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 repositories {
  23   jcenter()
  24   mavenCentral()
  25   mavenLocal()
  26   flatDir {
  27     dirs gradlePluginsDir
  28   }
  29 }
  30
  31 dependencies {
  32   compile 'org.apache.commons:commons-compress:1.18'
  33 }
  34
  35 mainClassName = launcherClass
  36 def cloverInstrDir = file("$buildDir/$cloverSourcesInstrDir")
  37 def classes = "$jalviewDir/$classesDir"
  38
  39 if (clover.equals("true")) {
  40   use_clover = true
  41   classes = "$buildDir/$cloverClassesDir"
  42 } else {
  43   use_clover = false
  44   classes = "$jalviewDir/$classesDir"
  45 }
  46
  47 // configure classpath/args for j8/j11 compilation
  48
  49 def jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
  50 def libDir
  51 def libDistDir
  52 def compile_source_compatibility
  53 def compile_target_compatibility
  54
  55 ext {
  56   getdownWebsiteDir = "${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}"
  57   getdownDir = ""
  58   reportRsyncCmd = false
  59   buildDist = true
  60   buildProperties = buildPropertiesFile
  61   getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher}"
  62   switch (CHANNEL) {
  63
  64     case "BUILD":
  65     // TODO: get bamboo build artifact URL for getdown artifacts
  66     getdown_channel_base = bamboo_channelbase
  67     getdown_channel_name = "${bamboo_planKey}/${JAVA_VERSION}"
  68     getdown_app_base = "${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}"
  69     getdown_app_dir = getdown_app_dir_alt
  70     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  71     break
  72
  73     case "RELEASE":
  74     getdown_channel_name = CHANNEL.toLowerCase()
  75     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
  76     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
  77     getdown_app_dir = getdown_app_dir_release
  78     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
  79     reportRsyncCommand = true
  80     break
  81
  82     case "ARCHIVE":
  83     getdown_channel_name = CHANNEL.toLowerCase()+"/${JALVIEW_VERSION}"
  84     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
  85     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
  86     getdown_app_dir = getdown_app_dir_alt
  87     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
  88       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
  89       exit
  90     } else {
  91       packageDir = "${ARCHIVEDIR}/${packageDir}"
  92       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
  93       buildDist = false
  94     }
  95     reportRsyncCommand = true
  96     break
  97
  98     case "ARCHIVELOCAL":
  99     getdown_channel_name = "archive/${JALVIEW_VERSION}"
 100     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 101     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 102     getdown_app_dir = getdown_app_dir_alt
 103     if (!file("${ARCHIVEDIR}/${packageDir}").exists()) {
 104       print "Must provide an ARCHIVEDIR value to produce an archive distribution"
 105       exit
 106     } else {
 107       packageDir = "${ARCHIVEDIR}/${packageDir}"
 108       buildProperties = "${ARCHIVEDIR}/${classesDir}/${buildPropertiesFile}"
 109       buildDist = false
 110     }
 111     reportRsyncCommand = true
 112     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 113     break
 114
 115     case "DEVELOP":
 116     getdown_channel_name = CHANNEL.toLowerCase()
 117     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 118     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 119     getdown_app_dir = getdown_app_dir_alt
 120     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 121     reportRsyncCommand = true
 122     break
 123
 124     case "TEST-RELEASE":
 125     getdown_channel_name = CHANNEL.toLowerCase()
 126     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 127     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 128     getdown_app_dir = getdown_app_dir_alt
 129     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 130     reportRsyncCommand = true
 131     break
 132
 133     case ~/^SCRATCH(|-[-\w]*)$/:
 134     getdown_channel_name = CHANNEL
 135     getdownDir = "${getdown_channel_name}/${JAVA_VERSION}"
 136     getdown_app_base = "${getdown_channel_base}/${getdownDir}"
 137     getdown_app_dir = getdown_app_dir_alt
 138     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 139     reportRsyncCommand = true
 140     break
 141
 142     case "LOCAL":
 143     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
 144     getdown_app_dir = getdown_app_dir_alt
 145     buildProperties = "${jalviewDir}/${classesDir}/${buildPropertiesFile}"
 146     getdownLauncher = "${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}"
 147     break
 148
 149     default: // something wrong specified
 150     print("CHANNEL must be one of BUILD, RELEASE, ARCHIVE, DEVELOP, TEST-RELEASE, SCRATCH-..., LOCAL [default]")
 151     exit
 152     break
 153
 154   }
 155
 156   println("Using a ${CHANNEL} profile. appbase=${getdown_app_base}")
 157   getdownAppDir = "${getdownWebsiteDir}/${getdown_app_dir}"
 158   //getdownJ11libDir = "${getdownWebsiteDir}/${getdown_j11lib_dir}"
 159   getdownResourceDir = "${getdownWebsiteDir}/${getdown_resource_dir}"
 160   getdownInstallDir = "${getdownWebsiteDir}/${getdown_install_dir}"
 161   getdownFilesDir = "${jalviewDir}/${getdown_files_dir}/${JAVA_VERSION}/"
 162   getdownFilesInstallDir = "${getdownFilesDir}/${getdown_install_dir}"
 163   /* compile without modules -- using classpath libraries
 164   modules_compileClasspath = fileTree(dir: "${jalviewDir}/${j11modDir}", include: ["*.jar"])
 165   modules_runtimeClasspath = modules_compileClasspath
 166   */
 167   gitHash = ""
 168   gitBranch = ""
 169
 170 }
 171
 172 def JAVA_INTEGER_VERSION
 173 def additional_compiler_args = []
 174 // these are getdown.txt properties defined dependent on the JAVA_VERSION
 175 def getdown_alt_java_min_version
 176 def getdown_alt_java_max_version
 177 // this property is assigned below and expanded to multiple lines in the getdown task
 178 def getdown_alt_multi_java_location
 179 // this property is for the Java library used in eclipse
 180 def eclipse_java_runtime_name
 181 if (JAVA_VERSION.equals("1.8")) {
 182   JAVA_INTEGER_VERSION = "8"
 183   //libDir = j8libDir
 184   libDir = j11libDir
 185   libDistDir = j8libDir
 186   compile_source_compatibility = 1.8
 187   compile_target_compatibility = 1.8
 188   getdown_alt_java_min_version = getdown_alt_java8_min_version
 189   getdown_alt_java_max_version = getdown_alt_java8_max_version
 190   getdown_alt_multi_java_location = getdown_alt_java8_txt_multi_java_location
 191   eclipse_java_runtime_name = "JavaSE-1.8"
 192 } else if (JAVA_VERSION.equals("11")) {
 193   JAVA_INTEGER_VERSION = "11"
 194   libDir = j11libDir
 195   libDistDir = j11libDir
 196   compile_source_compatibility = 11
 197   compile_target_compatibility = 11
 198   getdown_alt_java_min_version = getdown_alt_java11_min_version
 199   getdown_alt_java_max_version = getdown_alt_java11_max_version
