build.gradle

import org.gradle.internal.os.OperatingSystem
import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
import org.jabref.build.xjc.XjcPlugin
import org.jabref.build.xjc.XjcTask

plugins {
    id 'application'

    id 'com.github.andygoossens.modernizer' version '1.9.2'

    id 'me.champeau.jmh' version '0.7.2'

    id 'org.javamodularity.moduleplugin' version '1.8.15'

    id 'org.openjfx.javafxplugin' version '0.1.0'

    id 'org.beryx.jlink' version '3.0.1'

    // nicer test outputs during running and completion
    // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
    id 'com.adarshr.test-logger' version '4.0.0'

    id 'jacoco'

    id 'checkstyle'

    id 'project-report'

    id 'idea'

    id 'org.openrewrite.rewrite' version '6.16.0'
}

// Enable following for debugging
// gradle.startParameter.showStacktrace = org.gradle.api.logging.configuration.ShowStacktrace.

apply plugin: XjcPlugin

apply from: 'eclipse.gradle'

group = "org.jabref"
version = project.findProperty('projVersion') ?: '100.0.0'

java {
    sourceCompatibility = JavaVersion.VERSION_21
    targetCompatibility = JavaVersion.VERSION_21
    // Workaround needed for Eclipse, probably because of https://github.com/gradle/gradle/issues/16922
    // Should be removed as soon as Gradle 7.0.1 is released ( https://github.com/gradle/gradle/issues/16922#issuecomment-828217060 )
    modularity.inferModulePath.set(false)

    toolchain {
        // If this is updated, also update
        // - .gitpod.Dockerfile
        // - .devcontainer/devcontainer.json#L34 and
        // - .github/workflows/deployment-jdk-ea.yml#L53
        languageVersion = JavaLanguageVersion.of(21)
        // See https://docs.gradle.org/current/javadoc/org/gradle/jvm/toolchain/JvmVendorSpec.html for a full list
        // vendor = JvmVendorSpec.AMAZON
    }
}

application {
    mainClass.set('org.jabref.Launcher')
    mainModule.set('org.jabref')

    applicationDefaultJvmArgs = [
        // On a change here, also adapt
        //   1. "run > moduleOptions"
        //   2. "deployment.yml" (macOS part)
        //   3. "deployment-arm64.yml"

        // Note that the arguments are cleared for the "run" task to avoid messages like "WARNING: Unknown module: org.jabref.merged.module specified to --add-exports"

        // Fix for https://github.com/JabRef/jabref/issues/11188
        '--add-exports=javafx.base/com.sun.javafx.event=org.jabref.merged.module',
        '--add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module',

        // Fix for https://github.com/JabRef/jabref/issues/11198
        '--add-opens=javafx.graphics/javafx.scene=org.jabref.merged.module',
        '--add-opens=javafx.controls/javafx.scene.control=org.jabref.merged.module',
        '--add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref.merged.module',

        // Fix for https://github.com/JabRef/jabref/issues/11225 on linux
        '--add-opens=javafx.controls/javafx.scene.control=org.jabref',
        '--add-exports=javafx.base/com.sun.javafx.event=org.jabref',
        '--add-exports=javafx.controls/com.sun.javafx.scene.control=org.jabref',
        '--add-opens=javafx.graphics/javafx.scene=org.jabref',
        '--add-opens=javafx.controls/javafx.scene.control=org.jabref',
        '--add-opens=javafx.controls/com.sun.javafx.scene.control=org.jabref'
    ]
}

