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build.gradle
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build.gradle
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import java.util.regex.Matcher
plugins {
id 'application'
id 'org.openjfx.javafxplugin' version '0.1.0'
id 'com.diffplug.spotless' version '6.25.0'
}
group 'de.unijena.cheminf'
version '1.2.0.0'
sourceCompatibility = 1.21
//Creates javadoc and sources jars
java {
withJavadocJar()
withSourcesJar()
}
repositories {
mavenCentral()
}
def javaFxVersion = '21.0.1'
def cdkVersion = '2.9'
dependencies {
implementation 'org.jetbrains:annotations:19.0.0'
testImplementation(platform('org.junit:junit-bom:5.9.3'))
testImplementation ('org.junit.jupiter:junit-jupiter')
implementation group: 'org.openscience.cdk', name: 'cdk-bundle', version: cdkVersion
implementation group: 'org.openscience.cdk', name: 'cdk-scaffold', version: '2.8'
implementation group: 'io.github.jonasschaub', name: 'sru', version: '1.4.0.0'
implementation group: 'io.github.jonasschaub', name: 'ErtlFunctionalGroupsFinder', version: '1.3.0.0'
implementation group: 'com.github.librepdf', name: 'openpdf', version: '1.3.26'
implementation group: 'org.openjfx', name: 'javafx-controls', version: javaFxVersion, classifier: 'win'
implementation group: 'org.openjfx', name: 'javafx-controls', version: javaFxVersion, classifier: 'linux'
implementation group: 'org.openjfx', name: 'javafx-controls', version: javaFxVersion, classifier: 'mac'
implementation group: 'org.openjfx', name: 'javafx-controls', version: javaFxVersion, classifier: 'linux-aarch64'
implementation group: 'org.openjfx', name: 'javafx-controls', version: javaFxVersion, classifier: 'mac-aarch64'
implementation group: 'org.openjfx', name: 'javafx-swing', version: javaFxVersion, classifier: 'win'
implementation group: 'org.openjfx', name: 'javafx-swing', version: javaFxVersion, classifier: 'linux'
implementation group: 'org.openjfx', name: 'javafx-swing', version: javaFxVersion, classifier: 'mac'
implementation group: 'org.openjfx', name: 'javafx-swing', version: javaFxVersion, classifier: 'linux-aarch64'
implementation group: 'org.openjfx', name: 'javafx-swing', version: javaFxVersion, classifier: 'mac-aarch64'
implementation group: 'org.openjfx', name: 'javafx-graphics', version: javaFxVersion, classifier: 'win'
implementation group: 'org.openjfx', name: 'javafx-graphics', version: javaFxVersion, classifier: 'linux'
implementation group: 'org.openjfx', name: 'javafx-graphics', version: javaFxVersion, classifier: 'mac'
implementation group: 'org.openjfx', name: 'javafx-graphics', version: javaFxVersion, classifier: 'linux-aarch64'
implementation group: 'org.openjfx', name: 'javafx-graphics', version: javaFxVersion, classifier: 'mac-aarch64'
implementation group: 'org.openjfx', name: 'javafx-base', version: javaFxVersion, classifier: 'win'
implementation group: 'org.openjfx', name: 'javafx-base', version: javaFxVersion, classifier: 'linux'
implementation group: 'org.openjfx', name: 'javafx-base', version: javaFxVersion, classifier: 'mac'
implementation group: 'org.openjfx', name: 'javafx-base', version: javaFxVersion, classifier: 'linux-aarch64'
implementation group: 'org.openjfx', name: 'javafx-base', version: javaFxVersion, classifier: 'mac-aarch64'
}
javafx {
modules = ['javafx.base','javafx.graphics', 'javafx.controls', 'javafx.swing']
}
test {
useJUnitPlatform()
testLogging {
events "passed", "skipped", "failed"
}
}
mainClassName = 'de.unijena.cheminf.mortar.main.Main'
applicationName = 'MORTAR'
applicationDefaultJvmArgs = ["-Xms4g", "-Xmx4g"]
/*
* The unix script still has to be tested!
