build.gradle

buildscript {
    apply from: '../gradle/repository.gradle'

	repositories repositoryConfig

    dependencies {
        classpath 'apache:commons-codec:1.10',
                  'owasp:dependency-check-gradle:6.2.2',
				  'paleozogt:symzip-plugin:0.10.1',
				  'com.moowork.gradle:gradle-node-plugin:1.2.0'
    }
}

apply plugin: org.owasp.dependencycheck.gradle.DependencyCheckPlugin
apply plugin: "org.paleozogt.symzip"
apply plugin: "com.moowork.node"

dependencyCheck {
  failBuildOnCVSS = 7 // 0 - 4 = low, 4 - 7 = medium, 7 - 9 = high, 9-10 = critical
  suppressionFile = "owasp_suppressing_false_positives.xml"
  analyzers{
    assemblyEnabled = false
  }
  proxy {
   server = 'proxy.ethz.ch'
   port = 3128
  }
}

evaluationDependsOn(':commonbase')
evaluationDependsOn(':common')
evaluationDependsOn(':openbis_api')
evaluationDependsOn(':openbis-common')
evaluationDependsOn(':authentication')
evaluationDependsOn(':dbmigration')
evaluationDependsOn(':openbis')
evaluationDependsOn(':datastore_server')
evaluationDependsOn(':screening')
evaluationDependsOn(':rtd_yeastx')
evaluationDependsOn(':deep_sequencing_unit')
evaluationDependsOn(':plasmid')
evaluationDependsOn(':big_data_link_server')
evaluationDependsOn(':openbis_ng_ui')


apply from: '../gradle/javaproject.gradle'
apply from: 'query-api.gradle'
apply from: 'screening-api.gradle'
apply from: 'clients.gradle'
apply from: 'admin-console.gradle'

apply plugin: 'war'

archivesBaseName = 'openBIS-server-standard-technologies'

configurations.create('gwt')
configurations.create('zipping')
configurations.create('datastore_server')
configurations.create('javadoc_sources')
configurations.create('javadoc_compilation')

def jettyVersion = '9.4.44'

dependencies {
	compile project(':screening')

	providedCompile 'google:gwt-user:2.4'

	providedRuntime "eclipse:jetty-deploy:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-xml:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-webapp:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-servlet:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-security:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-server:${jettyVersion}.v20210927@jar",
                    "eclipse:jetty-continuation:${jettyVersion}.v20210927@jar"

	gwt 'reveregroup:gwt-image-loader:1.1.4',
                'google:gwt-dev:2.4'

	zipping "eclipse:jetty-distribution:${jettyVersion}@zip"

	datastore_server project(':deep_sequencing_unit'),
					 project(':rtd_yeastx'),
					 project(':screening'),
					 project(':plasmid'),
					 'bioformats:bioformats:6.5.1',
					 'imagej:ij:1.43u',
					 'cisd:cisd-openbis-knime-server:13.6.0.r29301',
					 'apache:xml-apis:1.3.03',
					 'slf4j:slf4j:1.6.2',
					 'slf4j:slf4j-log4j12:1.6.2',
					 'sybit:image-viewer:0.3.6'

	javadoc_sources	project(path:':commonbase', configuration: 'archives'),
		    	project(path:':common', configuration: 'archives'),
		    	project(path:':openbis_api', configuration: 'archives'),
		    	project(path:':openbis-common', configuration: 'archives'),
		    	project(path:':openbis', configuration: 'archives'),
		    	project(path:':datastore_server', configuration: 'archives'),
		    	project(path:':screening', configuration: 'archives'),
		    	'sis:sis-base:18.09.0:sources',
		    	'cisd:cisd-args4j:9.11.2:sources',
		    	'cisd:cisd-hotdeploy:13.01.0:sources'

	javadoc_compilation	project(path:':screening')

    testCompile (project(path: ':openbis', configuration: 'tests')) {
         exclude group: 'google', module: 'gwt-user'
    }

