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 = "${jalviewDir}/local.properties"
  24 if (file(localProps).exists()) {
  25   try {
  26     def p = new Properties()
  27     def localPropsFIS = new FileInputStream(localProps)
  28     p.load(localPropsFIS)
  29     localPropsFIS.close()
  30     p.each {
  31       key, val ->
  32         def over = getProperty(key) != null
  33         setProperty(key, val)
  34         if (over) {
  35           println("Overriding property '${key}' with local.properties value '${val}'")
  36         }
  37     }
  38   } catch (Exception e) {
  39   }
  40 }
  41
  42 repositories {
  43   jcenter()
  44   mavenCentral()
  45   mavenLocal()
  46   flatDir {
  47     dirs gradlePluginsDir
  48   }
  49 }
  50
  51 dependencies {
  52   compile 'org.apache.commons:commons-compress:1.18'
  53 }
  54
  55 mainClassName = launcherClass
  56 def cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
  57 def classes = "${jalviewDir}/${classesDir}"
  58
  59 if (clover.equals("true")) {
  60   use_clover = true
  61   classes = "${buildDir}/${cloverClassesDir}"
  62 } else {
  63   use_clover = false
  64   classes = "${jalviewDir}/${classesDir}"
  65 }
  66
  67 // configure classpath/args for j8/j11 compilation
  68
  69 def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
  70 def libDir
  71 def libDistDir
  72 def compile_source_compatibility
  73 def compile_target_compatibility
  74
  75 ext {
  76   getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}"
  77   getdownDir = ""
  78   reportRsyncCmd = false
  79   buildDist = true
  80   buildProperties = buildPropertiesFile
  81   getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
  82   switch (CHANNEL) {
  83
  84     case "BUILD":
  85     // TODO: get bamboo build artifact URL for getdown artifacts
  86     getdown_channel_base = bamboo_channelbase
  87     getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
  88     getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
  89     getdown_app_dir = getdown_app_dir_alt
  90     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  91     break
  92
  93     case "RELEASE":
  94     getdown_channel_name = CHANNEL.toLowerCase()
  95     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
  96     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
  97     getdown_app_dir = getdown_app_dir_release
  98     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  99     reportRsyncCommand = true
 100     break
 101
 102     case "ARCHIVE":
 103     getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
 104     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 105     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 106     getdown_app_dir = getdown_app_dir_alt
 107     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
 108       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
 109       exit
 110     } else {
 111       packageDir = "${ARCHIVEDIR}/${packageDir}"
 112       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
 113       buildDist = false
 114     }
 115     reportRsyncCommand = true
 116     break
 117
 118     case "ARCHIVELOCAL":
 119     getdown_channel_name = "archive/${JALVIEW_VERSION}"
 120     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 121     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 122     getdown_app_dir = getdown_app_dir_alt
 123     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
 124       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
 125       exit
 126     } else {
 127       packageDir = "${ARCHIVEDIR}/${packageDir}"
 128       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
 129       buildDist = false
 130     }
 131     reportRsyncCommand = true
 132     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 133     break
 134
 135     case "DEVELOP":
 136     getdown_channel_name = CHANNEL.toLowerCase()
 137     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 138     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 139     getdown_app_dir = getdown_app_dir_alt
 140     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 141     reportRsyncCommand = true
 142     break
 143
 144     case "TEST-RELEASE":
 145     getdown_channel_name = CHANNEL.toLowerCase()
 146     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 147     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 148     getdown_app_dir = getdown_app_dir_alt
 149     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 150     reportRsyncCommand = true
 151     break
 152
 153     case ~/^SCRATCH(|-[-\w]*)$/:
 154     getdown_channel_name = CHANNEL
 155     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 156     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 157     getdown_app_dir = getdown_app_dir_alt
 158     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 159     reportRsyncCommand = true
 160     break
 161
 162     case "LOCAL":
 163     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 164     getdown_app_dir = getdown_app_dir_alt
 165     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 166     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 167     break
 168
 169     default: // something wrong specified
 170     print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
 171     exit
 172     break
 173
 174   }
 175
 176   getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}"
 177   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
 178   getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}"
 179   getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}"
 180   getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/"
 181   getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_dir}"
 182   /* compile without modules -- using classpath libraries
 183   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
 184   modules_runtimeClasspath = modules_compileClasspath
 185   */
 186   gitHash = ""
 187   gitBranch = ""
 188
 189   println("Using a ${CHANNEL} profile.")
 190 }
 191
 192 def JAVA_INTEGER_VERSION
 193 def additional_compiler_args = []
 194 // these are getdown.txt properties defined dependent on the JAVA_VERSION
 195 def getdown_alt_java_min_version
 196 def getdown_alt_java_max_version
 197 // this property is assigned below and expanded to multiple lines in the getdown task
 198 def getdown_alt_multi_java_location
 199 // this property is for the Java library used in eclipse
 200 def eclipse_java_runtime_name
 201 if (JAVA_VERSION.equals("1.8")) {
 202   JAVA_INTEGER_VERSION = "8"
 203   //libDir = j8libDir
 204   libDir = j11libDir
 205   libDistDir = j8libDir
 206   compile_source_compatibility = 1.8
 207   compile_target_compatibility = 1.8
 208   getdown_alt_java_min_version = getdown_alt_java8_min_version
 209   getdown_alt_java_max_version = getdown_alt_java8_max_version
 210   getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 211   eclipse_java_runtime_name = "JavaSE-1.8"
 212 } else if (JAVA_VERSION.equals("11")) {
