build.gradle

buildscript {
    repositories {
        mavenLocal()
        mavenCentral()
        maven {
            url 'https://plugins.gradle.org/m2/'
        }
    }

    dependencies {
        classpath 'gradle.plugin.org.kt3k.gradle.plugin:coveralls-gradle-plugin:2.12.0'
        classpath "gradle.plugin.com.github.jengelman.gradle.plugins:shadow:7.0.0"
    }
}

apply plugin: 'application'
apply plugin: 'java'
apply plugin: 'java-library'
//apply plugin: 'maven'
apply plugin: 'maven-publish'
apply plugin: 'com.github.johnrengelman.shadow'

group 'com.scienceminer.glutton'
version '0.3-SNAPSHOT'

//sourceCompatibility = 1.8
sourceCompatibility = 1.11
targetCompatibility = 1.11

// The main class of the application
mainClassName = 'com.scienceminer.glutton.web.LookupServiceApplication'
tasks.run.workingDir = rootProject.rootDir

repositories {
    mavenLocal()
    mavenCentral()
}

sourceSets.main.resources {
    srcDirs = ["src/main/resources"];
}

configurations {
    all*.exclude group: 'org.slf4j', module: "slf4j-log4j12"
    all*.exclude group: 'log4j', module: "log4j"
    all*.exclude group: 'log4j2', module: "log4j2"
    implementation.setCanBeResolved(true)
}

processResources {
    filesMatching('config/glutton.yml') {
        filter {
            it.replace('project.version', project.property('version_placeholder'))
        }
    }
}

task install(dependsOn: installShadowDist)

dependencies {
    testImplementation group: 'junit', name: 'junit', version: '4.12'
    testImplementation "org.hamcrest:hamcrest-all:1.3"
    testImplementation "org.easymock:easymock:3.5"

    implementation "com.google.code.gson:gson:2.8.1"

    //Dropwizard
    implementation 'ru.vyarus:dropwizard-guicey:7.0.0'

    implementation 'io.dropwizard:dropwizard-bom:4.0.0'
    implementation 'io.dropwizard:dropwizard-core:4.0.0'
    implementation 'io.dropwizard:dropwizard-assets:4.0.0'
    implementation 'io.dropwizard:dropwizard-testing:4.0.0'
    implementation 'io.dropwizard.modules:dropwizard-testing-junit4:4.0.0'
    implementation 'io.dropwizard:dropwizard-forms:4.0.0'
    implementation 'io.dropwizard:dropwizard-client:4.0.0'
    implementation 'io.dropwizard:dropwizard-auth:4.0.0'
    implementation 'io.dropwizard.metrics:metrics-core:4.2.22'
    implementation 'io.dropwizard.metrics:metrics-servlets:4.2.22'

    implementation 'jakarta.validation:jakarta.validation-api:2.0.2'

    implementation 'org.slf4j:slf4j-api:1.7.30'
    implementation 'ch.qos.logback:logback-classic:1.2.3'
    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.8.2'

    implementation "com.rockymadden.stringmetric:stringmetric-core_2.10:0.27.3"

    //Parsing XML/Json
    implementation group: 'org.codehaus.woodstox', name: 'stax2-api', version: '4.0.0'
    implementation group: 'org.codehaus.woodstox', name: 'woodstox-core-asl', version: '4.4.1'

    implementation 'org.lmdbjava:lmdbjava:0.9.0'
    implementation 'de.ruedigermoeller:fst:2.56'
    implementation 'org.xerial.snappy:snappy-java:1.1.7.2'

    implementation 'org.elasticsearch.client:elasticsearch-rest-high-level-client:7.17.2'
    implementation 'co.elastic.clients:elasticsearch-java:8.12.1'
    implementation ('org.apache.solr:solr-solrj:9.5.0') {
        exclude group: 'org.eclipse.jetty', module: 'jetty-http2'
        exclude group: 'org.eclipse.jetty.http2', module: 'http2-client'
    }

    implementation 'org.apache.commons:commons-collections4:4.1'
    implementation 'commons-beanutils:commons-beanutils:1.9.4'
    implementation 'commons-io:commons-io:2.6'
    implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.20'

    implementation group: 'org.tukaani', name: 'xz', version: '1.8'

    implementation "com.fasterxml.jackson.core:jackson-core:2.14.3"
    implementation "com.fasterxml.jackson.core:jackson-databind:2.14.3"
    implementation "com.fasterxml.jackson.module:jackson-module-afterburner:2.14.3"
    implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.14.3"

    implementation group: 'com.opencsv', name: 'opencsv', version: '5.0'
}

distributions {
    shadow {
        /*contents {
            from(new File(rootProject.rootDir, "data/config")) {
                into "data/config"
            }
        }*/
    }
}

shadowJar {
    classifier = 'onejar'
    mergeServiceFiles()
    zip64 true
    manifest {
        attributes 'Main-Class': mainClassName
    }
    exclude("logback.xml")
    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
}

distTar.enabled = false
distZip.enabled = false
shadowDistTar.enabled = false

artifacts {
    archives shadowJar
}

// arguments for exec tasks
ext.getArg = { propName, defaultVal ->
    return project.hasProperty(propName) ? project.getProperty(propName) : defaultVal;
}

task server(dependsOn: 'classes', type: JavaExec, group: 'service') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'server', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED"  
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task crossref(dependsOn: 'classes', type: JavaExec, group: 'data') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'crossref', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task gap_crossref(dependsOn: 'classes', type: JavaExec, group: 'data') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'gap_crossref', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task hal(dependsOn: 'classes', type: JavaExec, group: 'data') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'hal', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED"
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task pmid(dependsOn: 'classes', type: JavaExec, group: 'service') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'pmid', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED"  
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task unpaywall(dependsOn: 'classes', type: JavaExec, group: 'data') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'unpaywall', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

task istex(dependsOn: 'classes', type: JavaExec, group: 'data') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'istex', '--input', getArg('input', ''), getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

// only used it to re-create the search index from scratch, keeping the LMDB unchanged
task index(dependsOn: 'classes', type: JavaExec, group: 'search') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'index', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

// experimental
task hal_audit(dependsOn: 'classes', type: JavaExec, group: 'search') {
    main = 'com.scienceminer.glutton.web.LookupServiceApplication'
    classpath = sourceSets.main.runtimeClasspath
    args 'hal_audit', getArg('config', 'config/glutton.yml') 
    if(JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Xmx3072m', "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    } else {
        jvmArgs '-Xmx3072m'
    }
}

test {
    useJUnitPlatform()
        
    testLogging.showStandardStreams = true
    // enable for having separate test executor for different tests
    forkEvery = 1
    maxHeapSize = "1024m"        

    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED", 
        "--add-opens", "java.base/java.nio=ALL-UNNAMED", "--add-opens", "java.base/sun.nio.ch=ALL-UNNAMED", "--add-opens", "java.base/java.text=ALL-UNNAMED", "--add-opens", "java.base/java.net=ALL-UNNAMED", "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-opens", "java.base/java.math=ALL-UNNAMED", "--add-opens", "java.base/java.util=ALL-UNNAMED", "--add-opens", "java.base/java.util.concurrent=ALL-UNNAMED", "--add-opens", "java.base/java.time=ALL-UNNAMED" 
    }
}