X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=21a4c81056a60c515957e814586fac298713a1bf;hb=e8a974af046e0ee231b09743c4299c89d3a95d87;hp=fc4d9cacaf21794ccff2acbcaff76d4da402d414;hpb=68ed70b0672bed174113443b6c0516d277d8ea07;p=jalview.git

diff --git a/build.gradle b/build.gradle
index fc4d9ca..21a4c81 100644
--- a/build.gradle
+++ b/build.gradle
@@ -42,6 +42,7 @@ def string(Object o) {
 
 ext {
   jalviewDirAbsolutePath = file(jalviewDir).getAbsolutePath()
+  jalviewDirRelativePath = jalviewDir
 
   // local build environment properties
   def localProps = "${jalviewDirAbsolutePath}/local.properties"
@@ -64,7 +65,6 @@ ext {
     }
   }
 
-
   // this property set when running Eclipse headlessly
   j2sHeadlessBuildProperty = string("net.sf.j2s.core.headlessbuild")
   // this property set by Eclipse
@@ -86,18 +86,31 @@ ext {
   System.properties.sort { it.key }.each {
     key, val -> println("SYSTEM PROPERTY ${key}='${val}'")
   }
+  if (false && IN_ECLIPSE) {
+    jalviewDir = jalviewDirAbsolutePath
+  }
   */
 
+  // essentials
+  bareSourceDir = string(source_dir)
+  sourceDir = string("${jalviewDir}/${bareSourceDir}")
+  resourceDir = string("${jalviewDir}/${resource_dir}")
+  bareTestSourceDir = string(test_source_dir)
+  testSourceDir = string("${jalviewDir}/${bareTestSourceDir}")
+
+  // clover
   cloverInstrDir = file("${buildDir}/${cloverSourcesInstrDir}")
-  classes = string("${jalviewDir}/${classesDir}")
+  classesDir = string("${jalviewDir}/${classes_dir}")
   if (clover.equals("true")) {
     use_clover = true
-    classes = string("${buildDir}/${cloverClassesDir}")
+    classesDir = string("${buildDir}/${cloverClassesDir}")
   } else {
     use_clover = false
-    classes = string("${jalviewDir}/${classesDir}")
+    classesDir = string("${jalviewDir}/${classes_dir}")
   }
 
+  classes = classesDir
+
   getdownWebsiteDir = string("${jalviewDir}/${getdown_website_dir}/${JAVA_VERSION}")
   getdownDir = string("")
   reportRsyncCmd = false
@@ -112,7 +125,7 @@ ext {
     getdown_channel_name = string("${bamboo_planKey}/${JAVA_VERSION}")
     getdown_app_base = string("${bamboo_channelbase}/${bamboo_planKey}${bamboo_getdown_channel_suffix}/${JAVA_VERSION}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     break
 
     case "RELEASE":
@@ -120,7 +133,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_release
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -134,7 +147,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -150,7 +163,7 @@ ext {
       exit
     } else {
       packageDir = string("${ARCHIVEDIR}/${packageDir}")
-      buildProperties = string("${ARCHIVEDIR}/${classesDir}/${build_properties_file}")
+      buildProperties = string("${ARCHIVEDIR}/${classes_dir}/${build_properties_file}")
       buildDist = false
     }
     reportRsyncCommand = true
@@ -162,7 +175,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -171,7 +184,7 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
@@ -180,14 +193,14 @@ ext {
     getdownDir = string("${getdown_channel_name}/${JAVA_VERSION}")
     getdown_app_base = string("${getdown_channel_base}/${getdownDir}")
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     reportRsyncCommand = true
     break
 
     case "LOCAL":
     getdown_app_base = file(getdownWebsiteDir).toURI().toString()
     getdown_app_dir = getdown_app_dir_alt
-    buildProperties = string("${jalviewDir}/${classesDir}/${build_properties_file}")
+    buildProperties = string("${classesDir}/${build_properties_file}")
     getdownLauncher = string("${jalviewDir}/${getdown_lib_dir}/${getdown_launcher_local}")
     break
 
