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knakul853
Apr 16th, 2020
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  1. import org.gradle.internal.os.OperatingSystem
  2.  
  3. plugins {
  4.     id "java"
  5.     id "application"
  6.     id "org.openjfx.javafxplugin" version "0.0.8"
  7.     id "org.javamodularity.moduleplugin" version "1.5.0"
  8.     id "org.beryx.jlink" version "2.16.4"
  9. }
  10.  
  11. group = "io.github.mzmine"
  12. version = "3.0"
  13. description = "MZmine"
  14. sourceCompatibility = "12"
  15. targetCompatibility = "12"
  16. defaultTasks "runtimeZip"
  17.  
  18.  
  19. // Check the OS
  20. project.ext.osSuffix = OperatingSystem.current().getName().replaceAll(" ", "_")
  21. if (OperatingSystem.current().isMacOsX())
  22.     project.ext.osSuffix = "macOS"
  23. if (OperatingSystem.current().isLinux())
  24.     project.ext.osSuffix = "Linux"
  25. if (OperatingSystem.current().isWindows())
  26.     project.ext.osSuffix = "Windows"
  27. println "OS detected as " + project.ext.osSuffix
  28.  
  29.  
  30. repositories {
  31.     maven {
  32.         url = "file://" + projectDir + "/src/main/lib"
  33.     }
  34.     maven { // For jmztab 3.0.9+ (https://github.com/PRIDE-Utilities/jmzTab)
  35.         url = "https://dl.bintray.com/lifs/maven/"
  36.     }
  37.     maven { // For jmzml, etc.
  38.         url = "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/"
  39.     }
  40.     maven {
  41.         url = "https://repo.maven.apache.org/maven2"
  42.     }
  43.     maven { // For SIRIUS ID modules
  44.         url = "https://bio.informatik.uni-jena.de/repository/libs-oss/"
  45.     }
  46.     maven {
  47.         url = "https://jitpack.io"
  48.     }
  49.     maven {
  50.         url = "https://www.xypron.de/repository/"
  51.     }
  52.     maven { // For cpdetector
  53.         url = "https://nexus.nuiton.org/nexus/content/groups/releases/"
  54.     }
  55. }
  56.  
  57. ext {
  58.     msdkVersion = "0.0.27"
  59.     cdkVersion = "2.3"
  60.     jmztabVersion = "3.0.9"
  61.     swaggerVersion = "1.5.22"
  62.     okhttpVersion = "2.7.5"
  63.     guavaVersion = "28.1-jre"
  64.     slf4jVersion = "1.7.28"
  65.     poiVersion = "4.1.0"
  66.     batikVersion = "1.11"
  67.     controlsfxVersion = "11.0.1"
  68. }
  69.  
  70. dependencies {
  71.     implementation "com.github.graphstream:gs-core:2.0-alpha"
  72.     implementation "com.github.graphstream:gs-ui-javafx:2.0-alpha"
  73.     implementation "org.jfree:jfreechart:1.5.0"
  74.     implementation "org.jfree:jfreechart-fx:1.0.1"
  75.     implementation "org.jfree:fxgraphics2d:1.8"
  76.     implementation "org.jfree:jfreesvg:3.3"
  77.     implementation "com.orsonpdf:orsonpdf:1.9"
  78.     implementation "com.google.guava:guava:$guavaVersion"
  79.     implementation "org.apache.commons:commons-math:2.2"
  80.     implementation "edu.ucar:netcdf4:4.5.5"
  81.     implementation "org.ostermiller:utils:1.07.00"
  82.     implementation "com.google.code.findbugs:jsr305:3.0.2"
  83.     implementation "nz.ac.waikato.cms.weka:weka-stable:3.8.3"
  84.     implementation "net.sourceforge.jmol:jmol:14.29.27"
  85.     implementation "org.slf4j:slf4j-api:$slf4jVersion"
  86.     implementation "org.slf4j:slf4j-jdk14:$slf4jVersion"
  87.     implementation "org.apache.poi:poi:$poiVersion"
  88.     implementation "org.apache.poi:poi-ooxml:$poiVersion"
  89.     implementation "org.openscience.cdk:cdk-core:$cdkVersion"
  90.     implementation "org.openscience.cdk:cdk-io:$cdkVersion"
  91.     implementation "org.openscience.cdk:cdk-standard:$cdkVersion"
  92.     implementation "org.openscience.cdk:cdk-silent:$cdkVersion"
  93.     implementation "org.openscience.cdk:cdk-formula:$cdkVersion"
  94.     implementation "org.openscience.cdk:cdk-sdg:$cdkVersion"
  95.     implementation "org.openscience.cdk:cdk-renderbasic:$cdkVersion"
  96.     implementation "org.openscience.cdk:cdk-renderawt:$cdkVersion"
  97.     implementation "org.openscience.cdk:cdk-data:$cdkVersion"
  98.     implementation "org.openscience.cdk:cdk-interfaces:$cdkVersion"
