build.gradle

   1 import org.apache.tools.ant.filters.ReplaceTokens
   2 import org.gradle.internal.os.OperatingSystem
   3
   4
   5 buildscript {
   6   dependencies {
   7         classpath 'org.openclover:clover:4.3.1'
   8   }
   9 }
  10
  11 plugins {
  12   id 'java'
  13   id 'application'
  14   id 'com.github.johnrengelman.shadow' version '4.0.3'
  15   id 'com.install4j.gradle' version '7.0.9'
  16 }
  17
  18 repositories {
  19   jcenter()
  20   mavenCentral()
  21   mavenLocal()
  22   flatDir {
  23     dirs gradlePluginsDir
  24   }
  25 }
  26
  27 mainClassName = launcherClass
  28 def cloverInstrDir = file("$buildDir/sources-instr")
  29
  30 sourceSets {
  31
  32   main {
  33     java {
  34       srcDirs "$jalviewDir/$sourceDir"
  35       outputDir = file("$jalviewDir/$classesDir")
  36     }
  37
  38     resources {
  39       srcDirs "$jalviewDir/$resourceDir"
  40       srcDirs "$jalviewDir/$libDir"
  41     }
  42
  43     jar.destinationDir = file("$jalviewDir/$packageDir")
  44
  45     compileClasspath = files(sourceSets.main.java.outputDir)
  46     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
  47     if (JAVA_VERSION.equals("1.8")) {
  48       print("ADDING J11LIBS TO CLASSPATH")
  49       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
  50     }
  51
  52     runtimeClasspath = compileClasspath
  53   }
  54
  55   modules {
  56     compileClasspath = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
  57
  58     runtimeClasspath = compileClasspath
  59   }
  60
  61   clover {
  62     java {
  63         srcDirs = [ cloverInstrDir ]
  64         outputDir = file("$jalviewDir/$testOutputDir")
  65     }
  66
  67     resources {
  68       srcDirs = sourceSets.main.resources.srcDirs
  69     }
  70     compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
  71     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
  72     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
  73     if (JAVA_VERSION.equals("1.8")) {
  74       print("ADDING J11LIBS TO CLASSPATH")
  75       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
  76     }
  77
  78     runtimeClasspath = compileClasspath
  79   }
  80
  81   test {
  82     java {
  83       srcDirs = [ cloverInstrDir ]
  84       outputDir = file("$jalviewDir/$testOutputDir")
  85     }
  86
  87     resources {
  88       srcDirs = sourceSets.main.resources.srcDirs
  89     }
  90
  91
  92     compileClasspath += configurations.cloverRuntime + files( sourceSets.test.java.outputDir )
  93     compileClasspath += fileTree(dir: "$jalviewDir/$utilsDir", include: ["**/*.jar"])
  94     compileClasspath += fileTree(dir: "$jalviewDir/$libDir", include: ["*.jar"])
  95     if (JAVA_VERSION.equals("1.8")) {
  96       print("ADDING J11LIBS TO CLASSPATH")
  97       compileClasspath += fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"])
  98     }
  99
 100     runtimeClasspath = compileClasspath
 101   }
 102 }
 103
 104 // clover bits
 105 dependencies {
 106   cloverCompile 'org.openclover:clover:4.3.1'
 107   testCompile 'org.openclover:clover:4.3.1'
 108 }
 109
 110 configurations {
 111     cloverRuntime
 112     cloverRuntime.extendsFrom cloverCompile
 113 }
 114
 115 task cloverInstr() {
 116     inputs.files files (sourceSets.main.allJava, fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
 117     outputs.dir cloverInstrDir
 118
 119     doFirst {
 120         delete cloverInstrDir
 121         def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 122                         "-d", "${buildDir}/sources-instr"]