 200   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 201   eclipse_java_runtime_name = "JavaSE-11"
 202   /* compile without modules -- using classpath libraries
 203   additional_compiler_args += [
 204   '--module-path', ext.modules_compileClasspath.asPath,
 205   '--add-modules', j11modules
 206   ]
 207   */
 208 } else if (JAVA_VERSION.equals("12") || JAVA_VERSION.equals("13")) {
 209   JAVA_INTEGER_VERSION = JAVA_VERSION
 210   libDir = j11libDir
 211   libDistDir = j11libDir
 212   compile_source_compatibility = JAVA_VERSION
 213   compile_target_compatibility = JAVA_VERSION
 214   getdown_alt_java_min_version = getdown_alt_java11_min_version
 215   getdown_alt_java_max_version = getdown_alt_java11_max_version
 216   getdown_alt_multi_java_location = getdown_alt_java11_txt_multi_java_location
 217   eclipse_java_runtime_name = "JavaSE-11"
 218   /* compile without modules -- using classpath libraries
 219   additional_compiler_args += [
 220   '--module-path', ext.modules_compileClasspath.asPath,
 221   '--add-modules', j11modules
 222   ]
 223   */
 224 } else {
 225   throw new GradleException("JAVA_VERSION=${JAVA_VERSION} not currently supported by Jalview")
 226 }
 227
 228 sourceSets {
 229
 230   main {
 231     java {
 232       srcDirs "${jalviewDir}/${sourceDir}"
 233       outputDir = file("${classes}")
 234     }
 235
 236     resources {
 237       srcDirs "${jalviewDir}/${resourceDir}"
 238     }
 239
 240     jar.destinationDir = file("${jalviewDir}/${packageDir}")
 241
 242     compileClasspath = files(sourceSets.main.java.outputDir)
 243     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 244
 245     runtimeClasspath = compileClasspath
 246   }
 247
 248   clover {
 249     java {
 250       srcDirs = [ cloverInstrDir ]
 251       outputDir = file("${buildDir}/${cloverClassesDir}")
 252     }
 253
 254     resources {
 255       srcDirs = sourceSets.main.resources.srcDirs
 256     }
 257     compileClasspath = configurations.cloverRuntime + files( sourceSets.clover.java.outputDir )
 258     compileClasspath += files(sourceSets.main.java.outputDir)
 259     compileClasspath += sourceSets.main.compileClasspath
 260     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["**/*.jar"])
 261     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 262
 263     runtimeClasspath = compileClasspath
 264   }
 265
 266   test {
 267     java {
 268       srcDirs "${jalviewDir}/${testSourceDir}"
 269       outputDir = file("${jalviewDir}/${testOutputDir}")
 270     }
 271
 272     resources {
 273       srcDirs = sourceSets.main.resources.srcDirs
 274     }
 275
 276     compileClasspath = files( sourceSets.test.java.outputDir )
 277
 278     if (use_clover) {
 279       compileClasspath += sourceSets.clover.compileClasspath
 280     } else {
 281       compileClasspath += files(sourceSets.main.java.outputDir)
 282     }
 283
 284     compileClasspath += fileTree(dir: "${jalviewDir}/${libDir}", include: ["*.jar"])
 285     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testnglibs", include: ["**/*.jar"])
 286     compileClasspath += fileTree(dir: "${jalviewDir}/${utilsDir}/testlibs", include: ["**/*.jar"])
 287
 288     runtimeClasspath = compileClasspath
 289   }
 290 }
 291
 292 // clover bits
 293 dependencies {
 294   if (use_clover) {
 295     cloverCompile 'org.openclover:clover:4.3.1'
 296     testCompile 'org.openclover:clover:4.3.1'
 297   }
 298 }
 299
 300 configurations {
 301   cloverRuntime
 302   cloverRuntime.extendsFrom cloverCompile
 303 }
 304
 305 eclipse {
 306   project {
 307     name = eclipse_project_name
 308
 309     natures 'org.eclipse.jdt.core.javanature',
 310     'org.eclipse.jdt.groovy.core.groovyNature',
 311     'org.eclipse.buildship.core.gradleprojectnature'
 312
 313     buildCommand 'org.eclipse.jdt.core.javabuilder'
 314     buildCommand 'org.eclipse.buildship.core.gradleprojectbuilder'
 315   }
 316
 317   classpath {
 318     //defaultOutputDir = sourceSets.main.java.outputDir
 319     def removeThese = []
 320     configurations.each{
 321       if (it.isCanBeResolved()) {
 322         removeThese += it
 323       }
 324     }
 325
 326     minusConfigurations += removeThese
 327     plusConfigurations = [ ]
 328     file {
 329
 330       whenMerged { cp ->
 331         def removeTheseToo = []
 332         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
 333         cp.entries.each { entry ->
 334           if (entry.kind == 'src') {
 335             if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
 336               removeTheseToo += entry
 337             } else {
 338               alreadyAddedSrcPath.putAt(entry.path, true)
 339             }
 340           }
 341         }
 342         cp.entries.removeAll(removeTheseToo)
 343
 344         if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
 345           cp.entries += new Output("${eclipse_bin_dir}/main")
 346         }
 347         if (file(helpParentDir).isDirectory()) {
 348           cp.entries += new Library(fileReference(helpParentDir))
 349         }
 350         if (file(resourceDir).isDirectory()) {
 351           cp.entries += new Library(fileReference(resourceDir))
 352         }
 353
 354         HashMap<String, Boolean> alreadyAddedLibPath = new HashMap<>();
 355
 356         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 357           //don't want to add outputDir as eclipse is using its own output dir in bin/main
 358           if (it.isDirectory() || ! it.exists()) {
 359             // don't add dirs to classpath
 360             return
 361           }
 362           def itPath = it.toString()
 363           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 364             // make relative path
 365             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 366           }
 367           if (alreadyAddedLibPath.get(itPath)) {
 368             //println("Not adding duplicate entry "+itPath)
 369           } else {
 370             //println("Adding entry "+itPath)
 371             cp.entries += new Library(fileReference(itPath))
 372             alreadyAddedLibPath.put(itPath, true)
 373           }
 374         }
 375
 376         //fileTree(dir: "$jalviewDir/$utilsDir", include: ["test*/*.jar"]).each {
 377         sourceSets.test.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
 378           //no longer want to add outputDir as eclipse is using its own output dir in bin/main
 379           if (it.isDirectory() || ! it.exists()) {
 380             // don't add dirs to classpath
 381             return false // groovy "break" in .each closure
 382           }
 383           def itPath = it.toString()
 384           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
 385             itPath = itPath.substring(jalviewDirAbsolutePath.length()+1)
 386           }
 387           if (alreadyAddedLibPath.get(itPath)) {
 388             // don't duplicate
 389           } else {
 390             def lib = new Library(fileReference(itPath))
 391             lib.entryAttributes["test"] = "true"
 392             cp.entries += lib
 393             alreadyAddedLibPath.put(itPath, true)
 394           }
 395         }
 396
 397       } // whenMerged
