build.gradle

import org.apache.tools.ant.filters.ReplaceTokens;
import org.gradle.api.tasks.Exec;
import org.apache.tools.ant.taskdefs.condition.Os

apply plugin: 'java'
apply plugin: 'war'
apply plugin: 'eclipse'
apply plugin: 'idea'

archivesBaseName = 'openspecimen'

Properties props = new Properties()
props.load(new FileInputStream("build.properties"))

def deploymentLocation = props.app_home + "/server/default/deploy"

if(new File(props.app_home + '/webapps').exists()) {
  deploymentLocation = props.app_home + "/webapps"
}

project.ext["deploy_location"]           = deploymentLocation

def environment = 'dev';
def envScript;

if (project.hasProperty("env")) {
  environment = env
}

if (environment == 'prod') {
  envScript = file("prod.gradle")
  if (!envScript.exists()) {
    throw new GradleException("Unknown environment: $env")
  }
} else if (environment == 'test') {
  envScript = file("test.gradle")
  if (!envScript.exists()) {
    throw new GradleException("Unknown environment: $env")
  }
} else {
  envScript = file("dev.gradle")
  if (!envScript.exists()) {
    throw new GradleException("Unknown environment: $env")
  }
}

sourceSets {
  main.java.srcDirs = ['WEB-INF/src']
  main.resources.srcDirs = ['WEB-INF/resources']
}

tasks.withType(JavaCompile) {
  options.compilerArgs += ['-parameters']
}

description = "openspecimen"

repositories {
  mavenCentral()

  maven {
    url "https://build.shibboleth.net/nexus/content/repositories/releases/"
  }
  maven {
    url "https://build.shibboleth.net/maven/releases/"
  }
}

configurations {
  ajc
  aspects
  aspectCompile
  
  compile {
    extendsFrom aspects
  }
}

configurations.all {
  transitive = false
}

dependencies {
  ajc       "org.aspectj:aspectjtools:1.9.19"
  implementation   "org.aspectj:aspectjrt:1.9.19"
  aspects   "org.springframework:spring-aspects:6.2.16"

  implementation fileTree(dir: 'lib', include: ['os-dynamic-forms-trunk.jar', 'os-tinymce.jar'])
  