 123         argsList.addAll(inputs.files.files.collect({ file ->
 124             file.absolutePath
 125         }))
 126         String[] args = argsList.toArray()
 127         println("About to instrument "+args.length +" files")
 128         com.atlassian.clover.CloverInstr.mainImpl(args)
 129     }
 130 }
 131
 132 test.dependsOn cloverInstr
 133
 134 task cloverReport {
 135     inputs.dir "${buildDir}/clover"
 136     outputs.dir "${reportsDir}/clover"
 137     onlyIf {
 138         file("${buildDir}/clover/clover.db").exists()
 139     }
 140     doFirst {
 141         def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 142                         "-o", "${reportsDir}/clover"]
 143         String[] args = argsList.toArray()
 144         com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
 145     }
 146 }
 147
 148 // end clover bits
 149
 150
 151 compileJava {
 152
 153   doFirst {
 154     if (JAVA_VERSION.equals("1.8")) {
 155       sourceCompatibility = 1.8
 156       targetCompatibility = 1.8
 157     } else if (JAVA_VERSION.equals("11")) {
 158       sourceCompatibility = 11
 159       targetCompatibility = 11
 160
 161       options.compilerArgs = [
 162         '--module-path', sourceSets.modules.compileClasspath.asPath,
 163         '--add-modules', j11modules
 164       ]
 165     }
 166     print ("Setting target compatibility to "+targetCompatibility+"\n")
 167   }
 168
 169 }
 170
 171 compileTestJava {
 172
 173   doFirst {
 174     if (JAVA_VERSION.equals("1.8")) {
 175       sourceCompatibility = 1.8
 176       targetCompatibility = 1.8
 177     } else if (JAVA_VERSION.equals("11")) {
 178       sourceCompatibility = 11
 179       targetCompatibility = 11
 180
 181       options.compilerArgs = [
 182         '--module-path', sourceSets.modules.compileClasspath.asPath,
 183         '--add-modules', j11modules
 184       ]
 185     }
 186     print ("Setting target compatibility to "+targetCompatibility+"\n")
 187   }
 188   classpath += configurations.cloverRuntime
 189 }
 190
 191
 192 //compileCloverJava {
 193 //
 194 //  doFirst {
 195 //    if (JAVA_VERSION.equals("1.8")) {
 196 //      sourceCompatibility = 1.8
 197 //      targetCompatibility = 1.8
 198 //    } else if (JAVA_VERSION.equals("11")) {
 199 //      sourceCompatibility = 11
 200 //      targetCompatibility = 11
 201 //
 202 //      options.compilerArgs += [
 203 //        '--module-path', sourceSets.modules.compileClasspath.asPath,
 204 //        '--add-modules', j11modules
 205 //      ]
 206 //    }
 207 //    print ("Setting target compatibility to "+targetCompatibility+"\n")
 208 //  }
 209 //  classpath += configurations.cloverRuntime
 210 //}
 211
 212 clean {
 213   delete sourceSets.main.java.outputDir
 214 }
 215
 216 cleanTest {
 217   delete sourceSets.test.java.outputDir
 218   delete cloverInstrDir
 219 }
 220
 221 def getDate(format) {
 222   def date = new Date()
 223   //return date.format("dd MMMM yyyy")
 224   return date.format(format)
 225 }
 226
 227 def getGitHash() {
 228   def stdout = new ByteArrayOutputStream()
 229   exec {
 230     commandLine "git", "rev-parse", "--short", "HEAD"
 231     standardOutput = stdout
 232     workingDir = jalviewDir
 233   }
 234   return stdout.toString().trim()
 235 }
 236
 237 def getGitBranch() {
 238   def stdout = new ByteArrayOutputStream()
 239   exec {
 240     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
 241     standardOutput = stdout
 242     workingDir = jalviewDir
 243   }
 244   return stdout.toString().trim()
 245 }
 246
 247 task createBuildProperties(type: WriteProperties) {