 213   JAVA_INTEGER_VERSION = "11"
 214   libDir = j11libDir
 215   libDistDir = j11libDir
 216   compile_source_compatibility = 11
 217   compile_target_compatibility = 11
 218   getdown_alt_java_min_version = getdown_alt_java11_min_version
 219   getdown_alt_java_max_version = getdown_alt_java11_max_version
 220   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 221   eclipse_java_runtime_name = "JavaSE-11"
 222   /* compile without modules -- using classpath libraries
 223   additional_compiler_args += [
 224   '--module-path', ext.modules_compileClasspath.asPath,
 225   '--add-modules', j11modules
 226   ]
 227   */
 228 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
 229   JAVA_INTEGER_VERSION = JAVA_VERSION
 230   libDir = j11libDir
 231   libDistDir = j11libDir
 232   compile_source_compatibility = JAVA_VERSION
 233   compile_target_compatibility = JAVA_VERSION
 234   getdown_alt_java_min_version = getdown_alt_java11_min_version
 235   getdown_alt_java_max_version = getdown_alt_java11_max_version
 236   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 237   eclipse_java_runtime_name = "JavaSE-11"
 238   /* compile without modules -- using classpath libraries
 239   additional_compiler_args += [
 240   '--module-path', ext.modules_compileClasspath.asPath,
 241   '--add-modules', j11modules
 242   ]
 243   */
 244 } else {
 245   throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
 246 }
 247
 248 sourceSets {
 249
 250   main {
 251     java {
 252       srcDirs "${jalviewDir}/${sourceDir}"
 253       outputDir = file("${classes}")
 254     }
 255
 256     resources {
 257       srcDirs "${jalviewDir}/${resourceDir}"
 258     }
 259
 260     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 261
 262     compileClasspath = files(sourceSets.main.java.outputDir)
 263     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 264
 265     runtimeClasspath = compileClasspath
 266   }
 267
 268   clover {
 269     java {
 270       srcDirs = [ cloverInstrDir ]
 271       outputDir = file("${buildDir}/${cloverClassesDir}")
 272     }
 273
 274     resources {
 275       srcDirs = sourceSets.main.resources.srcDirs
 276     }
 277     compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
 278     compileClasspath += files(sourceSets.main.java.outputDir)
 279     compileClasspath += sourceSets.main.compileClasspath
 280     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
 281     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 282
 283     runtimeClasspath = compileClasspath
 284   }
 285
 286   test {
 287     java {
 288       srcDirs "${jalviewDir}/${testSourceDir}"
 289       outputDir = file("${jalviewDir}/${testOutputDir}")
 290     }
 291
 292     resources {
 293       srcDirs = sourceSets.main.resources.srcDirs
 294     }
 295
 296     compileClasspath = files( sourceSets.test.java.outputDir )
 297
 298     if (use_clover) {
 299       compileClasspath += sourceSets.clover.compileClasspath
 300     } else {
 301       compileClasspath += files(sourceSets.main.java.outputDir)
 302     }
 303
 304     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 305     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
 306     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
 307
 308     runtimeClasspath = compileClasspath
 309   }
 310 }
 311
 312 // clover bits
 313 dependencies {
 314   if (use_clover) {
 315     cloverCompile 'org.openclover:clover:4.3.1'
 316     testCompile 'org.openclover:clover:4.3.1'
 317   }
 318 }
 319
 320 configurations {
 321   cloverRuntime
 322   cloverRuntime.extendsFrom cloverCompile
 323 }
 324
 325 eclipse {
 326   project {
 327     name = eclipse_project_name
 328
 329     natures 'org.eclipse.jdt.core.javanature',
 330     'org.eclipse.jdt.groovy.core.groovyNature',
 331     'org.eclipse.buildship.core.gradleprojectnature'
 332
 333     buildCommand 'org.eclipse.jdt.core.javabuilder'
 334     buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
 335   }
 336
 337   classpath {
 338     //defaultOutputDir = sourceSets.main.java.outputDir
 339     def removeThese = []
 340     configurations.each{
 341       if (it.isCanBeResolved()) {
 342         removeThese += it
 343       }
 344     }
 345
 346     minusConfigurations += removeThese
 347     plusConfigurations = [ ]
 348     file {
 349
 350       whenMerged { cp ->
 351         def removeTheseToo = []
 352         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
 353         cp.entries.each { entry ->
 354           if (entry.kind == 'src') {
 355             if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
 356               removeTheseToo += entry
 357             } else {
 358               alreadyAddedSrcPath.putAt(entry.path, true)
 359             }
 360           }
 361         }
 362         cp.entries.removeAll(removeTheseToo)
 363
 364         if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
 365           cp.entries += new Output("${eclipse_bin_dir}/main")
 366         }
 367         if (file(helpParentDir).isDirectory()) {
 368           cp.entries += new Library(fileReference(helpParentDir))
 369         }
 370         if (file(resourceDir).isDirectory()) {
 371           cp.entries += new Library(fileReference(resourceDir))
 372         }
 373
 374         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 375
 376         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 377           //don't want to add outputDir as eclipse is using its own output dir in bin/main
 378           if (it.isDirectory() || ! it.exists()) {
 379             // don't add dirs to classpath
 380             return
 381           }
 382           def itPath = it.toString()
 383           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 384             // make relative path
 385             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 386           }
 387           if (alreadyAddedLibPath.get(itPath)) {
 388             //println("Not adding duplicate entry "+itPath)
 389           } else {
 390             //println("Adding entry "+itPath)
 391             cp.entries += new Library(fileReference(itPath))
 392             alreadyAddedLibPath.put(itPath, true)
 393           }
 394         }
 395
 396         //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
 397         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 398           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
 399           if (it.isDirectory() || ! it.exists()) {
 400             // don't add dirs to classpath
 401             return false // groovy "break" in .each closure
 402           }
 403           def itPath = it.toString()
 404           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 405             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 406           }
 407           if (alreadyAddedLibPath.get(itPath)) {
 408             // don't duplicate
 409           } else {
 410             def lib = new Library(fileReference(itPath))
