build.gradle

evaluationDependsOn(':common')
evaluationDependsOn(':openbis_api')
evaluationDependsOn(':openbis-common')
evaluationDependsOn(':authentication')
evaluationDependsOn(':dbmigration')
evaluationDependsOn(':openbis')
evaluationDependsOn(':datastore_server')
evaluationDependsOn(':rtd_phosphonetx')
evaluationDependsOn(':screening')
evaluationDependsOn(':rtd_yeastx')
evaluationDependsOn(':deep_sequencing_unit')

apply from: 'http://svncisd.ethz.ch/repos/cisd/gradle/trunk/javaproject.gradle'
apply from: 'query-api.gradle'
apply from: 'screening-api.gradle'
apply from: 'proteomics-api.gradle'
apply from: 'dss-client.gradle'
apply from: 'dss-upload-gui.gradle'

apply plugin: 'war'

archivesBaseName = 'openBIS-server-standard-technologies'

configurations.create('gwt')
configurations.create('zipping')
configurations.create('admin_partial')
configurations.create('admin_full')
configurations.create('datastore_server')
configurations.create('webStartJars')

def jettyVersion = '8.1.8'

dependencies {
	compile project(':screening'),
			project(':rtd_phosphonetx')
	
	providedCompile 'google:gwt-user:2.4'
					
	providedRuntime	"eclipse:jetty-util:${jettyVersion}.v20121106",
					"eclipse:jetty-deploy:${jettyVersion}.v20121106"
		
	gwt 'reveregroup:gwt-image-loader:1.1.4',
                'google:gwt-dev:+'
	
	zipping "eclipse:jetty-distribution:${jettyVersion}@zip"
	
	admin_partial 'google:gwt-user:2.4'
	
	admin_full 'cisd:cisd-base:+',
				'apache:commons-httpclient:+',
				'apache:commons-logging:+',
				'apache:commons-io:+',
				'apache:log4j:+',
				'springframework:spring-core:+',
				'springframework:spring-context:+',
				'springframework:spring-jdbc:+',
				'springframework:spring-orm:+',
				'springframework:spring-aop:+',
				'marathon:marathon-spring-util:+',
				'springframework:spring-beans:+',
				'jline:jline:0.9.94'	
	
	datastore_server project(':deep_sequencing_unit'),
					 project(':rtd_yeastx'),
					 project(':screening'),
					 project(':rtd_phosphonetx'),
					 'bioformats:bioformats:+',
					 'imagej:ij:+',
					 'cisd:cisd-openbis-knime-server:+',
					 'apache:xml-apis:+',
					 'javax:jaxb:+',
					 'slf4j:slf4j:+',
					 'slf4j:slf4j-log4j12:+',
					 'sybit:image-viewer:+'
					 
    webStartJars 'cisd:cisd-base:+',
                 'apache:commons-codec:+',
                 'apache:commons-io:+',
                 'apache:commons-httpclient:+',
                 'apache:commons-lang:+',
                 'apache:commons-logging:+',
                 'apache:log4j:+',
                 'apache:geronimo-stax:+',
                 'apache:poi:+',
                 'apache:poi-ooxml:+',
                 'apache:poi-ooxml-schemas:+',
                 'apache:xmlbeans:+',
                 'dom4j:dom4j:+',
                 'imagej:ij:+',
                 'python:jython:+',
                 'sybit:image-viewer:+',
                 'springframework:spring:+',
                 'springframework:spring-aop:+',
                 'springframework:spring-beans:+',
                 'springframework:spring-context:+',
                 'springframework:spring-core:+',
                 'springframework:spring-web:+',
                 'marathon:marathon-spring-util:+',
                 'aopalliance:aopalliance:+'
                 
}

buildscript {
    apply from: '../gradle/repository.gradle'
    
    repositories repositoryConfig
    
    dependencies {
        classpath 'apache:commons-codec:+'
    }
}

task compileGwt (dependsOn: classes, type: JavaExec) {

	buildDir = "${project.buildDir}/gwt"
	extraDir = "${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.classesDir,
			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,
			project(":rtd_phosphonetx").sourceSets.main.java.srcDirs,
			project(":rtd_phosphonetx").sourceSets.main.output.resourcesDir,			
			configurations.gwt
		]   
	}
     
	args =
		[
			'ch.systemsx.cisd.openbis.OpenBIS',
			'-war', buildDir,
			'-logLevel', 'INFO',
			'-localWorkers', '2',
			'-compileReport', 
			'-extra', extraDir,
		]
	
