X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.gradle;h=c5c16c3933180ee895810fe0c03a9d6b637e7d2f;hb=refs%2Fheads%2Fbug%2FJAL-3473_SpinnerNumberModel_causing_IllegalArgumentException;hp=b7f21620d9e825fbe1f8199a8d75a0a784ec29ef;hpb=ce0d0a188dc7362f95bb966dc4634d58aee8eb28;p=jalview.git

diff --git a/build.gradle b/build.gradle
index b7f2162..c5c16c3 100644
--- a/build.gradle
+++ b/build.gradle
@@ -22,17 +22,21 @@ plugins {
 // local build environment properties
 def localProps = "${jalviewDir}/local.properties"
 if (file(localProps).exists()) {
-  def p = new Properties()
-  def localPropsFIS = new FileInputStream(localProps)
-  p.load(localPropsFIS)
-  localPropsFIS.close()
-  p.each {
-    key, val -> 
-      def over = getProperty(key) != null
-      setProperty(key, val)
-      if (over) {
-        println("Overriding property '${key}' with local.properties value '${val}'")
-      }
+  try {
+    def p = new Properties()
+    def localPropsFIS = new FileInputStream(localProps)
+    p.load(localPropsFIS)
+    localPropsFIS.close()
+    p.each {
+      key, val -> 
+        def over = getProperty(key) != null
+        setProperty(key, val)
+        if (over) {
+          println("Overriding property '${key}' with local.properties value '${val}'")
+        }
+    }
+  } catch (Exception e) {
+    System.out.println("Exception reading local.properties")
   }
 }
 
@@ -642,9 +646,9 @@ task copyHelp(type: Copy) {
   def outputDir = "${classes}/${helpDir}"
   from(inputDir) {
     exclude '**/*.gif'
-      exclude '**/*.jpg'
-      exclude '**/*.png'
-      filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
+    exclude '**/*.jpg'
+    exclude '**/*.png'
+    filter(ReplaceTokens, beginToken: '$$', endToken: '$$', tokens: ['Version-Rel': JALVIEW_VERSION,'Year-Rel': getDate("yyyy")])
   }
   from(inputDir) {
     include '**/*.gif'
@@ -737,21 +741,27 @@ task compileLinkCheck(type: JavaCompile) {
   outputs.file("${jalviewDir}/${utilsDir}/BufferedLineReader.class")
 }
 
-def helplinkscheckertouchfile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.touch")
 task linkCheck(type: JavaExec) {
   dependsOn prepare, compileLinkCheck
+
+  def helpLinksCheckerOutFile = file("${jalviewDir}/${utilsDir}/HelpLinksChecker.out")
   classpath = files("${jalviewDir}/${utilsDir}")
   main = "HelpLinksChecker"
   workingDir = jalviewDir
   def help = "${classes}/${helpDir}"
   args = [ "${classes}/${helpDir}", "-nointernet" ]
 
-  doLast {
-    helplinkscheckertouchfile.createNewFile()
-  }
+  def outFOS = new FileOutputStream(helpLinksCheckerOutFile, false) // false == don't append
+  def errFOS = outFOS
+  standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    standardOutput)
+  errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+    outFOS,
+    errorOutput)
 
   inputs.dir("${classes}/${helpDir}")
-  outputs.file(helplinkscheckertouchfile)
+  outputs.file(helpLinksCheckerOutFile)
 }
 
 // import the pubhtmlhelp target
@@ -1265,11 +1275,7 @@ def jalviewjsTransferSiteDir
 task jalviewjsSitePath {
   def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
   jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
-  if (jalviewjs_site_dir.startsWith('/')) {
-    jalviewjsSiteDir = jalviewjs_site_dir
-  } else {
-    jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
-  }
+  jalviewjsSiteDir = "${jalviewjsBuildDir}/${jalviewjs_site_dir}"
   jalviewjsTransferSiteDir = "${jalviewjsBuildDir}/tmp/site"
 }
 
@@ -1283,12 +1289,13 @@ task jalviewjsSetEclipseWorkspace {
       propVal = System.getProperty("user.home") + propVal.substring(1)
     }
   }
-  def propsFileName = "${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_workspace_location_file}"
+  def propsFile = file(propsFileName)
   def eclipseWsDir = propVal
   def props = new Properties()
 
-  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && file(propsFileName).exists()) {
-    def ins = new FileInputStream("${jalviewDirAbsolutePath}/${propsFileName}")
+  if (( eclipseWsDir == null || !file(eclipseWsDir).exists() ) && propsFile.exists()) {
+    def ins = new FileInputStream(propsFileName)
     props.load(ins)
     ins.close()
     if (props.getProperty(propKey, null) != null) {
@@ -1296,30 +1303,32 @@ task jalviewjsSetEclipseWorkspace {
     }
   }
 
