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build.gradle
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import org.gradle.nativeplatform.platform.internal.DefaultNativePlatform
import java.nio.file.Files
import java.nio.file.StandardOpenOption
buildscript {
repositories {
maven { url "https://plugins.gradle.org/m2/" }
mavenCentral()
}
dependencies {
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 "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 = '8.12'
}
//Global Properties
ext {
logger.lifecycle('reading build properties file...')
props = new Properties()
file("${projectDir}/chemistry_base/src/main/resources/sirius.build.properties").withReader("UTF8", {
props.load(it)
})
file("${projectDir}/fingerid_base_oss/src/main/resources/csi_fingerid.build.properties").withReader("UTF8", {
props.load(it)
})
file("${projectDir}/sirius_cli/src/main/resources/sirius_frontend.build.properties").withReader("UTF8", {
props.load(it)
})
file("${projectDir}/sirius_rest_service/src/main/resources/application.properties").withReader("UTF8", {
props.load(it)
})
siriusVersion = props.getProperty('de.unijena.bioinf.sirius.version')
fingeridVersion = props.getProperty('de.unijena.bioinf.fingerid.version')
siriusFrontendVersion = props.getProperty('de.unijena.bioinf.siriusFrontend.version')
siriusAPIVersion = props.getProperty('de.unijena.bioinf.siriusNightsky.version')
appName = props.getProperty('de.unijena.bioinf.utils.errorReport.softwareName').toLowerCase()
mztabm_version = props.getProperty('de.unijena.bioinf.mztabm.version')
//version for external libraries
jre_version = '21.0.5'
jjobs_version = '0.10.0'
slf4j_version = '1.7.36'
jackson_version = '2.16.1'
lombok_version = '1.18.34'
cbc_version = props.getProperty('de.unijena.bioinf.sirius.build.cbc_version')
glpk_version = props.getProperty('de.unijena.bioinf.sirius.build.glpk_version')
gurobi_version = props.getProperty('de.unijena.bioinf.sirius.build.gurobi_version')
cplex_version = props.getProperty('de.unijena.bioinf.sirius.build.cplex_version')
cdk_version = "2.9"
jetbrains_version = "26.0.1"
okhttp_version = "4.12.0"
trove_version = '3.1.0' //DEPRECATED -> user fast util instead
fastutil_version = '8.5.12' //replaces trove
//not recommended anymore -> use pico cli instead
jewelcli_version = '0.8.9'
//apache commons
commons_math_version = '3.6.1'
commons_email_version = '1.6.0'
commons_text_version = '1.12.0'
commons_lang_version = '3.15.0'
commons_compress_version = '1.26.2'
commons_io_version = '2.16.1'//'2.11.0'
commons_configuration_version = '2.11.0'
json_version = '1.0'
json_impl_version = "1.0.4"
psql_version = "42.2.1"
jdbi_version = '3.34.0'
liblinear_version = "1.95"
libsvm_version = "3.20"
swagger_version = "2.2.26"
jaxb_version = "2.3.9"
picocli_version = '4.7.5'
jakarta_version = '3.1.0'
jakarta_annotation_version = "3.0.0"
spring_boot_version = "3.4.0"
springdoc_version = "2.6.0"
junit_version = '5.11.4'
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
lib_path = 'lib'
native_path = 'native'
libDir = project.findProperty("build.sirius.location.lib")
System.out.println("----> LibDir: " + libDir)
includeRuntime = Boolean.parseBoolean((project.findProperty("build.sirius.starter.jdk.include") ?: "true") as String)
System.out.println("----> includeRuntime: ${includeRuntime} | ${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")}")
}
/*################### 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: 'java'
apply plugin: 'java-library'
apply plugin: 'maven-publish'
sourceCompatibility = 21
compileJava.options.encoding = "UTF-8"
compileTestJava.options.encoding = "UTF-8"
javadoc.options.encoding = 'UTF-8'
group = 'io.sirius-ms'
repositories {
// mavenLocal()
mavenCentral()
maven {
url 'https://gitlab.com/api/v4/projects/66031889/packages/maven'
name "BG GitLab Common Public"
}
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://eulergui.sourceforge.net/maven2/" //FTAlign stuff
allowInsecureProtocol = true
}
// This is just needed to load sirius-ms testing dependencies.