 411             lib.entryAttributes["test"] = "true"
 412             cp.entries += lib
 413             alreadyAddedLibPath.put(itPath, true)
 414           }
 415         }
 416
 417       } // whenMerged
 418
 419     } // file
 420
 421     containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
 422
 423   } // classpath
 424
 425   jdt {
 426     // for the IDE, use java 11 compatibility
 427     sourceCompatibility = compile_source_compatibility
 428     targetCompatibility = compile_target_compatibility
 429     javaRuntimeName = eclipse_java_runtime_name
 430
 431     // add in jalview project specific properties/preferences into eclipse core preferences
 432     file {
 433       withProperties { props ->
 434         def jalview_prefs = new Properties()
 435         def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
 436         jalview_prefs.load(ins)
 437         ins.close()
 438         jalview_prefs.forEach { t, v ->
 439           if (props.getAt(t) == null) {
 440             props.putAt(t, v)
 441           }
 442         }
 443       }
 444     }
 445
 446   } // jdt
 447
 448 }
 449
 450 task cloverInstr() {
 451   // only instrument source, we build test classes as normal
 452   inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
 453   outputs.dir cloverInstrDir
 454
 455   doFirst {
 456     delete cloverInstrDir
 457     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 458     "-d", "${buildDir}/${cloverSourcesInstrDir}"]
 459     argsList.addAll(inputs.files.files.collect({ file ->
 460       file.absolutePath
 461     }))
 462     String[] args = argsList.toArray()
 463     println("About to instrument "+args.length +" files")
 464     com.atlassian.clover.CloverInstr.mainImpl(args)
 465   }
 466 }
 467
 468
 469 task cloverReport {
 470   group = "Verification"
 471     description = "Createst the Clover report"
 472     inputs.dir "${buildDir}/clover"
 473     outputs.dir "${reportsDir}/clover"
 474     onlyIf {
 475       file("${buildDir}/clover/clover.db").exists()
 476     }
 477   doFirst {
 478     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 479     "-o", "${reportsDir}/clover"]
 480     String[] args = argsList.toArray()
 481     com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
 482
 483     // and generate ${reportsDir}/clover/clover.xml
 484     args = ["--initstring", "${buildDir}/clover/clover.db",
 485     "-o", "${reportsDir}/clover/clover.xml"].toArray()
 486     com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
 487   }
 488 }
 489
 490 // end clover bits
 491
 492
 493 compileJava {
 494
 495   doFirst {
 496     sourceCompatibility = compile_source_compatibility
 497     targetCompatibility = compile_target_compatibility
 498     options.compilerArgs = additional_compiler_args
 499     print ("Setting target compatibility to "+targetCompatibility+"\n")
 500   }
 501
 502 }
 503
 504 compileTestJava {
 505   if (use_clover) {
 506     dependsOn compileCloverJava
 507     classpath += configurations.cloverRuntime
 508   } else {
 509     classpath += sourceSets.main.runtimeClasspath
 510   }
 511   doFirst {
 512     sourceCompatibility = compile_source_compatibility
 513     targetCompatibility = compile_target_compatibility
 514     options.compilerArgs = additional_compiler_args
 515     print ("Setting target compatibility to "+targetCompatibility+"\n")
 516   }
 517 }
 518
 519
 520 compileCloverJava {
 521
 522   doFirst {
 523     sourceCompatibility = compile_source_compatibility
 524     targetCompatibility = compile_target_compatibility
 525     options.compilerArgs += additional_compiler_args
 526     print ("Setting target compatibility to "+targetCompatibility+"\n")
 527   }
 528   classpath += configurations.cloverRuntime
 529 }
 530
 531 clean {
 532   doFirst {
 533     delete sourceSets.main.java.outputDir
 534   }
 535 }
 536
 537 cleanTest {
 538   doFirst {
 539     delete sourceSets.test.java.outputDir
 540     delete cloverInstrDir
 541   }
 542 }
 543
 544 // format is a string like date.format("dd MMMM yyyy")
 545 def getDate(format) {
 546   def date = new Date()
 547   return date.format(format)
 548 }
 549
 550 task setGitVals {
 551   def hashStdOut = new ByteArrayOutputStream()
 552   exec {
 553     commandLine "git", "rev-parse", "--short", "HEAD"
 554     standardOutput = hashStdOut
 555     ignoreExitValue true
 556   }
 557
 558   def branchStdOut = new ByteArrayOutputStream()
 559   exec {
 560     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
 561     standardOutput = branchStdOut
 562     ignoreExitValue true
 563   }
 564
 565   project.ext.gitHash = hashStdOut.toString().trim()
 566   project.ext.gitBranch = branchStdOut.toString().trim()
 567
 568   outputs.upToDateWhen { false }
 569 }
 570
 571 task createBuildProperties(type: WriteProperties) {
 572   dependsOn setGitVals
 573   inputs.dir("${jalviewDir}/${sourceDir}")
 574   inputs.dir("${classes}")
 575   inputs.dir("${jalviewDir}/${resourceDir}")
 576   outputFile (buildProperties)
 577   // taking time specific comment out to allow better incremental builds
 578   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
 579   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
 580   property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
 581   property "VERSION", JALVIEW_VERSION
 582   property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
 583   outputs.file(outputFile)
 584 }
 585
 586 def buildingHTML = "${jalviewDir}/${docDir}/building.html"
 587 task cleanBuildingHTML(type: Delete) {
 588   doFirst {
 589     delete buildingHTML
 590   }
 591 }
 592
 593 task convertBuildingMD(type: Exec) {
 594   dependsOn cleanBuildingHTML
 595   def buildingMD = "${jalviewDir}/${docDir}/building.md"
 596   def css = "${jalviewDir}/${docDir}/github.css"
 597
 598   def pandoc = null
 599   pandoc_exec.split(",").each {
 600     if (file(it.trim()).exists()) {
 601       pandoc = it.trim()
 602       return true
 603     }
 604   }
 605
 606   def hostname = "hostname".execute().text.trim()
 607   if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
 608     pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
 609   }
 610
 611   doFirst {
 612     if (pandoc != null && file(pandoc).exists()) {
 613         commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
 614     } else {
 615         println("Cannot find pandoc. Skipping convert building.md to HTML")
 616         throw new StopExecutionException()
 617     }
 618   }
 619
 620   ignoreExitValue true
 621
 622   inputs.file(buildingMD)
 623   inputs.file(css)
 624   outputs.file(buildingHTML)
 625 }
 626
 627 clean {
 628   doFirst {
 629     delete buildingHTML
 630   }
 631 }
 632
 633 task syncDocs(type: Sync) {
 634   dependsOn convertBuildingMD
 635   def syncDir = "${classes}/${docDir}"
 636   from fileTree("${jalviewDir}/${docDir}")
 637   into syncDir
 638
 639 }
 640
 641 def helpFile = "${classes}/${helpDir}/help.jhm"
 642
 643 task copyHelp(type: Copy) {
 644   def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