 248   inputs.dir("$jalviewDir/$sourceDir")
 249   inputs.dir("$jalviewDir/$resourceDir")
 250   outputFile "$jalviewDir/$classesDir/$buildPropertiesFile"
 251   /* taking time/date specific comment out to allow better incremental builds */
 252   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
 253   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
 254   property "BUILD_DATE", getDate("dd MMMM yyyy")
 255   property "VERSION", JALVIEW_VERSION
 256   property "INSTALLATION", INSTALLATION+" git-commit:"+getGitHash()+" ["+getGitBranch()+"]"
 257   outputs.file(outputFile)
 258   outputs.dir("$jalviewDir/$classesDir")
 259 }
 260
 261 task syncDocs(type: Sync) {
 262   def syncDir = "$jalviewDir/$classesDir/$docDir"
 263   from fileTree("$jalviewDir/$docDir")
 264   into syncDir
 265
 266 }
 267
 268 def helpFile = "$jalviewDir/$classesDir/$helpDir/help.jhm"
 269 task syncHelp(type: Sync) {
 270   inputs.files("$jalviewDir/$helpDir")
 271   outputs.files(helpFile)
 272
 273   def syncDir = "$jalviewDir/$classesDir/$helpDir"
 274   from fileTree("$jalviewDir/$helpDir")
 275   into syncDir
 276 }
 277
 278 task copyHelp(type: Copy) {
 279   def inputDir = "$jalviewDir/$helpDir"
 280   def outputDir = "$jalviewDir/$classesDir/$helpDir"
 281   from inputDir
 282   into outputDir
 283   filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': "USING_FILTER"])
 284   inputs.dir(inputDir)
 285   outputs.files(helpFile)
 286   outputs.dir(outputDir)
 287 }
 288
 289 task syncLib(type: Sync) {
 290   def syncDir = "$jalviewDir/$classesDir/$libDir"
 291   from fileTree("$jalviewDir/$libDir")
 292   into syncDir
 293 }
 294
 295 task syncResources(type: Sync) {
 296   from "$jalviewDir/$resourceDir"
 297   include "**/*.*"
 298   exclude "install4j"
 299   into "$jalviewDir/$classesDir"
 300   preserve {
 301     include "**"
 302   }
 303 }
 304
 305 task prepare {
 306   dependsOn syncResources
 307   dependsOn syncDocs
 308   dependsOn copyHelp
 309 }
 310
 311
 312 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 313 test {
 314   dependsOn prepare
 315
 316
 317   useTestNG()
 318   options {
 319     includeGroups testngGroups
 320     preserveOrder true
 321   }
 322
 323   workingDir = jalviewDir
 324   //systemProperties 'clover.jar' System.properties.clover.jar
 325   if (JAVA_VERSION.equals("1.8")) {
 326     sourceCompatibility = 1.8
 327     targetCompatibility = 1.8
 328   } else if (JAVA_VERSION.equals("11")) {
 329     sourceCompatibility = 11
 330     targetCompatibility = 11
 331
 332     jvmArgs += [
 333       '--module-path',
 334       sourceSets.modules.compileClasspath.asPath,
 335       '--add-modules',
 336       j11modules
 337     ]
 338   }
 339   print ("Setting target compatibility to "+targetCompatibility+"\n")
 340 }
 341
 342 task buildIndices(type: JavaExec) {
 343   dependsOn copyHelp
 344   classpath = sourceSets.main.compileClasspath
 345   main = "com.sun.java.help.search.Indexer"
 346   workingDir = "$jalviewDir/$classesDir/$helpDir"
 347   def argDir = "html"
 348   args = [ argDir ]
 349   inputs.dir("$workingDir/$argDir")
 350
 351   outputs.dir("$jalviewDir/$classesDir/doc")
 352   outputs.dir("$jalviewDir/$classesDir/help")
 353   outputs.file("$workingDir/JavaHelpSearch/DOCS")
 354   outputs.file("$workingDir/JavaHelpSearch/DOCS.TAB")
 355   outputs.file("$workingDir/JavaHelpSearch/OFFSETS")
 356   outputs.file("$workingDir/JavaHelpSearch/POSITIONS")
 357   outputs.file("$workingDir/JavaHelpSearch/SCHEMA")
 358   outputs.file("$workingDir/JavaHelpSearch/TMAP")
 359 }
 360
 361 task compileLinkCheck(type: JavaCompile) {
