build.gradle

import org.gradle.internal.os.OperatingSystem

import javax.tools.ToolProvider

buildscript {
    repositories {
        mavenCentral()
    }
}

plugins {
    id "java"
    id 'maven'
    id 'signing'
    id 'jacoco'
    id 'application'
    id 'com.palantir.git-version' version '0.5.1'
    id 'com.github.johnrengelman.shadow' version '1.2.3'
    id "com.github.kt3k.coveralls" version '2.6.3'
    id 'org.ajoberstar.grgit' version '1.4.2'
    id 'org.ajoberstar.github-pages' version '1.4.2'
}

mainClassName = "picard.cmdline.PicardCommandLine"

repositories {
    mavenLocal()
    mavenCentral()
    maven {
        url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" //for htsjdk snapshots
    }
}

jacocoTestReport {
    dependsOn test
    group = "Reporting"
    description = "Generate Jacoco coverage reports after running tests."
    additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)

    reports {
        xml.enabled = true // coveralls plugin depends on xml format report
        html.enabled = true
    }
}

jacoco {
    toolVersion = "0.7.5.201505241946"
}

final htsjdkVersion = System.getProperty('htsjdk.version', '2.8.0')

dependencies {
    compile 'com.google.guava:guava:15.0'
    compile 'com.github.samtools:htsjdk:' + htsjdkVersion
    //tools dependency for doclet requires sdk devel
    compile(files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs()))
    testCompile 'org.testng:testng:6.9.10'
}

sourceCompatibility = 1.8
targetCompatibility = 1.8

final isRelease = Boolean.getBoolean("release")
final gitVersion = gitVersion().replaceAll(".dirty", "")
version = isRelease ? gitVersion : gitVersion + "-SNAPSHOT"

logger.info("build for version:" + version)
group = 'com.github.broadinstitute'

defaultTasks 'all'

task all(dependsOn: ['jar', 'distZip', 'documentAll', 'shadowJar', 'currentJar'])

jar {
    manifest {
        attributes 'Main-Class': 'picard.cmdline.PicardCommandLine',
                'Implementation-Title': 'Picard',
                'Implementation-Vendor': 'Broad Institute',
                'Implementation-Version': version
    }
}
// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting
if (JavaVersion.current().isJava8Compatible()) {
    tasks.withType(Javadoc) {
        options.addStringOption('Xdoclint:none', '-quiet')
    }
}

task currentJar(type: Copy){
    from shadowJar
    into new File(buildDir, "libs")
    rename { string -> "picard.jar"}
}

shadowJar {
    finalizedBy currentJar
}

tasks.withType(Test) {
    outputs.upToDateWhen { false } // tests will always rerun
    description = "Runs the unit tests"

    useTestNG {
        if (OperatingSystem.current().isUnix()) {
            excludeGroups "slow", "broken"
        } else {
            excludeGroups "slow", "broken", "unix"
        }
    }

    // set heap size for the test JVM(s)
    minHeapSize = "1G"
    maxHeapSize = "2G"
    if (System.env.CI == "true") {  //if running under a CI output less into the logs
        int count = 0

        beforeTest { descriptor ->
            count++
            if( count % 100 == 0) {
                logger.lifecycle("Finished "+ Integer.toString(count++) + " tests")
            }
        }
    } else {
        // show standard out and standard error of the test JVM(s) on the console
        testLogging.showStandardStreams = true
        beforeTest { descriptor ->
            logger.lifecycle("Running Test: " + descriptor)
        }

        // listen to standard out and standard error of the test JVM(s)
        onOutput { descriptor, event ->
            logger.lifecycle("Test: " + descriptor + " produced standard out/err: " + event.message )
        }
    }

    testLogging {
        testLogging {
            events "skipped", "failed"
            exceptionFormat = "full"
        }
        afterSuite { desc, result ->
            if (!desc.parent) { // will match the outermost suite
                println "Results: ${result.resultType} (${result.testCount} tests, ${result.successfulTestCount} successes, ${result.failedTestCount} failures, ${result.skippedTestCount} skipped)"
            }
        }
    }
}

