From: Ben Soares <bsoares@dundee.ac.uk>
Date: Fri, 8 Nov 2019 10:18:12 +0000 (+0000)
Subject: Revert "JAL-3210 Added jalviewjsBuildAllClosures. Improved incrementality of jalviewj... 
X-Git-Tag: Release_2_11_4_0~45^2~18^2~57^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=db3936d2efd977012b614888cf5b186725a662af;p=jalview.git

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

This reverts commit 9fe5286cbcbbfdca0e9548e6ab1b6543871a8073.

Seems to have broken development in Eclipse IDE. Reverting.
---

diff --git a/build.gradle b/build.gradle
index 52c0385..a88c42f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1331,9 +1331,8 @@ task jalviewjsSetEclipseWorkspace {
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
   }
 
-  //inputs.property(propKey, eclipseWsDir) // eclipseWsDir only gets set once this task runs, so will be out-of-date
+  inputs.property(propKey, eclipseWsDir)
   outputs.file(propsFileName)
-  outputs.upToDateWhen { eclipseWorkspace.exists() }
 }
 
 
@@ -1620,8 +1619,7 @@ 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"
+  def projdir = eclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", eclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
   if (eclipseDebug) {
@@ -1630,9 +1628,7 @@ 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) {
@@ -1653,7 +1649,7 @@ task jalviewjsTranspile(type: Exec) {
     stdout = new ByteArrayOutputStream()
     stderr = new ByteArrayOutputStream()
 
-    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_transpile_stdout}"
+    def logOutFileName = "${jalviewDirAbsolutePath}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"
     def logOutFile = file(logOutFileName)
     logOutFile.createNewFile()
     logOutFile.text = """ROOT: ${jalviewjs_eclipse_root}
@@ -1695,7 +1691,7 @@ 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}/${jalviewjs_j2s_transpile_stdout}'")
+      throw new GradleException("Error during transpilation:\n${stderr}\nSee eclipse transpile log file '${jalviewDir}/${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}'")
     }
   }
 
@@ -1704,15 +1700,15 @@ DEBUG: ${eclipseDebug}
   outputs.upToDateWhen( { file("${jalviewDir}/${jalviewjsTransferSiteJsDir}${jalviewjs_server_resource}").exists() } )
 }
 
-// this Copy version of TransferSiteJs will delete anything else in the target dir
-task jalviewjsCopyTransferSiteJs(type: Copy) {
+// this Copy version of TransferSite will delete anything else in the target dir
+task jalviewjsCopyTransferSite(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 jalviewjsSyncTransferSiteJs(type: Sync) {
+task jalviewjsSyncTransferSite(type: Sync) {
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   include "**/*.*"
   into "${jalviewDir}/${jalviewjsSiteDir}"
@@ -1721,15 +1717,15 @@ task jalviewjsSyncTransferSiteJs(type: Sync) {
   }
 }
 
-jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSiteJs
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSiteJs
+jalviewjsSyncLib.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncResources.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsCopyTransferSite
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsCopyTransferSite
 
-jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSiteJs
-jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSiteJs
-jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSiteJs
-jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSiteJs
+jalviewjsSyncLib.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncResources.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncSiteResources.mustRunAfter jalviewjsSyncTransferSite
+jalviewjsSyncBuildProperties.mustRunAfter jalviewjsSyncTransferSite
 
 task jalviewjsPrepareSite {
   group "JalviewJS"
@@ -1738,21 +1734,18 @@ task jalviewjsPrepareSite {
   dependsOn jalviewjsSyncResources
   dependsOn jalviewjsSyncSiteResources
   dependsOn jalviewjsSyncBuildProperties
-  dependsOn jalviewjsSyncCore
 }
 
 task jalviewjsBuildSite {
   group "JalviewJS"
   description "Builds the whole website including transpiled code"
-  dependsOn jalviewjsCopyTransferSiteJs
+  dependsOn jalviewjsCopyTransferSite
   dependsOn jalviewjsPrepareSite
 }
 
 task cleanJalviewjsSite {
   doFirst {
     delete "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
-    delete "${jalviewDir}/${jalviewjsTransferSiteLibDir}"
-    delete "${jalviewDir}/${jalviewjsTransferSiteCoreDir}"
     delete "${jalviewDir}/${jalviewjsSiteDir}"
   }
 }
@@ -1840,12 +1833,12 @@ task jalviewjs {
 }
 
 
-task jalviewjsIDE_CopyTransferSiteJs(type: Copy) {
+task jalviewjsIDE_CopyTransferSite(type: Copy) {
   from "${jalviewDir}/${jalviewjsTransferSiteJsDir}"
   into "${jalviewDir}/${jalviewjsSiteDir}"
 }
 
