JAL-3210 Improvements to how incremental build and gradle artefacts play with j2s

diff --git a/build.gradle b/build.gradle
index dec0765..9aef0ff 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -2,7 +2,8 @@ import org.apache.tools.ant.filters.ReplaceTokens
 import org.gradle.internal.os.OperatingSystem
 import org.gradle.plugins.ide.eclipse.model.*
 import groovy.transform.ExternalizeMethods
-import org.eclipse.osgi.*
+//import org.eclipse.osgi.*
+import com.diffplug.gradle.GoomphCacheLocations
 
 /*
 buildscript {
@@ -293,6 +294,20 @@ clean {
 
 
 
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+GoomphCacheLocations.override_workspaces = file(jalviewDirAbsolutePath+"/"+goomph_workspace)
 oomphIde {
   repoEclipse goomph_eclipse_version
   jdt {
@@ -358,18 +373,32 @@ ideJalviewjsBuild.dependsOn ideCopyDropins
 
 
 
-def tempEclipseWorkspace = ""
 
+def jalviewjsBuildDir
+def jalviewjsSiteDir
+task jalviewjsSitePath {
+  if (jalviewjs_site_dir.startsWith("/")) {
+    jalviewjsSiteDir = jalviewjs_site_dir
+  } else {
+    def relativeBuildDir = file(jalviewDirAbsolutePath).toPath().relativize(buildDir.toPath())
+    jalviewjsBuildDir = "${relativeBuildDir}/jalviewjs"
+    jalviewjsSiteDir = jalviewjsBuildDir + "/" + jalviewjs_site_dir
+  }
+}
+
+def tempEclipseWorkspace
 task jalviewjsSetTempEclipseWorkspace {
   tempEclipseWorkspace = file(jalviewjs_eclipse_workspace)
   if (!tempEclipseWorkspace.exists()) {
-    tempEclipseWorkspace = File.createTempDir()
-    tempEclipseWorkspace.deleteOnExit()
+    tempEclipseWorkspace = file("${buildDir}/tmp/eclipse-workspace")
+    //tempEclipseWorkspace.deleteOnExit()
   }
   println("ECLIPSE WORKSPACE: "+tempEclipseWorkspace.getPath())
 }
 
 task jalviewjsUnzipFiles {
+  dependsOn jalviewjsSitePath
+
   def zipFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_libjs_dir).include("*.zip")
   zipFiles += jalviewjs_utils_dir+"/"+jalviewjs_swingjs_zip
 
@@ -377,18 +406,17 @@ task jalviewjsUnzipFiles {
     zipFiles.each { file_zip -> 
       copy {
         from zipTree(file_zip)
-        into jalviewjs_site_dir
+        into jalviewjsSiteDir
       }
     }
   }
 
   inputs.files zipFiles
-  outputs.dir jalviewjs_site_dir
+  outputs.dir jalviewjsSiteDir
 }
 
-def eclipseBinary
 def eclipseDropinsDir
-def eclipsePluginsDir
+def eclipseBinary
 task jalviewjsEclipsePaths {
   def eclipseRoot = jalviewjs_eclipse_root
   if (eclipseRoot.startsWith("~")) {
@@ -397,18 +425,14 @@ task jalviewjsEclipsePaths {
        if (OperatingSystem.current().isMacOsX()) {
     eclipseRoot += "/Eclipse.app"
                eclipseDropinsDir = eclipseRoot+"/Contents/Eclipse/dropins"
-               eclipsePluginsDir = eclipseRoot+"/Contents/Eclipse/plugins"
                eclipseBinary = eclipseRoot+"/Contents/MacOS/eclipse"
        } else if (OperatingSystem.current().isWindows()) { // check these paths!!
                eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipsePluginsDir = eclipseRoot+"/plugins"
                eclipseBinary = eclipseRoot+"/eclipse"
        } else { // linux or unix
                eclipseDropinsDir = eclipseRoot+"/dropins"
-               eclipsePluginsDir = eclipseRoot+"/plugins"
                eclipseBinary = eclipseRoot+"/eclipse"
        }
-  println("ECLIPSE ROOT: "+eclipseRoot)
 }
 
 task jalviewjsEclipseCopyDropins (type: Copy) {
@@ -427,43 +451,39 @@ task jalviewjsEclipseCopyDropins (type: Copy) {
   inputs.files inputFiles
 }
 
-task jalviewjsEclipseCopyPlugins (type: Copy) {
-  dependsOn jalviewjsEclipsePaths
-  def inputFiles = fileTree(jalviewjs_utils_dir+"/"+jalviewjs_eclipse_plugins_dir)
-  def outputDir = eclipsePluginsDir
-
-  from inputFiles
-  into outputDir
-  def outputFiles = []
-  rename { filename ->
-    outputFiles += outputDir+"/"+filename
-    null
-  }
-  outputs.files outputFiles
-  inputs.files inputFiles
-}
-
 task jalviewjsEclipseSetup {
   dependsOn jalviewjsEclipseCopyDropins
-  dependsOn jalviewjsEclipseCopyPlugins
   dependsOn jalviewjsSetTempEclipseWorkspace
 }
 
