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build.gradle
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/*
grep -F "call compile-htsjdk-cmd," Makefile | cut -d, -f 2 | while read F; do grep -w "\"${F}\"" build.gradle > /dev/null || echo $F; done | grep -v -F 'biostar$(1)' | head -n 1 | xargs -I{} grep ",{}," Makefile
gradle -Djvarkit.delete.jar=true -Djvarkit.disable.test=true all all2
gradle -Djvarkit.generate.doc=false all all2
*/
//import org.gradle.internal.logging.text.StyledTextOutput
//import org.gradle.internal.logging.text.StyledTextOutput.Style
import java.util.stream.Collectors ;
defaultTasks 'top'
ext {
libraries = new HashMap<>();
htsjdkVersion = "4.1.1"
jettyVersion = "9.4.26.v20200117"
}
class JarFile
{
private final String repo;
String server;
boolean test=false;
JarFile(final String repo) {
this.repo = repo.trim();
}
boolean isTest() {
return this.test;
}
JarFile setTest() {
this.test=true;
return this;
}
JarFile setServer(String s) {
this.server=s;
return this;
}
@Override
public int hashCode() { return this.repo.hashCode();}
@Override
public boolean equals(Object o) {
if(o==this) return true;
if(o==null || !(o instanceof JarFile)) return false;
return this.repo.equals(JarFile.class.cast(o).repo);
}
@Override
public String toString() {
return this.repo+" -> "+getUrl()+" "+ getRelativeFile();
}
private String[] split() {
return this.repo.split("[\\:]");
}
String getGroup() { return split()[0];}
String getArctifact() { return split()[1];}
String getVersion() { return split()[3];}
boolean isSameArctifact(JarFile other) {
if( !this.getGroup().equals(other.getGroup())) return false;
if( !this.getArctifact().equals(other.getArctifact())) return false;
return true;
}
boolean isReplacing(JarFile other) {
if( !isSameArctifact(other) ) return false;
def t1 = this.getVersion().split("[\\.]");
def t2 = other.getVersion().split("[\\.]");
for(int i=0;i< t1.length && i<t2.length;i++) {
try {
int i1 = Integer.parseInt(t1[i]);
int i2 = Integer.parseInt(t2[i]);
if(i1!=i2) return i1>i2;
}
catch(Exception err)
{
return false;
}
}
return false;
}
public String getServer() {
return this.server==null?"https://repo1.maven.org/maven2":this.server;
}
public String getUrl() {
return getServer() + "/" + getRelativeFile();
}
public String getRelativeDirectory() {
return getGroup().replace('.','/')+"/"+getArctifact()+"/"+getVersion();
}
public String getRelativeFile() {
return getRelativeDirectory()+"/"+getArctifact()+"-"+getVersion()+".jar";
}
public void download(project)
{
final File f= this.toFile(project);
if(!f.exists())
{
project.logger.lifecycle("Downloading "+this.getUrl()+" to "+ f);
project.ant.mkdir(dir:f.getParent());
project.ant.get(
src:getUrl(),
verbose: true,
dest: f
);
}
}
public File toFile(project)
{
def baseDir = project.projectDir.getPath()+"/lib";
final File f= new File(baseDir,getRelativeFile());
return f;
}
}
class Library
{
private final def files = new ArrayList<>();
Library() {
}
Library add(String s) {
return this.add(new JarFile(s));
}
Library add(JarFile f) {
for(int i=0;i< this.files.size();i++)
{
JarFile fold = this.files.get(i);
if(fold.isSameArctifact(f))
{
if(f.isReplacing(fold)) {
//System.err.println("##replace "+fold+" with "+f);
this.files.set(i,f);
}
return this;
}
}
this.files.add(f);
return this;
}
Library add(Library L) {
if(L!=this) {
for(int i=0;i< L.files.size();i++)
{
this.add(L.files.get(i));
}
}
if(this.isEmpty() && !L.isEmpty()) throw new GradleException("uh ?"+L);
return this;
}
Library withoutTest() {
final Library L=new Library().add(this);
L.files.removeIf{it->it.isTest()};
return L;
}
boolean isEmpty() { return files.isEmpty();}
public String toString() {
return files.toString();
}
}
libraries.put("htsjdk",new Library().