  99.     implementation "org.openscience.cdk:cdk-smiles:$cdkVersion"
  100.     implementation "uk.ac.ebi.jmzml:jmzml:1.7.11"
  101.     implementation "org.postgresql:postgresql:9.3-1102-jdbc41"
  102.     implementation "mysql:mysql-connector-java:5.1.34"
  103.     implementation "org.nuiton.thirdparty:REngine:1.8-5"
  104.     implementation "org.nuiton.thirdparty:Rserve:1.8-5"
  105.     implementation "com.github.jbytecode:RCaller:3.0"
  106.     implementation "uk.ac.ebi.pride:jmztab-modular-model:$jmztabVersion"
  107.     implementation "uk.ac.ebi.pride:jmztab-modular-util:$jmztabVersion"
  108.     implementation "org.apache.xmlgraphics:fop:1.0"
  109.     implementation "org.freehep:freehep-graphicsio-emf:2.4"
  110.     implementation "org.xerial:sqlite-jdbc:3.8.11.2"
  111.     implementation "it.unimi.dsi:fastutil:8.2.2"
  112.     implementation "com.itextpdf:itextpdf:5.5.13.1"
  113.     implementation "org.apache.xmlgraphics:xmlgraphics-commons:2.3"
  114.     implementation "org.apache.xmlgraphics:batik-util:$batikVersion"
  115.     implementation "org.apache.xmlgraphics:batik-transcoder:$batikVersion"
  116.     implementation "org.apache.xmlgraphics:batik-codec:$batikVersion"
  117.     implementation "org.apache.xmlgraphics:batik-ext:$batikVersion"
  118.     implementation "org.apache.xmlgraphics:batik-awt-util:$batikVersion"
  119.     implementation "org.apache.xmlgraphics:batik-dom:$batikVersion"
  120.     implementation "org.apache.xmlgraphics:batik-svggen:$batikVersion"
  121.     implementation "org.apache.xmlgraphics:batik-svg-dom:$batikVersion"
  122.     implementation "org.apache.xmlgraphics:batik-anim:$batikVersion"
  123.     implementation "org.apache.xmlgraphics:batik-rasterizer:$batikVersion"
  124.     implementation "org.apache.xmlgraphics:batik-swing:$batikVersion"
  125.     implementation "org.apache.xmlgraphics:batik-gui-util:$batikVersion"
  126.     implementation "org.apache.xmlgraphics:batik-ttf2svg:$batikVersion"
  127.     implementation "org.apache.xmlgraphics:batik-parser:$batikVersion"
  128.     implementation "net.sf.epsgraphics:epsgraphics:1.2"
  129.     implementation "com.miglayout:miglayout:3.7.4"
  130.     implementation "javax.xml.bind:jaxb-api:2.3.1"
  131.     implementation "com.sun.xml.bind:jaxb-core:2.3.0.1"
  132.     implementation "com.sun.xml.bind:jaxb-impl:2.3.2"
  133.     implementation "javax.activation:javax.activation-api:1.2.0"
  134.     implementation "javax.mail:javax.mail-api:1.6.2"
  135.     implementation "io.swagger:swagger-annotations:$swaggerVersion"
  136.     implementation "com.squareup.okhttp:okhttp:$okhttpVersion"
  137.     implementation "com.squareup.okhttp:logging-interceptor:$okhttpVersion"
  138.     implementation "com.google.code.gson:gson:2.8.5"
  139.     implementation "io.gsonfire:gson-fire:1.8.0"
  140.     implementation "org.threeten:threetenbp:1.3.8"
  141.     implementation "org.controlsfx:controlsfx:$controlsfxVersion"
  142.     implementation "org.drjekyll:fontchooser:2.4"
  143.     implementation "org.json:json:20190722"
  144.     implementation "com.panemu:tiwulfx:3.0" // For DetachableTabPane
  145.     implementation "com.github.oshi:oshi-core:4.5.2" // because the version that is pulled by SIRIUS crashes
  146.     implementation "io.github.msdk:msdk-io-mzml:$msdkVersion"
  147.  
  148. }
  149.  
  150. /*
  151.  * Remove the xml-apis dependencies to avoid a compilation error in Eclipse.
  152.  * The org.w3c.dom package is present in the java.xml module as well as in these dependencies.
  153.  * That is illegal (https://bugs.eclipse.org/bugs/show_bug.cgi?id=536928).
  154.  */
  155. configurations.all {
  156.   exclude group: "xml-apis", module: "xml-apis"
  157.   exclude group: "xml-apis", module: "xml-apis-ext"
  158.   exclude group: "xom", module: "xom"
  159.   exclude group: "ch.qos.logback", module: "logback-core"
  160.   exclude group: "ch.qos.logback", module: "logback-classic"
  161.   exclude group: "gurobi", module: "gurobi-linux64"
  162.   exclude group: "cplex", module: "cplex"
  163.     exclude group: "cdk", module:"cdk-formula"
  164. }
  165.  
