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build.gradle
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build.gradle
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import java.nio.file.Files
import java.nio.file.StandardOpenOption
import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
buildscript {
repositories {
maven { url "https://plugins.gradle.org/m2/" }
mavenCentral()
}
dependencies {
// classpath 'edu.sc.seis.gradle:launch4j:2.4.9'
classpath 'commons-configuration:commons-configuration:1.10'
classpath 'com.github.viswaramamoorthy:gradle-util-plugins:0.1.0-RELEASE'
classpath 'org.yaml:snakeyaml:1.29'
}
}
plugins {
id "com.jfrog.artifactory" version "4.25.1"
id "de.undercouch.download" version "4.1.1"
}
//this task is used to update the gradle wrapper properties to a new version
// it also ensures that wrapper scripts and gradle-wrapper.jar are updates if necessary
wrapper {
gradleVersion = '7.6'
}
//Global Properties
ext {
junit_version = '5.10.0'
jackson_version = "2.16.1"
spring_boot_version = "3.2.3"
springdoc_version = "2.3.0"
//version for external libraries
slf4j_version = '1.7.36'
jjobs_version = '0.9.36-SNAPSHOT'
jaxb_version = "2.3.9"
cdk_version = "2.8"
picocli_version = '4.7.5'//'3.9.5'
siriusTargetPlatform = SiriusPlatform.fromDescriptor((
project.findProperty('build.sirius.platform') ?:
"${DefaultNativePlatform.getCurrentOperatingSystem().getName()}-${DefaultNativePlatform.getCurrentArchitecture().getName()}"
) as String)
System.out.println("----> Following platform detected: " + siriusTargetPlatform)
javaFX_modules = ['javafx-base', 'javafx-controls', 'javafx-swing', 'javafx-web', 'javafx-graphics', 'javafx-fxml', 'javafx-media']
//locations of runtime libraries
//jre path relative tu app home
jre_path = 'zulu'
lib_path = 'lib'
native_path = 'native'
libDir = project.findProperty("build.sirius.location.lib")
System.out.println("----> LibDir: " + libDir)
includeJreFX = Boolean.parseBoolean((project.findProperty("build.sirius.starter.jdk.include") ?: "false") as String)
System.out.println("----> includeJreFX: ${includeJreFX} | ${project.findProperty("build.sirius.starter.jdk.include")}")
launch4jJDKPath = project.findProperty("build.sirius.starter.jdk.location")
System.out.println("----> launch4jJDKPath: ${launch4jJDKPath}")
excludeCbcNative = project.findProperty("build.sirius.native.cbc.exclude")
System.out.println("----> excludeCbcNative: " + excludeCbcNative)
excludeJFX = Boolean.parseBoolean((project.findProperty("build.sirius.native.openjfx.exclude") ?: "false") as String)
System.out.println("----> excludeJFX: ${excludeJFX} | ${project.findProperty("build.sirius.native.openjfx.exclude")}")
jetbrains_version = "22.0.0"
// mainly for IDE execution, ilp libs are not shipped with distributions anyways
cplex_version = '12.7.1'
// cplex_version = '20.1.0'
gurobi_version = '9.1.1'
cbc_version = '2.10.8.1'
jakarta_version = '3.1.0'
logger.lifecycle('reading build properties file...')
