build.gradle

   1 import org.apache.tools.ant.filters.ReplaceTokens
   2 import org.gradle.internal.os.OperatingSystem
   3 import org.gradle.plugins.ide.eclipse.model.Output
   4 import org.gradle.plugins.ide.eclipse.model.Library
   5
   6 import groovy.transform.ExternalizeMethods
   7
   8 buildscript {
   9   dependencies {
  10     classpath 'org.openclover:clover:4.3.1'
  11   }
  12 }
  13
  14 plugins {
  15   id 'java'
  16   id 'application'
  17   id 'eclipse'
  18   id 'com.github.johnrengelman.shadow' version '4.0.3'
  19   id 'com.install4j.gradle' version '7.0.9'
  20 }
  21
  22 // local build environment properties
  23 def localProps = "${jalviewDir}/local.properties"
  24 if (file(localProps).exists()) {
  25   def p = new Properties()
  26   def localPropsFIS = new FileInputStream(localProps)
  27   p.load(localPropsFIS)
  28   localPropsFIS.close()
  29   p.each {
  30     key, val ->
  31       def over = getProperty(key) != null
  32       setProperty(key, val)
  33       if (over) {
  34         println("Overriding property '${key}' with local.properties value '${val}'")
  35       }
  36   }
  37 }
  38
  39 repositories {
  40   jcenter()
  41   mavenCentral()
  42   mavenLocal()
  43   flatDir {
  44     dirs gradlePluginsDir
  45   }
  46 }
  47
  48 dependencies {
  49   compile 'org.apache.commons:commons-compress:1.18'
  50 }
  51
  52 mainClassName = launcherClass
  53 def cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
  54 def classes = "${jalviewDir}/${classesDir}"
  55
  56 if (clover.equals("true")) {
  57   use_clover = true
  58   classes = "${buildDir}/${cloverClassesDir}"
  59 } else {
  60   use_clover = false
  61   classes = "${jalviewDir}/${classesDir}"
  62 }
  63
  64 // configure classpath/args for j8/j11 compilation
  65
  66 def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
  67 def libDir
  68 def libDistDir
  69 def compile_source_compatibility
  70 def compile_target_compatibility
  71
  72 ext {
  73   getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}"
  74   getdownDir = ""
  75   reportRsyncCmd = false
  76   buildDist = true
  77   buildProperties = buildPropertiesFile
  78   getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
  79   switch (CHANNEL) {
  80
  81     case "BUILD":
  82     // TODO: get bamboo build artifact URL for getdown artifacts
  83     getdown_channel_base = bamboo_channelbase
  84     getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
  85     getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
  86     getdown_app_dir = getdown_app_dir_alt
  87     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  88     break
  89
  90     case "RELEASE":
  91     getdown_channel_name = CHANNEL.toLowerCase()
  92     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
  93     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
  94     getdown_app_dir = getdown_app_dir_release
  95     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  96     reportRsyncCommand = true
  97     break
  98
  99     case "ARCHIVE":
 100     getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
 101     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 102     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 103     getdown_app_dir = getdown_app_dir_alt
 104     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
 105       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
 106       exit
 107     } else {
 108       packageDir = "${ARCHIVEDIR}/${packageDir}"
 109       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
 110       buildDist = false
 111     }
 112     reportRsyncCommand = true
 113     break
 114
 115     case "ARCHIVELOCAL":
 116     getdown_channel_name = "archive/${JALVIEW_VERSION}"
 117     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 118     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 119     getdown_app_dir = getdown_app_dir_alt
 120     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
 121       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
 122       exit
 123     } else {
 124       packageDir = "${ARCHIVEDIR}/${packageDir}"
 125       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
 126       buildDist = false
 127     }
 128     reportRsyncCommand = true
 129     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 130     break
 131
 132     case "DEVELOP":
 133     getdown_channel_name = CHANNEL.toLowerCase()
 134     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 135     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 136     getdown_app_dir = getdown_app_dir_alt
 137     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 138     reportRsyncCommand = true
 139     break
 140
 141     case "TEST-RELEASE":
 142     getdown_channel_name = CHANNEL.toLowerCase()
 143     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 144     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 145     getdown_app_dir = getdown_app_dir_alt
 146     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 147     reportRsyncCommand = true
 148     break
 149
 150     case ~/^SCRATCH(|-[-\w]*)$/:
 151     getdown_channel_name = CHANNEL
 152     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 153     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 154     getdown_app_dir = getdown_app_dir_alt
 155     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 156     reportRsyncCommand = true
 157     break
 158
 159     case "LOCAL":
 160     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 161     getdown_app_dir = getdown_app_dir_alt
 162     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 163     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 164     break
 165
 166     default: // something wrong specified
 167     print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
 168     exit
 169     break
 170
 171   }
 172
 173   getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}"
 174   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
 175   getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}"
 176   getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}"
 177   getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/"
 178   getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_dir}"
 179   /* compile without modules -- using classpath libraries
 180   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
 181   modules_runtimeClasspath = modules_compileClasspath
 182   */
 183   gitHash = ""
 184   gitBranch = ""
 185
 186   println("Using a ${CHANNEL} profile.")