}

sourceSets {
	test {
		resources {
			srcDirs = ['source/java', 'sourceTest/java']
		}
	}
}

def gwtBuildDir = "${project.buildDir}/gwt"
def gwtCacheBuildDir = "${project.buildDir}/gwt-unitCache"
def gwtModuleName = 'ch.systemsx.cisd.openbis.OpenBIS'
def gwtModuleBuildDir = "${gwtBuildDir}/${gwtModuleName}"
def gwtArchivePath = 'resource'
def gwtArchiveFileName = 'gwt.tar.gz'

task compileGwt (dependsOn: classes, type: JavaExec) {
	ext.buildDir = gwtBuildDir
	def extraDir = "${project.buildDir}/extra"

	// inputs.source
	sourceSets.main.java.srcDirs
	// inputs.dir
	sourceSets.main.output.resourcesDir
	outputs.dir buildDir

	doFirst {
		file(buildDir).mkdirs()
	}

	main = 'com.google.gwt.dev.Compiler'

	classpath {
		[
			sourceSets.main.java.srcDirs,
			project(":openbis").sourceSets.main.java.srcDirs,
			project(":openbis").sourceSets.main.output.resourcesDir,
			project(":openbis").sourceSets.main.output.classesDirs,
			project(":openbis").sourceSets.main.compileClasspath,
			project(":common").sourceSets.main.java.srcDirs,
			project(":openbis_api").sourceSets.main.java.srcDirs,
			project(":screening").sourceSets.main.java.srcDirs,
			project(":screening").sourceSets.main.output.resourcesDir,
			configurations.gwt
		]
	}

	args =
		[
			gwtModuleName,
			'-war', buildDir,
			'-logLevel', 'INFO',
			'-localWorkers', '2',
			'-compileReport',
			'-extra', extraDir,
		]

	maxHeapSize = '1024m'

	systemProperty "javax.xml.parsers.SAXParserFactory", "org.apache.xerces.jaxp.SAXParserFactoryImpl"
}

task buildCoreUIPackageUsingJDK8(type: Tar, dependsOn: compileGwt) {
	from gwtBuildDir
	destinationDirectory = file(gwtArchivePath)
	archiveFileName = gwtArchiveFileName
	compression = Compression.GZIP
	doLast { // Cleanup, the rest of the build should not use these
		delete gwtBuildDir
		delete gwtCacheBuildDir
	}
}

task untarGwt(type: Copy) {
	from tarTree(resources.gzip("${gwtArchivePath}/${gwtArchiveFileName}"))
	into gwtBuildDir
}

node {
	download = true
	version = '10.22.0'
	workDir = file("${projectDir}/node/nodejs")
	nodeModulesDir = file("${projectDir}")
}

task bundleOpenbisStaticResources(type: Exec) {
	dependsOn 'untarGwt'
	dependsOn 'npmInstall'
	commandLine 'bash', '-c', "${projectDir}/resource/js/v3/build.sh"
}

task copyOpenbisStaticResources(type: Copy) {
	dependsOn 'bundleOpenbisStaticResources'
	from "${project(':openbis').projectDir}/source/java/ch/systemsx/cisd/openbis/public"
	into gwtModuleBuildDir
}

ext.classpathEntries = files(
	project(':openbis').file('source/java/applicationContext.xml'),
	project(':openbis').file('source/java/dbConfigurationContext.xml'),
	project(':openbis').file('source/java/ehcache.xml'),
	project(':openbis').file('source/java/genericApplicationContext.xml'),
	project(':openbis').file('source/java/hibernateContext.xml'),
	project(':openbis').file('source/java/schema-for-xslt20.xsd'),
	project(':openbis').file('source/java/XMLSchema.xsd'),
	project(':screening').file('source/java/screening-applicationContext.xml'),
	project(':screening').file('source/java/screening-dssApplicationContext.xml'),
	project(':screening').file('source/java/screening-plugin-applicationContext.xml'),
	project(':common').file('source/java/genericCommonContext.xml'),
	'source/java/standard-technologies-applicationContext.xml'
)