// All artifacts needed to build SIRIUS should be public.
// however some acceptance test data is not.
if ((System.getenv("CI_JOB_TOKEN") != null) || (project.findProperty("com.bright-giant.build.gitlab.username") != null
&& project.findProperty("com.bright-giant.build.gitlab.token") != null)) {
maven {
url "https://gitlab.com/api/v4/groups/bright-giant/-/packages/maven"
name "BG GitLab"
if (System.getenv("CI_JOB_TOKEN") != null) {
credentials(HttpHeaderCredentials) {
name = "Job-Token"
value = System.getenv("CI_JOB_TOKEN")
}
authentication {
header(HttpHeaderAuthentication)
}
} else if (project.findProperty("com.bright-giant.build.gitlab.username") != null
&& project.findProperty("com.bright-giant.build.gitlab.token") != null
) {
credentials(PasswordCredentials) {
username = project.findProperty("com.bright-giant.build.gitlab.username") as String
password = project.findProperty("com.bright-giant.build.gitlab.token") as String
// the variable resides in $GRADLE_USER_HOME/gradle.properties
// https://docs.gradle.org/current/userguide/directory_layout.html#dir:gradle_user_home
}
authentication {
basic(BasicAuthentication)
}
}
}
}
}
dependencies {
compileOnly "org.projectlombok:lombok:$lombok_version"
annotationProcessor "org.projectlombok:lombok:$lombok_version"
// Annotations
api "org.jetbrains:annotations:$jetbrains_version"
api "io.swagger.core.v3:swagger-annotations:$swagger_version"
api "it.unimi.dsi:fastutil:$fastutil_version"
api "org.apache.commons:commons-lang3:$commons_lang_version"
api "org.apache.commons:commons-math3:$commons_math_version"
api "org.apache.commons:commons-compress:$commons_compress_version"
api "commons-io:commons-io:$commons_io_version"
api "com.fasterxml.jackson.core:jackson-databind:$jackson_version"
api "com.fasterxml.jackson.core:jackson-annotations:$jackson_version"
api 'com.googlecode.concurrent-locks:concurrent-locks:1.0.0'
api "de.unijena.bioinf:jjobs-core:$jjobs_version"
api "org.slf4j:slf4j-api:$slf4j_version"
//NOTE: cannot be provided as transitive dependency
implementation "jakarta.persistence:jakarta.persistence-api:$jakarta_version"
implementation "jakarta.annotation:jakarta.annotation-api:$jakarta_annotation_version"
implementation "org.glassfish.jaxb:jaxb-runtime:$jaxb_version"
// TEST DEPENDENCIES
testCompileOnly "org.projectlombok:lombok:$lombok_version"
testAnnotationProcessor "org.projectlombok:lombok:$lombok_version"
testImplementation "org.slf4j:log4j-over-slf4j:$slf4j_version"
testImplementation "org.slf4j:jcl-over-slf4j:$slf4j_version"
// Aggregator dependency that also brings JUnit 5 parameterized tests etc.
testImplementation "org.junit.jupiter:junit-jupiter:$junit_version"
testImplementation "org.junit.jupiter:junit-jupiter-params:$junit_version"
testImplementation "org.mockito:mockito-junit-jupiter:5.12.0"
// The Vintage engine is needed to be able to run JUnit 4 tests
testImplementation "org.junit.vintage:junit-vintage-engine:$junit_version"
testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:$junit_version"
}
//there are some outdated incompatible trove dependencies in some libs.
// this is to exclude them and enforce the one we need.