add("com.github.samtools:htsjdk:jar:" + ext.htsjdkVersion ).
add("commons-logging:commons-logging:jar:1.3.0").
add("org.apache.commons:commons-jexl:jar:2.1.1").
add("org.apache.commons:commons-compress:jar:1.25.0").
add("org.tukaani:xz:jar:1.9").
add("org.json:json:jar:20231013").
add("org.openjdk.nashorn:nashorn-core:jar:15.4").
add("org.xerial.snappy:snappy-java:jar:1.1.10.5")
);
libraries.put("jcommander",new Library().
add("com.beust:jcommander:jar:1.82")
);
libraries.put("testng",new Library().
add(libraries.get("jcommander")).
add(new JarFile("org.testng:testng:jar:6.14.3").setTest())
);
libraries.put("jaxb",new Library().
add("jakarta.xml.bind:jakarta.xml.bind-api:jar:4.0.2").
add("org.glassfish.jaxb:jaxb-core:jar:4.0.5").
add("com.sun.istack:istack-commons-runtime:jar:4.2.0").
//add("com.sun.xml.bind:jaxb-core:jar:2.2.11").
//add("org.glassfish.jaxb:txw2:jar:2.2.11").
add("org.glassfish.jaxb:jaxb-runtime:jar:4.0.5").
add("jakarta.activation:jakarta.activation-api:jar:2.1.3")
);
libraries.put("berkeleydb",new Library().
add(new JarFile("com.sleepycat:je:jar:7.3.7").setServer("http://download.oracle.com/maven"))
);
libraries.put("xjc",new Library().
add("jakarta.xml.bind:jakarta.xml.bind-api:jar:4.0.2").
// add("javax.xml.bind:jaxb-api:jar:2.2.11").
add("org.glassfish.jaxb:jaxb-xjc:jar:4.0.5").
add("org.glassfish.jaxb:jaxb-core:jar:4.0.5").
add("org.glassfish.jaxb:codemodel:jar:4.0.5").
add("org.glassfish.jaxb:xsom:jar:4.0.5").
add("com.sun.xml.bind.external:relaxng-datatype:jar:4.0.5").
add("com.sun.xml.bind.external:rngom:jar:4.0.5").
// add("com.sun.istack:istack-commons-tools:jar:3.0.7").
add("com.sun.istack:istack-commons-runtime:jar:4.2.0").
add("com.sun.xml.dtd-parser:dtd-parser:jar:1.5.1").
add("org.glassfish.jaxb:jaxb-runtime:jar:4.0.5").
add("jakarta.activation:jakarta.activation-api:jar:2.1.3")
);
libraries.put("math",new Library().
add("org.apache.commons:commons-math3:jar:3.6.1")
);
libraries.put("mysql",new Library().
add("mysql:mysql-connector-java:jar:5.1.47")
);
libraries.put("gson",new Library().
add("com.google.code.gson:gson:jar:2.6.2")
);
libraries.put("httpclient",new Library().
add("commons-logging:commons-logging:jar:1.2").
add("org.apache.httpcomponents:httpcore:jar:4.4.11").
add("org.apache.httpcomponents:httpclient:jar:4.5.9").
add("commons-codec:commons-codec:jar:1.11")
);
libraries.put("jetty",new Library().
add("javax.servlet:javax.servlet-api:jar:4.0.1").
add("org.eclipse.jetty:jetty-webapp:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-http:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-server:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-io:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-security:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-servlet:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-util:jar:" + ext.jettyVersion).
add("org.eclipse.jetty:jetty-xml:jar:" + ext.jettyVersion)
);
libraries.put("derby",new Library().
add("org.apache.derby:derby:jar:10.12.1.1").
add("org.apache.derby:derbyclient:jar:10.12.1.1")
);
libraries.put("jena",new Library().
add("commons-io:commons-io:jar:2.12.0").
add("commons-cli:commons-cli:jar:1.4").
add("commons-codec:commons-codec:jar:1.11").
add("org.apache.jena:jena-iri:jar:3.10.0").
add("org.apache.jena:jena-base:jar:3.10.0").
add("org.apache.jena:jena-core:jar:3.10.0").
add("org.slf4j:slf4j-api:jar:1.7.25").
add("org.apache.jena:jena-shaded-guava:jar:3.7.0")
);
libraries.put("arq",new Library().
