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

group = "com.scienceminer.nerd"
version = '0.0.6'

description = """entity recognition and disambiguation against Wikidata and Wikipedia in a raw text, partially-annotated text segment, PDF or weighted term vector"""

sourceCompatibility = 1.8
targetCompatibility = 1.8

import org.apache.tools.ant.taskdefs.condition.Os

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

repositories {
    mavenLocal()
    mavenCentral()
    maven { url "https://grobid.s3.eu-west-1.amazonaws.com/repo/" }
    //jcenter()
    maven {
        url 'lib/'
    }
}

dependencies {
    // Tests
    testImplementation group: 'junit', name: 'junit', version: '4.13.1'
    testImplementation "org.hamcrest:hamcrest-all:1.3"
    testImplementation group: 'org.easymock', name: 'easymock', version: '3.5'

    // to be removed?
    testImplementation group: 'com.googlecode.json-simple', name: 'json-simple', version: '1.1.1'

    // GROBID
    implementation (group: 'org.grobid', name: 'grobid-core', version: '0.8.0') {
        //exclude(module: 'log4j-over-slf4j')
        exclude(group: 'ch.qos.logback', module: 'logback-classic')
    }
    implementation (group: 'org.grobid', name: 'grobid-trainer', version: '0.8.0') {
        //exclude(module: 'log4j-over-slf4j')
        exclude(group: 'ch.qos.logback', module: 'logback-classic')
    }
    implementation (group: 'org.grobid', name: 'grobid-ner', version: '0.8.0') {
        //exclude(module: 'log4j-over-slf4j')
        exclude(group: 'ch.qos.logback', module: 'logback-classic')
    }

    implementation 'black.ninia:jep:4.0.2'
    implementation 'org.apache.opennlp:opennlp-tools:1.9.1'
    implementation "joda-time:joda-time:2.9.9"
    implementation "org.apache.lucene:lucene-analyzers-common:4.5.1"
    implementation group: 'org.jruby', name: 'jruby-complete', version: '9.2.13.0'

    //implementation group: 'directory-naming', name: 'naming-java', version: '0.8'
    implementation group: 'fr.limsi.wapiti', name: 'wapiti', version: '1.5.0'
    implementation group: 'org.wipo.analysers', name: 'wipo-analysers', version: '0.0.1'

    // Apache commons
    implementation 'org.apache.commons:commons-collections4:4.1'
    implementation 'org.apache.commons:commons-lang3:3.6'
    implementation 'commons-logging:commons-logging:1.2'
    implementation 'commons-io:commons-io:2.7'
    implementation 'commons-pool:commons-pool:1.6'
    implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.13'
    implementation group: 'org.apache.httpcomponents', name: 'httpmime', version: '4.5.13'
    implementation group: 'org.apache.commons', name: 'commons-text', version: '1.1'
    implementation group: 'com.google.guava', name: 'guava', version: '29.0-jre'

    // json and yaml
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.10.1'
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.10.1'
    implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.10.1'
    implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.10.1'

    // Web services
    implementation "io.dropwizard:dropwizard-core:1.3.29"
    implementation "io.dropwizard:dropwizard-assets:1.3.29"
    implementation "com.hubspot.dropwizard:dropwizard-guicier:1.3.5.2"
    implementation "io.dropwizard:dropwizard-testing:1.3.29"
    implementation "io.dropwizard:dropwizard-forms:1.3.29"
    implementation "io.dropwizard:dropwizard-client:1.3.29"
    implementation "io.dropwizard:dropwizard-auth:1.3.29"
    implementation "io.dropwizard.metrics:metrics-core:4.0.5"
    implementation "io.dropwizard.metrics:metrics-servlets:4.0.5"
    implementation "io.prometheus:simpleclient_dropwizard:0.11.0"
    implementation "io.prometheus:simpleclient_servlet:0.11.0"

    implementation group: 'net.arnx', name: 'jsonic', version: '1.3.10'

    implementation "com.google.code.gson:gson:2.8.1"
    implementation 'javax.mail:javax.mail-api:1.6.2'
    implementation group: 'javax.activation', name: 'activation', version: '1.1.1'