props = new Properties()
File propertiesFileIn = new File("${projectDir}/sirius_cli/src/main/resources/sirius_frontend.build.properties")
propertiesFileIn.withReader("UTF8", {
props.load(it)
})
// edit all these versions in sirius_cli/src/main/resources/....build.properties
appName = props.getProperty('de.unijena.bioinf.utils.errorReport.softwareName').toLowerCase()
siriusFrontendVersion = props.getProperty('de.unijena.bioinf.siriusFrontend.version')
siriusVersion = props.getProperty('de.unijena.bioinf.sirius.version')
fingeridVersion = props.getProperty('de.unijena.bioinf.fingerid.version')
mztabm_version = props.getProperty('de.unijena.bioinf.mztabm.version')
}
/*################### DISTRIBUTION STUFF ################### */
project.ext.set("linSuffix", "linux")
project.ext.set("winSuffix", "win")
project.ext.set("macSuffix", "osx")
project.ext.set("arch", ['64', '32'])
project.ext.set("distPath", file('dist').absolutePath)
allprojects {
apply plugin: "com.jfrog.artifactory"
apply plugin: 'java'
apply plugin: 'maven-publish'
targetCompatibility = 17
compileJava.options.encoding = "UTF-8"
compileTestJava.options.encoding = "UTF-8"
javadoc.options.encoding = 'UTF-8'
version = "$siriusFrontendVersion"
group = 'de.unijena.bioinf.ms'
repositories {
mavenLocal()
mavenCentral()
maven {//public libs only so anybody can build the frontend without login
url "https://bio.informatik.uni-jena.de/repository/libs-oss"
metadataSources {
mavenPom()
artifact()
}
}
maven {
url "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/"
}
maven {
url "https://repo1.maven.org/maven2/" //glazed lists
}
maven {
url "http://gose.fiehnlab.ucdavis.edu:55000/content/groups/public"
allowInsecureProtocol = true
// only used for spectral hashs (Splash)
}
}
dependencies {
annotationProcessor "de.unijena.bioinf.ms:processor:$siriusVersion"
implementation 'net.sf.trove4j:core:3.1.0'
implementation "org.jetbrains:annotations:$jetbrains_version"
implementation "org.slf4j:log4j-over-slf4j:$slf4j_version"
implementation "org.slf4j:jcl-over-slf4j:$slf4j_version"
implementation "org.slf4j:slf4j-api:$slf4j_version"
//NOTE: cannot be provided as transitive dependency
implementation "jakarta.persistence:jakarta.persistence-api:$jakarta_version"
implementation "org.glassfish.jaxb:jaxb-runtime:$jaxb_version"
// Aggregator dependency that also brings JUnit 5 parameterized tests etc.
testImplementation("org.junit.jupiter:junit-jupiter:$junit_version")
testImplementation("org.junit.jupiter:junit-jupiter-params:$junit_version")
// The Vintage engine is needed to be able to run JUnit 4 tests
testImplementation("org.junit.vintage:junit-vintage-engine:$junit_version")
testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:$junit_version"
}
test {
useJUnitPlatform()
maxHeapSize = "16G"
}
//there are some outdated incompatible trove dependencies in some libs.
// this is to exclude them and enforce the one we need.
configurations.all {
//replaced by log4j-over-slf4j
it.exclude group: "log4j", module: "log4j"
//replaced by jcl-over-slf4j
it.exclude group: "commons-logging", module: "commons-logging"
it.exclude module: 'trove4j'
}
configurations {
compileClasspath {
resolutionStrategy.force 'net.sf.trove4j:core:3.1.0'
}
}
}
subprojects {
apply plugin: 'application'
}
task sourceJar(type: Jar) {
group = 'build'
archiveClassifier.set('sources')
from sourceSets.main.allSource
}
task javadocJar(type: Jar, dependsOn: javadoc) {
group = 'documentation'
archiveClassifier.set('javadoc')
from javadoc.destinationDir
}
def javaProjects() {
subprojects.findAll { new File(it.projectDir, 'src').directory }
}
allprojects {
configure(javaProjects()) {
publishing {
publications {
mavenJava(MavenPublication) {
if (version.toString().endsWith('-SNAPSHOT'))
setArtifacts([jar, sourceJar])
else
setArtifacts([jar, sourceJar, javadocJar])
}
}
}
}
publishing {
publications {
mavenJava(MavenPublication) {
from project.components.java
//adding submodules to pom
pom.withXml {
if (!project.subprojects.isEmpty()) {
def modlules = asNode().appendNode('modules', '')
project.subprojects.each {
new Node(modlules, 'module', it.name)
}
}
}
setArtifacts([])
}
}
}
}
task refreshDownloadLinks {
File webPath = getBuildDir().toPath().resolve('tmp/webSite/').toFile()
group = 'publishing'
File outfile = new File(webPath, "sirius-download.md")
outputs.file(outfile)
doLast {
webPath.mkdirs()
