From ff6abf8a5e1e34d0dd06a63cf3a856376c6efb84 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Wed, 8 Dec 2021 13:58:53 -0800
Subject: [PATCH 1/2] update versions for hotfix

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index be2aabfb..3f3b66ae 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1</version>
+	<version>1.1.1</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

From 9d79a3e24d47efcfd2717af1a8a507c624329939 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Wed, 8 Dec 2021 13:53:51 -0800
Subject: [PATCH 2/2] Fix null URI in OntologyTerm.getChildren

It's mentioned in jena that the URI can be null of the term is a bnode.

This is causing the following issue: https://github.com/PavlidisLab/Gemma/issues/247
---
 src/ubic/basecode/ontology/model/OntologyTermImpl.java | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/ubic/basecode/ontology/model/OntologyTermImpl.java b/src/ubic/basecode/ontology/model/OntologyTermImpl.java
index 129e4a02..0d5186a1 100644
--- a/src/ubic/basecode/ontology/model/OntologyTermImpl.java
+++ b/src/ubic/basecode/ontology/model/OntologyTermImpl.java
@@ -385,8 +385,9 @@ private void getChildren( boolean direct, Collection<OntologyTerm> work ) {
         ExtendedIterator<OntClass> iterator = ontResource.listSubClasses( true );
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
+            // URI can be null if the ont is a bnode (no idea what it is, but we have to handle this)
             // some reasoners will infer owl#Nothing as a subclass of everything
-            if ( c.getURI().equals( NOTHING ) ) continue;
+            if ( c.getURI() == null || c.getURI().equals( NOTHING ) ) continue;
 
             if ( USE_PROPER_PART_RESTRICTIONS && c.isRestriction() ) {