From f81fed58a85dcf39e0557ad730d23619fc2015fa Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Sat, 26 Nov 2022 01:50:30 -0800
Subject: [PATCH 1/3] Update versions for hotfix

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

diff --git a/pom.xml b/pom.xml
index d0b120db..9b9b0792 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.4</version>
+	<version>1.1.5</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

From 440fce256a217610704207734d6ed7d4ca8b04bb Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Sat, 26 Nov 2022 01:50:01 -0800
Subject: [PATCH 2/3] Add support for comma-delimited entries in configuration

---
 src/ubic/basecode/util/ConfigUtils.java      | 16 +++++++++++++---
 test/data/test.properties                    |  1 +
 test/ubic/basecode/util/ConfigUtilsTest.java |  7 +++----
 3 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/ubic/basecode/util/ConfigUtils.java b/src/ubic/basecode/util/ConfigUtils.java
index 61c11842..c1b446a7 100644
--- a/src/ubic/basecode/util/ConfigUtils.java
+++ b/src/ubic/basecode/util/ConfigUtils.java
@@ -22,6 +22,8 @@
 import org.apache.commons.configuration2.PropertiesConfiguration;
 import org.apache.commons.configuration2.builder.FileBasedBuilderParametersImpl;
 import org.apache.commons.configuration2.builder.FileBasedConfigurationBuilder;
+import org.apache.commons.configuration2.convert.DefaultListDelimiterHandler;
+import org.apache.commons.configuration2.convert.ListDelimiterHandler;
 import org.apache.commons.configuration2.ex.ConfigurationException;
 import org.apache.commons.configuration2.io.FileHandler;
 import org.apache.commons.configuration2.io.FileLocator;
@@ -36,6 +38,8 @@
  */
 public class ConfigUtils {
 
+    private static final ListDelimiterHandler LIST_DELIMITER_HANDLER = new DefaultListDelimiterHandler( ',' );
+
     /**
      * @param file
      * @return
@@ -51,7 +55,7 @@ public static FileBasedConfigurationBuilder<PropertiesConfiguration> getConfigBu
         }
         FileBasedConfigurationBuilder<PropertiesConfiguration> builder = new FileBasedConfigurationBuilder<PropertiesConfiguration>(
                 PropertiesConfiguration.class );
-        builder.configure( new FileBasedBuilderParametersImpl().setFile( file ) );
+        builder.configure( new FileBasedBuilderParametersImpl().setFile( file ).setListDelimiterHandler( LIST_DELIMITER_HANDLER ) );
         return builder;
     }
 
@@ -96,7 +100,7 @@ public static PropertiesConfiguration loadClasspathConfig( String name ) throws
             throw new ConfigurationException( "Couldn't locate: " + name );
         }
 
-        PropertiesConfiguration pc = new PropertiesConfiguration();
+        PropertiesConfiguration pc = createConfiguration();
         FileHandler handler = new FileHandler( pc );
         handler.setURL( url );
         handler.load();
@@ -116,7 +120,7 @@ public static PropertiesConfiguration loadConfig( File file ) throws Configurati
                 throw new ConfigurationException( "Couldn't create the file: " + e.getMessage() );
             }
         }
-        PropertiesConfiguration pc = new PropertiesConfiguration();
+        PropertiesConfiguration pc = createConfiguration();
         FileHandler handler = new FileHandler( pc );
         handler.setFile( file );
         handler.load();
@@ -187,4 +191,10 @@ public static URL locate( String name ) {
         FileLocator fl = FileLocatorUtils.fileLocator().fileName( name ).create();
         return FileLocatorUtils.locate( fl );
     }
+
+    private static PropertiesConfiguration createConfiguration() {
+        PropertiesConfiguration pc = new PropertiesConfiguration();
+        pc.setListDelimiterHandler( LIST_DELIMITER_HANDLER );
+        return pc;
+    }
 }
diff --git a/test/data/test.properties b/test/data/test.properties
index 0bd430bc..04d98701 100644
--- a/test/data/test.properties
+++ b/test/data/test.properties
@@ -1,3 +1,4 @@
 foo=bar
 ack=yup
 tek=6
+list=1,2 ,3
diff --git a/test/ubic/basecode/util/ConfigUtilsTest.java b/test/ubic/basecode/util/ConfigUtilsTest.java
index ff26e8a7..6018267c 100644
--- a/test/ubic/basecode/util/ConfigUtilsTest.java
+++ b/test/ubic/basecode/util/ConfigUtilsTest.java
@@ -14,10 +14,6 @@
  */
 package ubic.basecode.util;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
 import java.io.File;
 
 import org.apache.commons.configuration2.PropertiesConfiguration;
@@ -27,6 +23,8 @@
 import org.junit.Before;
 import org.junit.Test;
 
+import static org.junit.Assert.*;
+
 /**
  * @author Paul
  *
@@ -58,6 +56,7 @@ public void testGetConfigBuilderFile() throws Exception {
                 testConfigPath ) );
         assertNotNull( config );
         assertEquals( "bar", config.getConfiguration().getProperty( "foo" ) );
+        assertArrayEquals( new String[] { "1", "2", "3" }, config.getConfiguration().getStringArray( "list" ) );
     }
 
     @Test

From e78d33aac836fdfcee5b0ba8f8b7f4c536000d44 Mon Sep 17 00:00:00 2001
From: Guillaume Poirier-Morency <guillaumepoiriermorency@gmail.com>
Date: Sat, 26 Nov 2022 01:58:43 -0800
Subject: [PATCH 3/3] Update dependencies

---
 pom.xml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index 9b9b0792..7a0adc25 100644
--- a/pom.xml
+++ b/pom.xml
@@ -142,7 +142,7 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>1.7.36</version>
+			<version>2.0.4</version>
 		</dependency>
 
 		<!-- Jena -->
@@ -224,7 +224,7 @@
 		<dependency>
 			<groupId>com.opencsv</groupId>
 			<artifactId>opencsv</artifactId>
-			<version>5.6</version>
+			<version>5.7.1</version>
 		</dependency>
 
 		<!-- Testing utilities -->
@@ -237,7 +237,7 @@
 		<dependency>
 			<groupId>org.mockito</groupId>
 			<artifactId>mockito-core</artifactId>
-			<version>4.6.1</version>
+			<version>4.8.0</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>