 645   def outputDir = "${classes}/${helpDir}"
 646   from(inputDir) {
 647     exclude '**/*.gif'
 648     exclude '**/*.jpg'
 649     exclude '**/*.png'
 650     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
 651   }
 652   from(inputDir) {
 653     include '**/*.gif'
 654     include '**/*.jpg'
 655     include '**/*.png'
 656   }
 657   into outputDir
 658
 659   inputs.dir(inputDir)
 660   outputs.files(helpFile)
 661   outputs.dir(outputDir)
 662 }
 663
 664 task syncLib(type: Sync) {
 665   def syncDir = "${classes}/${libDistDir}"
 666   from fileTree("${jalviewDir}/${libDistDir}")
 667   into syncDir
 668 }
 669
 670 task syncResources(type: Sync) {
 671   from "${jalviewDir}/${resourceDir}"
 672   include "**/*.*"
 673   into "${classes}"
 674   preserve {
 675     include "**"
 676   }
 677 }
 678
 679 task prepare {
 680   dependsOn syncResources
 681   dependsOn syncDocs
 682   dependsOn copyHelp
 683 }
 684
 685
 686 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 687 test {
 688   dependsOn prepare
 689   dependsOn compileJava
 690   if (use_clover) {
 691     dependsOn cloverInstr
 692   }
 693
 694   if (use_clover) {
 695     print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
 696   }
 697
 698   useTestNG() {
 699     includeGroups testngGroups
 700     preserveOrder true
 701     useDefaultListeners=true
 702   }
 703
 704   workingDir = jalviewDir
 705   //systemProperties 'clover.jar' System.properties.clover.jar
 706   sourceCompatibility = compile_source_compatibility
 707   targetCompatibility = compile_target_compatibility
 708   jvmArgs += additional_compiler_args
 709
 710 }
 711
 712 task buildIndices(type: JavaExec) {
 713   dependsOn copyHelp
 714   classpath = sourceSets.main.compileClasspath
 715   main = "com.sun.java.help.search.Indexer"
 716   workingDir = "${classes}/${helpDir}"
 717   def argDir = "html"
 718   args = [ argDir ]
 719   inputs.dir("${workingDir}/${argDir}")
 720
 721   outputs.dir("${classes}/doc")
 722   outputs.dir("${classes}/help")
 723   outputs.file("${workingDir}/JavaHelpSearch/DOCS")
 724   outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
 725   outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
 726   outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
 727   outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
 728   outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 729 }
 730
 731 task compileLinkCheck(type: JavaCompile) {
 732   options.fork = true
 733   classpath = files("${jalviewDir}/${utilsDir}")
 734   destinationDir = file("${jalviewDir}/${utilsDir}")
 735   source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 736
 737   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 738   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 739   outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
 740   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 741 }
 742
 743 task linkCheck(type: JavaExec) {
 744   dependsOn prepare, compileLinkCheck
 745
 746   def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
 747   classpath = files("${jalviewDir}/${utilsDir}")
 748   main = "HelpLinksChecker"
 749   workingDir = jalviewDir
 750   def help = "${classes}/${helpDir}"
 751   args = [ "${classes}/${helpDir}", "-nointernet" ]
 752
 753   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
 754   def errFOS = outFOS
 755   standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
 756     outFOS,
 757     standardOutput)
 758   errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
 759     outFOS,
 760     errorOutput)
 761
 762   inputs.dir("${classes}/${helpDir}")
 763   outputs.file(helpLinksCheckerOutFile)
 764 }
 765
 766 // import the pubhtmlhelp target
 767 ant.properties.basedir = "${jalviewDir}"
 768 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
 769 ant.importBuild "${utilsDir}/publishHelp.xml"
 770
 771
 772 task cleanPackageDir(type: Delete) {
 773   doFirst {
 774     delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
 775   }
 776 }
 777
 778 jar {
 779   dependsOn linkCheck
 780   dependsOn buildIndices
 781   dependsOn createBuildProperties
 782
 783   manifest {
 784     attributes "Main-Class": mainClass,
 785     "Permissions": "all-permissions",
 786     "Application-Name": "Jalview Desktop",
 787     "Codebase": application_codebase
 788   }
 789
 790   destinationDir = file("${jalviewDir}/${packageDir}")
 791   archiveName = rootProject.name+".jar"
 792
 793   exclude "cache*/**"
 794   exclude "*.jar"
 795   exclude "*.jar.*"
 796   exclude "**/*.jar"
 797   exclude "**/*.jar.*"
 798
 799   inputs.dir("${classes}")
 800   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 801 }
 802
 803 task copyJars(type: Copy) {
 804   from fileTree(dir: "${classes}", include: "**/*.jar").files
 805   into "${jalviewDir}/${packageDir}"
 806 }
 807
 808 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 809 task syncJars(type: Sync) {
 810   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
 811   into "${jalviewDir}/${packageDir}"
 812   preserve {
 813     include jar.archiveName
 814   }
 815 }
 816
 817 task makeDist {
 818   group = "build"
 819   description = "Put all required libraries in dist"
 820   // order of "cleanPackageDir", "copyJars", "jar" important!
 821   jar.mustRunAfter cleanPackageDir
 822   syncJars.mustRunAfter cleanPackageDir
 823   dependsOn cleanPackageDir
 824   dependsOn syncJars
 825   dependsOn jar
 826   outputs.dir("${jalviewDir}/${packageDir}")
 827 }
 828
 829 task cleanDist {
 830   dependsOn cleanPackageDir
 831   dependsOn cleanTest
 832   dependsOn clean
 833 }
 834
 835 shadowJar {
 836   group = "distribution"
 837   if (buildDist) {
 838     dependsOn makeDist
 839   }
 840   from ("${jalviewDir}/${libDistDir}") {
 841     include("*.jar")
 842   }
 843   manifest {
 844     attributes 'Implementation-Version': JALVIEW_VERSION
 845   }
 846   mainClassName = shadowJarMainClass
 847   mergeServiceFiles()
 848   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
 849   minimize()
 850 }
 851
 852 task getdownWebsite() {
 853   group = "distribution"
 854   description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
 855   if (buildDist) {
 856     dependsOn makeDist
 857   }
 858
 859   def getdownWebsiteResourceFilenames = []
 860   def getdownTextString = ""
 861   def getdownResourceDir = project.ext.getdownResourceDir
 862   def getdownAppDir = project.ext.getdownAppDir
 863   def getdownResourceFilenames = []
 864
 865   doFirst {
 866     // clean the getdown website and files dir before creating getdown folders
 867     delete project.ext.getdownWebsiteDir
 868     delete project.ext.getdownFilesDir
 869
 870     copy {
 871       from buildProperties
 872       rename(buildPropertiesFile, getdown_build_properties)
 873       into project.ext.getdownAppDir
 874     }
 875     getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
 876
 877     // go through properties looking for getdown_txt_...