def repoKey = "${project.version.toString().endsWith('-SNAPSHOT') ? 'dist-snapshot-local' : 'dist-release-local'}"
List<String> lines = [
"### SIRIUS+CSI:FingerID GUI and CLI - Version $version (${new Date().format('yyyy-MM-dd')})",
"##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.",
"- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64.msi) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64.zip) / " +
"- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64.pkg) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64.zip) / " +
"- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-linux64.zip)",
"",
"### SIRIUS+CSI:FingerID Command-Line Interface only - Version $version (${new Date().format('yyyy-MM-dd')})",
"##### These versions include the Java Runtime Environment, so there is no need to install Java separately! Just download, install/unpack and execute.",
"- for Windows (64bit): [msi](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64-headless.msi) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-win64-headless.zip) / " +
"- for Mac (64bit): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64-headless.pkg) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-osx64-headless.zip) / " +
"- for Linux (64bit): [zip](https://github.com/sirius-ms/sirius/releases/download/v$version/sirius-$version-linux64-headless.zip)",
""
] as List
Files.deleteIfExists(outfile.toPath())
Files.write(outfile.toPath(), lines, StandardOpenOption.CREATE)
}
}
String cleanVersion = fingeridVersion.toString().replace('-SNAPSHOT', '')
String minorVersion = "${cleanVersion.split('[.]')[0]}.${cleanVersion.split('[.]')[1]}"
task refreshTrainingLinks {
File webPath = getBuildDir().toPath().resolve('tmp/webSite/').toFile()
group = 'publishing'
File outfile = new File(webPath, "sirius-training.md")
outputs.file(outfile)
doLast {
webPath.mkdirs()
List<String> lines = [
"- https://www.csi-fingerid.uni-jena.de/v$minorVersion/api/fingerid/trainingstructures?predictor=1 (training structures for positive ion mode)",
"- https://www.csi-fingerid.uni-jena.de/v$minorVersion/api/fingerid/trainingstructures?predictor=2 (training structures for negative ion mode)"
] as List
Files.deleteIfExists(outfile.toPath())
Files.write(outfile.toPath(), lines, StandardOpenOption.CREATE)
}
}
task refreshReadMe {
inputs.files(refreshDownloadLinks.outputs.files.singleFile, refreshTrainingLinks.outputs.files.singleFile)
outputs.file("${getRootDir()}/README.md")
group = 'publishing'
doFirst {
File dld = inputs.files.getAt(0)
File clg = inputs.files.getAt(1)
File out = outputs.files.singleFile
List<String> links = Files.readAllLines(dld.toPath())
List<String> training = Files.readAllLines(clg.toPath())
Map<String, String> keywords = ['<!--begin download-->': '<!--end download-->', '<!--begin training-->': '<!--end training-->']
Map<String, List<String>> replacements = ['<!--begin download-->': links, '<!--begin training-->': training]
List<String> lines = Files.readAllLines(out.toPath())
List<String> nuLines = new LinkedList<>()
String keyword = null
String keywordEnd = null
lines.each { String line ->
if (line.startsWith("[![Generic badge](https://img.shields.io/badge/Version-")) {
nuLines.add("[![Generic badge](https://img.shields.io/badge/Version-${project.version.replace("-", "--")}-informational.svg)](https://shields.io/)")
} else if (keyword == null) {
keywordEnd = keywords.get(line)
nuLines.add(line)
if (keywordEnd != null) {
keyword = line
def r = replacements.get(keyword)
nuLines.add('')
nuLines.addAll(r)
}
} else if (line.equals(keywordEnd)) {
nuLines.add('')
nuLines.add(line)
keyword = null
keywordEnd = null
}
}
Files.deleteIfExists(out.toPath())
Files.write(out.toPath(), nuLines, StandardOpenOption.CREATE)
}
}
refreshReadMe.dependsOn refreshTrainingLinks
refreshReadMe.dependsOn refreshDownloadLinks
// publication artifactory
artifactory {
contextUrl = 'https://bio.informatik.uni-jena.de/repository/'
publish {
repository {
repoKey = "${project.version.toString().endsWith('-SNAPSHOT') ? 'dist-snapshot-local' : 'dist-release-local'}"
username = project.findProperty('de.unijena.bioinf.build.artifactory.username')
password = project.findProperty('de.unijena.bioinf.build.artifactory.password')
}
defaults {
//Publish every distribution to Artifactory
publications("siriusMS")
publications("manual")
}
}
}
artifactoryPublish.dependsOn 'refreshDownloadLinks'
artifactoryPublish.dependsOn 'refreshReadMe'