ext.htmlDir = new File("build/docs/html")
ext.htmlDirInc = new File(htmlDir, "_includes")
ext.commandClasses = ["picard.sam.AddCommentsToBam", "picard.sam.AddOrReplaceReadGroups", "picard.util.BaitDesigner", "picard.fastq.BamToBfq",
                          "picard.sam.BamIndexStats", "picard.util.BedToIntervalList", "picard.sam.BuildBamIndex", "picard.analysis.directed.CalculateHsMetrics",
                          "picard.sam.CalculateReadGroupChecksum", "picard.sam.CleanSam", "picard.analysis.CollectAlignmentSummaryMetrics",
                          "picard.analysis.CollectBaseDistributionByCycle", "picard.analysis.CollectGcBiasMetrics", "picard.illumina.quality.CollectHiSeqXPfFailMetrics",
                          "picard.analysis.directed.CollectHsMetrics", "picard.illumina.CollectIlluminaBasecallingMetrics", "picard.illumina.CollectIlluminaLaneMetrics",
                          "picard.analysis.CollectInsertSizeMetrics", "picard.analysis.CollectJumpingLibraryMetrics", "picard.analysis.CollectMultipleMetrics",
                          "picard.analysis.CollectOxoGMetrics", "picard.analysis.CollectQualityYieldMetrics", "picard.analysis.CollectRawWgsMetrics",
                          "picard.analysis.directed.CollectTargetedPcrMetrics", "picard.analysis.CollectRnaSeqMetrics", "picard.analysis.CollectRrbsMetrics",
                          "picard.analysis.artifacts.CollectSequencingArtifactMetrics", "picard.vcf.CollectVariantCallingMetrics", "picard.analysis.CollectWgsMetrics",
                          "picard.analysis.CollectWgsMetricsFromQuerySorted", "picard.analysis.CollectWgsMetricsFromSampledSites",
                          "picard.analysis.CollectWgsMetricsWithNonZeroCoverage", "picard.analysis.CompareMetrics", "picard.sam.CompareSAMs",
                          "picard.analysis.artifacts.ConvertSequencingArtifactToOxoG", "picard.sam.CreateSequenceDictionary", "picard.sam.DownsampleSam",
                          "picard.illumina.ExtractIlluminaBarcodes", "picard.sam.markduplicates.EstimateLibraryComplexity", "picard.sam.FastqToSam", "picard.util.FifoBuffer",
                          "picard.vcf.MendelianViolations.FindMendelianViolations",
                          "picard.sam.FilterSamReads", "picard.vcf.filter.FilterVcf", "picard.sam.FixMateInformation", "picard.sam.GatherBamFiles", "picard.vcf.GatherVcfs",
                          "picard.vcf.GenotypeConcordance", "picard.illumina.IlluminaBasecallsToFastq", "picard.illumina.IlluminaBasecallsToSam", "picard.illumina.CheckIlluminaDirectory",
                          "picard.sam.CheckTerminatorBlock", "picard.util.IntervalListTools", "picard.util.LiftOverIntervalList", "picard.vcf.LiftoverVcf", "picard.vcf.MakeSitesOnlyVcf",
                          "picard.sam.markduplicates.MarkDuplicates", "picard.sam.markduplicates.MarkDuplicatesWithMateCigar", "picard.analysis.MeanQualityByCycle",
                          "picard.sam.MergeBamAlignment", "picard.sam.MergeSamFiles", "picard.vcf.MergeVcfs", "picard.reference.NormalizeFasta", "picard.sam.PositionBasedDownsampleSam",
                          "picard.reference.ExtractSequences", "picard.analysis.QualityScoreDistribution", "picard.vcf.RenameSampleInVcf", "picard.sam.ReorderSam",
                          "picard.sam.ReplaceSamHeader", "picard.sam.RevertSam", "picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar", "picard.sam.SamFormatConverter",
                          "picard.sam.SamToFastq", "picard.util.ScatterIntervalsByNs", "picard.sam.SetNmMdAndUqTags",
                          "picard.sam.SortSam", "picard.vcf.SortVcf", "picard.sam.SplitSamByLibrary", "picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar",
                          "picard.vcf.UpdateVcfSequenceDictionary", "picard.vcf.VcfFormatConverter", "picard.illumina.MarkIlluminaAdapters", "picard.vcf.SplitVcfs",
                          "picard.sam.ValidateSamFile", "picard.sam.ViewSam", "picard.vcf.VcfToIntervalList"]

//generate documentation

task documentAll(dependsOn: ['documentCommands', 'createMetricsDoc', 'documentStandardOptions']){
  doFirst{
    htmlDirInc.mkdirs()
  }
}

task documentCommands  {
    def previousDocTask = null
    def usageFile = new File(htmlDirInc, "command-line-usage.html")
    def sidebarFile = new File(htmlDirInc, "command-line-sidebar.html")

    commandClasses.each { mainClass ->
       task "document_${mainClass}"(type: JavaExec) {
           main ='picard.cmdline.CreateHtmlDocForProgram'
           classpath = sourceSets.main.runtimeClasspath
           args mainClass
           def outputFile = new File(htmlDirInc, mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html")
           doFirst {
                htmlDirInc.mkdirs()
                standardOutput = new FileOutputStream(outputFile)
            }
           outputs.file outputFile