 878     def props = project.properties.sort { it.key }
 879     if (getdown_alt_java_min_version.length() > 0) {
 880       props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
 881     }
 882     if (getdown_alt_java_max_version.length() > 0) {
 883       props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
 884     }
 885     props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
 886
 887     props.put("getdown_txt_appbase", getdown_app_base)
 888     props.each{ prop, val ->
 889       if (prop.startsWith("getdown_txt_") && val != null) {
 890         if (prop.startsWith("getdown_txt_multi_")) {
 891           def key = prop.substring(18)
 892           val.split(",").each{ v ->
 893             def line = "${key} = ${v}\n"
 894             getdownTextString += line
 895           }
 896         } else {
 897           // file values rationalised
 898           if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
 899             def r = null
 900             if (val.indexOf('/') == 0) {
 901               // absolute path
 902               r = file(val)
 903             } else if (val.indexOf('/') > 0) {
 904               // relative path (relative to jalviewDir)
 905               r = file( "${jalviewDir}/${val}" )
 906             }
 907             if (r.exists()) {
 908               val = "${getdown_resource_dir}/" + r.getName()
 909               getdownWebsiteResourceFilenames += val
 910               getdownResourceFilenames += r.getPath()
 911             }
 912           }
 913           if (! prop.startsWith("getdown_txt_resource")) {
 914             def line = prop.substring(12) + " = ${val}\n"
 915             getdownTextString += line
 916           }
 917         }
 918       }
 919     }
 920
 921     getdownWebsiteResourceFilenames.each{ filename ->
 922       getdownTextString += "resource = ${filename}\n"
 923     }
 924     getdownResourceFilenames.each{ filename ->
 925       copy {
 926         from filename
 927         into project.ext.getdownResourceDir
 928       }
 929     }
 930
 931     def codeFiles = []
 932     fileTree(file(packageDir)).each{ f ->
 933       if (f.isDirectory()) {
 934         def files = fileTree(dir: f, include: ["*"]).getFiles()
 935         codeFiles += files
 936       } else if (f.exists()) {
 937         codeFiles += f
 938       }
 939     }
 940     codeFiles.sort().each{f ->
 941       def name = f.getName()
 942       def line = "code = ${getdown_app_dir}/${name}\n"
 943       getdownTextString += line
 944       copy {
 945         from f.getPath()
 946         into project.ext.getdownAppDir
 947       }
 948     }
 949
 950     // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
 951     /*
 952     if (JAVA_VERSION.equals("11")) {
 953     def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
 954     j11libFiles.sort().each{f ->
 955     def name = f.getName()
 956     def line = "code = ${getdown_j11lib_dir}/${name}\n"
 957     getdownTextString += line
 958     copy {
 959     from f.getPath()
 960     into project.ext.getdownJ11libDir
 961     }
 962     }
 963     }
 964      */
 965
 966     // 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.
 967     //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
 968     getdownTextString += "resource = ${getdown_launcher_new}\n"
 969     getdownTextString += "class = ${mainClass}\n"
 970
 971     def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt")
 972     getdown_txt.write(getdownTextString)
 973
 974     def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}")
 975     launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
 976
 977     copy {
 978       from getdownLauncher
 979       rename(file(getdownLauncher).getName(), getdown_launcher_new)
 980       into project.ext.getdownWebsiteDir
 981     }
 982
 983     copy {
 984       from getdownLauncher
 985       if (file(getdownLauncher).getName() != getdown_launcher) {
 986         rename(file(getdownLauncher).getName(), getdown_launcher)
 987       }
 988       into project.ext.getdownWebsiteDir
 989     }
 990
 991     if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
 992       copy {
 993         from getdown_txt
 994         from getdownLauncher
 995         from "${getdownWebsiteDir}/${getdown_build_properties}"
 996         if (file(getdownLauncher).getName() != getdown_launcher) {
 997           rename(file(getdownLauncher).getName(), getdown_launcher)
 998         }
 999         into getdownInstallDir
1000       }
1001
1002       copy {
1003         from getdownInstallDir
1004         into getdownFilesInstallDir
1005       }
1006     }
1007
1008     copy {
1009       from getdown_txt
1010       from launch_jvl
1011       from getdownLauncher
1012       from "${getdownWebsiteDir}/${getdown_build_properties}"
1013       if (file(getdownLauncher).getName() != getdown_launcher) {
1014         rename(file(getdownLauncher).getName(), getdown_launcher)
1015       }
1016       into getdownFilesDir
1017     }
1018
1019     copy {
1020       from getdownResourceDir
1021       into "${project.ext.getdownFilesDir}/${getdown_resource_dir}"
1022     }
1023   }
1024
1025   if (buildDist) {
1026     inputs.dir("${jalviewDir}/${packageDir}")
1027   }
1028   outputs.dir(project.ext.getdownWebsiteDir)
1029   outputs.dir(project.ext.getdownFilesDir)
1030 }
1031
1032 task getdownDigest(type: JavaExec) {
1033   group = "distribution"
1034   description = "Digest the getdown website folder"
1035   dependsOn getdownWebsite
1036   doFirst {
1037     classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
1038   }
1039   main = "com.threerings.getdown.tools.Digester"
1040   args project.ext.getdownWebsiteDir
1041   inputs.dir(project.ext.getdownWebsiteDir)
1042   outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
1043 }
1044
1045 task getdown() {
1046   group = "distribution"
1047   description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1048   dependsOn getdownDigest
1049   doLast {
1050     if (reportRsyncCommand) {
1051       def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1052       def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1053       println "LIKELY RSYNC COMMAND:"
1054       println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1055       if (RUNRSYNC == "true") {
1056         exec {
1057           commandLine "mkdir", "-p", toDir
1058         }
1059         exec {
1060           commandLine "rsync", "-avh", "--delete", fromDir, toDir
1061         }
1062       }
1063     }
1064   }
1065 }
1066
1067 clean {
1068   doFirst {
1069     delete project.ext.getdownWebsiteDir
1070     delete project.ext.getdownFilesDir
1071   }
1072 }
1073
1074 install4j {
1075   def install4jHomeDir = "/opt/install4j"
1076   def hostname = "hostname".execute().text.trim()
1077   if (hostname.equals("jv-bamboo")) {
1078     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1079   } else if (OperatingSystem.current().isMacOsX()) {
1080     install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
1081     if (! file(install4jHomeDir).exists()) {
1082       install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
1083     }
1084   } else if (OperatingSystem.current().isLinux()) {
1085     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1086   }
1087   installDir = file(install4jHomeDir)
1088   mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
1089   if (install4jFaster.equals("true")) {
1090     faster = true
1091   }
1092 }
1093
1094 def install4jConf
1095 def macosJavaVMDir
1096 def macosJavaVMTgz
1097 def windowsJavaVMDir
1098 def windowsJavaVMTgz
1099 def install4jDir = "${jalviewDir}/${install4jResourceDir}"
1100 def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j"
1101 install4jConf = "${install4jDir}/${install4jConfFile}"
1102
1103 task copyInstall4jTemplate(type: Copy) {
1104   macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre"
1105   macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz"
1106   windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre"
1107   windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz"
1108   from (install4jDir) {
1109     include install4jTemplate
1110     rename (install4jTemplate, install4jConfFile)
1111     filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