+  def writeProps = false
   if (eclipseWsDir == null || !file(eclipseWsDir).exists()) {
     def tempDir = File.createTempDir()
     eclipseWsDir = tempDir.getAbsolutePath()
-    props.setProperty(propKey, eclipseWsDir)
-    def propsFile = file(propsFileName)
-    propsFile.parentFile.mkdirs()
-    propsFile.createNewFile() // doesn't affect existing file
-    def outs = new FileOutputStream(propsFile, false)
-    props.store(outs, null)
-    outs.close()
+    writeProps = true
   }
-
   eclipseWorkspace = file(eclipseWsDir)
 
   doFirst {
+    if (writeProps) {
+      props.setProperty(propKey, eclipseWsDir)
+      propsFile.parentFile.mkdirs()
+      def bytes = new ByteArrayOutputStream()
+      props.store(bytes, null)
+      def propertiesString = bytes.toString()
+      propsFile.text = propertiesString
+    }
+
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
+
   inputs.property(propKey, eclipseWsDir)
   outputs.file(propsFileName)
 }
 
 
-def eclipseDropinsDir
-def utilsDropinsDir
 def eclipseBinary
 def eclipseVersion
 def eclipseDebug = false
@@ -1333,21 +1342,18 @@ task jalviewjsEclipsePaths {
   }
   if (OperatingSystem.current().isMacOsX()) {
     eclipseRoot += "/Eclipse.app"
-    eclipseDropinsDir = "${eclipseRoot}/Contents/Eclipse/dropins"
     eclipseBinary = "${eclipseRoot}/Contents/MacOS/eclipse"
     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   } else { // linux or unix
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
     }
-    eclipseDropinsDir = "${eclipseRoot}/dropins"
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   }
@@ -1371,16 +1377,15 @@ task jalviewjsEclipsePaths {
   } else {
     eclipseVersionSuffix = "_4.13"
   }
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}${eclipseVersionSuffix}"
   */
 
-  utilsDropinsDir = "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}"
+  
   def propKey = "eclipse_debug"
   eclipseDebug = (project.hasProperty(propKey) && project.getProperty(propKey).equals("true"))
 
   doFirst {
     if (!assumedVersion) {
-      println("ECLIPSE_VERSION=${eclipseVersion}")
+      println("ECLIPSE VERSION=${eclipseVersion}")
     }
   }
 }
@@ -1395,9 +1400,9 @@ task eclipseSetup {
 task OLDjalviewjsEclipseCopyDropins {
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsCleanEclipse
-  def inputFiles = fileTree(dir: utilsDropinsDir, include: "*.jar")
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
   inputFiles += file(jalviewjs_j2s_plugin)
-  def outputDir = eclipseDropinsDir
+  def outputDir = "${buildDir}/jalviewjs
 
   inputs.files inputFiles
   inputFiles.each { file ->
@@ -1419,15 +1424,12 @@ task OLDjalviewjsEclipseCopyDropins {
 task jalviewjsEclipseCopyDropins(type: Copy) {
   dependsOn jalviewjsEclipsePaths
 
-  from utilsDropinsDir
-  into eclipseDropinsDir
+  def inputFiles = fileTree(dir: "${jalviewDir}/${jalviewjs_eclipse_dropins_dir}", include: "*.jar")
+  inputFiles += file("${jalviewDir}/${jalviewjs_j2s_plugin}")
+  def outputDir = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}"
 
-  doLast {
-    copy {
-      from jalviewjs_j2s_plugin
-      into eclipseDropinsDir
-    }
-  }
+  from inputFiles
+  into outputDir
 }
 
 // this eclipse -clean doesn't actually work
@@ -1448,10 +1450,6 @@ y
 """
   def inputByteStream = new ByteArrayInputStream(inputString.getBytes())
   standardInput = inputByteStream
-
-  doFirst {
-    println("CLEAN ECLIPSE_DEBUG=${eclipseDebug}")
-  }
 }
 /* not really working yet
 jalviewjsEclipseCopyDropins.finalizedBy jalviewjsCleanEclipse
@@ -1477,7 +1475,11 @@ task jalviewjsUnzipFiles {
 }
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+  group "JalviewJS"
+  description "Create the .j2s file from the j2s.* properties"
+
   dependsOn jalviewjsSitePath
+
   outputFile ("${jalviewDir}/${jalviewjs_j2s_settings}")
   def j2s_props = project.properties.findAll { it.key.startsWith("j2s.") }.sort { it.key }
   def siteDirProperty = "j2s.site.directory"
@@ -1486,14 +1488,14 @@ task jalviewjsCreateJ2sSettings(type: WriteProperties) {
     if (val != null) {
       if (prop == siteDirProperty) {
         if (!(val.startsWith('/') || val.startsWith("file://") )) {
-          val = "${jalviewjsTransferSiteDir}/${val}"
+          val = "${jalviewDir}/${jalviewjsTransferSiteDir}/${val}"
         }
         setSiteDir = true
       }
       property(prop,val)
     }
     if (!setSiteDir) { // default site location, don't override specifically set property
-      property(siteDirProperty,jalviewjsTransferSiteDir)
+      property(siteDirProperty,"${jalviewDir}/${jalviewjsTransferSiteDir}")
     }
   }
   inputs.properties(j2s_props)
@@ -1555,14 +1557,9 @@ task jalviewjsProjectImport(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=utils/jalviewjs/eclipse/dropins"] here? (instead of copying plugins to eclipse dropins dir)
-
-  doFirst {
-    println("IMPORT ECLIPSE_DEBUG=${eclipseDebug}")
-  }
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   inputs.file("${jalviewDir}/.project")
-  outputs.dir(projdir)
   outputs.upToDateWhen { file(projdir).exists() }
 }
 