 187 }
 188
 189 def JAVA_INTEGER_VERSION
 190 def additional_compiler_args = []
 191 // these are getdown.txt properties defined dependent on the JAVA_VERSION
 192 def getdown_alt_java_min_version
 193 def getdown_alt_java_max_version
 194 // this property is assigned below and expanded to multiple lines in the getdown task
 195 def getdown_alt_multi_java_location
 196 // this property is for the Java library used in eclipse
 197 def eclipse_java_runtime_name
 198 if (JAVA_VERSION.equals("1.8")) {
 199   JAVA_INTEGER_VERSION = "8"
 200   //libDir = j8libDir
 201   libDir = j11libDir
 202   libDistDir = j8libDir
 203   compile_source_compatibility = 1.8
 204   compile_target_compatibility = 1.8
 205   getdown_alt_java_min_version = getdown_alt_java8_min_version
 206   getdown_alt_java_max_version = getdown_alt_java8_max_version
 207   getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 208   eclipse_java_runtime_name = "JavaSE-1.8"
 209 } else if (JAVA_VERSION.equals("11")) {
 210   JAVA_INTEGER_VERSION = "11"
 211   libDir = j11libDir
 212   libDistDir = j11libDir
 213   compile_source_compatibility = 11
 214   compile_target_compatibility = 11
 215   getdown_alt_java_min_version = getdown_alt_java11_min_version
 216   getdown_alt_java_max_version = getdown_alt_java11_max_version
 217   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 218   eclipse_java_runtime_name = "JavaSE-11"
 219   /* compile without modules -- using classpath libraries
 220   additional_compiler_args += [
 221   '--module-path', ext.modules_compileClasspath.asPath,
 222   '--add-modules', j11modules
 223   ]
 224   */
 225 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
 226   JAVA_INTEGER_VERSION = JAVA_VERSION
 227   libDir = j11libDir
 228   libDistDir = j11libDir
 229   compile_source_compatibility = JAVA_VERSION
 230   compile_target_compatibility = JAVA_VERSION
 231   getdown_alt_java_min_version = getdown_alt_java11_min_version
 232   getdown_alt_java_max_version = getdown_alt_java11_max_version
 233   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 234   eclipse_java_runtime_name = "JavaSE-11"
 235   /* compile without modules -- using classpath libraries
 236   additional_compiler_args += [
 237   '--module-path', ext.modules_compileClasspath.asPath,
 238   '--add-modules', j11modules
 239   ]
 240   */
 241 } else {
 242   throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
 243 }
 244
 245 sourceSets {
 246
 247   main {
 248     java {
 249       srcDirs "${jalviewDir}/${sourceDir}"
 250       outputDir = file("${classes}")
 251     }
 252
 253     resources {
 254       srcDirs "${jalviewDir}/${resourceDir}"
 255     }
 256
 257     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 258
 259     compileClasspath = files(sourceSets.main.java.outputDir)
 260     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 261
 262     runtimeClasspath = compileClasspath
 263   }
 264
 265   clover {
 266     java {
 267       srcDirs = [ cloverInstrDir ]
 268       outputDir = file("${buildDir}/${cloverClassesDir}")
 269     }
 270
 271     resources {
 272       srcDirs = sourceSets.main.resources.srcDirs
 273     }
 274     compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
 275     compileClasspath += files(sourceSets.main.java.outputDir)
 276     compileClasspath += sourceSets.main.compileClasspath
 277     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
 278     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 279
 280     runtimeClasspath = compileClasspath
 281   }
 282
 283   test {
 284     java {
 285       srcDirs "${jalviewDir}/${testSourceDir}"
 286       outputDir = file("${jalviewDir}/${testOutputDir}")
 287     }
 288
 289     resources {
 290       srcDirs = sourceSets.main.resources.srcDirs
 291     }
 292
 293     compileClasspath = files( sourceSets.test.java.outputDir )
 294
 295     if (use_clover) {
 296       compileClasspath += sourceSets.clover.compileClasspath
 297     } else {
 298       compileClasspath += files(sourceSets.main.java.outputDir)
 299     }
 300
 301     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 302     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
 303     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
 304
 305     runtimeClasspath = compileClasspath
 306   }
 307 }
 308
 309 // clover bits
 310 dependencies {
 311   if (use_clover) {
 312     cloverCompile 'org.openclover:clover:4.3.1'
 313     testCompile 'org.openclover:clover:4.3.1'
 314   }
 315 }
 316
 317 configurations {
 318   cloverRuntime
 319   cloverRuntime.extendsFrom cloverCompile
 320 }
 321
 322 eclipse {
 323   project {
 324     name = eclipse_project_name
 325
 326     natures 'org.eclipse.jdt.core.javanature',
 327     'org.eclipse.jdt.groovy.core.groovyNature',
 328     'org.eclipse.buildship.core.gradleprojectnature'
 329
 330     buildCommand 'org.eclipse.jdt.core.javabuilder'
 331     buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
 332   }
 333
 334   classpath {
 335     //defaultOutputDir = sourceSets.main.java.outputDir
 336     def removeThese = []
 337     configurations.each{
 338       if (it.isCanBeResolved()) {
 339         removeThese += it
 340       }
 341     }
 342
 343     minusConfigurations += removeThese
 344     plusConfigurations = [ ]
 345     file {
 346
 347       whenMerged { cp ->
 348         def removeTheseToo = []
 349         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
 350         cp.entries.each { entry ->
 351           if (entry.kind == 'src') {
 352             if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
 353               removeTheseToo += entry
 354             } else {
 355               alreadyAddedSrcPath.putAt(entry.path, true)
 356             }
 357           }
 358         }
 359         cp.entries.removeAll(removeTheseToo)
 360
 361         if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
 362           cp.entries += new Output("${eclipse_bin_dir}/main")
 363         }
 364         if (file(helpParentDir).isDirectory()) {
 365           cp.entries += new Library(fileReference(helpParentDir))
 366         }
 367         if (file(resourceDir).isDirectory()) {
 368           cp.entries += new Library(fileReference(resourceDir))
 369         }
 370
 371         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 372
 373         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 374           //don't want to add outputDir as eclipse is using its own output dir in bin/main
 375           if (it.isDirectory() || ! it.exists()) {
 376             // don't add dirs to classpath
 377             return
 378           }
 379           def itPath = it.toString()
 380           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 381             // make relative path
 382             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 383           }
 384           if (alreadyAddedLibPath.get(itPath)) {
 385             //println("Not adding duplicate entry "+itPath)
 386           } else {
 387             //println("Adding entry "+itPath)
 388             cp.entries += new Library(fileReference(itPath))
 389             alreadyAddedLibPath.put(itPath, true)
 390           }
 391         }
 392
 393         //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
