Merge pull request #94 from opencb/TASK-6780

TASK-6780 - Port Patch 5.2.1 -> 6.0.0 - Xetabase 2.2.1 -> 3.0.0

.github/workflows/develop.yml

@@ -10,12 +10,7 @@ jobs:
   build:
     uses: ./.github/workflows/build-java-app-workflow.yml
 
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
-
   deploy-maven:
     uses: ./.github/workflows/deploy-maven-repository-workflow.yml
-    needs: test
+    needs: build
     secrets: inherit

.github/workflows/scripts/get-xetabase-branch.sh

@@ -22,6 +22,7 @@ get_xetabase_branch() {
 
   # Check if the branch name starts with "release-" and follows the patterns "release-a.x.x" or "release-a.b.x"
   if [[ "$input_branch" =~ ^release-([0-9]+)\.x\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]]; then
+
     # Extract the MAJOR part of the branch name
     MAJOR=${BASH_REMATCH[1]}
     # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR

commons-lib/pom.xml

@@ -67,6 +67,13 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+            <version>2.8.0</version>
+            <scope>compile</scope>
         </dependency>
     </dependencies>
 </project>

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);