    //Specialised libraries
    implementation group: 'com.github.haifengl', name: 'smile-core', version: '1.3.1'
    implementation(group: 'it.unimi.dsi', name: 'sux4j', version: '3.1.2') {
        exclude(module: 'log4j-over-slf4j')
        exclude(group: 'ch.qos.logback', module: 'logback-classic')
    }
    implementation group: 'it.unimi.dsi', name: 'fastutil', version: '6.5.12'
    implementation group: 'it.unimi.dsi', name: 'dsiutils', version: '2.1.9'

    implementation group: 'de.ruedigermoeller', name: 'fst', version: '2.56'

    //Wikipedia
    implementation group: 'org.sweble.wikitext', name: 'swc-parser-lazy', version: '3.1.9'
    implementation(group: 'org.sweble.wikitext', name: 'swc-engine', version: '3.1.9') {
        exclude(module: 'jaxb-impl')   
    }

    //XML
    implementation group: 'com.thoughtworks.xstream', name: 'xstream', version: '1.4.19'

    //LMDB
    implementation group: 'org.deephacks.lmdbjni', name: 'lmdbjni', version: '0.4.6'
    implementation group: 'org.deephacks.lmdbjni', name: 'lmdbjni-linux64', version: '0.4.6'
    implementation group: 'org.deephacks.lmdbjni', name: 'lmdbjni-osx64', version: '0.4.6'
    implementation group: 'org.deephacks.lmdbjni', name: 'lmdbjni-win64', version: '0.4.6'

    //Hadoop
    implementation(group: 'org.apache.hadoop', name: 'hadoop-core', version: '1.2.1') {
        exclude(module: 'jaxb-impl')   
        exclude(module: 'jersey-core')
        exclude(module: 'jersey-json')
        exclude(module: 'jersey-server')
    }
    implementation group: 'org.apache.avro', name: 'avro', version: '1.7.5'
}

configurations.all {
    resolutionStrategy {
        force 'xml-apis:xml-apis:1.4.01'
    }

    exclude group: "ch.qos.logback", module: "logback-classic"
    exclude group: 'org.slf4j', module: "slf4j-log4j12"
    exclude group: 'org.slf4j', module: "slf4j-jdk14"
    exclude group: 'log4j', module: "log4j"
    exclude group: 'org.slf4j', module: "log4j-over-slf4j"
}

test {
    testLogging.showStandardStreams = true
    exclude '**/**IntegrationTest**'

    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs "--add-opens", "java.base/java.util.stream=ALL-UNNAMED", 
        "--add-opens", "java.base/java.io=ALL-UNNAMED", "--add-modules", "jdk.incubator.foreign"
    }
}

/*tasks.withType(JavaCompile) {
    options.compilerArgs << "-Xlint:deprecation"
    options.compilerArgs << "-Xlint:unchecked"
}*/

//distTar.enabled = false
//distZip.enabled = false

wrapper {
    gradleVersion "7.2"
}

// return the default value if the property has not been specified in command line
ext.getArg = { propName, defaultVal ->
    return project.hasProperty(propName) ? project.getProperty(propName) : defaultVal;
}

// Training with Wikipedia
// Run like this: ./gradlew train_wikipedia -Plang=en
// ./gradlew train_wikipedia -Plang=fr
// etc.
task(train_wikipedia, dependsOn: 'classes', type: JavaExec, group: 'training') {
    main = 'com.scienceminer.nerd.training.WikipediaTrainer'
    classpath = sourceSets.main.runtimeClasspath
    args 'data/wikipedia/training/', getArg('lang', 'en')
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g', "--add-opens", "java.base/java.lang=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" 
    } else {
        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g'
    }
}

// Training with an annotated corpus
// Run like this: ./gradlew train_corpus -Pcorpus=aquaint -Plang=en
// ./gradlew train_corpus -Pcorpus=aida-train -Plang=en 
// etc.
task(train_corpus, dependsOn: 'classes', type: JavaExec, group: 'training') {
    main = 'com.scienceminer.nerd.training.CorpusTrainer'
    classpath = sourceSets.main.runtimeClasspath
    args getArg('corpus', ''), getArg('lang', 'en')
    jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g'
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g', "--add-opens", "java.base/java.lang=ALL-UNNAMED", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Djdk.xml.totalEntitySizeLimit=2147480000', '-Xms2g', '-Xmx8g'
    }
}