-task jalviewjsIDE_j2sFile {
+task jalviewjsIDE_j2s {
   group "00 JalviewJS in Eclipse"
   description "Creates the .j2s file"
   dependsOn jalviewjsCreateJ2sSettings
@@ -1854,7 +1847,7 @@ task jalviewjsIDE_j2sFile {
 task jalviewjsIDE_AssembleSite {
   group "00 JalviewJS in Eclipse"
   description "Assembles the Eclipse transpiled site and unzips supporting zipfiles"
-  dependsOn jalviewjsIDE_CopyTransferSiteJs
+  dependsOn jalviewjsIDE_CopyTransferSite
   dependsOn jalviewjsPrepareSite
 }
 
@@ -1873,12 +1866,12 @@ task jalviewjsIDE_Server {
 // buildship runs this at import
 task eclipseSynchronizationTask {
   dependsOn eclipseSetup
-  dependsOn jalviewjsIDE_j2sFile
+  dependsOn jalviewjsIDE_j2s
 }
 
 // buildship runs this at build time
 task eclipseAutoBuildTask {
-  dependsOn jalviewjsSyncTransferSiteJs
+  dependsOn jalviewjsSyncTransferSite
   dependsOn jalviewjsPrepareSite
 }
 
@@ -1890,21 +1883,14 @@ task eclipseAutoBuildTask {
 
 
 // closure
-
-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 ${jsfile}"
-  println(msg)
-  logOutFile.createNewFile()
-  logOutFile.append(msg+"\n")
-
-  def coreTop = file(prefixFile)
-  def coreBottom = file(suffixFile)
+def jalviewjsCallCore(String name, FileCollection list, String jsDir, String outputDir) {
+  def coreFileName = "core${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")
   coreFile.getParentFile().mkdirs()
   coreFile.createNewFile()
   coreFile.write( coreTop.text )
@@ -1916,53 +1902,43 @@ def jalviewjsCallCore(FileCollection list, String prefixFile, String suffixFile,
       t.replaceAll("Class__","Clazz._")
       coreFile.append( t )
     } else {
-      msg = "...file "+f.getPath()+" does not exist, skipping"
-      println(msg)
-      logOutFile.append(msg+"\n")
+      println("...file ${line} does not exist, skipping")
     }
   }
   coreFile.append( coreBottom.text )
 
-  msg = "Generating ${zjsfile}"
-  println(msg)
-  logOutFile.append(msg+"\n")
-  def logOutFOS = new FileOutputStream(logOutFile, true) // true == append
-  def logErrFOS = logOutFOS
+  def coreZFileName = "core${name}.z.js"
+  def coreZFilePath = "${outputDir}/${coreZFileName}"
+  def coreZFile = file(coreZFilePath)
+  println("...Generating ${coreZFilePath}")
 
   javaexec {
     classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
-    args = [ "--js", jsfile, "--js_output_file", zjsfile ]
-
-    msg = "\nRunning '"+commandLine.join(' ')+"'\n"
-    println(msg)
-    logOutFile.append(msg+"\n")
-
-    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)
-    }
+    args = [ "--js", coreFileName, "--js_output_file", coreZFileName ]
+    workingDir = outputDir
   }
-  msg = "--"
-  println(msg)
-  logOutFile.append(msg+"\n")
+
+  return [ coreFile, coreZFile ]
 }
 
+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}")
+  }
+  */
 
+  return jalviewjsCallCore(name, list, jsDir, outputDir)
+// publish-core-template ... here?
+}
 
 task jalviewjsBuildAllCores {
   group "JalviewJS"
@@ -1972,54 +1948,10 @@ 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"
 
-    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}/${jalviewjs_j2s_closure_stdout}")
-    logOutFile.getParentFile().mkdirs()
-    logOutFile.createNewFile()
-    logOutFile.write(getDate("yyyy-MM-dd HH:mm:ss")+" jalviewjsBuildAllCores\n----\n")
-
-    classlists.each {
-      jalviewjsCallCore(it.list, prefixFile, suffixFile, it.jsfile, it.zjsfile, logOutFile, jalviewjs_j2s_to_console.equals("true"))
-    }
+    jalviewjsToJs(name, file.getAbsolutePath(), "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_js_subdir}", "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}", "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core")
   }
-
 }
diff --git a/gradle.properties b/gradle.properties
index 444d333..d602a9c 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -195,10 +195,9 @@ 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_transpile_stdout = j2s-transpile.out
+jalviewjs_j2s_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