 394         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 395           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
 396           if (it.isDirectory() || ! it.exists()) {
 397             // don't add dirs to classpath
 398             return false // groovy "break" in .each closure
 399           }
 400           def itPath = it.toString()
 401           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 402             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 403           }
 404           if (alreadyAddedLibPath.get(itPath)) {
 405             // don't duplicate
 406           } else {
 407             def lib = new Library(fileReference(itPath))
 408             lib.entryAttributes["test"] = "true"
 409             cp.entries += lib
 410             alreadyAddedLibPath.put(itPath, true)
 411           }
 412         }
 413
 414       } // whenMerged
 415
 416     } // file
 417
 418     containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
 419
 420   } // classpath
 421
 422   jdt {
 423     // for the IDE, use java 11 compatibility
 424     sourceCompatibility = compile_source_compatibility
 425     targetCompatibility = compile_target_compatibility
 426     javaRuntimeName = eclipse_java_runtime_name
 427
 428     // add in jalview project specific properties/preferences into eclipse core preferences
 429     file {
 430       withProperties { props ->
 431         def jalview_prefs = new Properties()
 432         def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
 433         jalview_prefs.load(ins)
 434         ins.close()
 435         jalview_prefs.forEach { t, v ->
 436           if (props.getAt(t) == null) {
 437             props.putAt(t, v)
 438           }
 439         }
 440       }
 441     }
 442
 443   } // jdt
 444
 445 }
 446
 447 task cloverInstr() {
 448   // only instrument source, we build test classes as normal
 449   inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
 450   outputs.dir cloverInstrDir
 451
 452   doFirst {
 453     delete cloverInstrDir
 454     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 455     "-d", "${buildDir}/${cloverSourcesInstrDir}"]
 456     argsList.addAll(inputs.files.files.collect({ file ->
 457       file.absolutePath
 458     }))
 459     String[] args = argsList.toArray()
 460     println("About to instrument "+args.length +" files")
 461     com.atlassian.clover.CloverInstr.mainImpl(args)
 462   }
 463 }
 464
 465
 466 task cloverReport {
 467   group = "Verification"
 468     description = "Createst the Clover report"
 469     inputs.dir "${buildDir}/clover"
 470     outputs.dir "${reportsDir}/clover"
 471     onlyIf {
 472       file("${buildDir}/clover/clover.db").exists()
 473     }
 474   doFirst {
 475     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 476     "-o", "${reportsDir}/clover"]
 477     String[] args = argsList.toArray()
 478     com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
 479
 480     // and generate ${reportsDir}/clover/clover.xml
 481     args = ["--initstring", "${buildDir}/clover/clover.db",
 482     "-o", "${reportsDir}/clover/clover.xml"].toArray()
 483     com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
 484   }
 485 }
 486
 487 // end clover bits
 488
 489
 490 compileJava {
 491
 492   doFirst {
 493     sourceCompatibility = compile_source_compatibility
 494     targetCompatibility = compile_target_compatibility
 495     options.compilerArgs = additional_compiler_args
 496     print ("Setting target compatibility to "+targetCompatibility+"\n")
 497   }
 498
 499 }
 500
 501 compileTestJava {
 502   if (use_clover) {
 503     dependsOn compileCloverJava
 504     classpath += configurations.cloverRuntime
 505   } else {
 506     classpath += sourceSets.main.runtimeClasspath
 507   }
 508   doFirst {
 509     sourceCompatibility = compile_source_compatibility
 510     targetCompatibility = compile_target_compatibility
 511     options.compilerArgs = additional_compiler_args
 512     print ("Setting target compatibility to "+targetCompatibility+"\n")
 513   }
 514 }
 515
 516
 517 compileCloverJava {
 518
 519   doFirst {
 520     sourceCompatibility = compile_source_compatibility
 521     targetCompatibility = compile_target_compatibility
 522     options.compilerArgs += additional_compiler_args
 523     print ("Setting target compatibility to "+targetCompatibility+"\n")
 524   }
 525   classpath += configurations.cloverRuntime
 526 }
 527
 528 clean {
 529   doFirst {
 530     delete sourceSets.main.java.outputDir
 531   }
 532 }
 533
 534 cleanTest {
 535   doFirst {
 536     delete sourceSets.test.java.outputDir
 537     delete cloverInstrDir
 538   }
 539 }
 540
 541 // format is a string like date.format("dd MMMM yyyy")
 542 def getDate(format) {
 543   def date = new Date()
 544   return date.format(format)
 545 }
 546
 547 task setGitVals {
 548   def hashStdOut = new ByteArrayOutputStream()
 549   exec {
 550     commandLine "git", "rev-parse", "--short", "HEAD"
 551     standardOutput = hashStdOut
 552     ignoreExitValue true
 553   }
 554
 555   def branchStdOut = new ByteArrayOutputStream()
 556   exec {
 557     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
 558     standardOutput = branchStdOut
 559     ignoreExitValue true
 560   }
 561
 562   project.ext.gitHash = hashStdOut.toString().trim()
 563   project.ext.gitBranch = branchStdOut.toString().trim()
 564
 565   outputs.upToDateWhen { false }
 566 }
 567
 568 task createBuildProperties(type: WriteProperties) {
 569   dependsOn setGitVals
 570   inputs.dir("${jalviewDir}/${sourceDir}")
 571   inputs.dir("${classes}")
 572   inputs.dir("${jalviewDir}/${resourceDir}")
 573   outputFile (buildProperties)
 574   // taking time specific comment out to allow better incremental builds
 575   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
 576   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
 577   property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
 578   property "VERSION", JALVIEW_VERSION
 579   property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
 580   outputs.file(outputFile)
 581 }
 582
 583 def buildingHTML = "${jalviewDir}/${docDir}/building.html"
 584 task cleanBuildingHTML(type: Delete) {
 585   doFirst {
 586     delete buildingHTML
 587   }
 588 }
 589
 590 task convertBuildingMD(type: Exec) {
 591   dependsOn cleanBuildingHTML
 592   def buildingMD = "${jalviewDir}/${docDir}/building.md"
 593   def css = "${jalviewDir}/${docDir}/github.css"
 594
 595   def pandoc = null
 596   pandoc_exec.split(",").each {
 597     if (file(it.trim()).exists()) {
 598       pandoc = it.trim()
 599       return true
 600     }
 601   }
 602
 603   def hostname = "hostname".execute().text.trim()
 604   if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
 605     pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
 606   }
 607
 608   doFirst {
 609     if (pandoc != null && file(pandoc).exists()) {
 610         commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
 611     } else {
 612         println("Cannot find pandoc. Skipping convert building.md to HTML")
 613         throw new StopExecutionException()
 614     }
 615   }
 616
 617   ignoreExitValue true
 618
 619   inputs.file(buildingMD)
 620   inputs.file(css)
 621   outputs.file(buildingHTML)
 622 }
 623
 624 clean {
 625   doFirst {
 626     delete buildingHTML
 627   }