@@ -277,7 +290,10 @@ ext {
 
 
   buildingHTML = string("${jalviewDir}/${docDir}/building.html")
-  helpFile = string("${classes}/${helpDir}/help.jhm")
+  helpFile = string("${classesDir}/${help_dir}/help.jhm")
+  helpParentDir = string("${jalviewDir}/${help_parent_dir}")
+  helpDir = string("${help_dir}")
+  helpSourceDir = string("${helpParentDir}/${helpDir}")
 
 
   relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
@@ -293,9 +309,10 @@ ext {
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
-  jalviewjsDefaultCoreName = string(jalviewjs_default_core)
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
+  jalviewjsJ2sSettingsFileName = string("${jalviewDir}/${jalviewjs_j2s_settings}")
+  jalviewjsJ2sProps = null
 
   eclipseWorkspace = null
   eclipseBinary = string("")
@@ -308,12 +325,12 @@ ext {
 sourceSets {
   main {
     java {
-      srcDirs "${jalviewDir}/${sourceDir}"
-      outputDir = file(project.classes)
+      srcDirs sourceDir
+      outputDir = file(classesDir)
     }
 
     resources {
-      srcDirs "${jalviewDir}/${resourceDir}"
+      srcDirs resourceDir
     }
 
     jar.destinationDir = file("${jalviewDir}/${packageDir}")
@@ -344,7 +361,7 @@ sourceSets {
 
   test {
     java {
-      srcDirs "${jalviewDir}/${testSourceDir}"
+      srcDirs testSourceDir
       outputDir = file("${jalviewDir}/${testOutputDir}")
     }
 
@@ -413,7 +430,7 @@ eclipse {
         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
           if (entry.kind == 'src') {
-            if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == sourceDir || entry.path == testSourceDir)) {
+            if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
               removeTheseToo += entry
             } else {
               alreadyAddedSrcPath.putAt(entry.path, true)
@@ -422,11 +439,9 @@ eclipse {
         }
         cp.entries.removeAll(removeTheseToo)
 
-        if (file("${jalviewDir}/${eclipse_bin_dir}/main").isDirectory()) {
-          cp.entries += new Output("${eclipse_bin_dir}/main")
-        }
-        if (file(helpParentDir).isDirectory()) {
-          cp.entries += new Library(fileReference(helpParentDir))
+        cp.entries += new Output("${eclipse_bin_dir}/main")
+        if (file(helpSourceDir).isDirectory()) {
+          cp.entries += new Library(fileReference(helpSourceDir))
         }
         if (file(resourceDir).isDirectory()) {
           cp.entries += new Library(fileReference(resourceDir))
@@ -509,7 +524,7 @@ eclipse {
 
   if (IN_ECLIPSE) {
     // Don't want these to be activated if in headless build
-    //synchronizationTasks "eclipseConfiguration"
+    synchronizationTasks "eclipseSynchronizationTask"
     autoBuildTasks "eclipseAutoBuildTask"
   }
 }
@@ -517,7 +532,7 @@ eclipse {
 
 task cloverInstr() {
   // only instrument source, we build test classes as normal
-  inputs.files files (sourceSets.main.allJava) // , fileTree(dir:"$jalviewDir/$testSourceDir", include: ["**/*.java"]))
+  inputs.files files (sourceSets.main.allJava) // , fileTree(dir: testSourceDir, include: ["**/*.java"]))
   outputs.dir cloverInstrDir
 
   doFirst {
@@ -643,8 +658,8 @@ task setGitVals {
 
 task createBuildProperties(type: WriteProperties) {
   dependsOn setGitVals
-  inputs.dir("${jalviewDir}/${sourceDir}")
-  inputs.dir("${jalviewDir}/${resourceDir}")
+  inputs.dir(sourceDir)
+  inputs.dir(resourceDir)
   file(buildProperties).getParentFile().mkdirs()
   outputFile (buildProperties)
   // taking time specific comment out to allow better incremental builds
@@ -708,7 +723,7 @@ clean {
 
 task syncDocs(type: Sync) {
   dependsOn convertBuildingMD
-  def syncDir = "${classes}/${docDir}"
+  def syncDir = "${classesDir}/${docDir}"
   from fileTree("${jalviewDir}/${docDir}")
   into syncDir
 
@@ -716,8 +731,8 @@ task syncDocs(type: Sync) {
 
 
 task copyHelp(type: Copy) {
-  def inputDir = "${jalviewDir}/${helpParentDir}/${helpDir}"
-  def outputDir = "${classes}/${helpDir}"
+  def inputDir = helpSourceDir
+  def outputDir = "${classesDir}/${helpDir}"
   from(inputDir) {
     exclude '**/*.gif'
     exclude '**/*.jpg'
@@ -745,16 +760,16 @@ task copyHelp(type: Copy) {
 
 
 task syncLib(type: Sync) {
-  def syncDir = "${classes}/${libDistDir}"
+  def syncDir = "${classesDir}/${libDistDir}"
   from fileTree("${jalviewDir}/${libDistDir}")
   into syncDir
 }
 
 
 task syncResources(type: Sync) {
-  from "${jalviewDir}/${resourceDir}"
+  from resourceDir
   include "**/*.*"
-  into "${classes}"
+  into "${classesDir}"
   preserve {
     include "**"
   }
@@ -799,13 +814,13 @@ task buildIndices(type: JavaExec) {
   dependsOn copyHelp
   classpath = sourceSets.main.compileClasspath
   main = "com.sun.java.help.search.Indexer"
-  workingDir = "${classes}/${helpDir}"
+  workingDir = "${classesDir}/${helpDir}"
   def argDir = "html"
   args = [ argDir ]
   inputs.dir("${workingDir}/${argDir}")
 