	maxHeapSize = '1024m'
}


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(':rtd_phosphonetx').file('source/java/proteomics-applicationContext.xml'),
	project(':rtd_phosphonetx').file('source/java/proteomics-plugin-applicationContext.xml'),
	project(':common').file('source/java/genericCommonContext.xml'),
	'source/java/standard-technologies-applicationContext.xml'
)

zipEntries = files(
	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/jetty.xml'),		
	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'),
	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()
    }    
  }
}

jarsToBeSignedFolder = "${buildDir}/jars_to_be_signed"
signedJarsFolder = "${buildDir}/signed_jars"
task createOpenbisJar(type: Jar) {
    archiveName = 'openbis.jar'
    destinationDir = file(jarsToBeSignedFolder)
    outputs.file new File(jarsToBeSignedFolder, archiveName)
    from zipTree(project(':common').jar.archivePath).plus(
         zipTree(project(':openbis-common').jar.archivePath).plus( 
         zipTree(project(':openbis_api').jar.archivePath).plus( 
         zipTree(project(':datastore_server').jar.archivePath).plus( 
         zipTree(project(':screening').jar.archivePath).plus( 
         zipTree(project(':openbis').jar.archivePath)))))).matching {
            include '**/ch/systemsx/cisd/common/**/*.class'
            include '**/ch/systemsx/cisd/openbis/common/**/*.class'
            include '**/ch/systemsx/cisd/openbis/generic/client/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/generic/client/cli/**/*.class'
            include '**/ch/systemsx/cisd/openbis/generic/shared/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/plugin/screening/client/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/plugin/screening/shared/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/dss/client/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/dss/generic/shared/api/**/*.class'
            include '**/ch/systemsx/cisd/openbis/dss/screening/shared/api/**/*.class'
            include '**/shared/I*.class'
            include '**/shared/basic/dto/**/*.class'
            include '**/shared/basic/*.class'
            include '**/*BuildAndEnvironmentInfo.class'
        }
}

task copyJarsForWebStart(type: Copy) {
    from configurations.webStartJars.files
    into jarsToBeSignedFolder
    rename '(.+)-[^-]*\\.jar', '$1.jar'
    rename 'dom4j.jar', 'dom4j-1.6.1.jar'
    rename 'poi-[^-]*\\.jar', 'poi.jar'
    rename 'poi-ooxml-[^-]*\\.jar', 'poi-ooxml.jar'
    rename 'poi-ooxml-schemas-[^-]*\\.jar', 'poi-ooxml-schemas.jar'
    rename 'geronimo-stax.jar', 'geronimo-stax-api_1.0_spec-1.0.jar'
    rename 'xmlbeans.jar', 'xmlbeans-2.3.0.jar'
    rename 'marathon-spring-util.*jar', 'stream-supporting-httpinvoker.jar'
}

keystoreFile = '../screening/etc/dev.keystore'
task signWebStartJars(type: Copy, dependsOn: [createOpenbisJar, dssGui, copyJarsForWebStart]) {
    from jarsToBeSignedFolder
    into signedJarsFolder
    inputs.file keystoreFile
    doLast {
        file(signedJarsFolder).listFiles().each { file ->
            ant.signjar(jar: file, keystore: keystoreFile,
                        alias: 'openbis', storepass: 'openbistest')
        }
    }
}

war.dependsOn compileGwt
war.dependsOn checkFilesExist
war.dependsOn signWebStartJars
war {
    rootSpec.eachFile { file ->
        if (file.name.startsWith('cisd-cifex') || file.name.startsWith('datastore_server')) {
            file.exclude()
        }
    }

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

    from('../rtd_phosphonetx/source/sql'){ 
        into("WEB-INF/classes") 
        include "proteomics/**/*.sql" 
    } 
    
