTemplates() {
   @Override
   public void addModelReferences() { }
 
+  @Override
+  public String getDefaultLinkCategory() {
+    return "CHIP Seq";
+  }
+
 
     @Override
 	public String[][] getPropertiesDeclaration() {