-  outputs.dir("${classes}/doc")
-  outputs.dir("${classes}/help")
+  outputs.dir("${classesDir}/doc")
+  outputs.dir("${classesDir}/help")
   outputs.file("${workingDir}/JavaHelpSearch/DOCS")
   outputs.file("${workingDir}/JavaHelpSearch/DOCS.TAB")
   outputs.file("${workingDir}/JavaHelpSearch/OFFSETS")
@@ -835,8 +850,8 @@ task linkCheck(type: JavaExec) {
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
-  def help = "${classes}/${helpDir}"
-  args = [ "${classes}/${helpDir}", "-nointernet" ]
+  def help = "${classesDir}/${helpDir}"
+  args = [ "${classesDir}/${helpDir}", "-nointernet" ]
 
   def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
   def errFOS = outFOS
@@ -847,13 +862,13 @@ task linkCheck(type: JavaExec) {
     outFOS,
     errorOutput)
 
-  inputs.dir("${classes}/${helpDir}")
+  inputs.dir("${classesDir}/${helpDir}")
   outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
 ant.properties.basedir = "${jalviewDir}"
-ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes}/${helpDir}"
+ant.properties.helpBuildDir = "${jalviewDirAbsolutePath}/${classes_dir}/${helpDir}"
 ant.importBuild "${utilsDir}/publishHelp.xml"
 
 
@@ -884,13 +899,13 @@ jar {
   exclude "**/*.jar"
   exclude "**/*.jar.*"
 
-  inputs.dir("${classes}")
+  inputs.dir(classesDir)
   outputs.file("${jalviewDir}/${packageDir}/${archiveName}")
 }
 
 
 task copyJars(type: Copy) {
-  from fileTree(dir: "${classes}", include: "**/*.jar").files
+  from fileTree(dir: classesDir, include: "**/*.jar").files
   into "${jalviewDir}/${packageDir}"
 }
 
@@ -1380,8 +1395,8 @@ task helppages  {
   dependsOn copyHelp
   dependsOn pubhtmlhelp
   
-  inputs.dir("${classes}/${helpDir}")
-  outputs.dir("${helpOutputDir}")
+  inputs.dir("${classesDir}/${helpDir}")
+  outputs.dir("${buildDir}/distributions/${helpDir}")
 }
 
 
@@ -1406,16 +1421,17 @@ task jalviewjsSetEclipseWorkspace {
   def eclipseWsDir = propVal
   def props = new Properties()
 
+  def writeProps = true
   if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
     def ins = new FileInputStream(propsFileName)
     props.load(ins)
     ins.close()
     if (props.getProperty(propKey, null) != null) {
       eclipseWsDir = props.getProperty(propKey)
+      writeProps = false
     }
   }
 
-  def writeProps = false
   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
     def tempDir = File.createTempDir()
     eclipseWsDir = tempDir.getAbsolutePath()
@@ -1439,6 +1455,9 @@ task jalviewjsSetEclipseWorkspace {
       props.store(bytes, null)
       def propertiesString = bytes.toString()
       propsFile.text = propertiesString
+      print("NEW ")
+    } else {
+      print("EXISTING ")
     }
 
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
@@ -1446,7 +1465,7 @@ task jalviewjsSetEclipseWorkspace {
 
   //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
   outputs.file(propsFileName)
-  outputs.upToDateWhen { eclipseWorkspace.exists() }
+  outputs.upToDateWhen { eclipseWorkspace.exists() && propsFile.exists() }
 }
 
 
@@ -1592,11 +1611,10 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
   group "JalviewJS"
   description "Create the .j2s file from the j2s.* properties"
 