 398
 399     } // file
 400
 401     containers 'org.eclipse.buildship.core.gradleclasspathcontainer'
 402
 403   } // classpath
 404
 405   jdt {
 406     // for the IDE, use java 11 compatibility
 407     sourceCompatibility = compile_source_compatibility
 408     targetCompatibility = compile_target_compatibility
 409     javaRuntimeName = eclipse_java_runtime_name
 410
 411     // add in jalview project specific properties/preferences into eclipse core preferences
 412     file {
 413       withProperties { props ->
 414         def jalview_prefs = new Properties()
 415         def ins = new FileInputStream("${jalviewDirAbsolutePath}/${eclipse_extra_jdt_prefs_file}")
 416         jalview_prefs.load(ins)
 417         ins.close()
 418         jalview_prefs.forEach { t, v ->
 419           if (props.getAt(t) == null) {
 420             props.putAt(t, v)
 421           }
 422         }
 423       }
 424     }
 425
 426   } // jdt
 427
 428 }
 429
 430 task cloverInstr() {
 431   // only instrument source, we build test classes as normal
 432   inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
 433   outputs.dir cloverInstrDir
 434
 435   doFirst {
 436     delete cloverInstrDir
 437     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 438     "-d", "${buildDir}/${cloverSourcesInstrDir}"]
 439     argsList.addAll(inputs.files.files.collect({ file ->
 440       file.absolutePath
 441     }))
 442     String[] args = argsList.toArray()
 443     println("About to instrument "+args.length +" files")
 444     com.atlassian.clover.CloverInstr.mainImpl(args)
 445   }
 446 }
 447
 448
 449 task cloverReport {
 450   group = "Verification"
 451     description = "Createst the Clover report"
 452     inputs.dir "${buildDir}/clover"
 453     outputs.dir "${reportsDir}/clover"
 454     onlyIf {
 455       file("${buildDir}/clover/clover.db").exists()
 456     }
 457   doFirst {
 458     def argsList = ["--initstring", "${buildDir}/clover/clover.db",
 459     "-o", "${reportsDir}/clover"]
 460     String[] args = argsList.toArray()
 461     com.atlassian.clover.reporters.html.HtmlReporter.runReport(args)
 462
 463     // and generate ${reportsDir}/clover/clover.xml
 464     args = ["--initstring", "${buildDir}/clover/clover.db",
 465     "-o", "${reportsDir}/clover/clover.xml"].toArray()
 466     com.atlassian.clover.reporters.xml.XMLReporter.runReport(args)
 467   }
 468 }
 469
 470 // end clover bits
 471
 472
 473 compileJava {
 474
 475   doFirst {
 476     sourceCompatibility = compile_source_compatibility
 477     targetCompatibility = compile_target_compatibility
 478     options.compilerArgs = additional_compiler_args
 479     print ("Setting target compatibility to "+targetCompatibility+"\n")
 480   }
 481
 482 }
 483
 484 compileTestJava {
 485   if (use_clover) {
 486     dependsOn compileCloverJava
 487     classpath += configurations.cloverRuntime
 488   } else {
 489     classpath += sourceSets.main.runtimeClasspath
 490   }
 491   doFirst {
 492     sourceCompatibility = compile_source_compatibility
 493     targetCompatibility = compile_target_compatibility
 494     options.compilerArgs = additional_compiler_args
 495     print ("Setting target compatibility to "+targetCompatibility+"\n")
 496   }
 497 }
 498
 499
 500 compileCloverJava {
 501
 502   doFirst {
 503     sourceCompatibility = compile_source_compatibility
 504     targetCompatibility = compile_target_compatibility
 505     options.compilerArgs += additional_compiler_args
 506     print ("Setting target compatibility to "+targetCompatibility+"\n")
 507   }
 508   classpath += configurations.cloverRuntime
 509 }
 510
 511 clean {
 512   doFirst {
 513     delete sourceSets.main.java.outputDir
 514   }
 515 }
 516
 517 cleanTest {
 518   doFirst {
 519     delete sourceSets.test.java.outputDir
 520     delete cloverInstrDir
 521   }
 522 }
 523
 524 // format is a string like date.format("dd MMMM yyyy")
 525 def getDate(format) {
 526   def date = new Date()
 527   return date.format(format)
 528 }
 529
 530 task setGitVals {
 531   def hashStdOut = new ByteArrayOutputStream()
 532   exec {
 533     commandLine "git", "rev-parse", "--short", "HEAD"
 534     standardOutput = hashStdOut
 535     ignoreExitValue true
 536   }
 537
 538   def branchStdOut = new ByteArrayOutputStream()
 539   exec {
 540     commandLine "git", "rev-parse", "--abbrev-ref", "HEAD"
 541     standardOutput = branchStdOut
 542     ignoreExitValue true
 543   }
 544
 545   project.ext.gitHash = hashStdOut.toString().trim()
 546   project.ext.gitBranch = branchStdOut.toString().trim()
 547
 548   outputs.upToDateWhen { false }
 549 }
 550
 551 task createBuildProperties(type: WriteProperties) {
 552   dependsOn setGitVals
 553   inputs.dir("${jalviewDir}/${sourceDir}")
 554   inputs.dir("${classes}")
 555   inputs.dir("${jalviewDir}/${resourceDir}")
 556   outputFile (buildProperties)
 557   // taking time specific comment out to allow better incremental builds
 558   comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd HH:mm:ss")
 559   //comment "--Jalview Build Details--\n"+getDate("yyyy-MM-dd")
 560   property "BUILD_DATE", getDate("HH:mm:ss dd MMMM yyyy")
 561   property "VERSION", JALVIEW_VERSION
 562   property "INSTALLATION", INSTALLATION+" git-commit:"+project.ext.gitHash+" ["+project.ext.gitBranch+"]"
 563   outputs.file(outputFile)
 564 }
 565
 566 def buildingHTML = "${jalviewDir}/${docDir}/building.html"
 567 task cleanBuildingHTML(type: Delete) {
 568   doFirst {
 569     delete buildingHTML
 570   }
 571 }
 572
 573 task convertBuildingMD(type: Exec) {
 574   dependsOn cleanBuildingHTML
 575   def buildingMD = "${jalviewDir}/${docDir}/building.md"
 576   def css = "${jalviewDir}/${docDir}/github.css"
 577
 578   def pandoc = null
 579   pandoc_exec.split(",").each {
 580     if (file(it.trim()).exists()) {
 581       pandoc = it.trim()
 582       return true
 583     }
 584   }
 585
 586   def hostname = "hostname".execute().text.trim()
 587   if ((pandoc == null || ! file(pandoc).exists()) && hostname.equals("jv-bamboo")) {
 588     pandoc = System.getProperty("user.home")+"/buildtools/pandoc/bin/pandoc"
 589   }
 590
 591   doFirst {
 592     if (pandoc != null && file(pandoc).exists()) {
 593         commandLine pandoc, '-s', '-o', buildingHTML, '--metadata', 'pagetitle="Building Jalview from Source"', '--toc', '-H', css, buildingMD
 594     } else {
 595         println("Cannot find pandoc. Skipping convert building.md to HTML")
 596         throw new StopExecutionException()
 597     }
 598   }
 599
 600   ignoreExitValue true
 601
 602   inputs.file(buildingMD)
 603   inputs.file(css)
 604   outputs.file(buildingHTML)
 605 }
 606
 607 clean {
 608   doFirst {
 609     delete buildingHTML
 610   }
 611 }
 612
 613 task syncDocs(type: Sync) {
 614   dependsOn convertBuildingMD
 615   def syncDir = "${classes}/${docDir}"
 616   from fileTree("${jalviewDir}/${docDir}")
 617   into syncDir
 618
 619 }
 620
 621 def helpFile = "${classes}/${helpDir}/help.jhm"
 622
 623 task copyHelp(type: Copy) {
 624   def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
 625   def outputDir = "${classes}/${helpDir}"
