Merge pull request #339 from AdamaJava/java21

feat(all projects): upgrade to java 21
AdamaJava · Nov 20, 2023 · 5a5c3b7 · 5a5c3b7
2 parents 559cee9 + 367a891
commit 5a5c3b7
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Showing 78 changed files with 1,010 additions and 1,394 deletions.
diff --git a/build.gradle b/build.gradle
@@ -1,5 +1,5 @@
 plugins {
-    id "com.github.spotbugs" version "4.2.0"
+  id("com.github.spotbugs") version "5.2.1"
 }
 
 defaultTasks "build"
@@ -18,11 +18,16 @@ allprojects {
     apply plugin: 'eclipse'
     apply plugin: 'checkstyle'
     apply plugin: 'com.github.spotbugs'
-    sourceCompatibility = 1.8
+    sourceCompatibility = 21
 
     //default value is libs according to java plugin
     libsDirName = "lib" 
 }
+java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
+}
 
 subprojects {
     //config spotbugs
@@ -44,7 +49,7 @@ subprojects {
     //config checkstyle
     checkstyle {
 	configFile = file('../config/google_check.xml')
-	toolVersion = '8.15'
+	toolVersion = '10.12.4'
 	checkstyleTest.enabled=false
     }
     checkstyleMain.onlyIf {project.hasProperty('checkstyle')}

diff --git a/config/google_check.xml b/config/google_check.xml
diff --git a/q3indel/build.gradle b/q3indel/build.gradle
@@ -6,24 +6,20 @@ def scriptname = 'q3indel'
 def isExecutable = true
 
 //control the ordering of jars, make sure junit before <tool>.jar
-configurations {
-    junit
-  }
 
 // q3indel has some scala classes that require the following task (along with the scalal plugin and api dependency)
 sourceSets {
         main { java.srcDirs=['src']; resources.srcDirs=['src']; scala.srcDirs=['scala/src'] }
         test { java.srcDirs=['test']; test.resources.srcDirs=['test'];scala.srcDirs=['scala/test'] }
     }
 dependencies {
-    configurations.compile.transitive = true
 
     api project(':qcommon')
     api project(':qio')
     api project(':qbamfilter')
     api project(':qpicard')
 
-    api 'org.scala-lang:scala-library:2.12.3'
+    api 'org.scala-lang:scala-library:2.12.18'
     api 'net.sf.jopt-simple:jopt-simple:4.6'
     api group: 'org.ini4j', name: 'ini4j', version: '0.5.2'
 }

diff --git a/q3panel/build.gradle b/q3panel/build.gradle
@@ -6,7 +6,6 @@ def isExecutable = true
 
 
 dependencies {
-    configurations.compile.transitive = true
 
     api project(':qcommon')
     api project(':qio')

diff --git a/q3tiledaligner/build.gradle b/q3tiledaligner/build.gradle
@@ -6,7 +6,6 @@ def isExecutable = true
 
 
 dependencies {
-    configurations.compile.transitive = true
     api project(':qcommon')
     api project(':qio')
 

diff --git a/q3vcftools/build.gradle b/q3vcftools/build.gradle
@@ -10,7 +10,6 @@ configurations {
 }
 
 dependencies {
-    configurations.compile.transitive = true
 
     api project(':qcommon')
     api project(':qio')

diff --git a/qannotate/build.gradle b/qannotate/build.gradle
@@ -25,8 +25,6 @@ dependencies {
     //this junit is required by snpEff-4.0
     junit ('junit:junit:4.10')
 
-    configurations.compile.transitive = true
-
     api project(':qcommon')
     api project(':qio')
     api project(':qbamfilter')

diff --git a/qbamannotate/build.gradle b/qbamannotate/build.gradle
@@ -5,14 +5,18 @@ def scriptname = 'qbamannotate'
 def isExecutable = true
 
 dependencies {
-    configurations.compile.transitive = true
 
     implementation project(':qcommon')
     implementation project(':qio')
     implementation project(':qpicard')
 
     implementation 'net.sf.jopt-simple:jopt-simple:4.6'
 