*/
startScripts {
doLast {
//suppress console window by using javaw instead of java
windowsScript.text = windowsScript.text.replaceAll("java.exe", "javaw.exe")
//use JRE shipped with MORTAR instead of Java installed on the machine and rename method to set the java home to use
windowsScript.text = windowsScript.text.replace("if defined JAVA_HOME goto findJavaFromJavaHome", "goto setJavaFromAppHome\n\n@rem unused because Java home is set in method called above")
windowsScript.text = windowsScript.text.replace(":findJavaFromJavaHome", ":setJavaFromAppHome")
windowsScript.text = windowsScript.text.replace("set JAVA_HOME=%JAVA_HOME:\"=%",
"set JAVA_HOME=%APP_HOME%\\jdk-21.0.1_12_jre\\")
//Merges the exact enumeration of all library jars into one single path giving all the files and subfolders in 'lib'
// This is necessary because lines that are too long cause errors in batch files.
windowsScript.text = windowsScript.text.replaceAll('set CLASSPATH=.*', 'set CLASSPATH=.;%APP_HOME%/lib/*')
//workaround to suppress command window by starting named process "MORTAR" - legacy
//windowsScript.text = windowsScript.text.replace("\"%JAVA_EXE%\" %DEFAULT_JVM_OPTS%", "start \"MORTAR\" \"%JAVA_EXE%\" %DEFAULT_JVM_OPTS%")
//workaround to suppress command window and pass CMD options to MORTAR to suppress the Java version check
windowsScript.text = windowsScript.text.replace("\"%JAVA_EXE%\" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %MORTAR_OPTS% -classpath \"%CLASSPATH%\" de.unijena.cheminf.mortar.main.Main %*",
"start \"MORTAR\" \"%JAVA_EXE%\" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %MORTAR_OPTS% -classpath \"%CLASSPATH%\" de.unijena.cheminf.mortar.main.Main \"-skipJavaVersionCheck\"")
//adjusting error messages
windowsScript.text = windowsScript.text.replace("Please set the JAVA_HOME variable in your environment to match the", "Please check your MORTAR installation,")
windowsScript.text = windowsScript.text.replace("location of your Java installation.", "something must be wrong with the Java Runtime Environment shipped with MORTAR.")
//Merges the exact enumeration of all library jars into one single path giving all the files and subfolders in 'lib' for unix script
unixScript.text = unixScript.text.replaceAll('CLASSPATH=\\Q$\\EAPP_HOME/lib.*', Matcher.quoteReplacement('CLASSPATH=$APP_HOME/lib/*'))
}
}
task updateHeapSpace20GbExtraRunApp(type: CreateStartScripts) {
mainClassName = 'de.unijena.cheminf.mortar.main.Main'
classpath = startScripts.classpath
outputDir = file('build/scripts')
applicationName = 'MORTAR_20GB'
defaultJvmOpts = ["-Xms20g", "-Xmx20g"]
updateHeapSpace20GbExtraRunApp {
doLast {
//suppress console window by using javaw instead of java
windowsScript.text = windowsScript.text.replaceAll("java.exe", "javaw.exe")
//use JRE shipped with MORTAR instead of Java installed on the machine and rename method to set the java home to use
windowsScript.text = windowsScript.text.replace("if defined JAVA_HOME goto findJavaFromJavaHome", "goto setJavaFromAppHome\n\n@rem unused because Java home is set in method called above")
windowsScript.text = windowsScript.text.replace(":findJavaFromJavaHome", ":setJavaFromAppHome")
windowsScript.text = windowsScript.text.replace("set JAVA_HOME=%JAVA_HOME:\"=%",
"set JAVA_HOME=%APP_HOME%\\jdk-21.0.1_12_jre\\")
//Merges the exact enumeration of all library jars into one single path giving all the files and subfolders in 'lib'
// This is necessary because lines that are too long cause errors in batch files.