 626   from(inputDir) {
 627     exclude '**/*.gif'
 628       exclude '**/*.jpg'
 629       exclude '**/*.png'
 630       filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
 631   }
 632   from(inputDir) {
 633     include '**/*.gif'
 634       include '**/*.jpg'
 635       include '**/*.png'
 636   }
 637   into outputDir
 638
 639   inputs.dir(inputDir)
 640   outputs.files(helpFile)
 641   outputs.dir(outputDir)
 642 }
 643
 644 task syncLib(type: Sync) {
 645   def syncDir = "${classes}/${libDistDir}"
 646   from fileTree("${jalviewDir}/${libDistDir}")
 647   into syncDir
 648 }
 649
 650 task syncResources(type: Sync) {
 651   from "${jalviewDir}/${resourceDir}"
 652   include "**/*.*"
 653   exclude "install4j"
 654   into "${classes}"
 655   preserve {
 656     include "**"
 657   }
 658 }
 659
 660 task prepare {
 661   dependsOn syncResources
 662   dependsOn syncDocs
 663   dependsOn copyHelp
 664 }
 665
 666
 667 //testReportDirName = "test-reports" // note that test workingDir will be $jalviewDir
 668 test {
 669   dependsOn prepare
 670   dependsOn compileJava
 671   if (use_clover) {
 672     dependsOn cloverInstr
 673   }
 674
 675   if (use_clover) {
 676     print("Running tests " + (use_clover?"WITH":"WITHOUT") + " clover [clover="+use_clover+"]\n")
 677   }
 678
 679   useTestNG() {
 680     includeGroups testngGroups
 681     preserveOrder true
 682     useDefaultListeners=true
 683   }
 684
 685   workingDir = jalviewDir
 686   //systemProperties 'clover.jar' System.properties.clover.jar
 687   sourceCompatibility = compile_source_compatibility
 688   targetCompatibility = compile_target_compatibility
 689   jvmArgs += additional_compiler_args
 690   print ("Setting target compatibility to "+targetCompatibility+"\n")
 691 }
 692
 693 task buildIndices(type: JavaExec) {
 694   dependsOn copyHelp
 695   classpath = sourceSets.main.compileClasspath
 696   main = "com.sun.java.help.search.Indexer"
 697   workingDir = "${classes}/${helpDir}"
 698   def argDir = "html"
 699   args = [ argDir ]
 700   inputs.dir("${workingDir}/${argDir}")
 701
 702   outputs.dir("${classes}/doc")
 703   outputs.dir("${classes}/help")
 704   outputs.file("${workingDir}/JavaHelpSearch/DOCS")
 705   outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
 706   outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
 707   outputs.file("${workingDir}/JavaHelpSearch/POSITIONS")
 708   outputs.file("${workingDir}/JavaHelpSearch/SCHEMA")
 709   outputs.file("${workingDir}/JavaHelpSearch/TMAP")
 710 }
 711
 712 task compileLinkCheck(type: JavaCompile) {
 713   options.fork = true
 714   classpath = files("${jalviewDir}/${utilsDir}")
 715   destinationDir = file("${jalviewDir}/${utilsDir}")
 716   source = fileTree(dir: "${jalviewDir}/${utilsDir}", include: ["HelpLinksChecker.java", "BufferedLineReader.java"])
 717
 718   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 719   inputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.java")
 720   outputs.file("${jalviewDir}/${utilsDir}/HelpLinksChecker.class")
 721   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 722 }
 723
 724 def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch")
 725 task linkCheck(type: JavaExec) {
 726   dependsOn prepare, compileLinkCheck
 727   classpath = files("${jalviewDir}/${utilsDir}")
 728   main = "HelpLinksChecker"
 729   workingDir = jalviewDir
 730   def help = "${classes}/${helpDir}"
 731   args = [ "${classes}/${helpDir}", "-nointernet" ]
 732
 733   doLast {
 734     helplinkscheckertouchfile.createNewFile()
 735   }
 736
 737   inputs.dir("${classes}/${helpDir}")
 738   outputs.file(helplinkscheckertouchfile)
 739 }
 740
 741 // import the pubhtmlhelp target
 742 ant.properties.basedir = "${jalviewDir}"
 743 ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
 744 ant.importBuild "${utilsDir}/publishHelp.xml"
 745
 746
 747 task cleanPackageDir(type: Delete) {
 748   doFirst {
 749     delete fileTree(dir: "${jalviewDir}/${packageDir}", include: "*.jar")
 750   }
 751 }
 752
 753 jar {
 754   dependsOn linkCheck
 755   dependsOn buildIndices
 756   dependsOn createBuildProperties
 757
 758   manifest {
 759     attributes "Main-Class": mainClass,
 760     "Permissions": "all-permissions",
 761     "Application-Name": "Jalview Desktop",
 762     "Codebase": application_codebase
 763   }
 764
 765   destinationDir = file("${jalviewDir}/${packageDir}")
 766   archiveName = rootProject.name+".jar"
 767
 768   exclude "cache*/**"
 769   exclude "*.jar"
 770   exclude "*.jar.*"
 771   exclude "**/*.jar"
 772   exclude "**/*.jar.*"
 773
 774   inputs.dir("${classes}")
 775   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 776 }
 777
 778 task copyJars(type: Copy) {
 779   from fileTree(dir: "${classes}", include: "**/*.jar").files
 780   into "${jalviewDir}/${packageDir}"
 781 }
 782
 783 // doing a Sync instead of Copy as Copy doesn't deal with "outputs" very well
 784 task syncJars(type: Sync) {
 785   from fileTree(dir: "${jalviewDir}/${libDistDir}", include: "**/*.jar").files
 786   into "${jalviewDir}/${packageDir}"
 787   preserve {
 788     include jar.archiveName
 789   }
 790 }
 791
 792 task makeDist {
 793   group = "build"
 794   description = "Put all required libraries in dist"
 795   // order of "cleanPackageDir", "copyJars", "jar" important!
 796   jar.mustRunAfter cleanPackageDir
 797   syncJars.mustRunAfter cleanPackageDir
 798   dependsOn cleanPackageDir
 799   dependsOn syncJars
 800   dependsOn jar
 801   outputs.dir("${jalviewDir}/${packageDir}")
 802 }
 803
 804 task cleanDist {
 805   dependsOn cleanPackageDir
 806   dependsOn cleanTest
 807   dependsOn clean
 808 }
 809
 810 shadowJar {
 811   group = "distribution"
 812   if (buildDist) {
 813     dependsOn makeDist
 814   }
 815   from ("${jalviewDir}/${libDistDir}") {
 816     include("*.jar")
 817   }
 818   manifest {
 819     attributes 'Implementation-Version': JALVIEW_VERSION
 820   }
 821   mainClassName = shadowJarMainClass
 822   mergeServiceFiles()
 823   classifier = "all-"+JALVIEW_VERSION+"-j"+JAVA_VERSION
 824   minimize()
 825 }
 826
 827 task getdownWebsite() {
 828   group = "distribution"
 829   description = "Create the getdown minimal app folder, and website folder for this version of jalview. Website folder also used for offline app installer"
 830   if (buildDist) {
 831     dependsOn makeDist
 832   }
 833
 834   def getdownWebsiteResourceFilenames = []
 835   def getdownTextString = ""
 836   def getdownResourceDir = project.ext.getdownResourceDir
 837   def getdownAppDir = project.ext.getdownAppDir
 838   def getdownResourceFilenames = []
 839
 840   doFirst {
 841     // clean the getdown website and files dir before creating getdown folders
 842     delete project.ext.getdownWebsiteDir
 843     delete project.ext.getdownFilesDir
 844
 845     copy {
 846       from buildProperties
 847       rename(buildPropertiesFile, getdown_build_properties)
 848       into project.ext.getdownAppDir
 849     }
 850     getdownWebsiteResourceFilenames += "${getdown_app_dir}/${getdown_build_properties}"
 851
 852     // go through properties looking for getdown_txt_...