1112     filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
1113     tokens: [
1114     'JAVA_VERSION': JAVA_VERSION,
1115     'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1116     'VERSION': JALVIEW_VERSION,
1117     'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1118     'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1119     'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1120     'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1121     'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
1122     'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
1123     'MACOS_BUNDLE_ID': install4jMacOSBundleId,
1124     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1125     'GETDOWN_DIST_DIR': getdown_app_dir,
1126     'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1127     'GETDOWN_INSTALL_DIR': getdown_install_dir
1128     ]
1129     )
1130     if (OSX_KEYPASS=="") {
1131       filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
1132       filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
1133     }
1134   }
1135   into install4jDir
1136   outputs.files(install4jConf)
1137
1138   doLast {
1139     // include file associations in installer
1140     def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text
1141     ant.replaceregexp(
1142       byline: false,
1143       flags: "s",
1144       match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
1145       replace: installerFileAssociationsXml,
1146       file: install4jConf
1147     )
1148     /*
1149     // include uninstaller applescript app files in dmg
1150     def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
1151     ant.replaceregexp(
1152     byline: false,
1153     flags: "s",
1154     match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
1155     replace: installerDMGUninstallerXml,
1156     file: install4jConf
1157     )
1158      */
1159   }
1160 }
1161
1162 task installers(type: com.install4j.gradle.Install4jTask) {
1163   group = "distribution"
1164   description = "Create the install4j installers"
1165   dependsOn getdown
1166   dependsOn copyInstall4jTemplate
1167   projectFile = file(install4jConf)
1168   variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
1169   destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}"
1170   buildSelected = true
1171
1172   if (OSX_KEYPASS) {
1173     macKeystorePassword=OSX_KEYPASS
1174   }
1175
1176   doFirst {
1177     println("Using projectFile "+projectFile)
1178   }
1179
1180   inputs.dir(project.ext.getdownWebsiteDir)
1181   inputs.file(install4jConf)
1182   inputs.dir(macosJavaVMDir)
1183   inputs.dir(windowsJavaVMDir)
1184   outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
1185 }
1186
1187 clean {
1188   doFirst {
1189     delete install4jConf
1190   }
1191 }
1192
1193 task sourceDist (type: Tar) {
1194
1195   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1196   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1197   // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1198   try {
1199     archiveFileName = outputFileName
1200   } catch (Exception e) {
1201     archiveName = outputFileName
1202   }
1203
1204   compression Compression.GZIP
1205
1206   into project.name
1207
1208   def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
1209   ,".*"
1210   ,"benchmarking/*"
1211   ,"**/.*"
1212   ,"*.class"
1213   ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
1214   ,"*locales/**",
1215   ,"utils/InstallAnywhere"]
1216   def PROCESS_FILES=[   "AUTHORS",
1217   "CITATION",
1218   "FEATURETODO",
1219   "JAVA-11-README",
1220   "FEATURETODO",
1221   "LICENSE",
1222   "**/README",
1223   "RELEASE",
1224   "THIRDPARTYLIBS","TESTNG",
1225   "build.gradle",
1226   "gradle.properties",
1227   "**/*.java",
1228   "**/*.html",
1229   "**/*.xml",
1230   "**/*.gradle",
1231   "**/*.groovy",
1232   "**/*.properties",
1233   "**/*.perl",
1234   "**/*.sh"]
1235
1236   from(jalviewDir) {
1237     exclude (EXCLUDE_FILES)
1238     include (PROCESS_FILES)
1239     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
1240   }
1241   from(jalviewDir) {
1242     exclude (EXCLUDE_FILES)
1243     exclude (PROCESS_FILES)
1244   exclude ("appletlib")
1245   exclude ("**/*locales")
1246   exclude ("*locales/**")
1247   exclude ("utils/InstallAnywhere")
1248
1249     exclude (getdown_files_dir)
1250   exclude (getdown_website_dir)
1251
1252   // exluding these as not using jars as modules yet
1253   exclude ("${j11modDir}/**/*.jar")
1254 }
1255 //  from (jalviewDir) {
1256 //    // explicit includes for stuff that seemed to not get included
1257 //    include(fileTree("test/**/*."))
1258 //    exclude(EXCLUDE_FILES)
1259 //    exclude(PROCESS_FILES)
1260 //  }
1261 }
1262
1263 task helppages  {
1264   dependsOn copyHelp
1265   dependsOn pubhtmlhelp
1266
1267   inputs.dir("${classes}/${helpDir}")
1268   outputs.dir("${helpOutputDir}")
1269 }
1270
1271 def jalviewjsBuildDir
1272 def jalviewjsSiteDir
1273 def jalviewjsTransferSiteDir
1274 task jalviewjsSitePath {
1275   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
1276   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
1277   jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
1278   jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
1279 }
1280
1281 def eclipseWorkspace
1282 task jalviewjsSetEclipseWorkspace {
1283   def propKey = "jalviewjs_eclipse_workspace"
1284   def propVal = null
1285   if (project.hasProperty(propKey)) {
1286     propVal = project.getProperty(propKey)
1287     if (propVal.startsWith("~/")) {
1288       propVal = System.getProperty("user.home") + propVal.substring(1)
1289     }
1290   }
1291   def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
1292   def propsFile = file(propsFileName)
1293   def eclipseWsDir = propVal
1294   def props = new Properties()
1295
1296   if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
1297     def ins = new FileInputStream(propsFileName)
1298     props.load(ins)
1299     ins.close()
1300     if (props.getProperty(propKey, null) != null) {
1301       eclipseWsDir = props.getProperty(propKey)
1302     }
1303   }
1304
1305   def writeProps = false
1306   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
1307     def tempDir = File.createTempDir()
1308     eclipseWsDir = tempDir.getAbsolutePath()
1309     writeProps = true
1310   }
1311   eclipseWorkspace = file(eclipseWsDir)
1312
1313   doFirst {
1314     if (writeProps) {
1315       props.setProperty(propKey, eclipseWsDir)
1316       propsFile.parentFile.mkdirs()
1317       def bytes = new ByteArrayOutputStream()
1318       props.store(bytes, null)
1319       def propertiesString = bytes.toString()
1320       propsFile.text = propertiesString
1321     }
1322
1323     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
1324   }
1325
1326   inputs.property(propKey, eclipseWsDir)
1327   outputs.file(propsFileName)
1328 }
1329
1330
1331 def eclipseBinary
1332 def eclipseVersion
1333 def eclipseDebug = false
1334 def eclipseVersionSuffix = ""
1335 task jalviewjsEclipsePaths {
1336   def eclipseProduct
1337
1338   def eclipseRoot = jalviewjs_eclipse_root
1339   if (eclipseRoot.startsWith("~/")) {
1340     eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
1341   }
1342   if (OperatingSystem.current().isMacOsX()) {
1343     eclipseRoot += "/Eclipse.app"
1344     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
1345     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
1346   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
1347     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1348       eclipseRoot += "/eclipse"
1349     }
1350     eclipseBinary = "${eclipseRoot}/eclipse"
1351     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1352   } else { // linux or unix
1353     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1354       eclipseRoot += "/eclipse"
1355     }
1356     eclipseBinary = "${eclipseRoot}/eclipse"
1357     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1358   }
1359
1360   eclipseVersion = "4.12" // default
1361   def assumedVersion = true
1362   if (file(eclipseProduct).exists()) {
1363     def fis = new FileInputStream(eclipseProduct)
1364     def props = new Properties()
1365     props.load(fis)
1366     eclipseVersion = props.getProperty("version")
1367     fis.close()