 628 }
 629
 630 task syncDocs(type: Sync) {
 631   dependsOn convertBuildingMD
 632   def syncDir = "${classes}/${docDir}"
 633   from fileTree("${jalviewDir}/${docDir}")
 634   into syncDir
 635
 636 }
 637
 638 def helpFile = "${classes}/${helpDir}/help.jhm"
 639
 640 task copyHelp(type: Copy) {
 641   def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
 642   def outputDir = "${classes}/${helpDir}"
 643   from(inputDir) {
 644     exclude '**/*.gif'
 645     exclude '**/*.jpg'
 646     exclude '**/*.png'
 647     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
 648   }
 649   from(inputDir) {
 650     include '**/*.gif'
 651     include '**/*.jpg'
 652     include '**/*.png'
 653   }
 654   into outputDir
 655
 656   inputs.dir(inputDir)
 657   outputs.files(helpFile)
 658   outputs.dir(outputDir)
 659 }
 660
 661 task syncLib(type: Sync) {
 662   def syncDir = "${classes}/${libDistDir}"
 663   from fileTree("${jalviewDir}/${libDistDir}")
 664   into syncDir
 665 }
 666
 667 task syncResources(type: Sync) {
 668   from "${jalviewDir}/${resourceDir}"
 669   include "**/*.*"
 670   into "${classes}"
 671   preserve {
 672     include "**"
 673   }
 674 }
 675
 676 task prepare {
 677   dependsOn syncResources
 678   dependsOn syncDocs
 679   dependsOn copyHelp
 680 }
 681
 682
 683 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 684 test {
 685   dependsOn prepare
 686   dependsOn compileJava
 687   if (use_clover) {
 688     dependsOn cloverInstr
 689   }
 690
 691   if (use_clover) {
 692     print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
 693   }
 694
 695   useTestNG() {
 696     includeGroups testngGroups
 697     preserveOrder true
 698     useDefaultListeners=true
 699   }
 700
 701   workingDir = jalviewDir
 702   //systemProperties 'clover.jar' System.properties.clover.jar
 703   sourceCompatibility = compile_source_compatibility
 704   targetCompatibility = compile_target_compatibility
 705   jvmArgs += additional_compiler_args
 706
 707 }
 708
 709 task buildIndices(type: JavaExec) {
 710   dependsOn copyHelp
 711   classpath = sourceSets.main.compileClasspath
 712   main = "com.sun.java.help.search.Indexer"
 713   workingDir = "${classes}/${helpDir}"
 714   def argDir = "html"
 715   args = [ argDir ]
 716   inputs.dir("${workingDir}/${argDir}")
 717
 718   outputs.dir("${classes}/doc")
 719   outputs.dir("${classes}/help")
 720   outputs.file("${workingDir}/JavaHelpSearch/DOCS")
 721   outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
 722   outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
 723   outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
 724   outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
 725   outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 726 }
 727
 728 task compileLinkCheck(type: JavaCompile) {
 729   options.fork = true
 730   classpath = files("${jalviewDir}/${utilsDir}")
 731   destinationDir = file("${jalviewDir}/${utilsDir}")
 732   source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 733
 734   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 735   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 736   outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
 737   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 738 }
 739
 740 task linkCheck(type: JavaExec) {
 741   dependsOn prepare, compileLinkCheck
 742
 743   def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
 744   classpath = files("${jalviewDir}/${utilsDir}")
 745   main = "HelpLinksChecker"
 746   workingDir = jalviewDir
 747   def help = "${classes}/${helpDir}"
 748   args = [ "${classes}/${helpDir}", "-nointernet" ]
 749
 750   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
 751   def errFOS = outFOS
 752   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
 753     outFOS,
 754     standardOutput)
 755   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
 756     outFOS,
 757     errorOutput)
 758
 759   inputs.dir("${classes}/${helpDir}")
 760   outputs.file(helpLinksCheckerOutFile)
 761 }
 762
 763 // import the pubhtmlhelp target
 764 ant.properties.basedir = "${jalviewDir}"
 765 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
 766 ant.importBuild "${utilsDir}/publishHelp.xml"
 767
 768
 769 task cleanPackageDir(type: Delete) {
 770   doFirst {
 771     delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
 772   }
 773 }
 774
 775 jar {
 776   dependsOn linkCheck
 777   dependsOn buildIndices
 778   dependsOn createBuildProperties
 779
 780   manifest {
 781     attributes "Main-Class": mainClass,
 782     "Permissions": "all-permissions",
 783     "Application-Name": "Jalview Desktop",
 784     "Codebase": application_codebase
 785   }
 786
 787   destinationDir = file("${jalviewDir}/${packageDir}")
 788   archiveName = rootProject.name+".jar"
 789
 790   exclude "cache*/**"
 791   exclude "*.jar"
 792   exclude "*.jar.*"
 793   exclude "**/*.jar"
 794   exclude "**/*.jar.*"
 795
 796   inputs.dir("${classes}")
 797   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 798 }
 799
 800 task copyJars(type: Copy) {
 801   from fileTree(dir: "${classes}", include: "**/*.jar").files
 802   into "${jalviewDir}/${packageDir}"
 803 }
 804
 805 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 806 task syncJars(type: Sync) {
 807   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
 808   into "${jalviewDir}/${packageDir}"
 809   preserve {
 810     include jar.archiveName
 811   }
 812 }
 813
 814 task makeDist {
 815   group = "build"
 816   description = "Put all required libraries in dist"
 817   // order of "cleanPackageDir", "copyJars", "jar" important!
 818   jar.mustRunAfter cleanPackageDir
 819   syncJars.mustRunAfter cleanPackageDir
 820   dependsOn cleanPackageDir
 821   dependsOn syncJars
 822   dependsOn jar
 823   outputs.dir("${jalviewDir}/${packageDir}")
 824 }
 825
 826 task cleanDist {
 827   dependsOn cleanPackageDir
 828   dependsOn cleanTest
 829   dependsOn clean
 830 }
 831
 832 shadowJar {
 833   group = "distribution"
 834   if (buildDist) {
 835     dependsOn makeDist
 836   }
 837   from ("${jalviewDir}/${libDistDir}") {
 838     include("*.jar")
 839   }
 840   manifest {
 841     attributes 'Implementation-Version': JALVIEW_VERSION
 842   }
 843   mainClassName = shadowJarMainClass
 844   mergeServiceFiles()
 845   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
 846   minimize()
 847 }
 848
 849 task getdownWebsite() {
 850   group = "distribution"
 851   description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
 852   if (buildDist) {
 853     dependsOn makeDist
 854   }
 855
 856   def getdownWebsiteResourceFilenames = []
 857   def getdownTextString = ""
 858   def getdownResourceDir = project.ext.getdownResourceDir
 859   def getdownAppDir = project.ext.getdownAppDir
 860   def getdownResourceFilenames = []
 861
 862   doFirst {
 863     // clean the getdown website and files dir before creating getdown folders
 864     delete project.ext.getdownWebsiteDir
 865     delete project.ext.getdownFilesDir
 866
 867     copy {
 868       from buildProperties
 869       rename(buildPropertiesFile, getdown_build_properties)
 870       into project.ext.getdownAppDir
 871     }
 872     getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
 873
 874     // go through properties looking for getdown_txt_...