add(libraries.get("jena")).
add("org.apache.jena:jena-arq:jar:3.10.0").
add("com.github.jsonld-java:jsonld-java:jar:0.12.1").
add("org.apache.commons:commons-lang3:jar:3.4").
add("org.apache.httpcomponents:httpclient:jar:4.5.5").
add("org.apache.httpcomponents:httpclient-cache:jar:4.5.5").
add("org.apache.jena:jena-shaded-guava:jar:3.10.0").
add("org.apache.thrift:libthrift:jar:0.10.0")
);
libraries.put("leveldb",new Library().
add("org.iq80.leveldb:leveldb:jar:0.12").
add("com.google.guava:guava:jar:21.0")
);
libraries.put("biojava",new Library().
add("org.biojava:biojava-alignment:jar:6.0.5").
add("org.biojava:biojava-core:jar:6.0.5").
add("org.biojava.thirdparty:forester:jar:1.039").
add("org.slf4j:slf4j-api:jar:1.7.30")
);
libraries.put("springcontext",new Library().
add("org.springframework:spring-context:jar:6.0.9").
add("org.springframework:spring-aop:jar:6.0.9").
add("org.springframework:spring-core:jar:6.0.9").
add("org.springframework:spring-expression:jar:6.0.9").
add("org.springframework:spring-beans:jar:6.0.9") //ORDER MATTERS because zip contains same files META-INF/spring.schemas
);
libraries.put("freemarker",new Library().
add("org.freemarker:freemarker:jar:2.3.32")
);
libraries.put("velocity",new Library().
add("org.slf4j:slf4j-api:jar:1.7.30").
add("org.apache.commons:commons-lang3:jar:3.16.0").
add("org.apache.velocity:velocity-engine-core:jar:2.3")
);
// https://stackoverflow.com/questions/28498688
public class CompileJVarkit extends DefaultTask {
@Input @Optional
String mainClass = ''
@Input @Optional
String srcDir =''
@Input @Optional
String testDir =''
@Input @Optional
String tmpDir = ""
@Input @Optional
String distDir = ""
@Input @Optional
String docDir = ""
@Input @Optional
String testNgDir=""
@Input @Optional
String jdkTarget = "17"
@Input @Optional
String jdkSource = "17"
@Input @Optional
Library jarLibs = new Library();
@Input
boolean requireJfx = false;
@Input @Optional
String deprecatedMsg = null;
@Input @Optional
def xsdFiles =[];
@Input @Optional
String endMsg = null;
@Input
boolean with_jni = false;
@Input @Optional
def otherJavaFiles = [];
@Input
boolean with_jaxb=false;
CompileJVarkit() {
def baseDir = this.getProject().projectDir.getPath();
this.srcDir = baseDir + "/src/main/java"
this.testDir = baseDir + "/src/test/java"
this.tmpDir = baseDir + "/tmp"
this.distDir = baseDir + "/dist"
this.docDir = baseDir + "/docs"
this.testNgDir = baseDir+"/tests-output"
String jvm = java.lang.System.getProperty("jvarkit.target",null);
if(jvm!=null && !jvm.isEmpty()) {
jdkTarget = jvm;
jdkSource = jvm;
}
}
void runXJC() /* see also https://dzone.com/articles/running-jaxb-xjc-compiler-with-openjdk-11 */
{
if(this.xsdFiles.size()==0) return;
/** download required lib for xjc */
def xjcjars = project.ext.libraries.get("xjc").files;
xjcjars.each{it->it.download(project)};
def params=[];
for(def src : this.xsdFiles)
{
project.logger.info("compiling xjc :" +src);
if(src.equals("gb"))
{
ant.java(
classname : "com.sun.tools.xjc.XJCFacade",
fork: true,
failonerror: true,
classpath : xjcjars.collect{it->it.toFile(project).path}.join(":")
) {
jvmarg(value:"-DenableExternalEntityProcessing=true")
arg(value: "-d")
arg(value: this.tmpDir)
arg(value: "-p")
arg(value:"gov.nih.nlm.ncbi.gb")
arg(value:"-dtd")
arg(value:"https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd")
}
}
else if(src.equals("pubmed"))
{
ant.java(
classname : "com.sun.tools.xjc.XJCFacade",
fork: true,
failonerror: true,