// Evaluation
// Run like this: ./gradlew evaluation -Pcorpus=[corpusname]
// e.g. ./gradlew evaluation -Pcorpus=aida-testb
task(evaluation, dependsOn: 'classes', type: JavaExec, group: 'evaluation') {
    main = 'com.scienceminer.nerd.evaluation.NEDCorpusEvaluation'
    classpath = sourceSets.main.runtimeClasspath
    args getArg('corpus', '')
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// training data generation
// Run like this: ./gradlew annotatedDataGeneration -Pcorpus=[corpusname]
// e.g. ./gradlew annotatedDataGeneration -Pcorpus=toto
task(annotatedDataGeneration, dependsOn: 'classes', type: JavaExec, group: 'training') {
    main = 'com.scienceminer.nerd.evaluation.AnnotatedDataGeneration'
    classpath = sourceSets.main.runtimeClasspath
    args getArg('corpus', '')
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// create entity description, necessary to then create entity embeddings
// Run like this: ./gradlew generate_entity_description -Plang=en
// ./gradlew generate_entity_description -Plang=fr
// etc.
task(generate_entity_description, dependsOn: 'classes', type: JavaExec, group: 'embeddings') {
    main = 'com.scienceminer.nerd.embeddings.EntityDescription'
    classpath = sourceSets.main.runtimeClasspath
    args 'data/embeddings/', getArg('lang', 'en')
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// tasks related to embeddings generation

// quantize word embeddings 
// Run like this: ./gradlew quantize_word_embeddings -Pi=word.embeddings.vec -Po=word.embeddings.quantized
task(quantize_word_embeddings, dependsOn: 'classes', type: JavaExec, group: 'embeddings') {
    main = 'com.scienceminer.nerd.embeddings.Quantizer'
    classpath = sourceSets.main.runtimeClasspath
    args '-i', getArg('i', 'word.embeddings.vec'), '-o', getArg('o', 'word.embeddings.quantized'), '-error', getArg('e', '0.01'), '-hashheader'
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// create entity embeddings from word embeddings and generated entity description 
// Run like this: ./gradlew generate_entity_embeddings -Pin=entity.description -Pv=word.embeddings.quantized -Pout=entity.embeddings.vec -Pn=10
task(generate_entity_embeddings, dependsOn: 'classes', type: JavaExec, group: 'embeddings') {
    main = 'com.scienceminer.nerd.embeddings.EntityEmbeddings'
    classpath = sourceSets.main.runtimeClasspath
    args '-in', getArg('in', 'entity.description'), '-v', getArg('v', 'word.embeddings.quantized'), '-out', getArg('out', 'entity.embeddings.vec'), '-n', getArg('n', '8')
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// quantize entity embeddings 
// Run like this: ./gradlew quantize_entity_embeddings -Pi=entity.embeddings.vec -Po=entity.embeddings.quantized
task(quantize_entity_embeddings, dependsOn: 'classes', type: JavaExec, group: 'embeddings') {
    main = 'com.scienceminer.nerd.embeddings.Quantizer'
    classpath = sourceSets.main.runtimeClasspath
    args '-i', getArg('i', 'entity.embeddings.vec'), '-o', getArg('o', 'entity.embeddings.quantized'), '-error', getArg('e', '0.01'), '-hashheader'
    if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
        jvmArgs '--Xms2g', '-Xmx8g', "--add-opens", "--add-modules", "jdk.incubator.foreign", "--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" 
    } else {
        jvmArgs '--Xms2g', '-Xmx8g'
    }
}

// service
apply plugin: 'application'
application {
    mainClassName = 'com.scienceminer.nerd.service.NerdApplication'

    run {
        if (JavaVersion.current().compareTo(JavaVersion.VERSION_1_8) > 0) {
            jvmArgs "--add-modules", "jdk.incubator.foreign", "--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" 
        }
    
        args = ['server', 'data/config/service.yaml']
    }
}