 875     def props = project.properties.sort { it.key }
 876     if (getdown_alt_java_min_version.length() > 0) {
 877       props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
 878     }
 879     if (getdown_alt_java_max_version.length() > 0) {
 880       props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
 881     }
 882     props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
 883
 884     props.put("getdown_txt_appbase", getdown_app_base)
 885     props.each{ prop, val ->
 886       if (prop.startsWith("getdown_txt_") && val != null) {
 887         if (prop.startsWith("getdown_txt_multi_")) {
 888           def key = prop.substring(18)
 889           val.split(",").each{ v ->
 890             def line = "${key} = ${v}\n"
 891             getdownTextString += line
 892           }
 893         } else {
 894           // file values rationalised
 895           if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
 896             def r = null
 897             if (val.indexOf('/') == 0) {
 898               // absolute path
 899               r = file(val)
 900             } else if (val.indexOf('/') > 0) {
 901               // relative path (relative to jalviewDir)
 902               r = file( "${jalviewDir}/${val}" )
 903             }
 904             if (r.exists()) {
 905               val = "${getdown_resource_dir}/" + r.getName()
 906               getdownWebsiteResourceFilenames += val
 907               getdownResourceFilenames += r.getPath()
 908             }
 909           }
 910           if (! prop.startsWith("getdown_txt_resource")) {
 911             def line = prop.substring(12) + " = ${val}\n"
 912             getdownTextString += line
 913           }
 914         }
 915       }
 916     }
 917
 918     getdownWebsiteResourceFilenames.each{ filename ->
 919       getdownTextString += "resource = ${filename}\n"
 920     }
 921     getdownResourceFilenames.each{ filename ->
 922       copy {
 923         from filename
 924         into project.ext.getdownResourceDir
 925       }
 926     }
 927
 928     def codeFiles = []
 929     fileTree(file(packageDir)).each{ f ->
 930       if (f.isDirectory()) {
 931         def files = fileTree(dir: f, include: ["*"]).getFiles()
 932         codeFiles += files
 933       } else if (f.exists()) {
 934         codeFiles += f
 935       }
 936     }
 937     codeFiles.sort().each{f ->
 938       def name = f.getName()
 939       def line = "code = ${getdown_app_dir}/${name}\n"
 940       getdownTextString += line
 941       copy {
 942         from f.getPath()
 943         into project.ext.getdownAppDir
 944       }
 945     }
 946
 947     // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
 948     /*
 949     if (JAVA_VERSION.equals("11")) {
 950     def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
 951     j11libFiles.sort().each{f ->
 952     def name = f.getName()
 953     def line = "code = ${getdown_j11lib_dir}/${name}\n"
 954     getdownTextString += line
 955     copy {
 956     from f.getPath()
 957     into project.ext.getdownJ11libDir
 958     }
 959     }
 960     }
 961      */
 962
 963     // getdown-launcher.jar should not be in main application class path so the main application can move it when updated.  Listed as a resource so it gets updated.
 964     //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
 965     getdownTextString += "resource = ${getdown_launcher_new}\n"
 966     getdownTextString += "class = ${mainClass}\n"
 967
 968     def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt")
 969     getdown_txt.write(getdownTextString)
 970
 971     def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}")
 972     launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
 973
 974     copy {
 975       from getdownLauncher
 976       rename(file(getdownLauncher).getName(), getdown_launcher_new)
 977       into project.ext.getdownWebsiteDir
 978     }
 979
 980     copy {
 981       from getdownLauncher
 982       if (file(getdownLauncher).getName() != getdown_launcher) {
 983         rename(file(getdownLauncher).getName(), getdown_launcher)
 984       }
 985       into project.ext.getdownWebsiteDir
 986     }
 987
 988     if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
 989       copy {
 990         from getdown_txt
 991         from getdownLauncher
 992         from "${getdownWebsiteDir}/${getdown_build_properties}"
 993         if (file(getdownLauncher).getName() != getdown_launcher) {
 994           rename(file(getdownLauncher).getName(), getdown_launcher)
 995         }
 996         into getdownInstallDir
 997       }
 998
 999       copy {
1000         from getdownInstallDir
1001         into getdownFilesInstallDir
1002       }
1003     }
1004
1005     copy {
1006       from getdown_txt
1007       from launch_jvl
1008       from getdownLauncher
1009       from "${getdownWebsiteDir}/${getdown_build_properties}"
1010       if (file(getdownLauncher).getName() != getdown_launcher) {
1011         rename(file(getdownLauncher).getName(), getdown_launcher)
1012       }
1013       into getdownFilesDir
1014     }
1015
1016     copy {
1017       from getdownResourceDir
1018       into "${project.ext.getdownFilesDir}/${getdown_resource_dir}"
1019     }
1020   }
1021
1022   if (buildDist) {
1023     inputs.dir("${jalviewDir}/${packageDir}")
1024   }
1025   outputs.dir(project.ext.getdownWebsiteDir)
1026   outputs.dir(project.ext.getdownFilesDir)
1027 }
1028
1029 task getdownDigest(type: JavaExec) {
1030   group = "distribution"
1031   description = "Digest the getdown website folder"
1032   dependsOn getdownWebsite
1033   doFirst {
1034     classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
1035   }
1036   main = "com.threerings.getdown.tools.Digester"
1037   args project.ext.getdownWebsiteDir
1038   inputs.dir(project.ext.getdownWebsiteDir)
1039   outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
1040 }
1041
1042 task getdown() {
1043   group = "distribution"
1044   description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1045   dependsOn getdownDigest
1046   doLast {
1047     if (reportRsyncCommand) {
1048       def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1049       def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1050       println "LIKELY RSYNC COMMAND:"
1051       println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1052       if (RUNRSYNC == "true") {
1053         exec {
1054           commandLine "mkdir", "-p", toDir
1055         }
1056         exec {
1057           commandLine "rsync", "-avh", "--delete", fromDir, toDir
1058         }
1059       }
1060     }
1061   }
1062 }
1063
1064 clean {
1065   doFirst {
1066     delete project.ext.getdownWebsiteDir
1067     delete project.ext.getdownFilesDir
1068   }
1069 }
1070
1071 install4j {
1072   def install4jHomeDir = "/opt/install4j"
1073   def hostname = "hostname".execute().text.trim()
1074   if (hostname.equals("jv-bamboo")) {
1075     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1076   } else if (OperatingSystem.current().isMacOsX()) {
1077     install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
1078     if (! file(install4jHomeDir).exists()) {
1079       install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
1080     }
1081   } else if (OperatingSystem.current().isLinux()) {
1082     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1083   }
1084   installDir = file(install4jHomeDir)
1085   mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
1086   if (install4jFaster.equals("true")) {
1087     faster = true
1088   }
1089 }
1090
1091 def install4jConf
1092 def macosJavaVMDir
1093 def macosJavaVMTgz
1094 def windowsJavaVMDir
1095 def windowsJavaVMTgz
1096 def install4jDir = "${jalviewDir}/${install4jResourceDir}"
1097 def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j"
1098 install4jConf = "${install4jDir}/${install4jConfFile}"
1099
1100 task copyInstall4jTemplate(type: Copy) {
1101   macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre"
1102   macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz"
1103   windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre"
1104   windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz"
1105   from (install4jDir) {
1106     include install4jTemplate
1107     rename (install4jTemplate, install4jConfFile)