+    // https://mvnrepository.com/artifact/jakarta.xml.bind/jakarta.xml.bind-api
+    implementation 'jakarta.xml.bind:jakarta.xml.bind-api:3.0.1'
+    // https://mvnrepository.com/artifact/org.eclipse.persistence/org.eclipse.persistence.moxy
+    implementation 'org.eclipse.persistence:org.eclipse.persistence.moxy:3.0.3'
+
     testImplementation  project(':qtesting')
 }
 
diff --git a/qbamannotate/src/org/qcmg/qbamannotate/FragBarCodeReport.java b/qbamannotate/src/org/qcmg/qbamannotate/FragBarCodeReport.java
@@ -14,12 +14,12 @@
 import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlSchemaType;
+import jakarta.xml.bind.annotation.XmlType;
 
 
 /**
@@ -67,7 +67,7 @@ public class FragBarCodeReport {
      * 
      * <p>
      * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
+     * not a snapshot. Therefore, any modification you make to the
      * returned list will be present inside the JAXB object.
      * This is why there is not a <CODE>set</CODE> method for the pairing property.
      * 
@@ -86,7 +86,7 @@ public class FragBarCodeReport {
      */
     public List<FragBarCodeReport.Pairing> getPairing() {
         if (pairing == null) {
-            pairing = new ArrayList<FragBarCodeReport.Pairing>();
+            pairing = new ArrayList<>();
         }
         return this.pairing;
     }

diff --git a/qbamannotate/src/org/qcmg/qbamannotate/FragReport.java b/qbamannotate/src/org/qcmg/qbamannotate/FragReport.java
@@ -14,12 +14,12 @@
 import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlSchemaType;
+import jakarta.xml.bind.annotation.XmlType;
 
 
 /**
@@ -67,7 +67,7 @@ public class FragReport {
      * 
      * <p>
      * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
+     * not a snapshot. Therefore, any modification you make to the
      * returned list will be present inside the JAXB object.
      * This is why there is not a <CODE>set</CODE> method for the uniquePairing property.
      * 
@@ -86,7 +86,7 @@ public class FragReport {
      */
     public List<FragReport.UniquePairing> getUniquePairing() {
         if (uniquePairing == null) {
-            uniquePairing = new ArrayList<FragReport.UniquePairing>();
+            uniquePairing = new ArrayList<>();
         }
         return this.uniquePairing;
     }

diff --git a/qbamannotate/src/org/qcmg/qbamannotate/LongMatePair.java b/qbamannotate/src/org/qcmg/qbamannotate/LongMatePair.java
@@ -6,27 +6,18 @@
  */
 package org.qcmg.qbamannotate;
 
+import htsjdk.samtools.SAMRecord;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.Marshaller;
+import org.eclipse.persistence.jaxb.JAXBContextFactory;
+import org.qcmg.qio.ma.MaDirection;
+import org.qcmg.qio.ma.MaRecord;
+
 import java.io.StringWriter;
 import java.math.BigInteger;
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.Marshaller;
-
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamSource;
-
-import org.qcmg.qio.ma.MaDirection;
-import org.qcmg.qio.ma.MaRecord;
-
-import javax.xml.transform.stream.StreamResult;
-import java.io.*;
-
-import htsjdk.samtools.SAMRecord;
-
 public class LongMatePair extends AnnotatorType {
 	final int isizeLowerLimit;
 	final int isizeUpperLimit;
@@ -87,7 +78,8 @@ public String generateReport() throws Exception {
 			report.getUniquePairing().add(pairing);
 		}
 		StringWriter writer = new StringWriter();
-		JAXBContext context = JAXBContext.newInstance(LongMatePairReport.class);
+		JAXBContext context = JAXBContextFactory.createContext(new Class[] {LongMatePairReport.class}, null);
+//		JAXBContext context = JAXBContext.newInstance(LongMatePairReport.class);
 		Marshaller m = context.createMarshaller();
 	    m.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); //pretty print XML
 		m.marshal(report, writer);

diff --git a/qbamannotate/src/org/qcmg/qbamannotate/LongMatePairReport.java b/qbamannotate/src/org/qcmg/qbamannotate/LongMatePairReport.java
@@ -14,13 +14,13 @@
 import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.List;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlAttribute;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlSchemaType;
+import jakarta.xml.bind.annotation.XmlType;
 
 
 /**

diff --git a/qbamannotate/src/org/qcmg/qbamannotate/ObjectFactory.java b/qbamannotate/src/org/qcmg/qbamannotate/ObjectFactory.java