  implementation group: 'jakarta.persistence', name: 'jakarta.persistence-api', version: '3.2.0'
  implementation group: 'jakarta.servlet', name: 'jakarta.servlet-api', version: '6.1.0'
  implementation group: 'org.antlr', name: 'antlr4', version:'4.13.2'
  implementation group: 'org.antlr', name: 'antlr4-runtime', version:'4.13.2'
  implementation group: 'aopalliance', name: 'aopalliance', version:'1.0'
  implementation group: 'asm', name: 'asm', version:'3.3.1'
  implementation group: 'org.aspectj', name: 'aspectjweaver', version:'1.9.19'
  implementation group: 'cglib', name: 'cglib', version:'3.1'
  implementation group: 'commons-beanutils', name: 'commons-beanutils', version:'1.9.4'
  implementation group: 'commons-codec', name: 'commons-codec', version:'1.15'
  implementation group: 'commons-fileupload', name: 'commons-fileupload', version:'1.4'
  implementation group: 'commons-httpclient', name: 'commons-httpclient', version:'3.1'
  implementation group: 'commons-io', name: 'commons-io', version:'2.18.0'
  implementation group: 'org.apache.commons', name: 'commons-collections4', version:'4.4'
  implementation group: 'org.apache.commons', name: 'commons-digester3', version:'3.2'
  implementation group: 'org.apache.commons', name: 'commons-lang3', version:'3.17.0'
  implementation group: 'org.apache.commons', name: 'commons-compress', version: '1.27.1'
  implementation group: 'org.apache.commons', name: 'commons-text', version: '1.15.0'
  implementation group: 'org.apache.taglibs', name: 'taglibs-standard-impl', version: '1.2.5'
  implementation group: 'org.apache.tika', name: 'tika-core', version: '3.3.1'
  implementation group: 'org.apache.tika', name: 'tika-parsers-standard-package', version: '3.3.1'
  implementation group: 'net.sf.kxml', name: 'kxml2-min', version:'2.3.0'
  implementation group: 'net.sf.ehcache', name: 'ehcache', version:'1.2.3'
  implementation group: 'net.sf.opencsv', name: 'opencsv', version:'2.3'
  implementation group: 'com.google.code.gson', name: 'gson', version:'2.8.9'
  implementation group: 'org.hibernate.common', name: 'hibernate-commons-annotations', version:'6.0.4.Final'
  implementation group: 'org.hibernate.orm', name: 'hibernate-core', version:'7.2.4.Final'
  implementation group: 'org.hibernate.orm', name: 'hibernate-envers', version:'7.2.4.Final'
  implementation group: 'org.hibernate.models', name: 'hibernate-models', version: '1.0.1'
  implementation group: 'net.bytebuddy', name: 'byte-buddy', version: '1.17.8'
  implementation group: 'com.fasterxml', name: 'classmate', version: '1.7.3'
  implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version:'2.22'
  implementation group: 'com.fasterxml.jackson.core', name: 'jackson-core', version:'2.22.1'
  implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version:'2.22.1'
  implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version:'2.22.1'
  implementation group: 'org.javassist', name: 'javassist', version:'3.19.0-GA'
  implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '4.0.6'
  implementation group: 'org.glassfish.jaxb', name: 'jaxb-core', version: '4.0.6'
  implementation group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '4.0.6'
  implementation group: 'org.glassfish.jaxb', name: 'txw2', version: '4.0.6'
  implementation group: 'com.sun.istack', name: 'istack-commons-runtime', version: '4.1.2'
  implementation group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version:'4.0.6'
  implementation group: 'org.jboss.logging', name: 'jboss-logging', version:'3.6.1.Final'
  implementation group: 'org.scijava', name: 'jep', version:'2.4.2'
  implementation group: 'org.json', name: 'json', version:'20140107'
  implementation group: 'jakarta.ws.rs', name: 'jakarta.ws.rs-api', version:'3.1.0'
  implementation group: 'jakarta.transaction', name: 'jakarta.transaction-api', version:'2.0.1'
  implementation group: 'com.sun.mail', name: 'jakarta.mail', version: '2.0.1'
  implementation group: 'org.liquibase', name: 'liquibase-core', version:'4.8.0'

  implementation group: 'commons-logging', name: 'commons-logging', version: '1.2'
  implementation group: 'org.apache.logging.log4j', name: 'log4j-api', version: '2.17.1'
  implementation group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.17.1'
  implementation group: 'org.slf4j', name: 'slf4j-api', version: '1.7.12'

  implementation group: 'quartz', name: 'quartz', version:'1.5.2'

  implementation group: 'org.springframework', name: 'spring-aspects', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-aop', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-beans', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-context', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-context-support', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-core', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-expression', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-instrument', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-jdbc', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-tx', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-web', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-webmvc', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-orm', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-messaging', version: '7.0.8'
  implementation group: 'org.springframework', name: 'spring-jms', version: '7.0.8'
  implementation group: 'org.springframework.integration', name: 'spring-integration-core', version: '7.0.5'
  implementation group: 'org.springframework.integration', name: 'spring-integration-mail', version: '7.0.5'
  implementation group: 'org.springframework.ldap', name: 'spring-ldap-core', version: '4.0.4'

  implementation group: 'org.springframework.security', name: 'spring-security-crypto', version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-config', version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-core',   version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-ldap',   version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-web',    version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-oauth2-core', version: '7.0.6'
  implementation group: 'org.springframework.security', name: 'spring-security-oauth2-jose', version: '7.0.6'

  implementation group: 'com.nimbusds', name: 'nimbus-jose-jwt', version: '9.31'

  implementation group: 'com.thoughtworks.xstream', name: 'xstream', version:'1.4.19'
  implementation group: 'com.itextpdf', name: 'itextpdf', version:'5.5.13.2'
  implementation group: 'dom4j', name: 'dom4j', version: '1.6.1'
  implementation group: 'com.jcraft', name: 'jsch', version: '0.1.54'

  implementation group: 'com.github.ua-parser', name: 'uap-java', version: '1.5.2'
  implementation group: 'org.yaml', name: 'snakeyaml', version: '1.28'

  implementation group: 'org.owasp.encoder', name: 'encoder', version: '1.2.3'