1108     filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
1109     filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
1110     tokens: [
1111     'JAVA_VERSION': JAVA_VERSION,
1112     'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1113     'VERSION': JALVIEW_VERSION,
1114     'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1115     'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1116     'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1117     'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1118     'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
1119     'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
1120     'MACOS_BUNDLE_ID': install4jMacOSBundleId,
1121     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1122     'GETDOWN_DIST_DIR': getdown_app_dir,
1123     'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1124     'GETDOWN_INSTALL_DIR': getdown_install_dir
1125     ]
1126     )
1127     if (OSX_KEYPASS=="") {
1128       filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
1129       filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
1130     }
1131   }
1132   into install4jDir
1133   outputs.files(install4jConf)
1134
1135   doLast {
1136     // include file associations in installer
1137     def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text
1138     ant.replaceregexp(
1139       byline: false,
1140       flags: "s",
1141       match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
1142       replace: installerFileAssociationsXml,
1143       file: install4jConf
1144     )
1145     /*
1146     // include uninstaller applescript app files in dmg
1147     def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
1148     ant.replaceregexp(
1149     byline: false,
1150     flags: "s",
1151     match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
1152     replace: installerDMGUninstallerXml,
1153     file: install4jConf
1154     )
1155      */
1156   }
1157 }
1158
1159 task installers(type: com.install4j.gradle.Install4jTask) {
1160   group = "distribution"
1161   description = "Create the install4j installers"
1162   dependsOn getdown
1163   dependsOn copyInstall4jTemplate
1164   projectFile = file(install4jConf)
1165   variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
1166   destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}"
1167   buildSelected = true
1168
1169   if (OSX_KEYPASS) {
1170     macKeystorePassword=OSX_KEYPASS
1171   }
1172
1173   doFirst {
1174     println("Using projectFile "+projectFile)
1175   }
1176
1177   inputs.dir(project.ext.getdownWebsiteDir)
1178   inputs.file(install4jConf)
1179   inputs.dir(macosJavaVMDir)
1180   inputs.dir(windowsJavaVMDir)
1181   outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
1182 }
1183
1184 clean {
1185   doFirst {
1186     delete install4jConf
1187   }
1188 }
1189
1190 task sourceDist (type: Tar) {
1191
1192   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1193   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1194   // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1195   try {
1196     archiveFileName = outputFileName
1197   } catch (Exception e) {
1198     archiveName = outputFileName
1199   }
1200
1201   compression Compression.GZIP
1202
1203   into project.name
1204
1205   def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
1206   ,".*"
1207   ,"benchmarking/*"
1208   ,"**/.*"
1209   ,"*.class"
1210   ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
1211   ,"*locales/**",
1212   ,"utils/InstallAnywhere"]
1213   def PROCESS_FILES=[   "AUTHORS",
1214   "CITATION",
1215   "FEATURETODO",
1216   "JAVA-11-README",
1217   "FEATURETODO",
1218   "LICENSE",
1219   "**/README",
1220   "RELEASE",
1221   "THIRDPARTYLIBS","TESTNG",
1222   "build.gradle",
1223   "gradle.properties",
1224   "**/*.java",
1225   "**/*.html",
1226   "**/*.xml",
1227   "**/*.gradle",
1228   "**/*.groovy",
1229   "**/*.properties",
1230   "**/*.perl",
1231   "**/*.sh"]
1232
1233   from(jalviewDir) {
1234     exclude (EXCLUDE_FILES)
1235     include (PROCESS_FILES)
1236     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
1237   }
1238   from(jalviewDir) {
1239     exclude (EXCLUDE_FILES)
1240     exclude (PROCESS_FILES)
1241   exclude ("appletlib")
1242   exclude ("**/*locales")
1243   exclude ("*locales/**")
1244   exclude ("utils/InstallAnywhere")
1245
1246     exclude (getdown_files_dir)
1247   exclude (getdown_website_dir)
1248
1249   // exluding these as not using jars as modules yet
1250   exclude ("${j11modDir}/**/*.jar")
1251 }
1252 //  from (jalviewDir) {
1253 //    // explicit includes for stuff that seemed to not get included
1254 //    include(fileTree("test/**/*."))
1255 //    exclude(EXCLUDE_FILES)
1256 //    exclude(PROCESS_FILES)
1257 //  }
1258 }
1259
1260 task helppages  {
1261   dependsOn copyHelp
1262   dependsOn pubhtmlhelp
1263
1264   inputs.dir("${classes}/${helpDir}")
1265   outputs.dir("${helpOutputDir}")
1266 }
1267
1268 def jalviewjsBuildDir
1269 def jalviewjsSiteDir
1270 def jalviewjsTransferSiteDir
1271 task jalviewjsSitePath {
1272   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
1273   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
1274   jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
1275   jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
1276 }
1277
1278 def eclipseWorkspace
1279 task jalviewjsSetEclipseWorkspace {
1280   def propKey = "jalviewjs_eclipse_workspace"
1281   def propVal = null
1282   if (project.hasProperty(propKey)) {
1283     propVal = project.getProperty(propKey)
1284     if (propVal.startsWith("~/")) {
1285       propVal = System.getProperty("user.home") + propVal.substring(1)
1286     }
1287   }
1288   def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
1289   def propsFile = file(propsFileName)
1290   def eclipseWsDir = propVal
1291   def props = new Properties()
1292
1293   if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
1294     def ins = new FileInputStream(propsFileName)
1295     props.load(ins)
1296     ins.close()
1297     if (props.getProperty(propKey, null) != null) {
1298       eclipseWsDir = props.getProperty(propKey)
1299     }
1300   }
1301
1302   def writeProps = false
1303   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
1304     def tempDir = File.createTempDir()
1305     eclipseWsDir = tempDir.getAbsolutePath()
1306     writeProps = true
1307   }
1308   eclipseWorkspace = file(eclipseWsDir)
1309
1310   doFirst {
1311     if (writeProps) {
1312       props.setProperty(propKey, eclipseWsDir)
1313       propsFile.parentFile.mkdirs()
1314       def bytes = new ByteArrayOutputStream()
1315       props.store(bytes, null)
1316       def propertiesString = bytes.toString()
1317       propsFile.text = propertiesString
1318     }
1319
1320     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
1321   }
1322
1323   inputs.property(propKey, eclipseWsDir)
1324   outputs.file(propsFileName)
1325 }
1326
1327
1328 def eclipseBinary
1329 def eclipseVersion
1330 def eclipseDebug = false
1331 def eclipseVersionSuffix = ""
1332 task jalviewjsEclipsePaths {
1333   def eclipseProduct
1334
1335   def eclipseRoot = jalviewjs_eclipse_root
1336   if (eclipseRoot.startsWith("~/")) {
1337     eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
1338   }
1339   if (OperatingSystem.current().isMacOsX()) {
1340     eclipseRoot += "/Eclipse.app"
1341     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
1342     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
1343   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
1344     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1345       eclipseRoot += "/eclipse"
1346     }
1347     eclipseBinary = "${eclipseRoot}/eclipse"
1348     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1349   } else { // linux or unix
1350     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1351       eclipseRoot += "/eclipse"
1352     }
1353     eclipseBinary = "${eclipseRoot}/eclipse"
1354     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1355   }
1356
1357   eclipseVersion = "4.12" // default
1358   def assumedVersion = true
1359   if (file(eclipseProduct).exists()) {
1360     def fis = new FileInputStream(eclipseProduct)
1361     def props = new Properties()
1362     props.load(fis)
1363     eclipseVersion = props.getProperty("version")
1364     fis.close()