 362   options.fork = true
 363   classpath = files("$jalviewDir/$utilsDir")
 364   destinationDir = file("$jalviewDir/$utilsDir")
 365   source = fileTree(dir: "$jalviewDir/$utilsDir", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 366
 367   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.class")
 368   outputs.file("$jalviewDir/$utilsDir/BufferedLineReader.class")
 369 }
 370
 371 task linkCheck(type: JavaExec) {
 372   dependsOn prepare, compileLinkCheck
 373   classpath = files("$jalviewDir/$utilsDir")
 374   main = "HelpLinksChecker"
 375   workingDir = "$jalviewDir"
 376   args = [ "$classesDir/$helpDir", "-nointernet" ]
 377
 378   doFirst {
 379     standardOutput new FileOutputStream("$jalviewDir/$utilsDir/HelpLinksChecker.out")
 380   }
 381
 382   outputs.file("$jalviewDir/$utilsDir/HelpLinksChecker.out")
 383 }
 384
 385 task cleanPackageDir(type: Delete) {
 386   delete fileTree("$jalviewDir/$packageDir").include("*.jar")
 387 }
 388
 389 jar {
 390   dependsOn linkCheck
 391   dependsOn buildIndices
 392   dependsOn createBuildProperties
 393
 394   manifest {
 395     attributes "Main-Class": mainClass,
 396     "Permissions": "all-permissions",
 397     "Application-Name": "Jalview Desktop",
 398     "Codebase": application_codebase
 399   }
 400
 401   destinationDir = file("$jalviewDir/$packageDir")
 402   archiveName = rootProject.name+".jar"
 403
 404   exclude "cache*/**"
 405   exclude "*.jar"
 406   exclude "*.jar.*"
 407   exclude "**/*.jar"
 408   exclude "**/*.jar.*"
 409
 410   inputs.dir("$jalviewDir/$classesDir")
 411   outputs.file("$jalviewDir/$packageDir/$archiveName")
 412 }
 413
 414 task copyJars(type: Copy) {
 415   from fileTree("$jalviewDir/$classesDir").include("**/*.jar").include("*.jar").files
 416   into "$jalviewDir/$packageDir"
 417 }
 418
 419 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 420 task syncJars(type: Sync) {
 421   from fileTree("$jalviewDir/$libDir").include("**/*.jar").include("*.jar").files
 422   into "$jalviewDir/$packageDir"
 423   preserve {
 424     include jar.archiveName
 425   }
 426 }
 427
 428 task makeDist {
 429   // order of "cleanPackageDir", "copyJars", "jar" important!
 430   jar.mustRunAfter cleanPackageDir
 431   syncJars.mustRunAfter cleanPackageDir
 432   dependsOn cleanPackageDir
 433   dependsOn syncJars
 434   dependsOn jar
 435   outputs.dir("$jalviewDir/$packageDir")
 436 }
 437
 438 task cleanDist {
 439   dependsOn cleanPackageDir
 440   dependsOn cleanTest
 441   dependsOn clean
 442 }
 443
 444 shadowJar {
 445   dependsOn makeDist
 446   if (JAVA_VERSION.equals("11")) {
 447     from ("$jalviewDir/$j11libDir") {
 448       include("*.jar")
 449     }
 450   }
 451   mainClassName = shadowJarMainClass
 452   mergeServiceFiles()
 453   classifier = "all"
 454   minimize()
 455 }
 456
 457 ext {
 458   getdownWebsiteDir = jalviewDir + '/' + getdown_website_dir
 459   getdownAppDir = getdownWebsiteDir + '/' + getdown_app_dir
 460   getdownJ11libDir = getdownWebsiteDir + '/' + getdown_j11lib_dir
 461   getdownResourceDir = getdownWebsiteDir + '/' + getdown_resource_dir
 462   getdownLauncher = jalviewDir + '/' + getdown_launcher
 463   getdownFilesDir = jalviewDir + '/' + getdown_files_dir
 464 }
 465
 466 task getdownWebsite() {
 467   dependsOn makeDist
 468   def getdownWebsiteResourceFilenames = []
 469   def getdownTextString = ""
 470   def getdownResourceDir = project.ext.getdownResourceDir
 471   def getdownAppDir = project.ext.getdownAppDir
 472   def getdownResourceFilenames = []
 473   doFirst {
 474     // go through properties looking for getdown_txt_...