// Workaround for https://github.com/openjfx/javafx-gradle-plugin/issues/89
// See also https://github.com/java9-modularity/gradle-modules-plugin/issues/165
modularity.disableEffectiveArgumentsAdjustment()

sourceSets {
    main {
        java {
            // src-gen reasoning: https://stackoverflow.com/a/64612308/873282
            srcDirs = ["src/main/java", "src-gen/main/java"]
        }
        resources {
            srcDirs = ["src/main/java", "src/main/resources"]
        }
    }
    test {
        java {
            srcDirs = ["src/test/java"]
        }
        resources {
            srcDirs = ["src/test/resources"]
        }
    }
}

repositories {
    mavenCentral()
    maven { url 'https://oss.sonatype.org/content/groups/public' }
    maven { url 'https://s01.oss.sonatype.org/content/repositories/snapshots/' }
    maven { url 'https://jitpack.io' }
    maven { url 'https://sandec.jfrog.io/artifactory/repo' }
}

configurations {
    antlr4
}

dependencyLocking {
    lockAllConfigurations()
}

javafx {
    version = "22.0.1"
    modules = [ 'javafx.controls', 'javafx.fxml', 'javafx.web', 'javafx.swing' ]
}

jacoco {
    toolVersion = "0.8.10"
}

dependencies {
    // Include all jar-files in the 'lib' folder as dependencies
    implementation fileTree(dir: 'lib', includes: ['*.jar'])

    def pdfbox = "3.0.2"
    implementation ("org.apache.pdfbox:pdfbox:$pdfbox") {
        exclude group: 'commons-logging'
    }
    implementation ("org.apache.pdfbox:fontbox:$pdfbox") {
        exclude group: 'commons-logging'
    }
    implementation ("org.apache.pdfbox:xmpbox:$pdfbox") {
        exclude group: 'org.junit.jupiter'
        exclude group: 'commons-logging'
    }

    def luceneVersion = "9.11.0"
    implementation "org.apache.lucene:lucene-core:$luceneVersion"
    implementation "org.apache.lucene:lucene-queryparser:$luceneVersion"
    implementation "org.apache.lucene:lucene-queries:$luceneVersion"
    implementation "org.apache.lucene:lucene-analysis-common:$luceneVersion"
    implementation "org.apache.lucene:lucene-highlighter:$luceneVersion"

    implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.11.0'
    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.12.0'
    implementation 'com.h2database:h2-mvstore:2.2.224'

    // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
    implementation 'org.bouncycastle:bcprov-jdk18on:1.78.1'

    implementation 'commons-cli:commons-cli:1.8.0'

    implementation 'org.libreoffice:unoloader:24.2.3'
    implementation 'org.libreoffice:libreoffice:24.2.3'

    implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
    implementation 'info.debatty:java-string-similarity:2.0.0'
    implementation 'com.github.javakeyring:java-keyring:1.0.4'

    antlr4 'org.antlr:antlr4:4.13.1'
    implementation 'org.antlr:antlr4-runtime:4.13.1'

    implementation group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '6.9.0.202403050737-r'

    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.17.1'
    implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.17.1'

    implementation 'com.fasterxml:aalto-xml:1.3.3'

    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.9'

    implementation 'org.postgresql:postgresql:42.7.3'

    implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
        // causing module issues
        exclude module: 'oraclepki'
    }

    implementation ('com.google.guava:guava:33.1.0-jre') {
        // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
        exclude module: "jsr305"
    }

    implementation 'jakarta.annotation:jakarta.annotation-api:2.1.1'
    implementation 'jakarta.inject:jakarta.inject-api:2.0.1'

    implementation('org.jabref:afterburner.fx:2.0.0') {
        exclude group: 'org.openjfx'
    }
    implementation 'org.kordamp.ikonli:ikonli-javafx:12.3.1'
    implementation 'org.kordamp.ikonli:ikonli-materialdesign2-pack:12.3.1'
    implementation 'com.github.sialcasa.mvvmFX:mvvmfx-validation:f195849ca9' //jitpack
    implementation 'de.saxsys:mvvmfx:1.8.0'
    implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT') {
        exclude group: 'org.openjfx'
    }
    implementation 'org.fxmisc.flowless:flowless:0.7.3'
    implementation 'org.fxmisc.richtext:richtextfx:0.11.2'
    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '2.23.0') {
        exclude module: 'javax.inject' // Split package, use only jakarta.inject
        exclude module: 'commons-lang3'
        exclude group: 'org.openjfx'
        exclude group: 'org.apache.logging.log4j'
        exclude group: 'tech.units'
    }
    // Required by gemsfx
    implementation 'tech.units:indriya:2.2'

    implementation 'org.controlsfx:controlsfx:11.2.1'

    implementation 'org.jsoup:jsoup:1.17.2'
    implementation 'com.konghq:unirest-java:3.14.5'

    implementation 'org.slf4j:slf4j-api:2.0.13'
    implementation "org.tinylog:tinylog-api:2.7.0"
    implementation "org.tinylog:slf4j-tinylog:2.7.0"
    implementation "org.tinylog:tinylog-impl:2.7.0"

    // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
    implementation 'org.slf4j:jul-to-slf4j:2.0.13'
    // route all requests to log4j to SLF4J
    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.23.1'

    implementation('de.undercouch:citeproc-java:3.1.0') {
        exclude group: 'org.antlr'
    }

    // jakarta.activation is already dependency of glassfish
    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.2'
    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '4.0.3'

    implementation ('com.github.tomtung:latex2unicode_2.13:0.3.2') {
        exclude module: 'fastparse_2.13'
    }

    implementation "de.rototor.snuggletex:snuggletex:1.3.0"
    implementation ("de.rototor.snuggletex:snuggletex-jeuclid:1.3.0") {
        exclude group: "org.apache.xmlgraphics"
    }

    implementation 'com.vladsch.flexmark:flexmark:0.64.8'
    implementation 'com.vladsch.flexmark:flexmark-html2md-converter:0.64.8'

    implementation group: 'net.harawata', name: 'appdirs', version: '1.2.2'

    implementation group: 'org.jooq', name: 'jool', version: '0.9.15'
    // JAX-RS implemented by Jersey
    // API
    implementation 'jakarta.ws.rs:jakarta.ws.rs-api:4.0.0'
    // Implementation of the API
    implementation 'org.glassfish.jersey.core:jersey-server:3.1.7'
    // injection framework
    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.7'
    implementation 'org.glassfish.hk2:hk2-api:3.1.0'
    // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
    // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
    // testImplementation 'org.glassfish.hk2:hk2-junitrunner:3.0.4'
    // HTTP server
    // implementation 'org.glassfish.jersey.containers:jersey-container-netty-http:3.1.1'
    implementation 'org.glassfish.jersey.containers:jersey-container-grizzly2-http:3.1.7'
    testImplementation 'org.glassfish.jersey.test-framework.providers:jersey-test-framework-provider-grizzly2:3.1.7'
    // Allow objects "magically" to be mapped to JSON using GSON
    // implementation 'org.glassfish.jersey.media:jersey-media-json-gson:3.1.1'

    // Because of GraalVM quirks, we need to ship that. See https://github.com/jspecify/jspecify/issues/389#issuecomment-1661130973 for details
    implementation 'org.jspecify:jspecify:0.3.0'

    // parse plist files
    implementation 'com.googlecode.plist:dd-plist:1.28'

    // Parse lnk files
    implementation 'com.github.vatbub:mslinks:1.0.6.2'

    // YAML formatting
    implementation 'org.yaml:snakeyaml:2.2'

    implementation 'commons-io:commons-io:2.16.1'

    testImplementation 'io.github.classgraph:classgraph:4.8.173'
    testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
    testImplementation 'org.junit.platform:junit-platform-launcher:1.10.2'

    testImplementation 'org.mockito:mockito-core:5.12.0'
    testImplementation 'org.xmlunit:xmlunit-core:2.10.0'
    testImplementation 'org.xmlunit:xmlunit-matchers:2.10.0'
    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:1.3.0'
    testImplementation 'com.tngtech.archunit:archunit-junit5-api:1.3.0'
    testImplementation "org.testfx:testfx-core:4.0.16-alpha"
    testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
    testImplementation "org.hamcrest:hamcrest-library:2.2"

    checkstyle 'com.puppycrawl.tools:checkstyle:10.17.0'
    // xjc needs the runtime as well for the ant task, otherwise it fails
    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
    xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