1368     assumedVersion = false
1369   }
1370   /*
1371   String[] v = eclipseVersion.split("\\.")
1372   def v0 = Integer.valueOf(v[0])
1373   def v1 = Integer.valueOf(v[1])
1374   if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
1375     eclipseVersionSuffix = "_4.12"
1376   } else {
1377     eclipseVersionSuffix = "_4.13"
1378   }
1379   */
1380
1381
1382   def propKey = "eclipse_debug"
1383   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
1384
1385   doFirst {
1386     if (!assumedVersion) {
1387       println("ECLIPSE VERSION=${eclipseVersion}")
1388     }
1389   }
1390 }
1391
1392 task eclipseSetup {
1393   dependsOn eclipseProject
1394   dependsOn eclipseClasspath
1395   dependsOn eclipseJdt
1396 }
1397
1398 /* using the Copy task below
1399 task OLDjalviewjsEclipseCopyDropins {
1400   dependsOn jalviewjsEclipsePaths
1401   dependsOn jalviewjsCleanEclipse
1402   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
1403   inputFiles += file(jalviewjs_j2s_plugin)
1404   def outputDir = "${buildDir}/jalviewjs
1405
1406   inputs.files inputFiles
1407   inputFiles.each { file ->
1408     outputs.file("${outputDir}/${file.name}")
1409   }
1410
1411   doLast {
1412     inputFiles.each { file ->
1413       copy {
1414         from file
1415         into outputDir
1416       }
1417     }
1418   }
1419 }
1420 */
1421
1422 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
1423 task jalviewjsEclipseCopyDropins(type: Copy) {
1424   dependsOn jalviewjsEclipsePaths
1425
1426   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
1427   inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
1428   def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
1429
1430   from inputFiles
1431   into outputDir
1432 }
1433
1434 // this eclipse -clean doesn't actually work
1435 task jalviewjsCleanEclipse(type: Exec) {
1436   dependsOn eclipseSetup
1437   dependsOn jalviewjsEclipsePaths
1438   dependsOn jalviewjsEclipseCopyDropins
1439
1440   executable(eclipseBinary)
1441   args(["-nosplash", "--launcher.suppressErrors", "-data", eclipseWorkspace.getPath(), "-clean", "-console", "-consoleLog"])
1442   if (eclipseDebug) {
1443     args += "-debug"
1444   }
1445   args += "-l"
1446
1447   def inputString = """exit
1448 y
1449 """
1450   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
1451   standardInput = inputByteStream
1452 }
1453 /* not really working yet
1454 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
1455 */
1456
1457 task jalviewjsUnzipFiles {
1458   dependsOn jalviewjsSitePath
1459
1460   def zipFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_libjs_dir}", include: "*.zip")
1461   zipFiles += "${jalviewDir}/${jalviewjs_swingjs_zip}"
1462
1463   doLast {
1464     zipFiles.each { file_zip ->
1465       copy {
1466         from zipTree(file_zip)
1467         into "${jalviewDir}/${jalviewjsSiteDir}"
1468       }
1469     }
1470   }
1471
1472   inputs.files zipFiles
1473   outputs.dir "${jalviewDir}/${jalviewjsSiteDir}"
1474 }
1475
1476 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
1477   group "JalviewJS"
1478   description "Create the .j2s file from the j2s.* properties"
1479
1480   dependsOn jalviewjsSitePath
1481
1482   outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
1483   def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
1484   def siteDirProperty = "j2s.site.directory"
1485   def setSiteDir = false
1486   j2s_props.each { prop, val ->
1487     if (val != null) {
1488       if (prop == siteDirProperty) {
1489         if (!(val.startsWith('/') || val.startsWith("file://") )) {
1490           val = "${jalviewDir}/${jalviewjsTransferSiteDir}/${val}"
1491         }
1492         setSiteDir = true
1493       }
1494       property(prop,val)
1495     }
1496     if (!setSiteDir) { // default site location, don't override specifically set property
1497       property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteDir}")
1498     }
1499   }
1500   inputs.properties(j2s_props)
1501   outputs.file(outputFile)
1502 }
1503
1504 task jalviewjsEclipseSetup {
1505   dependsOn jalviewjsEclipseCopyDropins
1506   dependsOn jalviewjsSetEclipseWorkspace
1507   dependsOn jalviewjsCreateJ2sSettings
1508 }
1509
1510 task jalviewjsCopyResources (type: Sync) {
1511   dependsOn jalviewjsSitePath
1512   def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
1513   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
1514
1515   from inputFiles
1516   into outputDir
1517   def outputFiles = []
1518   rename { filename ->
1519     outputFiles += "${outputDir}/${filename}"
1520     null
1521   }
1522   preserve {
1523     include "**"
1524   }
1525   outputs.files outputFiles
1526   inputs.files inputFiles
1527 }
1528
1529 task jalviewjsCopySiteResources (type: Sync) {
1530   dependsOn jalviewjsSitePath
1531   def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_site_resource_dir}")
1532   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}"
1533
1534   from inputFiles
1535   into outputDir
1536   def outputFiles = []
1537   rename { filename ->
1538     outputFiles += "${outputDir}/${filename}"
1539     null
1540   }
1541   preserve {
1542     include "**"
1543   }
1544   outputs.files outputFiles
1545   inputs.files inputFiles
1546 }
1547
1548 task jalviewjsProjectImport(type: Exec) {
1549   dependsOn eclipseSetup
1550   dependsOn jalviewjsEclipsePaths
1551   dependsOn jalviewjsEclipseSetup
1552
1553   def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
1554   executable(eclipseBinary)
1555   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
1556   if (eclipseDebug) {
1557     args += "-debug"
1558   }
1559   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
1560
1561   inputs.file("${jalviewDir}/.project")
1562   outputs.upToDateWhen { file(projdir).exists() }
1563 }
1564
1565 task jalviewjsTranspile(type: Exec) {
1566   dependsOn jalviewjsEclipseSetup
1567   dependsOn jalviewjsProjectImport
1568   dependsOn jalviewjsEclipsePaths
1569
1570   executable(eclipseBinary)
1571   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipse_build_arg}", eclipse_project_name ])
1572   if (eclipseDebug) {
1573     args += "-debug"
1574   }
1575   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
1576
1577   def stdout
1578   def stderr
1579   doFirst {
1580     stdout = new ByteArrayOutputStream()
1581     stderr = new ByteArrayOutputStream()
1582
1583     def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
1584     def logOutFile = file(logOutFileName)