configurations.configureEach {
//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'
}
}
test {
useJUnitPlatform()
}
tasks.named('test') {
useJUnitPlatform {
filter { //filter test groups that do not have to run on every commit
excludeTestsMatching "*IntegrationTest"
excludeTestsMatching "*ApiTest"
excludeTestsMatching "*AcceptanceTest"
failOnNoMatchingTests false // to prevent failing if no test passes the filter for some module
}
}
}
//We usually just do them for the sirius-sdk. Maybe also for the cli
def integrationTest = tasks.register("integrationTest", Test) {
group = 'verification'
useJUnitPlatform {
filter {
includeTestsMatching "*IntegrationTest"
includeTestsMatching "*ApiTest"
failOnNoMatchingTests false // to prevent failing if no test passes the filter for some module
}
}
}
def acceptanceTest = tasks.register("acceptanceTest", Test) {
group = 'verification'
useJUnitPlatform {
filter {
includeTestsMatching "*AcceptanceTest"
failOnNoMatchingTests false // to prevent failing if no test passes the filter for some module
}
maxHeapSize = "16G"
}
}
}
subprojects {
java {
withJavadocJar()
withSourcesJar()
}
//do not build javadoc for snapshot version to reduce build time
components.java.withVariantsFromConfiguration(configurations.javadocElements) {
if (version.toString().endsWith('-SNAPSHOT'))
skip()
}
//build only artifacts from modules that contain code
if (new File(projectDir, "src/main").isDirectory() && !"sirius_rest_service".equalsIgnoreCase(project.name) && !"buildSrc".equalsIgnoreCase(project.name)) {
publishing {
publications {
mavenJava(MavenPublication) {
from project.components.java
pom {
licenses {
license {
name = 'GNU Affero General Public License, Version 3.0'
url = 'https://www.gnu.org/licenses/agpl-3.0.txt'
}
}
}
}
}
repositories {
maven {
name = "GitLab"
if (System.getenv("CI_JOB_TOKEN") != null) {
url = "${System.getenv('CI_API_V4_URL')}/projects/${System.getenv('CI_PROJECT_ID')}/packages/maven"
credentials(HttpHeaderCredentials) {
name = "Job-Token"
value = System.getenv("CI_JOB_TOKEN")
}
authentication {
header(HttpHeaderAuthentication)
}
} else {
url = project.findProperty("io.sirius-ms.build.artifactory.url") as String
credentials(PasswordCredentials) {
username = project.findProperty("io.sirius-ms.build.artifactory.username") as String
password = project.findProperty("io.sirius-ms.build.artifactory.token") as String
// the variable resides in $GRADLE_USER_HOME/gradle.properties
// https://docs.gradle.org/current/userguide/directory_layout.html#dir:gradle_user_home
}
authentication {
basic(BasicAuthentication)
}
}
}
}
}
}
}
tasks.register('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()
List<String> lines = [
"### SIRIUS+CSI:FingerID GUI and CLI - Version $siriusFrontendVersion (${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 (x86-64/amd64/x64): [msi](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-win-x64.msi) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-win-x64.zip)",
"- for Mac (x86-64/amd64/x64): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-macos-x64.pkg) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-macos-x64.zip)",
"- for Mac (arm64/aarch64/apple silicon): [pkg](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-macos-arm64.pkg) / " +
"[zip](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-macos-arm64.zip)",
"- for Linux (x86-64/amd64/x64): [zip](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-linux-x64.zip)",
"- for Linux (arm64/aarch64): [zip](https://github.com/sirius-ms/sirius/releases/download/v$siriusFrontendVersion/sirius-$siriusFrontendVersion-linux-arm64.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]}"
tasks.register('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)
}
}
tasks.register('refreshReadMe') {
inputs.files(refreshDownloadLinks.outputs.files.singleFile, refreshTrainingLinks.outputs.files.singleFile)
outputs.file("${getRootDir()}/README.md")
group = 'publishing'
doFirst {
File dld = inputs.files.getAt(0)
File clg = inputs.files.getAt(1)
File out = outputs.files.singleFile
List<String> links = Files.readAllLines(dld.toPath())
List<String> training = Files.readAllLines(clg.toPath())
Map<String, String> keywords = ['<!--begin download-->': '<!--end download-->', '<!--begin training-->': '<!--end training-->']
Map<String, List<String>> replacements = ['<!--begin download-->': links, '<!--begin training-->': training]
List<String> lines = Files.readAllLines(out.toPath())
List<String> nuLines = new LinkedList<>()
String keyword = null
String keywordEnd = null
lines.each { String line ->
if (line.startsWith("[![Generic badge](https://img.shields.io/badge/Version-")) {
nuLines.add("[![Generic badge](https://img.shields.io/badge/Version-${siriusFrontendVersion.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