classpath : xjcjars.collect{it->it.toFile(project).path}.join(":")
) {
jvmarg(value:"-DenableExternalEntityProcessing=true")
arg(value: "-d")
arg(value: this.tmpDir)
arg(value: "-p")
arg(value:"gov.nih.nlm.ncbi.pubmed")
arg(value:"-dtd")
arg(value:"https://www.ncbi.nlm.nih.gov/corehtml/query/DTD/pubmed_100101.dtd")
}
}
else if(src.equals("dbsnp"))
{
ant.java(
classname : "com.sun.tools.xjc.XJCFacade",
fork: true,
failonerror: true,
classpath : xjcjars.collect{it->it.toFile(project).path}.join(":")
) {
jvmarg(value:"-DenableExternalEntityProcessing=true")
arg(value: "-d")
arg(value: this.tmpDir)
arg(value: "-p")
arg(value:"gov.nih.nlm.ncbi.dbsnp")
arg(value:"src/main/resources/xsd/ncbi/docsum_3.4.xsd")
}
}
else if(src.equals("genoex"))
{
ant.java(
classname : "com.sun.tools.xjc.XJCFacade",
fork: true,
failonerror: true,
classpath : xjcjars.collect{it->it.toFile(project).path}.join(":")
) {
jvmarg(value:"-DenableExternalEntityProcessing=true")
arg(value: "-d")
arg(value: this.tmpDir)
arg(value: "-p")
arg(value:"gov.nih.nlm.ncbi.dbsnp.gt")
arg(value:"src/main/resources/xsd/ncbi/genoex_1_5.xsd")
}
}
else
{
throw new GradleException("Unknown xsd target "+src);
}
}
}
@Input
boolean isJavaFxAvailable() {
try {
this.getClass().getClassLoader().loadClass("javafx.embed.swing.JFXPanel");
return null;
}
catch (ClassNotFoundException e) {
return false;
}
}
@Input
boolean isFatJar() {
return java.lang.System.getProperty("jvarkit.fat.jar","true").equals("true");
}
private boolean isGeneratingDoc() {
if(!java.lang.System.getProperty("jvarkit.generate.doc","true").equals("true")) return false;
return true;
}
@Input
String getMainPackage() {
String s= this.mainClass;
int dollar = s.indexOf('$');
if(dollar!=-1) s=s.substring(0,dollar);
int dot = s.lastIndexOf('.');
if(dot==-1) return "";
return s.substring(0,dot);
}
private File getMainJavaTestFile() {
String travis = java.lang.System.getenv("TRAVIS");
if(travis!=null && travis.equals("true")) return null;
if(java.lang.System.getProperty("jvarkit.disable.test","false").equals("true")) return null;
String s = this.testDir +"/"+ getTestNgClass().replace('.','/')+".java";
File f = new File(s);
if(!f.exists()) return null;
return f;
}
@Input
String getMainJavaSource() {
String s = this.mainClass;
int dollar = s.indexOf('$');
if(dollar!=-1) s=s.substring(0,dollar);
s = this.srcDir + "/" + s.replace('.','/')+".java";
return s;
}
@Input
String getTestNgClass() {
String s = this.mainClass;
int dollar = s.indexOf('$');
if(dollar!=-1) s=s.substring(0,dollar);
return s+"Test";
}
@Input
String getAntInclude() {
final String s= this.getMainJavaSource();
final int slash = s.lastIndexOf('/');
String s2 = "**"+s.substring(slash);
return s2;
}
@Input
String getAntTestInclude() {
String s= this.getMainJavaSource();
int slash = s.lastIndexOf('/');
s= s.substring(slash);
int dot = s.lastIndexOf('.');
s= s.substring(0,dot);
return "**"+s+"Test.java";
}
public String toString() {
return ""+this.getName()+" "+this.mainClass;
}
private String getExecutablePath(String exe) {
try {
def stdout = new ByteArrayOutputStream()
project.exec {
commandLine 'which', exe
standardOutput = stdout
}
return stdout.toString().trim();
}
catch(Exception err) { return "";}
}
@Input
public String getGitHash() {
try {
def stdout = new ByteArrayOutputStream()
project.exec {
commandLine 'git', 'rev-parse', '--short', 'HEAD'
standardOutput = stdout
}
return stdout.toString().trim()
}
catch(Exception err) { return "undefined";}