  // HTML to PDF lib
  implementation group: 'org.apache.pdfbox', name: 'pdfbox', version: '2.0.24'
  implementation group: 'org.apache.pdfbox', name: 'xmpbox', version: '2.0.24'
  implementation group: 'org.apache.pdfbox', name: 'fontbox', version: '2.0.24'
  implementation group: 'de.rototor.pdfbox', name: 'graphics2d', version: '0.32'
  implementation group: 'com.openhtmltopdf', name: 'openhtmltopdf-core', version: '1.0.9'
  implementation group: 'com.openhtmltopdf', name: 'openhtmltopdf-pdfbox', version: '1.0.9'

  // Java APIs to access MS format files
  implementation group: 'org.apache.poi', name: 'poi', version: '5.3.0'
  implementation group: 'org.apache.poi', name: 'poi-ooxml', version: '5.3.0'
  implementation group: 'org.apache.poi', name: 'poi-ooxml-lite', version: '5.3.0'
  implementation group: 'org.apache.xmlbeans', name: 'xmlbeans', version: '5.2.2'

  implementation group: 'com.google.zxing', name: 'core', version: '3.4.1'

  implementation group: 'org.owasp.esapi', name: 'esapi', version: '2.2.0.0'
  implementation group: 'xerces', name: 'xercesImpl', version: '2.12.2'
  implementation group: 'xalan', name: 'xalan', version: '2.7.3'
  implementation group: 'xalan', name: 'serializer', version: '2.7.3'
  implementation group: 'joda-time', name: 'joda-time', version: '2.10'
  implementation group: 'org.apache.velocity', name: 'velocity-engine-core', version:'2.3'

  implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '2.1.2'
  implementation group: 'org.eclipse.angus',  name: 'angus-activation', version: '2.0.2'

  implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '4.0.4'
  implementation group: 'jakarta.inject', name: 'jakarta.inject-api', version: '2.0.1'
  implementation group: 'org.jspecify', name: 'jspecify', version: '1.0.0'

  // New SAML library
  implementation group: 'org.springframework.security', name: 'spring-security-saml2-service-provider', version: '7.0.6'
  implementation group: 'org.opensaml', name: 'opensaml-core-api', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-core-impl', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-saml-api', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-saml-impl', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-soap-api', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-soap-impl', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-xmlsec-api', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-xmlsec-impl', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-security-api', version: '5.1.6'
  implementation group: 'org.opensaml', name: 'opensaml-security-impl', version: '5.1.6'
  implementation group: 'net.shibboleth.utilities', name: 'java-support', version: '8.1.0'
  implementation group: 'net.shibboleth', name: 'shib-support', version: '9.1.6'
  implementation group: 'net.shibboleth', name: 'shib-security', version: '9.1.6'
  implementation group: 'com.google.guava', name: 'guava', version: '33.0.0-jre'
  implementation group: 'io.dropwizard.metrics', name: 'metrics-core', version: '4.2.37'
  implementation group: 'org.cryptacular', name: 'cryptacular', version: '1.2.7'
  implementation group: 'org.apache.httpcomponents', name: 'httpcore', version: '4.4.16'  // Core HTTP functionality
  implementation group: 'org.apache.httpcomponents', name: 'httpclient', version: '4.5.14'
  implementation group: 'org.apache.httpcomponents.client5', name: 'httpclient5', version: '5.4.1'
  implementation group: 'org.apache.httpcomponents.core5', name: 'httpcore5', version: '5.2.5'
  implementation group: 'org.bouncycastle', name: 'bcprov-jdk18on', version: '1.84'
  implementation group: 'org.bouncycastle', name: 'bcpkix-jdk18on', version: '1.84'
  implementation group: 'org.bouncycastle', name: 'bcutil-jdk18on', version: '1.84'
  implementation group: 'org.apache.santuario', name: 'xmlsec', version: '2.3.0'

  implementation group: 'io.micrometer', name: 'micrometer-commons', version: '1.16.1'
  implementation group: 'io.micrometer', name: 'micrometer-core', version: '1.16.1'
  implementation group: 'io.micrometer', name: 'micrometer-observation', version: '1.16.1'
  implementation group: 'io.micrometer', name: 'micrometer-registry-prometheus', version: '1.16.1'
  implementation group: 'io.prometheus', name: 'prometheus-metrics-model', version: '1.3.1'
  implementation group: 'io.prometheus', name: 'prometheus-metrics-core', version: '1.3.1'
  implementation group: 'io.prometheus', name: 'prometheus-metrics-config', version: '1.3.1'
  implementation group: 'io.prometheus', name: 'prometheus-metrics-exposition-formats', version: '1.3.1'
  implementation group: 'io.prometheus', name: 'prometheus-metrics-shaded-protobuf', version: '1.3.1'

