build(all projects): gradle updates, now works with vscode

build.gradle

@@ -1,8 +1,14 @@
-plugins {
-  id("com.github.spotbugs") version "5.2.1"
+buildscript {
+  repositories {
+    maven {
+      url = uri("https://plugins.gradle.org/m2/")
+    }
+  }
+  dependencies {
+    classpath("com.github.spotbugs.snom:spotbugs-gradle-plugin:6.0.4")
+  }
 }
-
-defaultTasks "build"
+apply plugin: 'base'
 
 ext {
     revision = "git rev-parse --short HEAD".execute().text.trim()
@@ -13,27 +19,18 @@ ext {
     // its better groovy/gradle too
     file('version.txt').withReader { verionId = it.readLine() + "-" + revision }
 }
-allprojects {
-    apply plugin: 'java-library'
-    apply plugin: 'eclipse'
+
+subprojects {
+    apply plugin: 'java'
     apply plugin: 'checkstyle'
-    apply plugin: 'com.github.spotbugs'
-    sourceCompatibility = 21
+    apply plugin: 'eclipse'
+    apply plugin: "com.github.spotbugs"
 
-    //default value is libs according to java plugin
-    libsDirName = "lib" 
-}
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(21)
-    }
-}
+    sourceCompatibility = 21
 
-subprojects {
-    //config spotbugs
     spotbugs {
-	ignoreFailures = true
-	spotbugsTest.enabled = false
+        ignoreFailures = true
+        spotbugsTest.enabled = false
     }
     //output to html, the default is xml
     spotbugsMain {
@@ -46,45 +43,25 @@ subprojects {
         }
     }
 
-    //config checkstyle
+    repositories {
+        mavenCentral()
+        flatDir(dirs:"$projectDir/../lib")
+    }
+
     checkstyle {
-	configFile = file('../config/google_check.xml')
-	toolVersion = '10.12.4'
-	checkstyleTest.enabled=false
+        configFile = file('../config/google_check.xml')
+        toolVersion = '10.12.4'
+        checkstyleTest.enabled=false
     }
     checkstyleMain.onlyIf {project.hasProperty('checkstyle')}
 
-    repositories { 
-	flatDir(dirs:"$projectDir/../lib")
-	mavenCentral()
-    }
-    dependencies {
-	testImplementation 'junit:junit:4.12' 
+     dependencies {
+        testImplementation 'junit:junit:4.13.2'
     }
 
     sourceSets {
-	main { java.srcDirs=['src']; resources.srcDirs=['src'] }
-	test { java.srcDirs=['test']; test.resources.srcDirs=['test'] }
-    }
-
-    jar.doFirst {
-	manifest { 
-	    if(project.hasProperty('mainClassName') && project.getProperty('mainClassName') != null ) {
-		attributes 'Main-Class' : project.mainClassName 
-	    }
-	    attributes  'Implementation-Title': project.name,
-		'Implementation-Version': verionId,
-		'SVN-Version': revision,
-		'Built-By': System.properties['user.name'],
-		'Date': new java.util.Date().toString(),
-		'Class-Path' : project.configurations.runtimeClasspath.collect { it.name }.join(' ')
-	}
-    }
-
-    build.doLast {
-	println "${project}: copy ${configurations.runtimeClasspath.collect { File file -> file.name }} to ${adamalib} and build/flat"
-	copy { from configurations.runtimeClasspath,libsDirectory; into file('build/flat') }
-	copy { from configurations.runtimeClasspath,libsDirectory; into adamalib }
+        main { java.srcDirs=['src']; resources.srcDirs=['src'] }
+        test { java.srcDirs=['test']; test.resources.srcDirs=['test'] }
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.4.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip

q3indel/build.gradle

@@ -7,21 +7,21 @@ def isExecutable = true
 
 //control the ordering of jars, make sure junit before <tool>.jar
 
-// q3indel has some scala classes that require the following task (along with the scalal plugin and api dependency)
+// q3indel has some scala classes that require the following task (along with the scalal plugin and implementation 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 {
 
-    api project(':qcommon')
-    api project(':qio')
-    api project(':qbamfilter')
-    api project(':qpicard')
+    implementation project(':qcommon')
+    implementation project(':qio')
+    implementation project(':qbamfilter')
+    implementation project(':qpicard')
 