ext.zipEntries = files(
	project(':openbis').file('dist/server/autosymlink.sh'),
	project(':openbis').file('dist/server/check.sh'),
	project(':openbis').file('dist/server/configure.sh'),
	project(':openbis').file('dist/server/export-master-data.py'),
	project(':openbis').file('dist/server/export-master-data.sh'),
	project(':openbis').file('dist/server/install.sh'),
	project(':openbis').file('dist/server/openBIS.keystore'),
	project(':openbis').file('dist/server/openbis.conf'),
	project(':openbis').file('dist/server/passwd.sh'),
	project(':openbis').file('dist/server/register-master-data.sh'),
	project(':openbis').file('dist/server/setup-env'),
	project(':openbis').file('dist/server/shutdown.sh'),
	project(':openbis').file('dist/server/startup.sh'),
	project(':openbis').file('dist/server/status.sh'),
	project(':openbis').file('dist/server/version.sh'),
	project(':openbis').file('dist/server/watchdog.sh'),
	project(':openbis').fileTree(dir: 'dist/server').matching {
	   include 'base/**'
	},
	file('dist/server/service.properties'),
	file('dist/server/web-client.properties')
)

task checkFilesExist {
  inputs.files files(classpathEntries, zipEntries)
  doLast {
    classpathEntries.each {
   	  x -> assert x.exists()
    }
    zipEntries.each {
   	  x -> assert x.exists()
    }
  }
}


war.dependsOn untarGwt
war.dependsOn copyOpenbisStaticResources
war.dependsOn checkFilesExist
war.dependsOn signWebStartJars
war {
    rootSpec.eachFile { file ->
        if (file.name.startsWith('cisd-cifex')
                || file.name.startsWith('datastore_server')
                || file.name.startsWith('bioformats')
                || file.name.startsWith('cisd-image-readers')
                ) {
            file.exclude()
        }
    }

    from "${project.buildDir}/gwt/ch.systemsx.cisd.openbis.OpenBIS"
    from signedJarsFolder
    webXml = file('resource/server/web.xml')
    webInf {
        from "${project.buildDir}/gwt/WEB-INF",
        project(':openbis').file('resource/server/bis-common.xml'),
        file('resource/server/spring-servlet.xml'),
        file('resource/server/jetty-web.xml'),
        project(':common').file('resource/server/web-common.xml')
    }

    from (classpathEntries) {
        into("WEB-INF/classes")
    }

    from('dist/server'){
        into("WEB-INF/classes")
        include "etc/log.xml"
    }

    from('targets/dist'){
        into("WEB-INF/classes")
        include 'BUILD*INFO'
        rename 'BUILD.*INFO', 'BUILD-openbis.INFO'
    }

    from('../screening/source'){
        into("WEB-INF/classes")
        include "sql/**/*.sql"
        exclude "sql/imaging/postgresql/_ERD"
    }

    from('../openbis/source'){
        into("WEB-INF/classes")
        include "sql/**/*.sql"
        exclude "sql/generic/_ERD"
        duplicatesStrategy 'exclude'
    }
}

def downloadCorePlugin(url, pluginname) {
  def file = project(':openbis').file("../openbis_standard_technologies/targets/downloads/${pluginname}.zip")
  if (file.exists() == false || System.currentTimeMillis() - file.lastModified() > 3600000) {
    file.getParentFile().mkdirs()
    ext.executeFunction('curl', [url, '-sLk', '-o', file.getAbsolutePath()])
    ext.executeFunction('unzip', ['-uqo', file.getAbsolutePath(), '-d', '../openbis_standard_technologies/targets/downloads/'])
  }
}

import org.paleozogt.gradle.zip.SymZip;

task zipCorePlugins(type: SymZip) {
  includeEmptyDirs = false
  archiveName 'core-plugins.zip'