1585     logOutFile.createNewFile()
1586     logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
1587 BINARY: ${eclipseBinary}
1588 VERSION: ${eclipseVersion}
1589 WORKSPACE: ${eclipseWorkspace}
1590 DEBUG: ${eclipseDebug}
1591 ----
1592 """
1593     def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
1594     //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
1595     //def logErrFile = file(logFileName)
1596     //logErrFile.createNewFile()
1597     //def logErrFOS = new FileErrputStream(logErrFile, false)
1598     // combine stdout and stderr
1599     def logErrFOS = logOutFOS
1600
1601     if (jalviewjs_j2s_to_console.equals("true")) {
1602       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1603         new org.apache.tools.ant.util.TeeOutputStream(
1604           logOutFOS,
1605           stdout),
1606         standardOutput)
1607       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1608         new org.apache.tools.ant.util.TeeOutputStream(
1609           logErrFOS,
1610           stderr),
1611         errorOutput)
1612     } else {
1613       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1614         logOutFOS,
1615         stdout)
1616       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1617         logErrFOS,
1618         stderr)
1619     }
1620   }
1621
1622   doLast {
1623     if (stdout.toString().contains("Error processing ")) {
1624       // j2s did not complete transpile
1625       throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
1626     }
1627   }
1628
1629   inputs.dir("${jalviewDir}/${sourceDir}")
1630   outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
1631   outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } )
1632 }
1633
1634 task jalviewjsCopyTransferSite(type: Copy) {
1635   dependsOn jalviewjsTranspile
1636   from "${jalviewDir}/${jalviewjsTransferSiteDir}"
1637   into "${jalviewDir}/${jalviewjsSiteDir}"
1638 }
1639
1640 jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
1641 jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
1642 jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
1643
1644 task jalviewjsPrepareSite {
1645   group "JalviewJS"
1646   description "Prepares the website folder including unzipping files and copying resources"
1647   dependsOn jalviewjsSitePath
1648   dependsOn jalviewjsUnzipFiles
1649   dependsOn jalviewjsCopyResources
1650   dependsOn jalviewjsCopySiteResources
1651 }
1652
1653 task jalviewjsBuildSite {
1654   group "JalviewJS"
1655   description "Builds the whole website including transpiled code"
1656   dependsOn jalviewjsCopyTransferSite
1657   dependsOn jalviewjsPrepareSite
1658 }
1659
1660 task cleanJalviewjsSite {
1661   doFirst {
1662     delete "${jalviewDir}/${jalviewjsTransferSiteDir}"
1663     delete "${jalviewDir}/${jalviewjsSiteDir}"
1664   }
1665 }
1666
1667 task jalviewjsSiteTar(type: Tar) {
1668   group "JalviewJS"
1669   description "Creates a tar.gz file for the website"
1670   dependsOn jalviewjsBuildSite
1671   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
1672   try {
1673     archiveFileName = outputFilename
1674   } catch (Exception e) {
1675     archiveName = outputFilename
1676   }
1677
1678   compression Compression.GZIP
1679
1680   from "${jalviewDir}/${jalviewjsSiteDir}"
1681   into jalviewjs_site_dir // this is inside the tar file
1682
1683   inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
1684 }
1685
1686 task jalviewjsServer {
1687   group "JalviewJS"
1688   description "Starts a webserver on localhost to test the website"
1689   dependsOn jalviewjsSitePath
1690   def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
1691   doLast {
1692
1693     SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
1694     def port = Integer.valueOf(jalviewjs_server_port)
1695     def start = port
1696     def running = false
1697     def url
1698     while(port < start+1000 && !running) {
1699       try {
1700         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
1701         def jalviewjsServer = factory.start(doc_root, port)
1702         running = true
1703         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
1704         println("SERVER STARTED with document root ${doc_root}.")
1705         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
1706         println("For debug: "+url+"?j2sdebug")
1707
1708         file(htmlFile).text = """
1709         <p><a href="${url}">Jalview JS Test. &lt;${url}&gt;</a></p>
1710         <p><a href="${url}?j2sdebug">Jalview JS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
1711         """
1712
1713       } catch (Exception e) {
1714         port++;
1715       }
1716     }
1717
1718   }
1719
1720   outputs.file(htmlFile)
1721   outputs.upToDateWhen({false})
1722 }
1723
1724 task cleanJalviewjsAll {
1725   group "JalviewJS"
1726   description "Delete all configuration and build artifacts to do with JalviewJS build"
1727   dependsOn cleanJalviewjsSite
1728   dependsOn jalviewjsEclipsePaths
1729
1730   doFirst {
1731     delete "${jalviewDir}/${jalviewjsBuildDir}"
1732     delete "${jalviewDir}/${eclipse_bin_dir}"
1733     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
1734       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
1735     }
1736     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
1737   }
1738
1739   outputs.upToDateWhen( { false } )
1740 }
1741
1742 task jalviewjs {
1743   group "JalviewJS"
1744   description "Build the site"
1745   dependsOn jalviewjsBuildSite
1746 }
1747
1748
1749 task jalviewjsIDECopyTransferSite(type: Copy) {
1750   from "${jalviewDir}/${jalviewjsTransferSiteDir}"
1751   into "${jalviewDir}/${jalviewjsSiteDir}"
1752 }
1753
1754 task jalviewjsIDEj2s {
1755   group "JalviewJS in Eclipse"
1756   description "Creates the .j2s file"
1757   dependsOn jalviewjsCreateJ2sSettings
1758 }
1759
1760 task jalviewjsIDEBuildSite {
1761   group "JalviewJS in Eclipse"
1762   description "Copies the Eclipse transpiled site and unzips supporting zipfiles"
1763   dependsOn jalviewjsIDECopyTransferSite
1764   dependsOn jalviewjsPrepareSite
1765 }
1766
1767 task jalviewjsIDESiteClean {
1768   group "JalviewJS in Eclipse"
1769   description "Deletes the Eclipse transpiled site"
1770   dependsOn cleanJalviewjsSite
1771 }
1772
1773 task jalviewjsIDEServer {
1774   group "JalviewJS in Eclipse"
1775   description "Starts a webserver on localhost to test the website"
1776   dependsOn jalviewjsServer
1777 }
1778