}
/**
def getConfiguration() {
//System.err.println("SEARCHING "+ this.configName);
//project.configurations.each{ System.err.println("conf : "+it.name); }
def c= project.configurations.find{it.name == this.configName}
//System.err.println("GOT::"+this.configName +" = "+c);
if(c==null) throw new GradleException("Cannot find config "+this.configName+" "+c);
return c;
}
*/
void installHtsJni() {
/** compile jni */
if(this.with_jni) {
try {
final File htsjniDir = new File("lib/htsjni");
if(!htsjniDir.exists()) {
project.logger.warn("downloading htsjni. Requires git");
project.exec {
workingDir "lib"
commandLine "git", "clone", "https://github.com/lindenb/htsjni", "htsjni"
standardOutput = System.err
}
}
project.logger.warn("updating htsjni. Requires git.");
project.exec {
workingDir htsjniDir.toString()
commandLine "git", "pull", "origin", "master"
standardOutput = System.err
}
project.logger.warn("compiling htsjni. Requires Linux/gcc/ and common C libraries like gz, threads, etc... ");
project.exec {
commandLine "make", "-C", "lib/htsjni"
standardOutput = System.err
}
}
catch(Exception err) {
throw new GradleException("java/jni Failed.",err);
}
}
/** end C Bindings */
}
@TaskAction
void doIt() {
if(this.deprecatedMsg!=null) {
project.logger.warn("[DEPRECATED] "+getName()+" : I won't create this project because it is deprecated : "+this.deprecatedMsg);
return;
}
if(this.requireJfx && !isJavaFxAvailable())
{
project.logger.warn("I won't compile "+getName()+" because the current jvm doesn't support javafx");
return;
}
// ignore for simple app if(this.jarLibs.isEmpty()) throw new GradleException("Empty ?? "+this.jarLibs);
/** BEGIN java annotation processor */
final File annotProcJar = new File(this.distDir+"/annotation_processor.jar")
if(true) {
ant.mkdir(dir:"${this.tmpDir}/META-INF/services")
ant.javac(
destdir: this.tmpDir,
srcdir: this.srcDir,
includeantruntime:false,
failonerror: true,
fork: true,
target: this.jdkTarget,
source: this.jdkSource,
debug: true,
) {
include(name: "**/JVarkitAnnotationProcessor.java")
compilerarg(value:'-Xlint')
}
ant.echo(message: "com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor\n",
file: "${this.tmpDir}/META-INF/services/javax.annotation.processing.Processor");
ant.jar(destfile: annotProcJar,
basedir:this.tmpDir
);
ant.delete( dir : this.tmpDir )
}
/** END java annotation processor */
/** prepare directories */
ant.mkdir(dir:"${this.tmpDir}/META-INF")
ant.mkdir(dir:"${this.distDir}")
/** download libraries */
for(final JarFile j: this.jarLibs.files)
{
j.download(this.project);
}
/** htsjni */
this.installHtsJni();
/** run xjc if needed */
this.runXJC();
/** copy main source */
// useless since java processor ant.mkdir(dir:"${this.tmpDir}/" + this.getMainPackage().replace('.','/') )
/** opendjk properties , required for external compilation */
final File distJar = new File(this.distDir+"/"+this.getName()+".jar")
ant.echo(message: "java="+getExecutablePath("java")+"\n"+
"javac="+getExecutablePath("javac")+"\n"+
"jar="+getExecutablePath("jar")+"\n"+
"self="+ distJar.getPath() +"\n"
,file: "${this.tmpDir}/META-INF/jdk.properties");
/** GATK4 stuff */
if(!System.getProperty('gatk4.local.jar',"").isEmpty() ) {
ant.echo(message: "gatk4="+ System.getProperty('gatk4.local.jar',""));
File gatk4jar = new File(System.getProperty('gatk4.local.jar',""));
System.err.println("COMPILATION WITH GATK4 enabled");
ant.javac(
destdir: this.tmpDir,
srcdir: this.srcDir+":"+this.tmpDir,