 853     def props = project.properties.sort { it.key }
 854         if (getdown_alt_java_min_version.length() > 0) {
 855                 props.put("getdown_txt_java_min_version", getdown_alt_java_min_version)
 856         }
 857         if (getdown_alt_java_max_version.length() > 0) {
 858                 props.put("getdown_txt_java_max_version", getdown_alt_java_max_version)
 859         }
 860         props.put("getdown_txt_multi_java_location", getdown_alt_multi_java_location)
 861
 862     props.put("getdown_txt_appbase", getdown_app_base)
 863     props.each{ prop, val ->
 864       if (prop.startsWith("getdown_txt_") && val != null) {
 865         if (prop.startsWith("getdown_txt_multi_")) {
 866           def key = prop.substring(18)
 867           val.split(",").each{ v ->
 868             def line = "${key} = ${v}\n"
 869             getdownTextString += line
 870           }
 871         } else {
 872           // file values rationalised
 873           if (val.indexOf('/') > -1 || prop.startsWith("getdown_txt_resource")) {
 874             def r = null
 875             if (val.indexOf('/') == 0) {
 876               // absolute path
 877               r = file(val)
 878             } else if (val.indexOf('/') > 0) {
 879               // relative path (relative to jalviewDir)
 880               r = file( "${jalviewDir}/${val}" )
 881             }
 882             if (r.exists()) {
 883               val = "${getdown_resource_dir}/" + r.getName()
 884               getdownWebsiteResourceFilenames += val
 885               getdownResourceFilenames += r.getPath()
 886             }
 887           }
 888           if (! prop.startsWith("getdown_txt_resource")) {
 889             def line = prop.substring(12) + " = ${val}\n"
 890             getdownTextString += line
 891           }
 892         }
 893       }
 894     }
 895
 896     getdownWebsiteResourceFilenames.each{ filename ->
 897       getdownTextString += "resource = ${filename}\n"
 898     }
 899     getdownResourceFilenames.each{ filename ->
 900       copy {
 901         from filename
 902         into project.ext.getdownResourceDir
 903       }
 904     }
 905
 906     def codeFiles = []
 907     fileTree(file(packageDir)).each{ f ->
 908       if (f.isDirectory()) {
 909         def files = fileTree(dir: f, include: ["*"]).getFiles()
 910         codeFiles += files
 911       } else if (f.exists()) {
 912         codeFiles += f
 913       }
 914     }
 915     codeFiles.sort().each{f ->
 916       def name = f.getName()
 917       def line = "code = ${getdown_app_dir}/${name}\n"
 918       getdownTextString += line
 919       copy {
 920         from f.getPath()
 921         into project.ext.getdownAppDir
 922       }
 923     }
 924
 925     // NOT USING MODULES YET, EVERYTHING SHOULD BE IN dist
 926     /*
 927     if (JAVA_VERSION.equals("11")) {
 928     def j11libFiles = fileTree(dir: "${jalviewDir}/${j11libDir}", include: ["*.jar"]).getFiles()
 929     j11libFiles.sort().each{f ->
 930     def name = f.getName()
 931     def line = "code = ${getdown_j11lib_dir}/${name}\n"
 932     getdownTextString += line
 933     copy {
 934     from f.getPath()
 935     into project.ext.getdownJ11libDir
 936     }
 937     }
 938     }
 939      */
 940
 941     // 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.
 942     //getdownTextString += "class = " + file(getdownLauncher).getName() + "\n"
 943     getdownTextString += "resource = ${getdown_launcher_new}\n"
 944     getdownTextString += "class = ${mainClass}\n"
 945
 946     def getdown_txt = file("${project.ext.getdownWebsiteDir}/getdown.txt")
 947     getdown_txt.write(getdownTextString)
 948
 949     def launch_jvl = file("${project.ext.getdownWebsiteDir}/${getdown_launch_jvl}")
 950     launch_jvl.write("appbase="+props.get("getdown_txt_appbase"))
 951
 952     copy {
 953       from getdownLauncher
 954       rename(file(getdownLauncher).getName(), getdown_launcher_new)
 955       into project.ext.getdownWebsiteDir
 956     }
 957
 958     copy {
 959       from getdownLauncher
 960       if (file(getdownLauncher).getName() != getdown_launcher) {
 961         rename(file(getdownLauncher).getName(), getdown_launcher)
 962       }
 963       into project.ext.getdownWebsiteDir
 964     }
 965
 966     if (! (CHANNEL.startsWith("ARCHIVE") || CHANNEL.startsWith("DEVELOP"))) {
 967       copy {
 968         from getdown_txt
 969         from getdownLauncher
 970         from "${getdownWebsiteDir}/${getdown_build_properties}"
 971         if (file(getdownLauncher).getName() != getdown_launcher) {
 972           rename(file(getdownLauncher).getName(), getdown_launcher)
 973         }
 974         into getdownInstallDir
 975       }
 976
 977       copy {
 978         from getdownInstallDir
 979         into getdownFilesInstallDir
 980       }
 981     }
 982
 983     copy {
 984       from getdown_txt
 985       from launch_jvl
 986       from getdownLauncher
 987       from "${getdownWebsiteDir}/${getdown_build_properties}"
 988       if (file(getdownLauncher).getName() != getdown_launcher) {
 989         rename(file(getdownLauncher).getName(), getdown_launcher)
 990       }
 991       into getdownFilesDir
 992     }
 993
 994     copy {
 995           from getdownResourceDir
 996       into "${project.ext.getdownFilesDir}/${getdown_resource_dir}"
 997     }
 998   }
 999
1000   if (buildDist) {
1001     inputs.dir("${jalviewDir}/${packageDir}")
1002   }
1003   outputs.dir(project.ext.getdownWebsiteDir)
1004   outputs.dir(project.ext.getdownFilesDir)
1005 }
1006
1007 task getdownDigest(type: JavaExec) {
1008   group = "distribution"
1009   description = "Digest the getdown website folder"
1010   dependsOn getdownWebsite
1011   doFirst {
1012     classpath = files("${getdownWebsiteDir}/${getdown_launcher}")
1013   }
1014   main = "com.threerings.getdown.tools.Digester"
1015   args project.ext.getdownWebsiteDir
1016   inputs.dir(project.ext.getdownWebsiteDir)
1017   outputs.file("${project.ext.getdownWebsiteDir}/digest2.txt")
1018 }
1019
1020 task getdown() {
1021   group = "distribution"
1022   description = "Create the minimal and full getdown app folder for installers and website and create digest file"
1023   dependsOn getdownDigest
1024   doLast {
1025     if (reportRsyncCommand) {
1026       def fromDir = getdownWebsiteDir + (getdownWebsiteDir.endsWith('/')?'':'/')
1027       def toDir = "${getdown_rsync_dest}/${getdownDir}" + (getdownDir.endsWith('/')?'':'/')
1028       println "LIKELY RSYNC COMMAND:"
1029       println "mkdir -p '$toDir'\nrsync -avh --delete '$fromDir' '$toDir'"
1030       if (RUNRSYNC == "true") {
1031         exec {
1032           commandLine "mkdir", "-p", toDir
1033         }
1034         exec {
1035           commandLine "rsync", "-avh", "--delete", fromDir, toDir
1036         }
1037       }
1038     }
1039   }
1040 }
1041
1042 clean {
1043   doFirst {
1044     delete project.ext.getdownWebsiteDir