-    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'
+    implementation 'org.scala-lang:scala-library:2.12.18'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation group: 'org.ini4j', name: 'ini4j', version: '0.5.2'
 }
 
 

q3indel/src/au/edu/qimr/indel/Main.java

@@ -2,7 +2,7 @@
 
 import au.edu.qimr.indel.pileup.IndelMT;
 import org.qcmg.common.log.QLogger;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 
 public class Main {
 

q3panel/build.gradle

@@ -7,13 +7,13 @@ def isExecutable = true
 
 dependencies {
 
-    api project(':qcommon')
-    api project(':qio')
+    implementation project(':qcommon')
+    implementation project(':qio')
 
-    api 'org.apache.commons:commons-lang3:3.4'
-    api 'net.sf.trove4j:core:3.1.0'
-    api 'net.sf.jopt-simple:jopt-simple:4.6'
-    api 'com.github.samtools:htsjdk:4.0.2'
+    implementation 'org.apache.commons:commons-lang3:3.4'
+    implementation 'net.sf.trove4j:core:3.1.0'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'com.github.samtools:htsjdk:4.0.2'
 
-    api group: 'com.io7m.xom',name: 'xom', version: '1.2.10'
+    implementation group: 'com.io7m.xom',name: 'xom', version: '1.2.10'
 }

q3panel/src/au/edu/qimr/panel/Q3ClinVar.java

@@ -65,7 +65,7 @@
 import org.qcmg.common.model.ChrRangePosition;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.Pair;
 import org.qcmg.common.util.TabTokenizer;
 

q3panel/src/au/edu/qimr/panel/Q3Panel.java

@@ -78,7 +78,7 @@
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
 import org.qcmg.common.util.IndelUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.Pair;
 import org.qcmg.common.util.SnpUtils;
 import org.qcmg.common.util.TabTokenizer;

q3tiledaligner/build.gradle

@@ -6,11 +6,11 @@ def isExecutable = true
 
 
 dependencies {
-    api project(':qcommon')
-    api project(':qio')
+    implementation project(':qcommon')
+    implementation project(':qio')
 
-    api 'com.github.samtools:htsjdk:4.0.2'
-    api 'net.sf.trove4j:core:3.1.0'
-    api 'org.apache.commons:commons-lang3:3.4'
-    api 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'com.github.samtools:htsjdk:4.0.2'
+    implementation 'net.sf.trove4j:core:3.1.0'
+    implementation 'org.apache.commons:commons-lang3:3.4'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
 }

q3vcftools/build.gradle

@@ -11,13 +11,13 @@ configurations {
 
 dependencies {
 
-    api project(':qcommon')
-    api project(':qio')
+    implementation project(':qcommon')
+    implementation project(':qio')
 
-    api 'com.github.samtools:htsjdk:4.0.2'
-    api 'net.sf.jopt-simple:jopt-simple:4.6'
-    api 'net.sf.trove4j:core:3.1.0'
-    api group: 'com.jcraft', name: 'jsch', version: '0.1.54'
-    api group: 'org.apache.commons', name: 'commons-lang3', version: '3.4'
+    implementation 'com.github.samtools:htsjdk:4.0.2'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'net.sf.trove4j:core:3.1.0'
+    implementation group: 'com.jcraft', name: 'jsch', version: '0.1.54'
+    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.4'
 }
 

q3vcftools/src/au/edu/qimr/vcftools/AmalAnalyser.java

@@ -20,7 +20,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.TabTokenizer;
 
 

q3vcftools/src/au/edu/qimr/vcftools/Amalgamator.java

@@ -22,7 +22,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.TabTokenizer;
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.VcfUtils;

q3vcftools/src/au/edu/qimr/vcftools/AmalgamatorGS.java

@@ -29,7 +29,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.TabTokenizer;
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.VcfUtils;

q3vcftools/src/au/edu/qimr/vcftools/Classify.java

@@ -24,7 +24,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.VcfUtils;
 import org.qcmg.common.vcf.header.VcfHeaderUtils;

q3vcftools/src/au/edu/qimr/vcftools/GoldStandardGenerator.java

@@ -20,7 +20,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.VcfUtils;
 import org.qcmg.common.vcf.header.VcfHeaderUtils;