includeantruntime:false,
failonerror: true,
fork: true,
classpath: gatk4jar.path,
target: this.jdkTarget,
source: this.jdkSource,
debug: true
) {
include(name:"**/Gatk4ProxyImpl.java")
compilerarg(value:'-Xlint')
}
}
else
{
//System.err.println("COMPILATION WITH GATK4 disabled.");
}
/* compile sources */
//System.err.println("JAVA_PATH="+getConfiguration().asPath);
final Set<File> classpath1 = this.jarLibs.withoutTest().files.collect{it->it.toFile(project)} as Set;
if(this.with_jni) classpath1.add(new File("lib/htsjni/htslib.jar"));
/** not the 'big test' */
ant.javac(
destdir: this.tmpDir,
srcdir: this.srcDir+":"+this.tmpDir,
includeantruntime:false,
failonerror: true,
fork: true,
classpath : annotProcJar.path + ":" + classpath1.collect{it->it.path}.join(":"),
target: this.jdkTarget,
source: this.jdkSource,
debug: true
) {
include(name: this.getAntInclude())
if(this.with_jaxb) {
include(name: "**/package-info.java")
include(name: "**/ObjectFactory.java")
}
include(name: "**/Program.java") // add this otherwise skipped because exists in annotation processor
for(def osrc: this.otherJavaFiles) {
include(name: osrc)
}
compilerarg(value:'-Xlint')
}
ant.copy(
file: this.getMainJavaSource(),
todir:"${this.tmpDir}/" + this.getMainPackage().replace('.','/')
)
/* shall we download Sequence Ontology ? */
File soTreeClassFile = new File("${this.tmpDir}/com/github/lindenb/jvarkit/util/so/SequenceOntologyTree.class");
if(soTreeClassFile.exists())
{
ant.mkdir(dir:"${this.tmpDir}/META-INF/so")
final File soOwlFile = new File( this.getProject().projectDir.getPath()+"/src/main/resources/so/so-simple.owl");
if(!soOwlFile.exists())
{
project.logger.warn("download to "+soOwlFile);
ant.mkdir(dir:soOwlFile.parent)
ant.get(
src:"https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so-simple.owl",
verbose:true,
dest:soOwlFile
);
}
System.err.println("copy to "+soOwlFile);
ant.copy(
file: soOwlFile,
todir:"${this.tmpDir}/META-INF/so"
)
}
/* copy resources ? */
ant.mkdir(dir:"${this.tmpDir}/META-INF/spring")
ant.copy(
file: new File( this.getProject().projectDir.getPath()+"/src/main/resources/spring/default-vcfstats-analyzers.xml") ,
todir:"${this.tmpDir}/META-INF/spring"
)
/** chromosome mapping file */
final File chromMappingFile = new File( this.getProject().projectDir.getPath()+"/src/main/resources/chromnames/mapping.tsv");
if(chromMappingFile.exists()) {
ant.mkdir(dir:"${this.tmpDir}/META-INF/chromnames")
ant.copy(
file: chromMappingFile ,
todir:"${this.tmpDir}/META-INF/chromnames"
)
}
if(isFatJar()) {
for(final File jf:classpath1) {
ant.unzip(src:jf,dest:this.tmpDir,overwrite:true)
}
}
/* jar tmp dir */
final String now = new Date().format("yyyyMMddHHmmss");
ant.jar(destfile: distJar,
basedir:this.tmpDir
){
manifest {
attribute(name:"Main-Class", value: this.mainClass )
attribute(name:"Htsjdk-Version", value: project.ext.htsjdkVersion)
attribute(name:"Git-Hash", value: getGitHash())
attribute(name:"Release", value: "v2024.08.25")
attribute(name:"Compile-Date", value: now)
attribute(name:(isFatJar()?"Ignore-Class-Path":"Class-Path"), value: classpath1.collect{it.path}.join(" "));
}
}
//remove tmpDir
ant.delete( dir : this.tmpDir )
// done : https://stackoverflow.com/questions/14516693/
project.logger.lifecycle("jar file generated :" + distJar)
if( isGeneratingDoc()) {
if(this.name.equals("jvarkit")) {
ant.java(
jar : this.distDir+"/${this.name}.jar" , fork: true
) {
arg(value: "--readthedocs")
arg(value: ".")