1045     delete project.ext.getdownFilesDir
1046   }
1047 }
1048
1049 install4j {
1050   def install4jHomeDir = "/opt/install4j"
1051   def hostname = "hostname".execute().text.trim()
1052   if (hostname.equals("jv-bamboo")) {
1053     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1054   } else if (OperatingSystem.current().isMacOsX()) {
1055     install4jHomeDir = '/Applications/install4j.app/Contents/Resources/app'
1056     if (! file(install4jHomeDir).exists()) {
1057       install4jHomeDir = System.getProperty("user.home")+install4jHomeDir
1058     }
1059   } else if (OperatingSystem.current().isLinux()) {
1060     install4jHomeDir = System.getProperty("user.home")+"/buildtools/install4j"
1061   }
1062   installDir = file(install4jHomeDir)
1063   mediaTypes = Arrays.asList(install4jMediaTypes.split(","))
1064   if (install4jFaster.equals("true")) {
1065     faster = true
1066   }
1067 }
1068
1069 def install4jConf
1070 def macosJavaVMDir
1071 def macosJavaVMTgz
1072 def windowsJavaVMDir
1073 def windowsJavaVMTgz
1074 def install4jDir = "${jalviewDir}/${install4jResourceDir}"
1075 def install4jConfFile = "jalview-installers-java${JAVA_VERSION}.install4j"
1076 install4jConf = "${install4jDir}/${install4jConfFile}"
1077
1078 task copyInstall4jTemplate(type: Copy) {
1079   macosJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/macos-jre${JAVA_VERSION}/jre"
1080   macosJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/macos-jre${JAVA_VERSION}.tar.gz"
1081   windowsJavaVMDir = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/getdown/windows-jre${JAVA_VERSION}/jre"
1082   windowsJavaVMTgz = "${System.env.HOME}/buildtools/jre/openjdk-java_vm/install4j/tgz/windows-jre${JAVA_VERSION}.tar.gz"
1083   from (install4jDir) {
1084     include install4jTemplate
1085     rename (install4jTemplate, install4jConfFile)
1086     filter(ReplaceTokens, beginToken: '', endToken: '', tokens: ['9999999999': JAVA_VERSION])
1087     filter(ReplaceTokens, beginToken: '$$', endToken: '$$',
1088     tokens: [
1089     'JAVA_VERSION': JAVA_VERSION,
1090     'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
1091     'VERSION': JALVIEW_VERSION,
1092     'MACOS_JAVA_VM_DIR': macosJavaVMDir,
1093     'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
1094     'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
1095     'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
1096     'INSTALL4JINFOPLISTFILEASSOCIATIONS': install4jInfoPlistFileAssociations,
1097     'COPYRIGHT_MESSAGE': install4jCopyrightMessage,
1098     'MACOS_BUNDLE_ID': install4jMacOSBundleId,
1099     'GETDOWN_RESOURCE_DIR': getdown_resource_dir,
1100     'GETDOWN_DIST_DIR': getdown_app_dir,
1101     'GETDOWN_ALT_DIR': getdown_app_dir_alt,
1102     'GETDOWN_INSTALL_DIR': getdown_install_dir
1103     ]
1104     )
1105     if (OSX_KEYPASS=="") {
1106       filter(ReplaceTokens, beginToken: 'codeSigning macEnabled="', endToken: '"', tokens: ['true':'codeSigning macEnabled="false"'])
1107       filter(ReplaceTokens, beginToken: 'runPostProcessor="true" ',endToken: 'Processor', tokens: ['post':'runPostProcessor="false" postProcessor'])
1108     }
1109   }
1110   into install4jDir
1111   outputs.files(install4jConf)
1112
1113   doLast {
1114     // include file associations in installer
1115     def installerFileAssociationsXml = file("${install4jDir}/${install4jInstallerFileAssociations}").text
1116     ant.replaceregexp(
1117       byline: false,
1118       flags: "s",
1119       match: '<action name="EXTENSIONS_REPLACED_BY_GRADLE".*?</action>',
1120       replace: installerFileAssociationsXml,
1121       file: install4jConf
1122     )
1123     /*
1124     // include uninstaller applescript app files in dmg
1125     def installerDMGUninstallerXml = file("$install4jDir/$install4jDMGUninstallerAppFiles").text
1126     ant.replaceregexp(
1127     byline: false,
1128     flags: "s",
1129     match: '<file name="UNINSTALL_OLD_JALVIEW_APP_REPLACED_IN_GRADLE" file=.*?>',
1130     replace: installerDMGUninstallerXml,
1131     file: install4jConf
1132     )
1133      */
1134   }
1135 }
1136
1137 task installers(type: com.install4j.gradle.Install4jTask) {
1138   group = "distribution"
1139   description = "Create the install4j installers"
1140   dependsOn getdown
1141   dependsOn copyInstall4jTemplate
1142   projectFile = file(install4jConf)
1143   println("Using projectFile "+projectFile)
1144   variables = [majorVersion: version.substring(2, 11), build: 001, OSX_KEYSTORE: OSX_KEYSTORE, JSIGN_SH: JSIGN_SH]
1145   destination = "${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}"
1146   buildSelected = true
1147
1148   if (OSX_KEYPASS) {
1149     macKeystorePassword=OSX_KEYPASS
1150
1151   }
1152
1153   inputs.dir(project.ext.getdownWebsiteDir)
1154   inputs.file(install4jConf)
1155   inputs.dir(macosJavaVMDir)
1156   inputs.dir(windowsJavaVMDir)
1157   outputs.dir("${jalviewDir}/${install4jBuildDir}/${JAVA_VERSION}")
1158
1159 }
1160
1161 clean {
1162   doFirst {
1163     delete install4jConf
1164   }
1165 }
1166
1167 task sourceDist (type: Tar) {
1168
1169   def VERSION_UNDERSCORES = JALVIEW_VERSION.replaceAll("\\.", "_")
1170   def outputFileName = "${project.name}_${VERSION_UNDERSCORES}.tar.gz"
1171   // cater for buildship < 3.1 [3.0.1 is max version in eclipse 2018-09]
1172   try {
1173     archiveFileName = outputFileName
1174   } catch (Exception e) {
1175     archiveName = outputFileName
1176   }
1177
1178   compression Compression.GZIP
1179
1180   into project.name
1181
1182   def EXCLUDE_FILES=["build/*","bin/*","test-output/","test-reports","tests","clover*/*"
1183   ,".*"
1184   ,"benchmarking/*"
1185   ,"**/.*"
1186   ,"*.class"
1187   ,"**/*.class","${j11modDir}/**/*.jar","appletlib","**/*locales"
1188   ,"*locales/**",
1189   ,"utils/InstallAnywhere"]
1190   def PROCESS_FILES=[   "AUTHORS",
1191   "CITATION",
1192   "FEATURETODO",
1193   "JAVA-11-README",
1194   "FEATURETODO",
1195   "LICENSE",
1196   "**/README",
1197   "RELEASE",
1198   "THIRDPARTYLIBS","TESTNG",
1199   "build.gradle",
1200   "gradle.properties",
1201   "**/*.java",
1202   "**/*.html",
1203   "**/*.xml",
1204   "**/*.gradle",
1205   "**/*.groovy",
1206   "**/*.properties",
1207   "**/*.perl",
1208   "**/*.sh"]
1209
1210   from(jalviewDir) {
1211     exclude (EXCLUDE_FILES)
1212     include (PROCESS_FILES)
1213     filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
1214   }
1215   from(jalviewDir) {
1216     exclude (EXCLUDE_FILES)
1217     exclude (PROCESS_FILES)
1218   exclude ("appletlib")
1219   exclude ("**/*locales")
1220   exclude ("*locales/**")
1221   exclude ("utils/InstallAnywhere")
1222
1223     exclude (getdown_files_dir)
1224   exclude (getdown_website_dir)
1225
1226   // exluding these as not using jars as modules yet
1227   exclude ("${j11modDir}/**/*.jar")
1228 }
1229 //  from (jalviewDir) {
1230 //    // explicit includes for stuff that seemed to not get included
1231 //    include(fileTree("test/**/*."))
