Update commons-lang3 to 3.17.0

Author: arteymix

pom.xml

@@ -92,13 +92,12 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-configuration2</artifactId>
-			<version>2.11.0</version>
+			<version>2.12.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<!-- 3.15.0 uses a secure random which is extremely slow, see #1194 in Gemma for details -->
-			<version>3.14.0</version>
+			<version>3.17.0</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
@@ -119,7 +118,7 @@
 		<dependency>
 			<groupId>commons-logging</groupId>
 			<artifactId>commons-logging</artifactId>
-			<version>1.3.2</version>
+			<version>1.3.5</version>
 			<scope>runtime</scope>
 		</dependency>
 		<dependency>

src/ubic/basecode/ontology/jena/AbstractOntologyService.java

@@ -130,7 +130,7 @@ public synchronized void startInitializationThread( boolean forceLoad, boolean f
             } catch ( Exception e ) {
                 log.error( "Initialization of {} failed.", this, e );
             }
-        }, getOntologyName() + "_load_thread_" + RandomStringUtils.randomAlphanumeric( 5 ) );
+        }, getOntologyName() + "_load_thread_" + RandomStringUtils.insecure().nextAlphanumeric( 5 ) );
         // To prevent VM from waiting on this thread to shut down (if shutting down).
         initializationThread.setDaemon( true );
         initializationThread.start();

src/ubic/basecode/util/r/AbstractRClient.java

@@ -55,7 +55,7 @@ public abstract class AbstractRClient implements RClient {
      * @return
      */
     public static String variableIdentityNumber( Object ob ) {
-        return Integer.toString( Math.abs( ob.hashCode() + 1 ) ) + RandomStringUtils.randomAlphabetic( 6 );
+        return Integer.toString( Math.abs( ob.hashCode() + 1 ) ) + RandomStringUtils.insecure().nextAlphabetic( 6 );
     }
 
     /**
@@ -455,7 +455,7 @@ public int[] intArrayEval( String command ) {
     @SuppressWarnings({ "unchecked" })
     public LinearModelSummary linearModel( double[] data, Map<String, List<?>> factors ) {
 
-        String datName = RandomStringUtils.randomAlphabetic( 10 );
+        String datName = RandomStringUtils.insecure().nextAlphabetic( 10 );
         assign( datName, data );
 
         for ( String factorName : factors.keySet() ) {
@@ -475,7 +475,7 @@ public LinearModelSummary linearModel( double[] data, Map<String, List<?>> facto
 
         String modelDeclaration = datName + " ~ " + StringUtils.join( factors.keySet(), "+" );
 
-        String lmName = RandomStringUtils.randomAlphabetic( 10 );
+        String lmName = RandomStringUtils.insecure().nextAlphabetic( 10 );
         String command = lmName + "<-lm(" + modelDeclaration + ", na.action=na.exclude)";
         log.debug( command );
         voidEval( command );
@@ -498,14 +498,14 @@ public LinearModelSummary linearModel( double[] data, Map<String, List<?>> facto
     @Override
     public LinearModelSummary linearModel( double[] data, ObjectMatrix<String, String, Object> d ) {
 
-        String datName = RandomStringUtils.randomAlphabetic( 10 );
+        String datName = RandomStringUtils.insecure().nextAlphabetic( 10 );
         assign( datName, data );
 
         String df = dataFrame( d );
 
         String varNames = StringUtils.join( d.getColNames(), "+" );
 
-        String lmName = RandomStringUtils.randomAlphabetic( 10 );
+        String lmName = RandomStringUtils.insecure().nextAlphabetic( 10 );
         String command = lmName + "<-lm(" + datName + " ~ " + varNames + ", data=" + df + ", na.action=na.exclude)";
         voidEval( command );
 
@@ -732,7 +732,7 @@ public void remove( String variableName ) {
     public Map<String, LinearModelSummary> rowApplyLinearModel( String dataMatrixVarName, String modelFormula,
             String[] factorNames ) {
 
-        String lmres = "lmlist." + RandomStringUtils.randomAlphanumeric( 10 );
+        String lmres = "lmlist." + RandomStringUtils.insecure().nextAlphanumeric( 10 );
 
         log.info( "Starting model fitting ..." );
 

test/ubic/basecode/util/FileToolsTest.java

@@ -86,7 +86,7 @@ public void setUp() throws Exception {
         tempoutput = File.createTempFile( "junkme", ".txt" );
 
         tempdir = FileTools.createDir( System.getProperty( "java.io.tmpdir" ) + File.separatorChar + "junk.tmpdir."
-                + RandomStringUtils.randomAlphabetic( 10 ) );
+                + RandomStringUtils.insecure().nextAlphabetic( 10 ) );
 
     }
 
@@ -140,7 +140,7 @@ public void testCheckPathIsReadableFile() {
     @Test
     public void testCheckPathIsReadableFileNot() {
         try {
-            FileTools.checkPathIsReadableFile( plain.getPath() + RandomStringUtils.randomNumeric( 10 ) );
+            FileTools.checkPathIsReadableFile( plain.getPath() + RandomStringUtils.insecure().nextNumeric( 10 ) );
             fail( "Should have thrown an IOException" );
         } catch ( IOException e ) {
             // ok