    rewrite(platform("org.openrewrite.recipe:rewrite-recipe-bom:2.12.0"))
    rewrite("org.openrewrite.recipe:rewrite-static-analysis")
    rewrite("org.openrewrite.recipe:rewrite-logging-frameworks")
    rewrite("org.openrewrite.recipe:rewrite-testing-frameworks")
    rewrite("org.openrewrite.recipe:rewrite-migrate-java")

    configurations.checkstyle {
        resolutionStrategy.capabilitiesResolution.withCapability("com.google.collections:google-collections") {
            select("com.google.guava:guava:0")
        }
    }

    configurations
            .matching(c -> c.name.contains("downloadSources"))
            .configureEach {
                attributes {
                    attribute(Usage.USAGE_ATTRIBUTE, objects.named(Usage, Usage.JAVA_RUNTIME))
                    attribute(OperatingSystemFamily.OPERATING_SYSTEM_ATTRIBUTE, objects.named(OperatingSystemFamily, DefaultNativePlatform.getCurrentOperatingSystem().getName()))
                    attribute(MachineArchitecture.ARCHITECTURE_ATTRIBUTE, objects.named(MachineArchitecture, DefaultNativePlatform.getCurrentArchitecture().getName()))
                }
            }
}

clean {
    delete "src/main/generated"
    delete "src-gen"
}

processResources {
    filteringCharset = 'UTF-8'

    filesMatching("build.properties") {
        expand(version: project.findProperty('projVersionInfo') ?: '100.0.0',
                "year": String.valueOf(Calendar.getInstance().get(Calendar.YEAR)),
                "maintainers": new File('MAINTAINERS').readLines().findAll { !it.startsWith("#") }.join(", "),
                "azureInstrumentationKey": System.getenv('AzureInstrumentationKey') ? System.getenv('AzureInstrumentationKey') : '',
                "springerNatureAPIKey": System.getenv('SpringerNatureAPIKey') ? System.getenv('SpringerNatureAPIKey') : '',
                "astrophysicsDataSystemAPIKey": System.getenv('AstrophysicsDataSystemAPIKey') ? System.getenv('AstrophysicsDataSystemAPIKey') : '',
                "ieeeAPIKey": System.getenv('IEEEAPIKey') ? System.getenv('IEEEAPIKey') : '',
                "scienceDirectApiKey": System.getenv('SCIENCEDIRECTAPIKEY') ? System.getenv('SCIENCEDIRECTAPIKEY') : '',
                "biodiversityHeritageApiKey": System.getenv('BiodiversityHeritageApiKey') ? System.getenv('BiodiversityHeritageApiKey') : '',
                "semanticScholarApiKey": System.getenv('SemanticScholarApiKey') ? System.getenv("SemanticScholarApiKey") : ''
        )
        filteringCharset = 'UTF-8'
    }

    filesMatching(["resources/resource/ods/meta.xml", "resources/resource/openoffice/meta.xml"]) {
        expand version: project.version
    }
}

tasks.register('generateSource') {
    dependsOn("generateBstGrammarSource",
            "generateSearchGrammarSource",
            "generateCitaviSource")
    group = 'JabRef'
    description 'Generates all necessary (Java) source files.'
}

tasks.register("generateBstGrammarSource", JavaExec) {
    group = "JabRef"
    description = 'Generates BstLexer.java and BstParser.java from the Bst.g grammar file using antlr4.'
    classpath = configurations.antlr4
    mainClass = "org.antlr.v4.Tool"
    javaLauncher.set(javaToolchains.launcherFor(java.toolchain))

    inputs.dir('src/main/antlr4/org/jabref/bst/')
    outputs.dir("src-gen/main/java/org/jabref/logic/bst/")
    args = ["-o", "src-gen/main/java/org/jabref/logic/bst/", "-visitor", "-no-listener", "-package", "org.jabref.logic.bst", "$projectDir/src/main/antlr4/org/jabref/bst/Bst.g4"]
}