  166.  
  167. /*
  168.  * Include JavaFX modules
  169.  */
  170. javafx {
  171.     version = "14"
  172.     modules = ["javafx.controls",
  173.                "javafx.swing",
  174.                "javafx.fxml",
  175.                "javafx.web",
  176.                "javafx.graphics"
  177.               ]
  178. }
  179.  
  180. tasks.withType(JavaCompile) {
  181.     options.encoding = "UTF-8"
  182. }
  183.  
  184.  
  185. /*
  186.  * Set the basic Java runtime parameters (heap size etc.)
  187.  */
  188. application {
  189.     mainClassName = "io.github.mzmine.main.MZmineCore"
  190.     applicationName = "MZmine"
  191.     executableDir = ""
  192.     applicationDefaultJvmArgs = ["-showversion",
  193.                                  "-XX:MaxHeapFreeRatio=100",
  194.                                  "-XX:InitialRAMPercentage=30",
  195.                                  "-XX:MinRAMPercentage=80",
  196.                                  "-XX:MaxRAMPercentage=80",
  197.                                  "-Djava.library.path=lib",
  198.                                  "-enableassertions",
  199.                                  "-Dapple.awt.application.name=MZmine ${version}"
  200.                                 ]
  201. }
  202.  
  203.  
  204. /*
  205.  * Provide a default start script for this platform
  206.  */
  207. startScripts {
  208.     applicationName = "startMZmine-" + osSuffix
  209.     classpath = files("lib/*")
  210.     doLast {
  211.         if (OperatingSystem.current().isWindows()) {
  212.             delete unixScript
  213.             // Temporary fix for https://github.com/gradle/gradle/issues/10387
  214.             windowsScript.text = windowsScript.text.replace('set JAVA_HOME=\"%~dp0.."', 'set JAVA_HOME="%~dp0"')
  215.         } else {
  216.             delete windowsScript
  217.         }
  218.     }
  219. }
  220.  
  221. /*
  222.  * Build the JVM runtime using jlink
  223.  */
  224. jlink {
  225.     mergedModule{
  226.         requires 'java.desktop'
  227.         requires "java.logging"
  228.         requires "java.rmi"
  229.         requires "java.sql"
  230.         requires "java.datatransfer"
  231.         requires "java.management"
  232.         requires "java.xml"
  233.         requires  "java.xml.crypto"
  234.         requires "jdk.xml.dom"
  235.         requires "java.naming"
  236.         requires "java.transaction.xa"
  237.         requires "java.scripting"
  238.         requires "jdk.jsobject"
  239.         requires "jdk.jfr"
  240.         requires "java.security.sasl"
  241.         requires "java.security.jgss"
  242.         requires "jdk.unsupported"
  243.         requires "jdk.unsupported.desktop"
  244.         requires "cdk.formula"
  245.         requires "cdk.data"
  246.         requires "cdk.interfaces"
  247.  
  248.     }
  249.     launcher{
  250.         name = 'mzmine'
  251.     }
  252.         options = ["--compress=2", "--vm=server", "--no-header-files", "--no-man-pages", "--output", "jre/jre"]
  253. }
  254.  
  255. /*
  256.  * Copy the resources and logging properties
  257.  */
  258. tasks.jlink.doLast {
  259.  
  260.     // Remove the "release" file produced by jlink
  261.     delete file(relativePath(imageDir) + "/release")
  262.  
  263.     copy {
  264.         from("log")
  265.         into("${buildDir}/${applicationName}-${version}-${osSuffix}" + "/log")
  266.     }
  267.     copy {
  268.         from("manual.pdf")
  269.         into("${buildDir}/${applicationName}-${version}-${osSuffix}")
  270.     }
  271.     copy {
  272.         from("LICENSE.txt")
  273.         into("${buildDir}/${applicationName}-${version}-${osSuffix}"+ "/legal/MZmine/")
  274.     }
  275.     copy {        
  276.         from("src/main/lib/vendor_lib")
  277.         into("${buildDir}/${applicationName}-${version}-${osSuffix}" + "/lib/vendor_lib")
  278.     }
  279.  
  280. }
  281.  
  282. /*
  283.  * This is important in order to copy all .java, .fxml, and help files into the final MZmine jar.
  284.  * The .java files are only for people who want to check the source codes.
  285.  * But the .fxml and help files are required for the GUI.
  286.  */
  287. jar {
  288.   sourceSets.main.resources.srcDirs += ["src/main/java"]
  289. }
  290.  
  291. /*
  292.  * Add MZmine version number to mzmineversion.properties
  293.  */
  294. processResources {
  295.     filesMatching("mzmineversion.properties") {
  296.         expand(project.properties)
  297.     }
  298. }
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