  downloadCorePlugin('https://github.com/aarpon/obit_flow_core_technology/archive/release/20.x.zip', 'flow')
  downloadCorePlugin('https://github.com/aarpon/obit_microscopy_core_technology/archive/release/20.x.zip', 'microscopy')
  downloadCorePlugin('https://github.com/aarpon/obit_shared_core_technology/archive/release/20.x.zip', 'shared')
  from project(':screening').fileTree(dir: 'source/core-plugins', includes:['screening/**', 'screening-optional/**'], excludes:['**/package-to-dist'])
  from project(':deep_sequencing_unit').fileTree(dir: 'source/core-plugins', includes:['illumina-ngs/**'], excludes:['**/package-to-dist'])
  from fileTree(dir: 'targets/downloads/obit_flow_core_technology-release-20.x/core-plugins', includes:['flow/**'])
  from fileTree(dir: 'targets/downloads/obit_microscopy_core_technology-release-20.x/core-plugins', includes:['microscopy/**'])
  from fileTree(dir: 'targets/downloads/obit_shared_core_technology-release-20.x/core-plugins', includes:['shared/**'])
  from 'dist/core-plugins'
  from 'dist/server/core-plugins.properties'
  into 'core-plugins'
}

def generateMD5(final file) {
   java.security.MessageDigest digest = java.security.MessageDigest.getInstance("MD5")
   file.withInputStream(){is->
   byte[] buffer = new byte[8192]
   int read = 0
      while( (read = is.read(buffer)) > 0) {
             digest.update(buffer, 0, read);
         }
     }
   byte[] md5sum = digest.digest()
   BigInteger bigInt = new BigInteger(1, md5sum)
   return bigInt.toString(16)
}

task checksums {
	ext.destFile = new File(buildDir, 'configuration.MD5')
	ext.inputFiles = war.getSource().filter({file -> file.name.endsWith('xml') || file.name.endsWith('.conf') || file.name.endsWith('.properties')})
    inputs.files inputFiles
    outputs.file destFile
	doLast {
		if (destFile.exists()) {
			destFile.delete()
		}
		destFile.createNewFile()

		def configFiles = classpathEntries.filter({file -> file.name.endsWith('xml') || file.name.endsWith('.conf') || file.name.endsWith('.properties')})
		configFiles.each {file ->
			destFile.text += generateMD5(file)+" webapps/openbis/WEB-INF/classes/"+file.name+"\n"
		}

		configFiles = war.getSource().filter({file -> file.name.endsWith('xml') || file.name.endsWith('.conf') || file.name.endsWith('.properties')}).minus(classpathEntries)
		configFiles.each {file ->
			destFile.text += generateMD5(file)+" webapps/openbis/WEB-INF/"+file.name+"\n"
		}
	}
}
checksums.dependsOn war

task createJettyVersionFile {
    ext.versionFile = new File(buildDir, 'jetty-version.txt')
    outputs.file versionFile
    doLast {
        versionFile.text = "${jettyVersion}"
    }
}

task zip(type: Zip, dependsOn: createJettyVersionFile) {
    from createJettyVersionFile
    from war
	from zipEntries
	from checksums
	from configurations.zipping
    from zipCorePlugins.archivePath
	from zipAdminConsole.archivePath
	rename 'jetty-distribution(.*).zip', 'jetty.zip'
	rename 'openBIS(.*).war', 'openBIS.war'
}
zip.dependsOn war
zip.dependsOn zipCorePlugins
zip.dependsOn zipAdminConsole
zip.dependsOn checksums

task zipDss(type: Zip, dependsOn: signWebStartJars) {
	baseName 'datastore_server-standard-technologies'
	includeEmptyDirs true

	from (configurations.datastore_server) {
		into 'datastore_server/lib'
		exclude '**/antlr*.jar'
		exclude '**/fastutil*.jar'
		exclude '**/gwt*.jar'
		exclude '**/gxt*.jar'
		exclude '**/hibernate*.jar'
		exclude '**/jmock*.jar'
		exclude '**/junit*.jar'
		exclude '**/lucene*.jar'
		exclude '**/restrictions*.jar'
		exclude '**/testng*.jar'
		rename 'common-.*jar', 'common.jar'
		rename 'commonbase-.*jar', 'commonbase.jar'
	}