tasks.register("generateSearchGrammarSource", JavaExec) {
    group = 'JabRef'
    description = "Generates java files for Search.g antlr4."
    classpath = configurations.antlr4
    mainClass = "org.antlr.v4.Tool"
    javaLauncher.set(javaToolchains.launcherFor(java.toolchain))

    inputs.dir("src/main/antlr4/org/jabref/search/")
    outputs.dir("src-gen/main/java/org/jabref/search/")
    args  = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
}

tasks.register("generateJournalListMV", JavaExec) {
    group = "JabRef"
    description = "Converts the comma-separated journal abbreviation file to a H2 MVStore"
    classpath = sourceSets.main.runtimeClasspath
    mainClass = "org.jabref.cli.JournalListMvGenerator"
    javaLauncher.set(javaToolchains.launcherFor(java.toolchain))
    onlyIf {
        !file("build/resources/main/journals/journal-list.mv").exists()
    }
}

jar.dependsOn("generateJournalListMV")
compileTestJava.dependsOn("generateJournalListMV")

tasks.register('generateCitaviSource', XjcTask) {
    group = 'JabRef'
    description = "Generates java files for the citavi importer."

    schemaFile = "src/main/resources/xjc/citavi/citavi.xsd"
    outputDirectory = "src-gen/main/java/"
    javaPackage = "org.jabref.logic.importer.fileformat.citavi"
}

tasks.withType(JavaCompile).configureEach {
    options.encoding = 'UTF-8'

    // hint by https://docs.gradle.org/current/userguide/performance.html#run_the_compiler_as_a_separate_process
    options.fork = true
}

compileJava {
    options.compilerArgs << "-Xlint:none"
    dependsOn "generateSource"

    options.generatedSourceOutputDirectory.set(file("src-gen/main/java"))

    moduleOptions {
        // TODO: Remove access to internal api
        addExports = [
                'javafx.controls/com.sun.javafx.scene.control' : 'org.jabref',
                'org.controlsfx.controls/impl.org.controlsfx.skin' : 'org.jabref'
        ]
    }
}

// Configures "application > run" task
run {
    doFirst {
        // Clear the default JVM arguments, to avoid messages like "WARNING: Unknown module: org.jabref.merged.module specified to --add-exports"
        application.applicationDefaultJvmArgs = []
    }

    // TODO: Remove access to internal api
    moduleOptions {
        // On a change here, also adapt "application > applicationDefaultJvmArgs"
        addExports = [
                'javafx.base/com.sun.javafx.event' : 'org.jabref.merged.module',
                'javafx.controls/com.sun.javafx.scene.control' : 'org.jabref',

                // We need to restate the ControlsFX exports, because we get following error otherwise:
                //   java.lang.IllegalAccessError:
                //     class org.controlsfx.control.textfield.AutoCompletionBinding (in module org.controlsfx.controls)
                //     cannot access class com.sun.javafx.event.EventHandlerManager (in module javafx.base) because
                //     module javafx.base does not export com.sun.javafx.event to module org.controlsfx.controls
                // Taken from here: https://github.com/controlsfx/controlsfx/blob/9.0.0/build.gradle#L1
                'javafx.graphics/com.sun.javafx.scene' : 'org.controlsfx.controls',
                'javafx.graphics/com.sun.javafx.scene.traversal' : 'org.controlsfx.controls',
                'javafx.graphics/com.sun.javafx.css' : 'org.controlsfx.controls',
                'javafx.controls/com.sun.javafx.scene.control' : 'org.controlsfx.controls',
                'javafx.controls/com.sun.javafx.scene.control.behavior' : 'org.controlsfx.controls',
                'javafx.controls/com.sun.javafx.scene.control.inputmap' : 'org.controlsfx.controls',
                'javafx.base/com.sun.javafx.event' : 'org.controlsfx.controls',
                'javafx.base/com.sun.javafx.collections' : 'org.controlsfx.controls',
                'javafx.base/com.sun.javafx.runtime': 'org.controlsfx.controls',
                'javafx.web/com.sun.webkit' : 'org.controlsfx.controls',
        ]

        addOpens = [
                'javafx.controls/javafx.scene.control' : 'org.jabref',
                'javafx.controls/com.sun.javafx.scene.control' : 'org.jabref',
                'org.controlsfx.controls/impl.org.controlsfx.skin' : 'org.jabref',
                'org.controlsfx.controls/org.controlsfx.control.textfield' : 'org.jabref',

