From 0deb3cd301ccdf60eff46651f0f0f49f70e88230 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 13 Jan 2026 14:21:14 +0000
Subject: [PATCH 1/3] Initial plan


From ac160ec562d72c311655a98bd14aa5aba1014721 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 13 Jan 2026 14:29:52 +0000
Subject: [PATCH 2/3] Fix Citation published field type mismatch - add
 NumericBooleanType annotation

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 .../main/java/org/cipres/treebase/domain/study/Citation.java    | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java b/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
index c1cfb93ab..480c626c5 100644
--- a/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
+++ b/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
@@ -30,6 +30,7 @@
 import org.hibernate.annotations.Fetch;
 import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.IndexColumn;
+import org.hibernate.annotations.Type;
 import org.springframework.beans.BeanUtils;
 
 import org.cipres.treebase.Constants;
@@ -285,6 +286,7 @@ public void setAbstract(String pNewAbstract) {
 	 * @return boolean mPublished
 	 */
 	@Column(name = "Published")
+	@Type(type = "org.hibernate.type.NumericBooleanType")
 	public boolean isPublished() {
 		return mPublished;
 	}

From 9b59d02c7eb6031b3d24944ca2be7889660a0722 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 13 Jan 2026 15:03:35 +0000
Subject: [PATCH 3/3] Revert NumericBooleanType and align schema: change
 published columns from smallint to boolean

Co-authored-by: rvosa <106490+rvosa@users.noreply.github.com>
---
 .../java/org/cipres/treebase/domain/study/Citation.java     | 2 --
 .../src/main/resources/TBASE2_POSTGRES_CREATION.sql         | 6 +++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java b/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
index 480c626c5..c1cfb93ab 100644
--- a/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
+++ b/treebase-core/src/main/java/org/cipres/treebase/domain/study/Citation.java
@@ -30,7 +30,6 @@
 import org.hibernate.annotations.Fetch;
 import org.hibernate.annotations.FetchMode;
 import org.hibernate.annotations.IndexColumn;
-import org.hibernate.annotations.Type;
 import org.springframework.beans.BeanUtils;
 
 import org.cipres.treebase.Constants;
@@ -286,7 +285,6 @@ public void setAbstract(String pNewAbstract) {
 	 * @return boolean mPublished
 	 */
 	@Column(name = "Published")
-	@Type(type = "org.hibernate.type.NumericBooleanType")
 	public boolean isPublished() {
 		return mPublished;
 	}
diff --git a/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql b/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
index 01bf2b5a8..f48925f51 100644
--- a/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
+++ b/treebase-core/src/main/resources/TBASE2_POSTGRES_CREATION.sql
@@ -220,7 +220,7 @@ CREATE TABLE citation
   keywords character varying(255),
   pages character varying(255),
   publishyear integer,
-  published smallint,
+  published boolean,
   title character varying(500),
   issue character varying(255),
   journal character varying(255),
@@ -515,7 +515,7 @@ CREATE TABLE matrix
   gapsymbol character(1),
   missingsymbol character(1),
   nexusfilename character varying(255),
-  published smallint,
+  published boolean,
   symbols character varying(255),
   title character varying(255),
   "nchar" integer,
@@ -677,7 +677,7 @@ CREATE TABLE phylotree
   ntax integer,
   newickstring text,
   nexusfilename character varying(255),
-  published smallint,
+  published boolean,
   rootedtree smallint,
   title character varying(255),
   rootnode_id bigint,