 475     def props = project.properties.sort { it.key }
 476     if (JAVA_VERSION.equals("11")) {
 477       props.put("getdown_txt_java_min_version", getdown_alt_java11_min_version)
 478     } else {
 479       props.put("getdown_txt_java_min_version", getdown_alt_java8_min_version)
 480     }
 481     props.each{ prop, val ->
 482       if (prop.startsWith("getdown_txt_") && val != null) {
 483         if (prop.startsWith("getdown_txt_multi_")) {
 484           def key = prop.substring(18)
 485           val.split(",").each{ v ->
 486             def line = key + " = " + v + "\n"
 487             getdownTextString += line
 488           }
 489         } else {
 490           // file values rationalised
 491           if (val.indexOf('/') > -1) {
 492             def r = null
 493             if (val.indexOf('/') == 0) {
 494               // absolute path
 495               r = file(val)
 496             } else if (val.indexOf('/') > 0) {
 497               // relative path (relative to jalviewDir)
 498               r = file( jalviewDir + '/' + val )
 499             }
 500             if (r.exists()) {
 501               val = getdown_resource_dir + '/' + r.getName()
 502               getdownWebsiteResourceFilenames += val
 503               getdownResourceFilenames += r.getPath()
 504             }
 505           }
 506           def line = prop.substring(12) + " = " + val + "\n"
 507           getdownTextString += line
 508         }
 509       }
 510     }
 511
 512     getdownWebsiteResourceFilenames.each{ filename ->
 513       getdownTextString += "resource = "+filename+"\n"
 514     }
 515     getdownResourceFilenames.each{ filename ->
 516       copy {
 517         from filename
 518         into project.ext.getdownResourceDir
 519       }
 520     }
 521
 522     def codeFiles = []
 523     makeDist.outputs.files.each{ f ->
 524       if (f.isDirectory()) {
 525         def files = fileTree(dir: f, include: ["*"]).getFiles()
 526         codeFiles += files
 527       } else if (f.exists()) {
 528         codeFiles += f
 529       }
 530     }
 531     codeFiles.sort().each{f ->
 532       def line = "code = " + getdown_app_dir + '/' + f.getName() + "\n"
 533       getdownTextString += line
 534       copy {
 535         from f.getPath()
 536         into project.ext.getdownAppDir
 537       }
 538     }
 539
 540     if (JAVA_VERSION.equals("11")) {
 541       def j11libFiles = fileTree(dir: "$jalviewDir/$j11libDir", include: ["*.jar"]).getFiles()
 542       j11libFiles.sort().each{f ->
 543         def line = "code = " + getdown_j11lib_dir + '/' + f.getName() + "\n"
 544         getdownTextString += line
 545         copy {
 546           from f.getPath()
 547           into project.ext.getdownJ11libDir
 548         }
 549       }
 550     }
 551
 552     getdownTextString += "code = " + file(getdownLauncher).getName() + "\n"
 553     getdownTextString += "class = " + mainClass + "\n"
 554
 555     def getdown_txt = file(project.ext.getdownWebsiteDir + "/getdown.txt")
 556     getdown_txt.write(getdownTextString)
 557
 558     copy {
 559       from getdown_txt
 560       into project.ext.getdownFilesDir
 561     }
 562
 563     copy {
 564       from getdownLauncher
 565       into project.ext.getdownWebsiteDir
 566     }
 567
 568     copy {
 569       from getdownLauncher
 570       into project.ext.getdownFilesDir
 571     }
 572
 573     copy {
 574       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.background_image')
 575       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.error_background')
 576       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.progress_image')
 577       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.icon')
 578       from jalviewDir + '/' + project.getProperty('getdown_txt_ui.mac_dock_icon')
 579       into project.ext.getdownFilesDir + '/' + getdown_resource_dir
 580     }
 581   }
 582
 583   inputs.dir(jalviewDir + '/' + packageDir)
 584   outputs.dir(project.ext.getdownWebsiteDir)
 585   outputs.dir(project.ext.getdownFilesDir)
 586 }
 587
 588 task getdownDigest(type: JavaExec) {
 589   dependsOn getdownWebsite
 590   classpath = files(jalviewDir + '/' + getdown_core)
 591   main = "com.threerings.getdown.tools.Digester"
 592   args project.ext.getdownWebsiteDir
 593   outputs.file(project.ext.getdownWebsiteDir + '/' + "digest2.txt")
 594 }
 595
 596 task getdown() {
 597   dependsOn getdownDigest
 598 }
 599
 600 clean {
 601   delete project.ext.getdownWebsiteDir
 602   delete project.ext.getdownFilesDir
 603 }
 604
 605 install4j {
 606   def install4jHomeDir = "/opt/install4j"
 607   def hostname = "hostname".execute().text.trim()
 608   if (hostname.equals("jv-bamboo")) {
 609     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
 610   } else if (OperatingSystem.current().isMacOsX()) {
 611     install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
 612     if (! file(install4jHomeDir).exists()) {
 613       install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
 614     }
 615   } else if (OperatingSystem.current().isLinux()) {
 616     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
 617   }
 618   installDir = file(install4jHomeDir)
 619 }
 620
 621 task installers(type: com.install4j.gradle.Install4jTask) {
 622   dependsOn getdown
 623   projectFile = "$jalviewDir/$install4jResourceDir/$install4jConf"
 624   variables = [majorVersion: version.substring(2, 11), build: 001]
 625   destination = "$jalviewDir/$install4jBuildDir"
 626   buildSelected = true
 627   inputs.dir(project.ext.getdownWebsiteDir)
 628   outputs.dir("$jalviewDir/$install4jBuildDir")
 629 }
 630