-  outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
-  def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
+  jalviewjsJ2sProps = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
   def setSiteDir = false
-  j2s_props.each { prop, val ->
+  jalviewjsJ2sProps.each { prop, val ->
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
@@ -1607,11 +1625,15 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteJsDir}")
+      property(siteDirProperty,"${jalviewDirRelativePath}/${jalviewjsTransferSiteJsDir}")
     }
   }
-  inputs.properties(j2s_props)
-  outputs.file(outputFile)
+  outputFile = jalviewjsJ2sSettingsFileName
+
+  if (! IN_ECLIPSE) {
+    inputs.properties(jalviewjsJ2sProps)
+    outputs.file(jalviewjsJ2sSettingsFileName)
+  }
 }
 
 
@@ -1644,7 +1666,7 @@ task jalviewjsSyncAllLibs (type: Sync) {
 
 
 task jalviewjsSyncResources (type: Sync) {
-  def inputFiles = fileTree(dir: "${jalviewDir}/${resourceDir}")
+  def inputFiles = fileTree(dir: resourceDir)
   def outputDir = "${jalviewDir}/${jalviewjsSiteDir}/${jalviewjs_j2s_subdir}"
 
   from inputFiles
@@ -1893,6 +1915,8 @@ task jalviewjsBuildAllCores {
   dependsOn jalviewjsTransferUnzipSwingJs
 
   def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+  def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+  def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
@@ -1913,7 +1937,7 @@ task jalviewjsBuildAllCores {
   }
 
   // _jmol and _jalview cores. Add any other peculiar classlist.txt files here
-  classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
+  //classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jmol}"), 'name': "_jvjmol" ]
   classlistFiles += [ 'file': file("${jalviewDir}/${jalviewjs_classlist_jalview}"), 'name': jalviewjsJalviewCoreName ]
 
   jalviewjsCoreClasslists = []
@@ -1969,10 +1993,31 @@ task jalviewjsBuildAllCores {
 
   // _all core
   def allClasslistName = "_all"
+  def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+  allJsFiles += fileTree(
+    dir: libJ2sDir,
+    include: "**/*.js",
+    excludes: [
+      // these exlusions are files that the closure-compiler produces errors for. Should fix them
+      "**/org/jmol/jvxl/readers/IsoIntersectFileReader.js",
+      "**/org/jmol/export/JSExporter.js"
+    ]
+  )
+  allJsFiles += fileTree(
+    dir: swingJ2sDir,
+    include: "**/*.js",
+    excludes: [
+      // these exlusions are files that the closure-compiler produces errors for. Should fix them
+      "**/sun/misc/Unsafe.js",
+      "**/swingjs/jquery/jquery-editable-select.js",
+      "**/swingjs/jquery/j2sComboBox.js",
+      "**/sun/misc/FloatingDecimal.js"
+    ]
+  )
   def allClasslist = [
     'jsfile': "${outputDir}/core${allClasslistName}.js",
     'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
-    'list': fileTree(dir: j2sDir, include: "**/*.js"),
+    'list': allJsFiles,
     'name': allClasslistName
   ]
   jalviewjsCoreClasslists += allClasslist
@@ -2155,36 +2200,35 @@ task jalviewjsServer {
     def start = port
     def running = false
     def url
+    def jalviewjsServer
     while(port < start+1000 && !running) {
       try {
         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
-        def jalviewjsServer = factory.start(doc_root, port)
+        jalviewjsServer = factory.start(doc_root, port)
         running = true
         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
         println("SERVER STARTED with document root ${doc_root}.")
         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
         println("For debug: "+url+"?j2sdebug")
-        println("For core: "+urlcore)
-
-        htmlText = """
-        <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
-        <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
-        """
-        jalviewjsCoreClasslists.each { cl ->
-          urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
-          htmlText += """
-          <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
-          """
-        }
-
-        file(htmlFile).text = htmlText
-
+        println("For verbose: "+url+"?j2sverbose")
       } catch (Exception e) {
-        e.printStackTrace()
         port++;
       }
     }
+    def htmlText = """
+      <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
+      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&gt;</a></p>
+      <p><a href="${url}?j2sverbose">JalviewJS Test with verbose. &lt;${url}?j2sdebug&gt;</a></p>
+      """
+    jalviewjsCoreClasslists.each { cl ->
+      def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+      htmlText += """
+      <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
+      """
+      println("For core ${cl.name}: "+urlcore)
+    }
 
+    file(htmlFile).text = htmlText
   }
 
   outputs.file(htmlFile)
@@ -2258,8 +2302,8 @@ task jalviewjsIDE_Server {
 
 
 // buildship runs this at import
-task eclipseConfiguration {
-  dependsOn eclipseSetup
+task eclipseSynchronizationTask {
+  //dependsOn eclipseSetup
   dependsOn jalviewjsIDE_j2sFile
 }