q3vcftools/src/au/edu/qimr/vcftools/MergeSameSamples.java

@@ -16,7 +16,7 @@
 import org.qcmg.common.model.ChrPosition;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.vcf.ContentType;
 import org.qcmg.common.vcf.VcfFileMeta;
 import org.qcmg.common.vcf.VcfRecord;

q3vcftools/src/au/edu/qimr/vcftools/Overlap.java

@@ -34,7 +34,7 @@
 import org.qcmg.common.meta.QExec;
 import org.qcmg.common.util.Constants;
 import org.qcmg.common.util.FileUtils;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.common.util.TabTokenizer;
 import org.qcmg.common.vcf.VcfRecord;
 import org.qcmg.common.vcf.VcfUtils;

qannotate/build.gradle

@@ -3,8 +3,6 @@ mainClassName = 'au.edu.qimr.qannotate.Main'
 def scriptname = 'qannotate'
 def isExecutable = true
 
-configurations { junit }
-
 /*
 * qannotate requires snpEff and the version currently used is 4.0e
 * This version of the snpEff jar file embedds a version of junit that is old,
@@ -25,14 +23,14 @@ dependencies {
     //this junit is required by snpEff-4.0
     junit ('junit:junit:4.10')
 
-    api project(':qcommon')
-    api project(':qio')
-    api project(':qbamfilter')
+    implementation project(':qcommon')
+    implementation project(':qio')
+    implementation project(':qbamfilter')
+    implementation project(':qpicard')
 
-    api 'com.github.samtools:htsjdk:4.0.2'
-    api 'net.sf.jopt-simple:jopt-simple:4.6'
-    api name: 'snpEff', version: '4.0e'
-    api 'com.fasterxml.jackson.core:jackson-databind:2.6.7'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation name: 'snpEff', version: '4.0e'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.6.7'
 }
 //have to specify test classpath for both snpEff and qannotate 
 sourceSets.test.runtimeClasspath = configurations.junit + sourceSets.test.runtimeClasspath

qannotate/test/au/edu/qimr/qannotate/modes/Vcf2mafIndelTest.java

@@ -31,7 +31,7 @@
 
 import au.edu.qimr.qannotate.utils.MafElement;
 import au.edu.qimr.qannotate.utils.SnpEffMafRecord;
-import junit.framework.Assert;
+import org.junit.Assert;
 
 
 public class Vcf2mafIndelTest {

qbamannotate/build.gradle

@@ -17,6 +17,9 @@ dependencies {
     // https://mvnrepository.com/artifact/org.eclipse.persistence/org.eclipse.persistence.moxy
     implementation 'org.eclipse.persistence:org.eclipse.persistence.moxy:3.0.3'
 
+
+    testImplementation project(':qpicard')
     testImplementation  project(':qtesting')
+    // testImplementation 'junit:junit:4.13.2'
 }
 

qbamfilter/build.gradle

@@ -6,10 +6,10 @@ def isExecutable = true
 
 dependencies {
 
-    api project(':qcommon')
-    api project(':qpicard')
+    implementation project(':qcommon')
+    implementation project(':qpicard')
 
-    api 'net.sf.jopt-simple:jopt-simple:4.6'
-    api 'org.antlr:antlr:3.2'
+    implementation 'net.sf.jopt-simple:jopt-simple:4.6'
+    implementation 'org.antlr:antlr:3.2'
 }
 

qbamfix/build.gradle

@@ -6,8 +6,8 @@ def isExecutable = true
 
 dependencies {
 
-    api project(':qcommon')
-    api project(':qpicard')
-    api 'commons-cli:commons-cli:1.2'
+    implementation project(':qcommon')
+    implementation project(':qpicard')
+    implementation 'commons-cli:commons-cli:1.2'
 }
 

qbamfix/src/org/qcmg/qbamfix/Main.java

@@ -12,7 +12,7 @@
 
 import org.qcmg.common.log.QLogger;
 import org.qcmg.common.log.QLoggerFactory;
-import org.qcmg.common.util.LoadReferencedClasses;
+
 import org.qcmg.picard.HeaderUtils;
 import org.qcmg.picard.SAMFileReaderFactory;
 

qbamfix/test/org/qcmg/qbamfix/NewOptionsTest.java

@@ -7,7 +7,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import junit.framework.Assert;
+import org.junit.Assert;
 
 import org.junit.AfterClass;
 import org.junit.BeforeClass;