1232 //    exclude(EXCLUDE_FILES)
1233 //    exclude(PROCESS_FILES)
1234 //  }
1235 }
1236
1237 task helppages  {
1238   dependsOn copyHelp
1239   dependsOn pubhtmlhelp
1240
1241   inputs.dir("${classes}/${helpDir}")
1242   outputs.dir("${helpOutputDir}")
1243 }
1244
1245 def jalviewjsBuildDir
1246 def jalviewjsSiteDir
1247 def jalviewjsTransferSiteDir
1248 task jalviewjsSitePath {
1249   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
1250   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
1251   if (jalviewjs_site_dir.startsWith('/')) {
1252     jalviewjsSiteDir = jalviewjs_site_dir
1253   } else {
1254     jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
1255   }
1256   jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
1257 }
1258
1259 def eclipseWorkspace
1260 task jalviewjsSetEclipseWorkspace {
1261   def propKey = "jalviewjs_eclipse_workspace"
1262   def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
1263   def props = new Properties()
1264   def eclipseWsDir
1265   def propVal = null
1266   if (project.hasProperty(propKey)) {
1267     propVal = project.getProperty(propKey)
1268     eclipseWsDir = propVal
1269   }
1270   if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
1271     def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
1272     props.load(ins)
1273     ins.close()
1274     if (props.getProperty(propKey, null) != null) {
1275       eclipseWsDir = props.getProperty(propKey)
1276     }
1277   }
1278
1279   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
1280     def tempDir = File.createTempDir()
1281     eclipseWsDir = tempDir.getAbsolutePath()
1282     props.setProperty(propKey, eclipseWsDir)
1283     def propsFile = file(propsFileName)
1284     propsFile.parentFile.mkdirs()
1285     propsFile.createNewFile() // doesn't affect existing file
1286     def outs = new FileOutputStream(propsFile, false)
1287     props.store(outs, null)
1288     outs.close()
1289   }
1290
1291   eclipseWorkspace = file(eclipseWsDir)
1292
1293   println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
1294
1295   inputs.property(propKey, propVal)
1296   outputs.file(propsFileName)
1297 }
1298
1299
1300 task jalviewjsUnzipFiles {
1301   dependsOn jalviewjsSitePath
1302
1303   def zipFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_libjs_dir}", include: "*.zip")
1304   zipFiles += "${jalviewjs_utils_dir}/${jalviewjs_swingjs_zip}"
1305
1306   doLast {
1307     zipFiles.each { file_zip ->
1308       copy {
1309         from zipTree(file_zip)
1310         into jalviewjsSiteDir
1311       }
1312     }
1313   }
1314
1315   inputs.files zipFiles
1316   outputs.dir jalviewjsSiteDir
1317 }
1318
1319 def eclipseDropinsDir
1320 def eclipseBinary
1321 def eclipseVersion
1322 def fromDropinsDir
1323 task jalviewjsEclipsePaths {
1324   def eclipseRoot
1325   def eclipseProduct
1326   eclipseRoot = jalviewjs_eclipse_root
1327   if (eclipseRoot.startsWith("~")) {
1328     eclipseRoot = System.getProperty("user.home") + eclipseRoot.substring(1)
1329   }
1330   if (OperatingSystem.current().isMacOsX()) {
1331     eclipseRoot += "/Eclipse.app"
1332     eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins"
1333     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
1334     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
1335   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
1336     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1337       eclipseRoot += "/eclipse"
1338     }
1339     eclipseDropinsDir = "${eclipseRoot}/dropins"
1340     eclipseBinary = "${eclipseRoot}/eclipse"
1341     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1342   } else { // linux or unix
1343     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
1344       eclipseRoot += "/eclipse"
1345     }
1346     eclipseDropinsDir = "${eclipseRoot}/dropins"
1347     eclipseBinary = "${eclipseRoot}/eclipse"
1348     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
1349   }
1350
1351   eclipseVersion = "4.12" // default
1352   if (file(eclipseProduct).exists()) {
1353     def fis = new FileInputStream(eclipseProduct)
1354     def props = new Properties()
1355     props.load(fis)
1356     eclipseVersion = props.getProperty("version")
1357     fis.close()
1358     println("ECLIPSE_VERSION=${eclipseVersion}")
1359   }
1360   String[] v = eclipseVersion.split("\\.")
1361   def v0 = Integer.valueOf(v[0])
1362   def v1 = Integer.valueOf(v[1])
1363   if (v0 < 4 || ( v0 == 4 && v1 < 13 )) {
1364     fromDropinsDir = "eclipse/dropins_4.12"
1365   } else {
1366     fromDropinsDir = "eclipse/dropins_4.13"
1367   }
1368 }
1369
1370 task jalviewjsEclipseCopyDropins {
1371   dependsOn jalviewjsEclipsePaths
1372   def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${fromDropinsDir}", include: "*.jar")
1373   def outputDir = eclipseDropinsDir
1374
1375   inputs.files inputFiles
1376   inputFiles.each { file ->
1377     outputs.file("${outputDir}/${file.name}")
1378   }
1379
1380   doLast {
1381     inputFiles.each { file ->
1382       copy {
1383         from file
1384         into outputDir
1385       }
1386     }
1387   }
1388 }
1389
1390 // this version (type: Copy) will delete anything in the eclipse dropins folder that isn't in fromDropinsDir
1391 task NEWjalviewjsEclipseCopyDropins(type: Copy) {
1392   dependsOn jalviewjsEclipsePaths
1393   from fromDropinsDir
1394   into eclipseDropinsDir
1395 }
1396
1397 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
1398   dependsOn jalviewjsSitePath
1399   outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
1400   def props = project.properties.sort { it.key }
1401   def siteDirProperty = "j2s.site.directory"
1402   def setSiteDir = false
1403   props.each { prop, val ->
1404     if (prop.startsWith("j2s.") && val != null) {
1405       if (prop == siteDirProperty) {
1406         if (!(val.startsWith('/') || val.startsWith("file://") )) {
1407           val = "${jalviewjsTransferSiteDir}/${val}"
1408         }
1409         setSiteDir = true
1410       }
1411       property(prop,val)
1412     }
1413     if (!setSiteDir) {
1414       property(siteDirProperty,jalviewjsTransferSiteDir)
1415     }
1416   }
1417   inputs.properties(props.findAll( { k, v -> k.startsWith("j2s.") } ))
1418   outputs.file(outputFile)
1419 }
1420
1421 task jalviewjsEclipseSetup {
1422   dependsOn jalviewjsEclipseCopyDropins
1423   dependsOn jalviewjsSetEclipseWorkspace
1424   dependsOn jalviewjsCreateJ2sSettings
1425 }
1426
1427 task jalviewjsCopyResources (type: Copy) {
1428   dependsOn jalviewjsSitePath
1429   def inputFiles = fileTree(dir: jalviewjs_resource_dir)
1430   def outputDir = "${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
1431
1432   from inputFiles
1433   into outputDir
1434   def outputFiles = []
1435   rename { filename ->
1436     outputFiles += "${outputDir}/${filename}"
1437     null
1438   }
1439   outputs.files outputFiles
1440   inputs.files inputFiles
1441 }
1442
1443 task jalviewjsCopySiteResources (type: Copy) {
1444   dependsOn jalviewjsSitePath
1445   def inputFiles = fileTree(dir: "${jalviewjs_utils_dir}/${jalviewjs_site_resource_dir}")
1446   def outputDir = jalviewjsSiteDir
1447
1448   from inputFiles
1449   into outputDir
1450   def outputFiles = []
1451   rename { filename ->
1452     outputFiles += "${outputDir}/${filename}"
1453     null
1454   }
1455   outputs.files outputFiles
1456   inputs.files inputFiles
1457 }
1458
1459 task jalviewjsProjectImport(type: Exec) {
1460   // work out how to do this!