  runtimeOnly group: 'antlr', name: 'antlr', version: '2.7.7'
  runtimeOnly group: 'org.apache.logging.log4j', name: 'log4j-slf4j-impl', version: '2.16.0'
  runtimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '2.16.0'

  testImplementation group: 'junit', name: 'junit', version:'4.13.1'
  testImplementation group: 'org.hamcrest', name: 'hamcrest-core', version: '1.3'
}

compileJava {
  options.release = 17

  afterEvaluate {
    tasks.withType(JavaCompile) {
      options.compilerArgs += ['-Xlint:deprecation', '-Xmaxwarns', '10000', '-Xmaxerrs',  '2000', '-parameters']
    }
  }

  doLast{
    ant.taskdef(resource: "org/aspectj/tools/ant/taskdefs/aspectjTaskdefs.properties", 
                classpath: configurations.ajc.asPath)
    ant.iajc(
      source: 17,
      target: 17,
      destDir: sourceSets.main.output.classesDirs.asPath,
      maxmem: "512m", 
      fork: "true",
      aspectPath: configurations.aspects.asPath,  
      sourceRootCopyFilter: "**/*.java",
      classpath: "${configurations.compileClasspath.asPath};${configurations.aspectCompile.asPath}"){
      sourceroots{
        sourceSets.main.java.srcDirs.each{
          pathelement(location:it.absolutePath)
        }
      }
    }
  }
}

def getTodayDate() {
  def today = new Date()
  return String.valueOf(today.getTime())
}

def getCommitRevision() {
  def revCmd = "git rev-parse --short HEAD"
  def revision = revCmd.execute()
  return revision.text.trim()
}

def getBranch() {
  def branchCmd = "git symbolic-ref -q --short HEAD";
  def branch = branchCmd.execute().text.trim();

  if (branch.length() == 0) {
    branchCmd = "git describe --tags --exact-match";
    branch = branchCmd.execute().text.trim();
  }
  return branch;
}

processResources {
  duplicatesStrategy(DuplicatesStrategy.INCLUDE)

  from(sourceSets.main.resources.srcDirs) {
    include 'application.properties'

    filter(
      ReplaceTokens, 
      tokens: [
        buildinfo_version : getBranch(),
        buildinfo_date : getTodayDate(),
        buildinfo_commit_revision : getCommitRevision()])
  }
}

task create_war(type: War) {
  from ('./') {
    include 'index.html'
    include 'index-redirect.js'
  }

  from ('./WEB-INF/') {
    include 'resources/**'
    include 'applicationContext.xml'
    include 'restApiContext.xml'
    include 'pluginUiContext.xml'
    include 'pluginVueUiContext.xml'
    include 'migrationContext.xml'
    include 'postInitContext.xml'
    include 'web.xml'
    
    into 'WEB-INF/'
  }
  
  from ('./build/') {
    include 'form-designer/**'
  }

  from ('./ui/dist') {
    include '**/**'

    into 'ui-app/'
  }
  
  manifest {
    attributes(
      "Implementation-Title": archivesBaseName,
      "Implementation-Version": getBranch(),
      "Implementation-Timestamp": new Date()
    )
  }
}

task vue_backup_src(type: Exec) {
  workingDir './ui'
  commandLine 'mv', 'src', 'src_bk'
}

task vue_install_dependencies(type: Exec) {
  workingDir './ui'
  commandLine 'npm', 'install'
}

task vue_restore_src(type: Exec) {
  workingDir './ui'
  commandLine 'mv', 'src_bk', 'src'
}

task vue_build(type: Exec) {
  workingDir './ui'
  commandLine 'npm', 'run', 'build'
}

vue_install_dependencies.dependsOn vue_backup_src
vue_restore_src.dependsOn vue_install_dependencies
vue_build.dependsOn vue_restore_src
create_war.dependsOn vue_build
build.dependsOn create_war

apply from: envScript