                'javafx.controls/javafx.scene.control.skin' : 'org.controlsfx.controls',
                'javafx.graphics/javafx.scene' : 'org.controlsfx.controls'
        ]
    }

    if (project.hasProperty('component')){
        if (component == 'httpserver'){
            main = 'org.jabref.http.server.Server'
        }
    }
}

javadoc {
    options {
        encoding = 'UTF-8'
        version = false
        author = false
        addMultilineStringsOption("-add-exports").setValue([
            'javafx.controls/com.sun.javafx.scene.control=org.jabref'
        ])
    }
}

test {
    useJUnitPlatform {
        excludeTags 'DatabaseTest', 'FetcherTest', 'GUITest'
    }

    moduleOptions {
        // TODO: Remove this as soon as ArchUnit is modularized
        runOnClasspath = true
    }
}

testlogger {
    // See https://github.com/radarsh/gradle-test-logger-plugin#configuration for configuration options

    theme 'standard'

    showPassed false
    showSkipped false

    showCauses false
    showStackTraces false
}

tasks.withType(Test) {
    reports.html.outputLocation.set(file("${reporting.baseDir}/${name}"))
    // Enable parallel tests. See https://docs.gradle.org/8.1/userguide/performance.html#execute_tests_in_parallel for details.
    maxParallelForks = Runtime.runtime.availableProcessors() - 1
    ignoreFailures = true
}

tasks.register('databaseTest', Test) {
    useJUnitPlatform {
        includeTags 'DatabaseTest'
    }

    testLogging {
        // set options for log level LIFECYCLE
        events = ["FAILED"]
        exceptionFormat "full"
    }

    maxParallelForks = 1
}

tasks.register('fetcherTest', Test) {
    useJUnitPlatform {
        includeTags 'FetcherTest'
    }

    maxParallelForks = 1
}

tasks.register('guiTest', Test) {
    useJUnitPlatform {
        includeTags 'GUITest'
    }

    testLogging {
        // set options for log level LIFECYCLE
        events = ["FAILED"]
        exceptionFormat "full"
    }

    maxParallelForks = 1
}

// Test result tasks
tasks.register('copyTestResources', Copy) {
    from "${projectDir}/src/test/resources"
    into "${buildDir}/classes/test"
}
processTestResources.dependsOn copyTestResources

tasks.register('jacocoPrepare') {
    doFirst {
        // Ignore failures of tests
        tasks.withType(Test).tap {
            configureEach {
                ignoreFailures = true
            }
        }
    }
}
test.mustRunAfter jacocoPrepare
databaseTest.mustRunAfter jacocoPrepare
fetcherTest.mustRunAfter jacocoPrepare

jacocoTestReport {
    dependsOn jacocoPrepare, test, fetcherTest, databaseTest

    executionData files(
            layout.buildDirectory.file('jacoco/test.exec').get().asFile,
            layout.buildDirectory.file('jacoco/fetcherTest.exec').get().asFile,
            layout.buildDirectory.file('jacoco/databaseTest.exec').get().asFile)

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

// Code quality tasks
checkstyle {
    // will only run when called explicitly from the command line
    sourceSets = []
}

rewrite {
    activeRecipe(
        'org.jabref.config.rewrite.cleanup'
    )
    exclusion (
        "build.gradle",
        "buildSrc/build.gradle",
        "eclipse.gradle",
        "settings.gradle",
        "src-gen/**",
        "src/main/resources/**",
        "src/test/resources/**",
        "**/module-info.java",
        "**/*.py",
        "**/*.xml",
        "**/*.yml"
    )
    plainTextMask("**/*.md")
    failOnDryRunResults = true
}

modernizer {
    failOnViolations = false
    includeTestClasses = true
    exclusions = [
        'java/util/Optional.get:()Ljava/lang/Object;'
    ]
}