}

task zipCorePlugins(type: Zip) {
    archiveName 'core-plugins.zip'
	from project(':rtd_phosphonetx').fileTree(dir: 'source/core-plugins', includes:['proteomics/**', 'proteomics-optional/**'], excludes:['**/dss/**', '**/package-to-dist'])
	from project(':screening').fileTree(dir: 'source/core-plugins', includes:['screening/**', 'screening-optional/**'], excludes:['**/dss/**', '**/package-to-dist'])
	from project(':deep_sequencing_unit').fileTree(dir: 'source/core-plugins', includes:['illumina-ngs/**'], excludes:['**/dss/**', '**/package-to-dist'])
	from 'dist/server/core-plugins.properties'
	into 'core-plugins'
}

task adminConsole(type: Jar) {
	archiveName 'openbis-admin-console.jar'
	includeEmptyDirs false
	from zipTree(project(':common').jar.archivePath).plus(
         zipTree(project(':openbis-common').jar.archivePath).plus( 
         zipTree(project(':screening').jar.archivePath).plus( 
         zipTree(project(':openbis').jar.archivePath)))).matching {
			include '**/ch/systemsx/cisd/common/spring/HttpInvokerUtils.class'
			include '**/ch/systemsx/cisd/common/**/*.class'
			include '**/ch/systemsx/cisd/openbis/common/**/*.class'
			include '**/ch/systemsx/cisd/openbis/generic/client/console/**/*.class'
			include '**/shared/I*.class'
			include '**/shared/basic/dto/**/*.class'
			include '**/shared/basic/*.class'
			include '**/shared/dto/**/*.class'
			include '**/shared/dto/*PE.class'
			include '**/shared/authorization/annotation/*.class'
			include '**/shared/authorization/ISessionProvider.class'
			include '**/*BuildAndEnvironmentInfo.class'
		}

	from zipTree(configurations.admin_partial.files.iterator().next()).matching {
			include '**/com/google/gwt/user/client/rpc/IsSerializable.class'
			include '**/com/google/gwt/user/client/rpc/SerializableException.class'
	}
	
	for (File f : configurations.admin_full.files) {
		from zipTree(f).matching {
			include '**/**'
		}
	}
    manifest {
	    attributes("Main-Class": "ch.systemsx.cisd.openbis.generic.client.console.AdminConsole",
    	           "Class-Path": "openbis-admin-console.jar cisd-base.jar commons-codec.jar commons-httpclient.jar commons-io.jar commons-logging.jar log4j.jar jline.jar spring.jar marathon-spring-util.jar")
    }	
}
adminConsole.dependsOn war

task zipAdminConsole(type: Zip) {
	archiveName 'openbis-admin-console.zip'
	from adminConsole.archivePath
	into 'openbis-admin-console'
}
zipAdminConsole.dependsOn adminConsole


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()
		
		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'
	}
	
	from (files(dssUploadGuiJars.collect({"${signedJarsFolder}/${it}"}))) {
	   into 'datastore_server/lib/dss_upload_gui'
	}
	
	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';
	}
	
	from (file('dist/server/service.properties')) {
		into 'datastore_server/server'
	}
	
	from (file('dist/server/etc/log.xml')) {
		into 'datastore_server/server/etc'
	}
	
	from(dssGuiZip.archivePath) {
		into 'datastore_server/lib/'
	}
	
	from (project(':rtd_phosphonetx').fileTree(dir: 'source/core-plugins', includes:['proteomics/**', 'proteomics-optional/**'], excludes:['**/as/**', '**/package-to-dist']).plus(
		 project(':screening').fileTree(dir: 'source/core-plugins', includes:['screening/**', 'screening-optional/**'], excludes:['**/as/**', '**/package-to-dist']).plus(
		 project(':deep_sequencing_unit').fileTree(dir: 'source/core-plugins', includes:['illumina-ngs/**'], excludes:['**/as/**', '**/package-to-dist'])))) {
		into 'core-plugins'
	}
}

task clientsAndApis(type: Zip) {
	baseName 'openBIS-clients-and-APIs'
	from dssClientZip.archivePath
	from dssGuiZip.archivePath
    from queryApiZip.archivePath
    from proteomicsApiZip.archivePath
    from screeningApiZip.archivePath


	from (dssClientZip.archivePath) {	
	    rename { String fileName -> fileName.replace('client', 'client-screening')}
    }

	from (dssGuiZip.archivePath) {	
	    rename { String fileName -> fileName.replace('gui', 'gui-screening')}
    }
    
    from ('../openbis_all/dist/readme.txt')
    
}
clientsAndApis.dependsOn dssClientZip
clientsAndApis.dependsOn dssGuiZip
clientsAndApis.dependsOn queryApiZip
clientsAndApis.dependsOn proteomicsApiZip
clientsAndApis.dependsOn screeningApiZip

build.dependsOn zip
build.dependsOn zipDss
build.dependsOn clientsAndApis