windowsScript.text = windowsScript.text.replaceAll('set CLASSPATH=.*', 'set CLASSPATH=.;%APP_HOME%/lib/*')
//workaround to suppress command window by starting named process "MORTAR" - legacy
//windowsScript.text = windowsScript.text.replace("\"%JAVA_EXE%\" %DEFAULT_JVM_OPTS%", "start \"MORTAR\" \"%JAVA_EXE%\" %DEFAULT_JVM_OPTS%")
//workaround to suppress command window and pass CMD options to MORTAR to suppress the Java version check
windowsScript.text = windowsScript.text.replace("\"%JAVA_EXE%\" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %MORTAR_20_GB_OPTS% -classpath \"%CLASSPATH%\" de.unijena.cheminf.mortar.main.Main %*",
"start \"MORTAR\" \"%JAVA_EXE%\" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %MORTAR_20_GB_OPTS% -classpath \"%CLASSPATH%\" de.unijena.cheminf.mortar.main.Main \"-skipJavaVersionCheck\"")
//adjusting error messages
windowsScript.text = windowsScript.text.replace("Please set the JAVA_HOME variable in your environment to match the", "Please check your MORTAR installation,")
windowsScript.text = windowsScript.text.replace("location of your Java installation.", "something must be wrong with the Java Runtime Environment shipped with MORTAR.")
//Merges the exact enumeration of all library jars into one single path giving all the files and subfolders in 'lib' for unix script
unixScript.text = unixScript.text.replaceAll('CLASSPATH=\\Q$\\EAPP_HOME/lib.*', Matcher.quoteReplacement('CLASSPATH=$APP_HOME/lib/*'))
}
}
}
applicationDistribution.into("bin") {
duplicatesStrategy= DuplicatesStrategy.EXCLUDE
from(updateHeapSpace20GbExtraRunApp)
fileMode = 0755
}
//Needed to make the created jar archives executable
jar {
manifest {
attributes 'Main-Class': mainClassName
}
}
//Creates a jar archive that includes all dependencies of the project, i.e. that MORTAR can be started by executing this jar
task fatJar(type: Jar) {
manifest {
attributes 'Implementation-Title': 'MORTAR Fat Jar File',
'Implementation-Version': archiveVersion,
'Main-Class': mainClassName
duplicatesStrategy = DuplicatesStrategy.INCLUDE
}
archiveAppendix = 'fat'
from {
// configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
configurations.runtimeClasspath.findAll { it.name.endsWith('jar') && !it.name.endsWith('aarch64.jar') }.collect { zipTree(it) }
}
with jar
}
task fatJarAarch64(type: Jar) {
manifest {
attributes 'Implementation-Title': 'MORTAR Fat Jar File for AArch64',
'Implementation-Version': archiveVersion,
'Main-Class': mainClassName
duplicatesStrategy = DuplicatesStrategy.INCLUDE
}
archiveAppendix = 'fat-aarch64'
from {
// configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
configurations.runtimeClasspath.findAll {it.name.endsWith('jar') && !it.name.endsWith('linux.jar') && !it.name.endsWith('mac.jar') }.collect { zipTree(it) }
}
with jar
}
//Archives artifacts executed with build
artifacts {
archives fatJar
archives fatJarAarch64
}
//Includes the Adopt Open JDK folder in the project's root directory in the created archives for distribution
distributions {
main {
contents {
from 'AdoptOpenJDK'
into('tutorial'){
from 'Tutorial'
}
}
}
}
spotless {
java {
toggleOffOn() //all code in between spotless:off / spotless:on will be ignored
licenseHeaderFile('License-header/License-header.txt')
encoding 'UTF-8'
cleanthat()
importOrder('com', 'de', 'javafx', 'org', 'javax', 'java')
removeUnusedImports()
indentWithSpaces(4) // doesn't really seem to work...
trimTrailingWhitespace()
endWithNewline()
//eclipse() //not optimal, because indents with tabs..
//googleJavaFormat() //not optimal, because indents with two spaces...
//palantirJavaFormat() //not optimal, because unnecessary line breaks in head of for loop and corrupts editor folds
//prettier() //needs npm installed, unsuitable...
//clangFormat() //also needs an installation...
custom 'Refuse wildcard imports', {
// Wildcard imports can't be resolved by spotless itself.
// This will require the developer themselves to adhere to best practices.
if (it =~ /\nimport .*\*;/) {
throw new AssertionError("Do not use wildcard imports. 'spotlessApply' cannot resolve this issue.")
}
}
}
}