// Release tasks
tasks.register('deleteInstallerTemp', Delete) {
    delete "$buildDir/installer"
}

jpackage.dependsOn deleteInstallerTemp
jlinkZip.dependsOn jpackage
jlink {
    // https://github.com/beryx/badass-jlink-plugin/issues/61#issuecomment-504640018
    addExtraDependencies("javafx")

    addOptions('--strip-debug', '--compress', 'zip-6', '--no-header-files', '--no-man-pages')
    launcher {
        name = 'JabRef'
    }

    addOptions("--bind-services")

    // TODO: Remove the following as soon as the dependencies are fixed (upstream)
    // forceMerge is usually needed when some non-modular artifacts in the dependency graph use code that was previously part of the JDK
    // but it was removed in the newer releases.
    // The pom.xml associated with such a non-modular artifact does not mention that the artifact depends on the removed code
    // (because the artifact was published when this code was still available in the JDK).
    forceMerge "controlsfx", "bcprov", "jaxb", "istack", "stax", "log4j"

    // TODO: Remove the following correction to the merged module
    // The module descriptor automatically generated by the plugin for the merged module contained some invalid entries.
    // This is based on ./gradlew suggestMergedModuleInfo, sort, strip ";"", comment non-used modules, and include the suggested directives here.
    //   However, we need to fine-tune this manually (non-alphabetic order)
    mergedModule {
        requires 'javafx.base'
        requires 'javafx.controls'
        requires 'javafx.fxml'
        requires 'javafx.graphics'
        requires 'javafx.media'
        requires 'javafx.swing'

        requires 'java.compiler'
        requires 'java.datatransfer'
        requires 'java.desktop'
        requires 'java.logging'
        requires 'java.management'
        requires 'java.naming'
        requires 'java.net.http'
        requires 'java.scripting'
        requires 'java.security.jgss'
        requires 'java.security.sasl'
        requires 'java.sql'
        requires 'java.sql.rowset'
        requires 'java.transaction.xa'
        requires 'java.rmi'
        requires 'java.xml'
        requires 'jdk.jsobject'
        requires 'jdk.unsupported'
        requires 'jdk.unsupported.desktop'
        requires 'jdk.security.jgss'
        requires 'jdk.xml.dom'
        requires 'com.google.gson'
        requires 'org.jsoup'
        requires 'org.slf4j'
        requires 'jakarta.xml.bind'
        requires 'org.apache.commons.lang3'
        requires 'org.apache.commons.text'
        uses 'org.mariadb.jdbc.credential.CredentialPlugin'
        uses 'org.mariadb.jdbc.authentication.AuthenticationPlugin'
        uses 'org.mariadb.jdbc.tls.TlsSocketPlugin'
        uses 'org.mariadb.jdbc.LocalInfileInterceptor'
        uses 'org.eclipse.jgit.transport.SshSessionFactory'
        uses 'org.eclipse.jgit.lib.GpgSigner'
        provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'
        provides 'java.sql.Driver' with 'org.postgresql.Driver'
        provides 'org.mariadb.jdbc.authentication.AuthenticationPlugin' with 'org.mariadb.jdbc.internal.com.send.authentication.CachingSha2PasswordPlugin',
                'org.mariadb.jdbc.internal.com.send.authentication.ClearPasswordPlugin',
                'org.mariadb.jdbc.internal.com.send.authentication.Ed25519PasswordPlugin',
                'org.mariadb.jdbc.internal.com.send.authentication.NativePasswordPlugin',
                'org.mariadb.jdbc.internal.com.send.authentication.OldPasswordPlugin',
                'org.mariadb.jdbc.internal.com.send.authentication.SendGssApiAuthPacket',
                'org.mariadb.jdbc.internal.com.send.authentication.SendPamAuthPacket',
                'org.mariadb.jdbc.internal.com.send.authentication.Sha256PasswordPlugin'
        provides 'org.mariadb.jdbc.credential.CredentialPlugin' with 'org.mariadb.jdbc.credential.aws.AwsIamCredentialPlugin',
                'org.mariadb.jdbc.credential.env.EnvCredentialPlugin',
                'org.mariadb.jdbc.credential.system.PropertiesCredentialPlugin'
        provides 'java.security.Provider' with 'org.bouncycastle.jce.provider.BouncyCastleProvider',
                'org.bouncycastle.pqc.jcajce.provider.BouncyCastlePQCProvider'
    }