           if (previousDocTask != null) delegate.dependsOn previousDocTask
           previousDocTask = delegate
           documentCommands.dependsOn(delegate)
           doLast {
             usageFile.append("{% include ${mainClass.substring(mainClass.lastIndexOf(".") + 1) + ".html"} %}")
             usageFile.append(System.getProperty("line.separator"))
             sidebarFile.append("<li><a href=\"command-line-overview.html#${mainClass.substring(mainClass.lastIndexOf(".") + 1)}\">${mainClass.substring(mainClass.lastIndexOf(".") + 1)}</a>")
             sidebarFile.append(System.getProperty("line.separator"))
           }
        }
    }
    outputs.dir htmlDirInc
}

task documentStandardOptions(type: JavaExec) {
    main = 'picard.cmdline.CreateHtmlDocForStandardOptions'
    classpath = sourceSets.main.runtimeClasspath
    def standardOptionsFile = new File(htmlDirInc, "standard-options.html")
    doFirst{
      htmlDirInc.mkdirs()
      standardOutput = new FileOutputStream(standardOptionsFile)
    }
    outputs.file standardOptionsFile
 }

task createMetricsDoc(dependsOn: classes, type: Javadoc) {
    doFirst {
        htmlDirInc.mkdirs()
    }
    
    source = sourceSets.main.allJava
    classpath = sourceSets.main.runtimeClasspath
    outputs.dir(htmlDirInc)

    options.destinationDirectory = htmlDirInc
    options.doclet = 'picard.util.MetricsDoclet'
    options.docletpath = sourceSets.main.runtimeClasspath.asType(List)
}
//end generate documentation

task wrapper(type: Wrapper) {
    description = "Regenerate the gradle wrapper"
    gradleVersion = '3.1'
}

task javadocJar(type: Jar, dependsOn: documentAll) {
    classifier = 'javadoc'
    from 'build/docs/javadoc'
}

task sourcesJar(type: Jar) {
    from sourceSets.main.allSource
    classifier = 'sources'
}

/**
 * This specifies what artifacts will be built and uploaded when performing a maven upload.
 */
artifacts {
    archives jar
    archives javadocJar
    archives sourcesJar
}

/**
 * Sign non-snapshot releases with our secret key.  This should never need to be invoked directly.
 */
signing {
    required { isRelease && gradle.taskGraph.hasTask("uploadArchives") }
    sign configurations.archives
}

/**
 * Upload a release to sonatype.  You must be an authorized uploader and have your sonatype
 * username and password information in your gradle properties file.  See the readme for more info.
 *
 * For releasing to your local maven repo, use gradle install
 */
uploadArchives {
    repositories {
        mavenDeployer {
            beforeDeployment { MavenDeployment deployment -> signing.signPom(deployment) }

            repository(url: "https://oss.sonatype.org/service/local/staging/deploy/maven2/") {
                authentication(userName: project.findProperty("sonatypeUsername"), password: project.findProperty("sonatypePassword"))
            }

            snapshotRepository(url: "https://artifactory.broadinstitute.org/artifactory/libs-snapshot-local/") {
                authentication(userName: System.env.ARTIFACTORY_USERNAME, password: System.env.ARTIFACTORY_PASSWORD)
            }

            pom.project {
                name 'Picard'
                packaging 'jar'
                description 'A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.'
                url 'http://broadinstitute.github.io/picard/'

                developers {
                    developer {
                        id 'picard'
                        name 'Picard Team'
                        url 'http://broadinstitute.github.io/picard'
                    }
                }

                scm {
                    url 'git@github.com:broadinstitute/picard.git'
                    connection 'scm:git:git@github.com:broadinstitute/picard.git'
                }

                licenses {
                    license {
                        name 'MIT License'
                        url 'http://opensource.org/licenses/MIT'
                        distribution 'repo'
                    }
                }
            }
        }
    }
    doFirst {
        System.out.println("Uploading version $version")
    }
}

//update static web docs
task copyJavadoc(dependsOn: 'javadoc', type: Copy) {
    from 'build/docs/javadoc'
    into "$htmlDir/javadoc"
}

task updateGhPages(dependsOn: ['copyJavadoc', 'documentAll']){
  outputs.dir htmlDir
}

updateGhPages.finalizedBy publishGhPages

githubPages {
  repoUri = 'git@github.com:broadinstitute/picard.git'
  targetBranch = 'gh-pages'
  deleteExistingFiles = false
  pages {
    from htmlDir
    into '.'
  }
}