From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 7 Nov 2019 15:36:48 +0000 (+0000)
Subject: JAL-3210 Added jalviewjsBuildAllClosures. Improved incrementality of jalviewjsSetEcli... 
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~75
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=9fe5286cbcbbfdca0e9548e6ab1b6543871a8073

JAL-3210 Added jalviewjsBuildAllClosures. Improved incrementality of jalviewjsSetEclipseWorkspace and jalviewjsProjectImport and hence jalviewjsTranspile :)
---

diff --git a/build.gradle b/build.gradle
index a88c42f..52c0385 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1331,8 +1331,9 @@ task jalviewjsSetEclipseWorkspace {
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
 
-  inputs.property(propKey, eclipseWsDir)
+  //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date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() }
 }
 
 
@@ -1619,7 +1620,8 @@ task jalviewjsProjectImport(type: Exec) {
   dependsOn jalviewjsEclipsePaths
   dependsOn jalviewjsEclipseSetup
 
-  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+  //def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
+  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview"
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
   if (eclipseDebug) {
@@ -1628,7 +1630,9 @@ task jalviewjsProjectImport(type: Exec) {
   args += [ "--launcher.appendVmargs", "-vmargs", "-Dorg.eclipse.equinox.p2.reconciler.dropins.directory=${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_eclipse_tmp_dropins_dir}" ]
 
   inputs.file("${jalviewDir}/.project")
-  outputs.upToDateWhen { file(projdir).exists() }
+  outputs.upToDateWhen { 
+    file(projdir).exists()
+  }
 }
 
 task jalviewjsTranspile(type: Exec) {
@@ -1649,7 +1653,7 @@ task jalviewjsTranspile(type: Exec) {
     stdout = new ByteArrayOutputStream()
     stderr = new ByteArrayOutputStream()
 
-    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
     def logOutFile = file(logOutFileName)
     logOutFile.createNewFile()
     logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
@@ -1691,7 +1695,7 @@ DEBUG: ${eclipseDebug}
   doLast {
     if (stdout.toString().contains("Error processing ")) {
       // j2s did not complete transpile
-      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}'")
     }
   }
 
@@ -1700,15 +1704,15 @@ DEBUG: ${eclipseDebug}
   outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
 }
 
-// this Copy version of TransferSite will delete anything else in the target dir
-task jalviewjsCopyTransferSite(type: Copy) {
+// this Copy version of TransferSiteJs will delete anything else in the target dir
+task jalviewjsCopyTransferSiteJs(type: Copy) {
   dependsOn jalviewjsTranspile
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
 // this Sync version of TransferSite is used by buildship to keep the website automatically up to date when a file changes
-task jalviewjsSyncTransferSite(type: Sync) {
+task jalviewjsSyncTransferSiteJs(type: Sync) {
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   include "**/*.*"
   into "${jalviewDir}/${jalviewjsSiteDir}"
@@ -1717,15 +1721,15 @@ task jalviewjsSyncTransferSite(type: Sync) {
   }
 }
 
-jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSite
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
 
-jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSite
-jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSite
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSite
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
 
 task jalviewjsPrepareSite {
   group "JalviewJS"
@@ -1734,18 +1738,21 @@ task jalviewjsPrepareSite {
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
   dependsOn jalviewjsSyncBuildProperties
+  dependsOn jalviewjsSyncCore
 }
 
 task jalviewjsBuildSite {
   group "JalviewJS"
   description "Builds the whole website including transpiled code"
-  dependsOn jalviewjsCopyTransferSite
+  dependsOn jalviewjsCopyTransferSiteJs
   dependsOn jalviewjsPrepareSite
 }
 
 task cleanJalviewjsSite {
   doFirst {
     delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
+    delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
     delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
@@ -1833,12 +1840,12 @@ task jalviewjs {
 }
 
 
-task jalviewjsIDE_CopyTransferSite(type: Copy) {
+task jalviewjsIDE_CopyTransferSiteJs(type: Copy) {
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-task jalviewjsIDE_j2s {
+task jalviewjsIDE_j2sFile {
   group "00 JalviewJS in Eclipse"
   description "Creates the .j2s file"
   dependsOn jalviewjsCreateJ2sSettings
@@ -1847,7 +1854,7 @@ task jalviewjsIDE_j2s {
 task jalviewjsIDE_AssembleSite {
   group "00 JalviewJS in Eclipse"
   description "Assembles the Eclipse transpiled site and unzips supporting zipfiles"
-  dependsOn jalviewjsIDE_CopyTransferSite
+  dependsOn jalviewjsIDE_CopyTransferSiteJs
   dependsOn jalviewjsPrepareSite
 }
 
@@ -1866,12 +1873,12 @@ task jalviewjsIDE_Server {
 // buildship runs this at import
 task eclipseSynchronizationTask {
   dependsOn eclipseSetup
-  dependsOn jalviewjsIDE_j2s
+  dependsOn jalviewjsIDE_j2sFile
 }
 
 // buildship runs this at build time
 task eclipseAutoBuildTask {
-  dependsOn jalviewjsSyncTransferSite
+  dependsOn jalviewjsSyncTransferSiteJs
   dependsOn jalviewjsPrepareSite
 }
 