1365     assumedVersion = false
1366   }
1367   /*
1368   String[] v = eclipseVersion.split("\\.")
1369   def v0 = Integer.valueOf(v[0])
1370   def v1 = Integer.valueOf(v[1])
1371   if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
1372     eclipseVersionSuffix = "_4.12"
1373   } else {
1374     eclipseVersionSuffix = "_4.13"
1375   }
1376   */
1377
1378
1379   def propKey = "eclipse_debug"
1380   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
1381
1382   doFirst {
1383     if (!assumedVersion) {
1384       println("ECLIPSE VERSION=${eclipseVersion}")
1385     }
1386   }
1387 }
1388
1389 task eclipseSetup {
1390   dependsOn eclipseProject
1391   dependsOn eclipseClasspath
1392   dependsOn eclipseJdt
1393 }
1394
1395 /* using the Copy task below
1396 task OLDjalviewjsEclipseCopyDropins {
1397   dependsOn jalviewjsEclipsePaths
1398   dependsOn jalviewjsCleanEclipse
1399   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
1400   inputFiles += file(jalviewjs_j2s_plugin)
1401   def outputDir = "${buildDir}/jalviewjs
1402
1403   inputs.files inputFiles
1404   inputFiles.each { file ->
1405     outputs.file("${outputDir}/${file.name}")
1406   }
1407
1408   doLast {
1409     inputFiles.each { file ->
1410       copy {
1411         from file
1412         into outputDir
1413       }
1414     }
1415   }
1416 }
1417 */
1418
1419 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
1420 task jalviewjsEclipseCopyDropins(type: Copy) {
1421   dependsOn jalviewjsEclipsePaths
1422
1423   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
1424   inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
1425   def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
1426
1427   from inputFiles
1428   into outputDir
1429 }
1430
1431 // this eclipse -clean doesn't actually work
1432 task jalviewjsCleanEclipse(type: Exec) {
1433   dependsOn eclipseSetup
1434   dependsOn jalviewjsEclipsePaths
1435   dependsOn jalviewjsEclipseCopyDropins
1436
1437   executable(eclipseBinary)
1438   args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
1439   if (eclipseDebug) {
1440     args += "-debug"
1441   }
1442   args += "-l"
1443
1444   def inputString = """exit
1445 y
1446 """
1447   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
1448   standardInput = inputByteStream
1449 }
1450 /* not really working yet
1451 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
1452 */
1453
1454 task jalviewjsUnzipFiles {
1455   dependsOn jalviewjsSitePath
1456
1457   def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
1458   zipFiles += "${jalviewDir}/${jalviewjs_swingjs_zip}"
1459
1460   doLast {
1461     zipFiles.each { file_zip ->
1462       copy {
1463         from zipTree(file_zip)
1464         into "${jalviewDir}/${jalviewjsSiteDir}"
1465       }
1466     }
1467   }
1468
1469   inputs.files zipFiles
1470   outputs.dir "${jalviewDir}/${jalviewjsSiteDir}"
1471 }
1472
1473 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
1474   dependsOn jalviewjsSitePath
1475   outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
1476   def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
1477   def siteDirProperty = "j2s.site.directory"
1478   def setSiteDir = false
1479   j2s_props.each { prop, val ->
1480     if (val != null) {
1481       if (prop == siteDirProperty) {
1482         if (!(val.startsWith('/') || val.startsWith("file://") )) {
1483           val = "${jalviewDir}/${jalviewjsTransferSiteDir}/${val}"
1484         }
1485         setSiteDir = true
1486       }
1487       property(prop,val)
1488     }
1489     if (!setSiteDir) { // default site location, don't override specifically set property
1490       property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteDir}")
1491     }
1492   }
1493   inputs.properties(j2s_props)
1494   outputs.file(outputFile)
1495 }
1496
1497 task jalviewjsEclipseSetup {
1498   dependsOn jalviewjsEclipseCopyDropins
1499   dependsOn jalviewjsSetEclipseWorkspace
1500   dependsOn jalviewjsCreateJ2sSettings
1501 }
1502
1503 task jalviewjsCopyResources (type: Sync) {
1504   dependsOn jalviewjsSitePath
1505   def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
1506   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
1507
1508   from inputFiles
1509   into outputDir
1510   def outputFiles = []
1511   rename { filename ->
1512     outputFiles += "${outputDir}/${filename}"
1513     null
1514   }
1515   preserve {
1516     include "**"
1517   }
1518   outputs.files outputFiles
1519   inputs.files inputFiles
1520 }
1521
1522 task jalviewjsCopySiteResources (type: Sync) {
1523   dependsOn jalviewjsSitePath
1524   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
1525   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
1526
1527   from inputFiles
1528   into outputDir
1529   def outputFiles = []
1530   rename { filename ->
1531     outputFiles += "${outputDir}/${filename}"
1532     null
1533   }
1534   preserve {
1535     include "**"
1536   }
1537   outputs.files outputFiles
1538   inputs.files inputFiles
1539 }
1540
1541 task jalviewjsProjectImport(type: Exec) {
1542   dependsOn eclipseSetup
1543   dependsOn jalviewjsEclipsePaths
1544   dependsOn jalviewjsEclipseSetup
1545
1546   def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
1547   executable(eclipseBinary)
1548   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
1549   if (eclipseDebug) {
1550     args += "-debug"
1551   }
1552   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
1553
1554   inputs.file("${jalviewDir}/.project")
1555   outputs.upToDateWhen { file(projdir).exists() }
1556 }
1557
1558 task jalviewjsTranspile(type: Exec) {
1559   dependsOn jalviewjsEclipseSetup
1560   dependsOn jalviewjsProjectImport
1561   dependsOn jalviewjsEclipsePaths
1562
1563   executable(eclipseBinary)
1564   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
1565   if (eclipseDebug) {
1566     args += "-debug"
1567   }
1568   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
1569
1570   def stdout
1571   def stderr
1572   doFirst {
1573     stdout = new ByteArrayOutputStream()
1574     stderr = new ByteArrayOutputStream()
1575
1576     def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
1577     def logOutFile = file(logOutFileName)
1578     logOutFile.createNewFile()
1579     logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