	from (signedJarsFolder) {
	   into 'datastore_server/lib/dss_upload_gui'
	   exclude openbisClientJarName
	   exclude dssCliClientJarName
	}

	from (project(':datastore_server').fileTree(dir: 'dist', includes: ['**/*'], excludes:['dss_client.sh', 'etc/**'])) {
		into 'datastore_server';
	}

	from (project(':datastore_server').files('dist/etc/datastore_server.conf', 'dist/etc/openBIS.keystore')) {
		into 'datastore_server/etc';
	}

	from (fileTree(dir: 'dist', includes: ['etc/service.properties', 'etc/log.xml'])) {
		into 'datastore_server'
	}

	from (project(':screening').file('dist/etc/tabular-data-graph.properties')) {
		into 'datastore_server/etc';
	}

}

task zipBdlServer(type: Zip, dependsOn: project(':big_data_link_server').tasks.distZip) {
	baseName 'big_data_link_server'
	from zipTree('../big_data_link_server/build/distributions/big_data_link_server.zip')
}

task pybisZip(type: Zip) {
  baseName 'pybis'
  from '../pybis/'
}

task obisZip(type: Zip) {
  baseName 'obis'
  from '../obis/'
}

task clientsAndApis(type: Zip, dependsOn: [dssClientZip, queryApiZip, apiV3Zip, screeningApiZip, pybisZip, obisZip]) {
  baseName 'openBIS-clients-and-APIs'
  from dssClientZip.archivePath
  from queryApiZip.archivePath
  from apiV3Zip.archivePath
  from screeningApiZip.archivePath
  from pybisZip.archivePath
  from obisZip.archivePath
  from ('dist/client/readme.txt')
  rename { filename ->
    if (filename.startsWith('pybis-')) {
      def contentOfSetUpFile = zipTree(pybisZip.archivePath).getFiles().findAll {it.path.endsWith('src/python/setup.py') }.iterator().next().text
      def pybisVersion = ( contentOfSetUpFile =~ /version.*=.*"(.*)"/)[0][1]
      'pybis-' + pybisVersion + '.zip'
    } else {
      filename
    }
  }
}

task deleteOpenbisNgUi(type: Delete) {
  delete 'dist/core-plugins/openbis-ng-ui'
}

task copyOpenbisNgUiToCorePlugins(type: Copy, dependsOn: [deleteOpenbisNgUi, ':openbis_ng_ui:build']) {
    from project(':openbis_ng_ui').file('build/core-plugins')
    into file('dist/core-plugins')
}

zipCorePlugins.dependsOn copyOpenbisNgUiToCorePlugins

task generateJavadoc(type: Javadoc) {
	source = configurations.javadoc_sources.collect { zipTree(it).matching {
		include "**/ch/ethz/sis/openbis/generic/asapi/**/*.java"
		include "**/ch/ethz/sis/openbis/generic/dssapi/**/*.java"
		include "**/ch/systemsx/cisd/**/api/**/*.java"
		include "**/ch/systemsx/cisd/common/annotation/*.java"
		include "**/ch/systemsx/cisd/base/**/*.java"
		include "**/OpenBISScreeningML.java"
		include "**/ch/systemsx/cisd/**/etlserver/TopLevelDataSetRegistratorGlobalState.java"
		include "**/ch/systemsx/cisd/**/etlserver/registrator/*.java"
		include "**/ch/systemsx/cisd/common/mail/*.java"
	}}
	classpath = configurations.javadoc_compilation
	maxMemory = "1024m"
	options.addStringOption("source", "1.8")
}

build.dependsOn zip
build.dependsOn zipDss
build.dependsOn zipBdlServer
build.dependsOn clientsAndApis
build.dependsOn dssUploadGuiStandaloneZip
build.dependsOn dssUploadGuiStandaloneJar
build.dependsOn generateJavadoc