1461   dependsOn eclipseProject
1462   dependsOn eclipseClasspath
1463   dependsOn eclipseJdt
1464   dependsOn jalviewjsEclipsePaths
1465   dependsOn jalviewjsEclipseSetup
1466   executable(eclipseBinary)
1467   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
1468   if (eclipse_debug == "true") {
1469     args += "-debug"
1470   }
1471
1472   def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
1473   inputs.file("${jalviewDir}/.project")
1474   outputs.dir(projdir)
1475   outputs.upToDateWhen { file(projdir).exists() }
1476 }
1477
1478 task jalviewjsTranspile(type: Exec) {
1479   dependsOn jalviewjsEclipseSetup
1480   dependsOn jalviewjsProjectImport
1481   dependsOn jalviewjsEclipsePaths
1482   executable(eclipseBinary)
1483   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", eclipseWorkspace, "-${jalviewjs_eclipseBuildArg}", eclipse_project_name ])
1484   if (eclipse_debug == "true") {
1485     args += "-debug"
1486   }
1487
1488   def stdout
1489   def stderr
1490   doFirst {
1491     stdout = new ByteArrayOutputStream()
1492     stderr = new ByteArrayOutputStream()
1493
1494     def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
1495     def logOutFile = file(logOutFileName)
1496     logOutFile.createNewFile()
1497     def logOutFOS = new FileOutputStream(logOutFile, false)
1498     //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
1499     //def logErrFile = file(logFileName)
1500     //logErrFile.createNewFile()
1501     //def logErrFOS = new FileErrputStream(logErrFile, false)
1502     // combine stdout and stderr
1503     def logErrFOS = logOutFOS
1504     if (jalviewjs_j2s_to_console.equals("true")) {
1505       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1506         new org.apache.tools.ant.util.TeeOutputStream(
1507           logOutFOS,
1508           stdout),
1509         standardOutput)
1510       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1511         new org.apache.tools.ant.util.TeeOutputStream(
1512           logErrFOS,
1513           stderr),
1514         errorOutput)
1515     } else {
1516       standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
1517         logOutFOS,
1518         stdout)
1519       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
1520         logErrFOS,
1521         stderr)
1522     }
1523   }
1524   doLast {
1525     if (stdout.toString().contains("Error processing ")) {
1526       // j2s did not complete transpile
1527       throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
1528     }
1529   }
1530
1531   inputs.dir(sourceDir)
1532   outputs.dir("${eclipse_bin_dir}/main")
1533   outputs.dir(jalviewjsTransferSiteDir)
1534   outputs.upToDateWhen { file("${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
1535
1536 }
1537
1538 task jalviewjsCopyTransferSite(type: Copy) {
1539   dependsOn jalviewjsTranspile
1540   from jalviewjsTransferSiteDir
1541   into jalviewjsSiteDir
1542 }
1543
1544 jalviewjsUnzipFiles.mustRunAfter jalviewjsCopyTransferSite
1545 jalviewjsCopyResources.mustRunAfter jalviewjsCopyTransferSite
1546 jalviewjsCopySiteResources.mustRunAfter jalviewjsCopyTransferSite
1547
1548 task jalviewjsPrepareSite {
1549   group "JalviewJS"
1550   description "Prepares the website folder including unzipping files and copying resources"
1551   dependsOn jalviewjsSitePath
1552   dependsOn jalviewjsUnzipFiles
1553   dependsOn jalviewjsCopyResources
1554   dependsOn jalviewjsCopySiteResources
1555 }
1556
1557 task jalviewjsBuildSite {
1558   group "JalviewJS"
1559   description "Builds the whole website including transpiled code"
1560   dependsOn jalviewjsCopyTransferSite
1561   dependsOn jalviewjsPrepareSite
1562 }
1563
1564 task cleanJalviewjsSite {
1565   doFirst {
1566     delete jalviewjsTransferSiteDir
1567     delete jalviewjsSiteDir
1568   }
1569 }
1570
1571 task jalviewjsSiteTar(type: Tar) {
1572   group "JalviewJS"
1573   description "Creates a tar.gz file for the website"
1574   dependsOn jalviewjsBuildSite
1575   def outputFilename = "jalviewjs-site-${JALVIEW_VERSION}.tar.gz"
1576   try {
1577     archiveFileName = outputFilename
1578   } catch (Exception e) {
1579     archiveName = outputFilename
1580   }
1581
1582   compression Compression.GZIP
1583
1584   from jalviewjsSiteDir
1585   into jalviewjs_site_dir // this is inside the tar file
1586
1587   inputs.dir(jalviewjsSiteDir)
1588 }
1589
1590 task jalviewjsServer {
1591   group "JalviewJS"
1592   description "Starts a webserver on localhost to test the website"
1593   dependsOn jalviewjsSitePath
1594   def htmlFile = "${jalviewDirAbsolutePath}/jalviewjsTest.html"
1595   doLast {
1596
1597     SimpleHttpFileServerFactory factory = new SimpleHttpFileServerFactory()
1598     def port = Integer.valueOf(jalviewjs_server_port)
1599     def start = port
1600     def running = false
1601     def url
1602     while(port < start+1000 && !running) {
1603       try {
1604         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
1605         def jalviewjsServer = factory.start(doc_root, port)
1606         running = true
1607         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
1608         println("SERVER STARTED with document root ${doc_root}.")
1609         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
1610         println("For debug: "+url+"?j2sdebug")
1611
1612         file(htmlFile).text = """
1613         <p><a href="${url}">Jalview JS Test. &lt;${url}&gt;</a></p>
1614         <p><a href="${url}?j2sdebug">Jalview JS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
1615         """
1616
1617       } catch (Exception e) {
1618         port++;
1619       }
1620     }
1621
1622   }
1623
1624   outputs.file(htmlFile)
1625 }
1626
1627 task cleanJalviewjsAll {
1628   group "JalviewJS"
1629   description "Delete all configuration and build artifacts to do with JalviewJS build"
1630   dependsOn cleanJalviewjsSite
1631
1632   doFirst {
1633     delete jalviewjsBuildDir
1634     delete "${jalviewDir}/${eclipse_bin_dir}"
1635     delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
1636     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
1637   }
1638 }
1639
1640 task jalviewjs {
1641   group "JalviewJS"
1642   description "Build the site"
1643   dependsOn jalviewjsBuildSite
1644 }
1645
1646
1647 task jalviewjsIDECopyTransferSite(type: Copy) {
1648   from jalviewjsTransferSiteDir
1649   into jalviewjsSiteDir
1650 }
1651
1652 task jalviewjsIDEj2s {
1653   group "JalviewJS in Eclipse"
1654   description "Creates the .j2s file"
1655   dependsOn jalviewjsCreateJ2sSettings
1656 }
1657
1658 task jalviewjsIDEBuildSite {
1659   group "JalviewJS in Eclipse"
1660   description "Copies the Eclipse transpiled site and unzips supporting zipfiles"
1661   dependsOn jalviewjsIDECopyTransferSite
1662   dependsOn jalviewjsPrepareSite
1663 }
1664
1665 task jalviewjsIDESiteClean {
1666   group "JalviewJS in Eclipse"
1667   description "Deletes the Eclipse transpiled site"
1668   dependsOn cleanJalviewjsSite
1669 }
1670
1671 task jalviewjsIDEServer {
1672   group "JalviewJS in Eclipse"
1673   description "Starts a webserver on localhost to test the website"
1674   dependsOn jalviewjsServer
1675 }
1676