@@ -1576,67 +1573,63 @@ task jalviewjsTranspile(type: Exec) {
   if (eclipseDebug) {
     args += "-debug"
   }
-  // can we use args += ["--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=swingjs"] here? (instead of copying plugins to eclipse dropins dir)
+  args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   def stdout
   def stderr
-  stdout = new ByteArrayOutputStream()
-  stderr = new ByteArrayOutputStream()
+  doFirst {
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
 
-  def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
-  def logOutFile = file(logOutFileName)
-  logOutFile.createNewFile()
-  logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
+    def logOutFile = file(logOutFileName)
+    logOutFile.createNewFile()
+    logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
 BINARY: ${eclipseBinary}
 VERSION: ${eclipseVersion}
 WORKSPACE: ${eclipseWorkspace}
 DEBUG: ${eclipseDebug}
 ----
 """
-  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
-  //def logErrFileName = "${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
-  //def logErrFile = file(logFileName)
-  //logErrFile.createNewFile()
-  //def logErrFOS = new FileErrputStream(logErrFile, false)
-  // combine stdout and stderr
-  def logErrFOS = logOutFOS
-
-  if (jalviewjs_j2s_to_console.equals("true")) {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      new org.apache.tools.ant.util.TeeOutputStream(
-        logOutFOS,
-        stdout),
-      standardOutput)
+    def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+    //def logErrFileName = "${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"
+    //def logErrFile = file(logFileName)
+    //logErrFile.createNewFile()
+    //def logErrFOS = new FileErrputStream(logErrFile, false)
+    // combine stdout and stderr
+    def logErrFOS = logOutFOS
+
+    if (jalviewjs_j2s_to_console.equals("true")) {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        new org.apache.tools.ant.util.TeeOutputStream(
+          logOutFOS,
+          stdout),
+        standardOutput)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         new org.apache.tools.ant.util.TeeOutputStream(
           logErrFOS,
           stderr),
         errorOutput)
-  } else {
-    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
-      logOutFOS,
-      stdout)
+    } else {
+      standardOutput = new org.apache.tools.ant.util.TeeOutputStream(
+        logOutFOS,
+        stdout)
       errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
         logErrFOS,
         stderr)
+    }
   }
 
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
     }
   }
 
-  doFirst {
-    println("TRANSPILE ECLIPSE_DEBUG=${eclipseDebug}")
-  }
-
   inputs.dir("${jalviewDir}/${sourceDir}")
-  outputs.dir("${jalviewDir}/${eclipse_bin_dir}/main")
   outputs.dir("${jalviewDir}/${jalviewjsTransferSiteDir}")
-  outputs.upToDateWhen { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() }
-
+  outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteDir}${jalviewjs_server_resource}").exists() } )
 }
 
 task jalviewjsCopyTransferSite(type: Copy) {
@@ -1667,8 +1660,8 @@ task jalviewjsBuildSite {
 
 task cleanJalviewjsSite {
   doFirst {
-    delete jalviewjsTransferSiteDir
-    delete jalviewjsSiteDir
+    delete "${jalviewDir}/${jalviewjsTransferSiteDir}"
+    delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
 
@@ -1685,10 +1678,10 @@ task jalviewjsSiteTar(type: Tar) {
 
   compression Compression.GZIP
 
-  from jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsSiteDir}"
   into jalviewjs_site_dir // this is inside the tar file
 
-  inputs.dir(jalviewjsSiteDir)
+  inputs.dir("${jalviewDir}/${jalviewjsSiteDir}")
 }
 
 task jalviewjsServer {
@@ -1736,13 +1729,15 @@ task cleanJalviewjsAll {
   dependsOn jalviewjsEclipsePaths
   
   doFirst {
-    delete jalviewjsBuildDir
+    delete "${jalviewDir}/${jalviewjsBuildDir}"
     delete "${jalviewDir}/${eclipse_bin_dir}"
     if (eclipseWorkspace != null && file(eclipseWorkspace.getAbsolutePath()+"/.metadata").exists()) {
       delete file(eclipseWorkspace.getAbsolutePath()+"/.metadata")
     }
     delete "${jalviewDir}/${jalviewjs_j2s_settings}"
   }
+
+  outputs.upToDateWhen( { false } )
 }
 
 task jalviewjs {
@@ -1753,8 +1748,8 @@ task jalviewjs {
 
 
 task jalviewjsIDECopyTransferSite(type: Copy) {
-  from jalviewjsTransferSiteDir
-  into jalviewjsSiteDir
+  from "${jalviewDir}/${jalviewjsTransferSiteDir}"
+  into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
 task jalviewjsIDEj2s {