@@ -1883,14 +1890,21 @@ task eclipseAutoBuildTask {
 
 
 // closure
-def jalviewjsCallCore(String name, FileCollection list, String jsDir, String outputDir) {
-  def coreFileName = "core${name}.js"
-  def coreFilePath = "${outputDir}/${coreFileName}"
-  def coreFile = file(coreFilePath)
-  println("...Generating ${coreFilePath}")
-
-  def coreTop = file("${jsDir}/core/coretop2.js")
-  def coreBottom = file("${jsDir}/core/corebottom2.js")
+
+def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile, String jsfile, String zjsfile, File logOutFile, Boolean logOutConsole) {
+
+  def stdout = new ByteArrayOutputStream()
+  def stderr = new ByteArrayOutputStream()
+
+  def coreFile = file(jsfile)
+  def msg = ""
+  msg = "Generating ${jsfile}"
+  println(msg)
+  logOutFile.createNewFile()
+  logOutFile.append(msg+"\n")
+
+  def coreTop = file(prefixFile)
+  def coreBottom = file(suffixFile)
   coreFile.getParentFile().mkdirs()
   coreFile.createNewFile()
   coreFile.write( coreTop.text )
@@ -1902,44 +1916,54 @@ def jalviewjsCallCore(String name, FileCollection list, String jsDir, String out
       t.replaceAll("Class__","Clazz._")
       coreFile.append( t )
     } else {
-      println("...file ${line} does not exist, skipping")
+      msg = "...file "+f.getPath()+" does not exist, skipping"
+      println(msg)
+      logOutFile.append(msg+"\n")
     }
   }
   coreFile.append( coreBottom.text )
 
-  def coreZFileName = "core${name}.z.js"
-  def coreZFilePath = "${outputDir}/${coreZFileName}"
-  def coreZFile = file(coreZFilePath)
-  println("...Generating ${coreZFilePath}")
+  msg = "Generating ${zjsfile}"
+  println(msg)
+  logOutFile.append(msg+"\n")
+  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
+  def logErrFOS = logOutFOS
 
   javaexec {
     classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
-    args = [ "--js", coreFileName, "--js_output_file", coreZFileName ]
-    workingDir = outputDir
-  }
+    args = [ "--js", jsfile, "--js_output_file", zjsfile ]
 
-  return [ coreFile, coreZFile ]
-}
+    msg = "\nRunning '"+commandLine.join(' ')+"'\n"
+    println(msg)
+    logOutFile.append(msg+"\n")
 
-def jalviewjsToJs(String name, String classlist, String jsDir, String j2sDir, String outputDir) {
-  def filelist = []
-  file(classlist).eachLine {
-    line ->
-    filelist += line
-  }
-  def list = fileTree(dir: j2sDir, includes: filelist)
-  /*
-  def list = files()
-  file(classlist).eachLine {
-    line ->
-    list += file("${j2sDir}/${line}")
+    if (logOutConsole) {
+      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)
+        errorOutput = new org.apache.tools.ant.util.TeeOutputStream(
+          logErrFOS,
+          stderr)
+    }
   }
-  */
-
-  return jalviewjsCallCore(name, list, jsDir, outputDir)
-// publish-core-template ... here?
+  msg = "--"
+  println(msg)
+  logOutFile.append(msg+"\n")
 }
 
+
+
 task jalviewjsBuildAllCores {
   group "JalviewJS"
   description "Build the core js lib closures"
@@ -1948,10 +1972,54 @@ task jalviewjsBuildAllCores {
   dependsOn jalviewjsTransferUnzipLib
   dependsOn jalviewjsTranspile
 
+  def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+  def jsDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_js_subdir}"
+  def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
+  def prefixFile = "${jsDir}/core/coretop2.js"
+  def suffixFile = "${jsDir}/core/corebottom2.js"
+
+  inputs.file prefixFile
+  inputs.file suffixFile
+
+  def classlists = []
   fileTree(dir: "${jalviewDir}/${jalviewjs_classlists_dir}", include: "*.txt").each {
     file ->
     def name = file.getName() - ".txt"
 
-    jalviewjsToJs(name, file.getAbsolutePath(), "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_js_subdir}", "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}", "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core")
+    def filelist = []
+    file.eachLine {
+      line ->
+      filelist += line
+    }
+    def list = fileTree(dir: j2sDir, includes: filelist)
+
+    def coreFileName = "core${name}.js"
+    def jsfile = "${outputDir}/${coreFileName}"
+    def coreZFileName = "core${name}.z.js"
+    def zjsfile = "${outputDir}/${coreZFileName}"
+
+    classlists += [
+      'jsfile': jsfile,
+      'zjsfile': zjsfile,
+      'list': list
+    ]
+
+    inputs.file(file)
+    inputs.files(list)
+    outputs.file(jsfile)
+    outputs.file(zjsfile)
+  } 
+
+
+  doFirst {
+    def logOutFile = file("${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_closure_stdout}")
+    logOutFile.getParentFile().mkdirs()
+    logOutFile.createNewFile()
+    logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
+
+    classlists.each {
+      jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
+    }
   }
+
 }
diff --git a/gradle.properties b/gradle.properties
index d602a9c..444d333 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -195,9 +195,10 @@ j2s.template.html = utils/jalviewjs/template.html
 #output will be comma-separated: called method,caller class 
 #j2s.prop.j2s.log.all.calls=true
 
-jalviewjs_j2s_stdout = j2s-transpile.out
+jalviewjs_j2s_transpile_stdout = j2s-transpile.out
 #jalviewjs_j2s_stderr = j2s-transpile.err # all going into out
 jalviewjs_j2s_to_console = true
+jalviewjs_j2s_closure_stdout = j2s-closure.out
 
 
 testp=gradle.properties