}
}
else
{
/* generate doc */
ant.java(
jar : this.distDir+"/${this.name}.jar" , fork: true
) {
jvmarg(value: "-Djvarkit.doc.dir=${this.docDir}");
arg(value: "--help")
arg(value: "--helpFormat")
arg(value: "make-doc")
}
}
}
/** test */
final File testJava = getMainJavaTestFile();
if(!isFatJar() || testJava==null)
{
project.logger.warn("No Test will be executed for "+this.getName());
project.logger.debug(" (test-file:"+testJava+" fat:"+isFatJar()+")");
}
else
{
ant.mkdir(dir: this.tmpDir)
project.logger.warn("Test will be executed in "+this.testNgDir+"/"+getName()+"/index.html");
final Set<File> classpath2 = new HashSet<>();
classpath2.add(distJar);
for(JarFile f:this.jarLibs.files)
{
if(!f.isTest()) continue;
classpath2.add(f.toFile(project));
}
if(this.with_jni) classpath2.add(new File("lib/htsjni/htslib.jar"));
ant.javac(
destdir: this.tmpDir,
srcdir: this.testDir+":"+ this.srcDir,
includeantruntime:false,
failonerror: true,
fork: true,
classpath : classpath2.collect{it->it.path}.join(":"),
target: this.jdkTarget,
source: this.jdkSource,
debug: true
)
{
include(name:"**/MiniTestNG.java")
include(name: getAntTestInclude())
compilerarg(value:'-Xlint')
}
ant.mkdir(dir: this.testNgDir+"/"+getName());
try {
ant.java(
classname : "com.github.lindenb.jvarkit.tools.tests.MiniTestNG",
fork: true,
failonerror: false,
classpath : this.tmpDir+":"+classpath2.collect{it->it.path}.join(":")
) {
arg(value: "-d")
arg(value: this.testNgDir+"/"+getName())
arg(value: getTestNgClass());
}
} catch(Throwable err) {
project.logger.warn("test failed.");
}
ant.delete( dir : this.tmpDir )
}
/** delete the jar at the if specified , jars can be big and I just want to generate the doc*/
if( java.lang.System.getProperty("jvarkit.delete.jar","false").equals("true")) {
project.logger.warn("delete jar "+ distJar);
ant.delete(file: distJar)
}
/** message at the end */
if(this.endMsg!=null && !this.endMsg.trim().isEmpty()) {
project.logger.info("\n#\n#\n# "+ this.endMsg+"\n#\n#\n");
}
}
}
String biostar2java(int i) {
return "com.github.lindenb.jvarkit.tools.biostar.Biostar"+i;
}
Library combineLibs(String...array)
{
final Library L= new Library();
for(String n: array)
{
final Library l2= libraries.get(n);
if(l2==null) throw new GradleException("Cannot find library "+n);
L.add(l2);
}
return L;
}
def all=new ArrayList<>();
def all2=new ArrayList<>();
/** simple tasks, just jcommander+htsjdk */
all2.add( task("bamindexreadnames", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.bamindexnames.BamIndexReadNames"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("bamqueryreadnames", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.bamindexnames.BamQueryReadNames"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("buildwpontology", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.misc.BuildWikipediaOntology"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("bwamemdigest", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.mem.BWAMemDigest"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("bwamemnop", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.mem.BWAMemNOp"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all.add( task("casectrlcanvas", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.burden.CaseControlCanvas"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("casectrljfx", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.burden.CaseControlJfx"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("vcfburdengtf", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.burden.VcfBurdenGtf"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("coveragenormalizer", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.misc.CoverageNormalizer"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("downsamplevcf", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.misc.DownSampleVcf"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all.add( task("faidxsplitter", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.misc.FaidxSplitter"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastgenotypegvcfs", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.gvcf.FastGenotypeGVCFs"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastq2fasta", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.misc.FastqToFasta"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastqentropy", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.fastq.FastqEntropy"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all.add( task("fastqjs", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.fastq.FastqJavascript"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastqphred64to33", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.fastq.ConvertPhred64toFastq33"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastqsplitinterleaved", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.fastq.FastqSplitInterleaved"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});
all2.add( task("fastqsplit", type: CompileJVarkit) {
mainClass = "com.github.lindenb.jvarkit.tools.fastq.FastqSplit"
jarLibs = combineLibs("htsjdk","testng","jcommander")
});