1580 BINARY: ${eclipseBinary}
1581 VERSION: ${eclipseVersion}
1582 WORKSPACE: ${eclipseWorkspace}
1583 DEBUG: ${eclipseDebug}
1584 ----
1585 """
1586     def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
1587     //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
1588     //def logErrFile = file(logFileName)
1589     //logErrFile.createNewFile()
1590     //def logErrFOS = new FileErrputStream(logErrFile, false)
1591     // combine stdout and stderr
1592     def logErrFOS = logOutFOS
1593
1594     if (jalviewjs_j2s_to_console.equals("true")) {
1595       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1596         new org.apache.tools.ant.util.TeeOutputStream(
1597           logOutFOS,
1598           stdout),
1599         standardOutput)
1600       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1601         new org.apache.tools.ant.util.TeeOutputStream(
1602           logErrFOS,
1603           stderr),
1604         errorOutput)
1605     } else {
1606       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1607         logOutFOS,
1608         stdout)
1609       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1610         logErrFOS,
1611         stderr)
1612     }
1613   }
1614
1615   doLast {
1616     if (stdout.toString().contains("Error processing ")) {
1617       // j2s did not complete transpile
1618       throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
1619     }
1620   }
1621
1622   inputs.dir("${jalviewDir}/${sourceDir}")
1623   outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
1624   outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } )
1625 }
1626
1627 task jalviewjsCopyTransferSite(type: Copy) {
1628   dependsOn jalviewjsTranspile
1629   from "${jalviewDir}/${jalviewjsTransferSiteDir}"
1630   into "${jalviewDir}/${jalviewjsSiteDir}"
1631 }
1632
1633 jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
1634 jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
1635 jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
1636
1637 task jalviewjsPrepareSite {
1638   group "JalviewJS"
1639   description "Prepares the website folder including unzipping files and copying resources"
1640   dependsOn jalviewjsSitePath
1641   dependsOn jalviewjsUnzipFiles
1642   dependsOn jalviewjsCopyResources
1643   dependsOn jalviewjsCopySiteResources
1644 }
1645
1646 task jalviewjsBuildSite {
1647   group "JalviewJS"
1648   description "Builds the whole website including transpiled code"
1649   dependsOn jalviewjsCopyTransferSite
1650   dependsOn jalviewjsPrepareSite
1651 }
1652
1653 task cleanJalviewjsSite {
1654   doFirst {
1655     delete "${jalviewDir}/${jalviewjsTransferSiteDir}"
1656     delete "${jalviewDir}/${jalviewjsSiteDir}"
1657   }
1658 }
1659
1660 task jalviewjsSiteTar(type: Tar) {
1661   group "JalviewJS"
1662   description "Creates a tar.gz file for the website"
1663   dependsOn jalviewjsBuildSite
1664   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
1665   try {
1666     archiveFileName = outputFilename
1667   } catch (Exception e) {
1668     archiveName = outputFilename
1669   }
1670
1671   compression Compression.GZIP
1672
1673   from "${jalviewDir}/${jalviewjsSiteDir}"
1674   into jalviewjs_site_dir // this is inside the tar file
1675
1676   inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
1677 }
1678
1679 task jalviewjsServer {
1680   group "JalviewJS"
1681   description "Starts a webserver on localhost to test the website"
1682   dependsOn jalviewjsSitePath
1683   def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
1684   doLast {
1685
1686     SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
1687     def port = Integer.valueOf(jalviewjs_server_port)
1688     def start = port
1689     def running = false
1690     def url
1691     while(port < start+1000 && !running) {
1692       try {
1693         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
1694         def jalviewjsServer = factory.start(doc_root, port)
1695         running = true
1696         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
1697         println("SERVER STARTED with document root ${doc_root}.")
1698         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
1699         println("For debug: "+url+"?j2sdebug")
1700
1701         file(htmlFile).text = """
1702         <p><a href="${url}">Jalview JS Test. &lt;${url}&gt;</a></p>
1703         <p><a href="${url}?j2sdebug">Jalview JS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
1704         """
1705
1706       } catch (Exception e) {
1707         port++;
1708       }
1709     }
1710
1711   }
1712
1713   outputs.file(htmlFile)
1714   outputs.upToDateWhen({false})
1715 }
1716
1717 task cleanJalviewjsAll {
1718   group "JalviewJS"
1719   description "Delete all configuration and build artifacts to do with JalviewJS build"
1720   dependsOn cleanJalviewjsSite
1721   dependsOn jalviewjsEclipsePaths
1722
1723   doFirst {
1724     delete "${jalviewDir}/${jalviewjsBuildDir}"
1725     delete "${jalviewDir}/${eclipse_bin_dir}"
1726     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
1727       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
1728     }
1729     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
1730   }
1731
1732   outputs.upToDateWhen( { false } )
1733 }
1734
1735 task jalviewjs {
1736   group "JalviewJS"
1737   description "Build the site"
1738   dependsOn jalviewjsBuildSite
1739 }
1740
1741
1742 task jalviewjsIDECopyTransferSite(type: Copy) {
1743   from "${jalviewDir}/${jalviewjsTransferSiteDir}"
1744   into "${jalviewDir}/${jalviewjsSiteDir}"
1745 }
1746
1747 task jalviewjsIDEj2s {
1748   group "JalviewJS in Eclipse"
1749   description "Creates the .j2s file"
1750   dependsOn jalviewjsCreateJ2sSettings
1751 }
1752
1753 task jalviewjsIDEBuildSite {
1754   group "JalviewJS in Eclipse"
1755   description "Copies the Eclipse transpiled site and unzips supporting zipfiles"
1756   dependsOn jalviewjsIDECopyTransferSite
1757   dependsOn jalviewjsPrepareSite
1758 }
1759
1760 task jalviewjsIDESiteClean {
1761   group "JalviewJS in Eclipse"
1762   description "Deletes the Eclipse transpiled site"
1763   dependsOn cleanJalviewjsSite
1764 }
1765
1766 task jalviewjsIDEServer {
1767   group "JalviewJS in Eclipse"
1768   description "Starts a webserver on localhost to test the website"
1769   dependsOn jalviewjsServer
1770 }
1771