From 195503565003989345370d88dcd4eb83ff8a2733 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Mon, 3 Jun 2024 10:22:22 +0200
Subject: [PATCH] utils: add the method FileUtils.copyFile, #TASK-6297,
 #TASK-6255

On branch TASK-6255
Changes to be committed:
	modified:   commons-lib/pom.xml
	modified:   commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java
---
 commons-lib/pom.xml                           |  6 +++++
 .../org/opencb/commons/utils/FileUtils.java   | 22 +++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml
index dccbe7ec9..0e057979e 100644
--- a/commons-lib/pom.xml
+++ b/commons-lib/pom.xml
@@ -68,5 +68,11 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.8.0</version>
+            <scope>compile</scope>
+        </dependency>
     </dependencies>
 </project>
diff --git a/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java b/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java
index 93fba0f0d..1ae5ba87d 100644
--- a/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java
+++ b/commons-lib/src/main/java/org/opencb/commons/utils/FileUtils.java
@@ -18,6 +18,7 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.opencb.commons.exec.Command;
+import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.nio.charset.Charset;
@@ -188,6 +189,27 @@ public static String[] getUserAndGroup(Path path, boolean numericId) throws IOEx
         return new String[]{split[2], split[3]};
     }
 
+
+    public static void copyFile(File src, File dest) throws IOException {
+        try {
+            org.apache.commons.io.FileUtils.copyFile(src, dest);
+        } catch (IOException e) {
+            try {
+                if (src.length() == dest.length()) {
+                    LoggerFactory.getLogger(FileUtils.class).warn(e.getMessage());
+                    return;
+                }
+                throw e;
+            } catch (Exception e1) {
+                throw e;
+            }
+        }
+    }
+
+    //-------------------------------------------------------------------------
+    // P R I V A T E     M E T H O D S
+    //-------------------------------------------------------------------------
+
     private static String getLsOutput(Path path, boolean numericId) throws IOException {
         FileUtils.checkPath(path);