    jpackage {
        outputDir = "distribution"

        if (OperatingSystem.current().isWindows()) {
            // This requires WiX to be installed: https://github.com/wixtoolset/wix3/releases
            installerType = "msi"
            imageOptions = [
                    '--icon', "${projectDir}/src/main/resources/icons/jabref.ico",
            ]
            installerOptions = [
                    '--vendor', 'JabRef',
                    '--app-version', "${project.version}",
                    '--verbose',
                    '--win-upgrade-uuid', 'd636b4ee-6f10-451e-bf57-c89656780e36',
                    '--win-dir-chooser',
                    '--win-shortcut',
                    '--win-menu',
                    '--win-menu-group', "JabRef",
                    '--temp', "$buildDir/installer",
                    '--resource-dir', "${projectDir}/buildres/windows",
                    '--license-file', "${projectDir}/buildres/LICENSE_with_Privacy.md",
                    '--file-associations', "${projectDir}/buildres/windows/bibtexAssociations.properties"
            ]
        }

        if (OperatingSystem.current().isLinux()) {
            imageOptions = [
                    '--icon', "${projectDir}/src/main/resources/icons/JabRef-icon-64.png",
                    '--app-version', "${project.version}",
            ]
            installerOptions = [
                    '--verbose',
                    '--vendor', 'JabRef',
                    '--app-version', "${project.version}",
                    // '--temp', "$buildDir/installer",
                    '--resource-dir', "${projectDir}/buildres/linux",
                    '--linux-menu-group', 'Office;',
                    '--linux-rpm-license-type', 'MIT',
                    // '--license-file', "${projectDir}/LICENSE.md",
                    '--description', 'JabRef is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format.',
                    '--linux-shortcut',
                    '--file-associations', "${projectDir}/buildres/linux/bibtexAssociations.properties"
            ]
        }

        if (OperatingSystem.current().isMacOsX()) {
            imageOptions = [
                    '--icon', "${projectDir}/src/main/resources/icons/jabref.icns",
                    '--resource-dir', "${projectDir}/buildres/mac"
            ]
            // Notarized mac images and packages are built on the pipeline only
            skipInstaller = true
            installerOptions = [
                    '--verbose',
                    '--vendor', 'JabRef',
                    '--mac-package-identifier', "JabRef",
                    '--mac-package-name', "JabRef",
                    '--app-version', "${project.version}",
                    '--file-associations', "${projectDir}/buildres/mac/bibtexAssociations.properties",
                    '--resource-dir', "${projectDir}/buildres/mac"
            ]
        }
    }
}

if (OperatingSystem.current().isWindows()) {
    tasks.jpackageImage.doLast {
        copy {
            from("${projectDir}/buildres/windows") {
                include "jabref-firefox.json", "jabref-chrome.json", "JabRefHost.bat", "JabRefHost.ps1"
            }
            into "$buildDir/distribution/JabRef"
        }
    }
}

if (OperatingSystem.current().isLinux()) {
    tasks.jpackageImage.doLast {
        copy {
            from("${projectDir}/buildres/linux") {
                include "native-messaging-host/**", "jabrefHost.py"
            }
            into "$buildDir/distribution/JabRef/lib"
        }
    }
}

if (OperatingSystem.current().isMacOsX()) {
    tasks.jpackageImage.doLast {
        copy {
            from("${projectDir}/buildres/mac") {
                include "native-messaging-host/**", "jabrefHost.py"
            }
            into "$buildDir/distribution/JabRef.app/Contents/Resources"
        }
    }
}

jmh {
    warmupIterations = 5
    iterations = 10
    fork = 2
}