 
 task jalviewjsCreateJ2sSettings(type: WriteProperties) {
+  dependsOn jalviewjsSitePath
   outputFile (jalviewDir+"/"+jalviewjs_j2s_settings)
   def props = project.properties.sort { it.key }
+  def siteDirProperty = "j2s.site.directory"
+  def setSiteDir = false
   props.each { prop, val ->
     if (prop.startsWith("j2s.") && val != null) {
+      if (prop == siteDirProperty) {
+        if (!(val.startsWith("/") || val.startsWith("file://") )) {
+          val = jalviewjsSiteDir+"/"+val
+        }
+        setSiteDir = true
+      }
       property(prop,val)
     }
+    if (!setSiteDir) {
+      property(siteDirProperty,"${jalviewjsSiteDir}")
+    }
   }
   outputs.file(outputFile)
 }
 
 task jalviewjsCopyResources (type: Copy) {
+  dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: jalviewjs_resource_dir)
-  def outputDir = jalviewjs_site_dir+"/"+jalviewjs_j2s_subdir
+  def outputDir = jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir
 
   from inputFiles
   into outputDir
@@ -477,8 +497,9 @@ task jalviewjsCopyResources (type: Copy) {
 }
 
 task jalviewjsCopySiteResources (type: Copy) {
+  dependsOn jalviewjsSitePath
   def inputFiles = fileTree(dir: jalviewjs_utils_dir+"/"+jalviewjs_site_resource_dir)
-  def outputDir = jalviewjs_site_dir
+  def outputDir = jalviewjsSiteDir
 
   from inputFiles
   into outputDir
@@ -492,8 +513,9 @@ task jalviewjsCopySiteResources (type: Copy) {
 }
 
 task cleanJalviewjs {
+  dependsOn jalviewjsSitePath
   /*
-  delete jalviewDir+"/"+jalviewjs_site_dir
+  delete jalviewDir+"/"+jalviewjsSiteDir
   delete jalviewDir+"/"+eclipse_bin_dir
   delete file(tempEclipseWorkspace.getAbsolutePath()+"/.metadata")
   delete jalviewDir+"/"+jalviewjs_j2s_settings
@@ -510,24 +532,58 @@ task jalviewjsProjectImport(type: Exec) {
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "com.seeq.eclipse.importprojects.headlessimport", "-data", tempEclipseWorkspace.getPath(), "-import", jalviewDirAbsolutePath])
 
-  def projdir = tempEclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core/"
+  def projdir = tempEclipseWorkspace.getPath()+"/.metadata/.plugins/org.eclipse.core.resources/.projects/jalview/org.eclipse.jdt.core"
   inputs.file(jalviewDir+"/.project")
   outputs.dir(projdir)
+  outputs.upToDateWhen { file(projdir).exists() }
 }
 
+
+
+
+
+
+
+
 task jalviewjsTranspile(type: Exec) {
   dependsOn jalviewjsCreateJ2sSettings 
   dependsOn jalviewjsProjectImport
   dependsOn jalviewjsEclipsePaths
   executable(eclipseBinary)
   args(["-nosplash", "--launcher.suppressErrors", "-application", "org.eclipse.jdt.apt.core.aptBuild", "-data", tempEclipseWorkspace, "-"+jalviewjs_eclipseBuildArg, eclipse_project_name ])
+
+  def stdout
+  def stderr
+  doFirst {
+    stdout = new ByteArrayOutputStream()
+    stderr = new ByteArrayOutputStream()
+    standardOutput = new org.apache.tools.ant.util.TeeOutputStream(new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stdout}"), stdout);
+    errorOutput = new org.apache.tools.ant.util.TeeOutputStream(new FileOutputStream("${jalviewjsBuildDir}/${jalviewjs_j2s_stderr}"), stderr);
+  }
+  doLast {
+    if (stdout.toString().contains("Error processing ")) {
+      // j2s did not complete transpile
+      throw new TaskExecutionException("Error during transpilation:\n${stderr}\n")
+    }
+  }
+
   inputs.dir(sourceDir)
   outputs.dir(eclipse_bin_dir+"/main")
-  outputs.file(eclipse_bin_dir+"/main/jalview/bin/Jalview.class")
-  outputs.dir(jalviewjs_site_dir+"/"+jalviewjs_j2s_subdir)
+  outputs.dir(jalviewjsSiteDir+"/"+jalviewjs_j2s_subdir)
+  outputs.file(jalviewjsSiteDir+jalviewjs_server_resource)
+  outputs.upToDateWhen { file(jalviewjsSiteDir+jalviewjs_server_resource).exists() }
+
 }
 
+
+
+
+
+
+
+
 task jalviewjsBuildSite {
+  dependsOn jalviewjsSitePath
   dependsOn jalviewjsUnzipFiles
   dependsOn jalviewjsCopyResources
   dependsOn jalviewjsCopySiteResources
@@ -545,10 +601,10 @@ task jalviewjsSiteTar(type: Tar) {
 
   compression Compression.GZIP
 
-  from jalviewjs_site_dir
+  from jalviewjsSiteDir
   into jalviewjs_site_dir // this is inside the tar file
 
-  inputs.dir(jalviewjs_site_dir)
+  inputs.dir(jalviewjsSiteDir)
 }
 
 task jalviewjs {
@@ -557,6 +613,7 @@ task jalviewjs {
 
 def jalviewjsServer = null
 task jalviewjsServerStart {
+  dependsOn jalviewjsSitePath
   doLast {
 
     if (jalviewjsServer != null) {
@@ -569,9 +626,10 @@ task jalviewjsServerStart {
       def running = false
       while(port < start+1000 && !running) {
         try {
-          jalviewjsServer = factory.start(new File(jalviewDirAbsolutePath+"/"+jalviewjs_site_dir), port)
+          def doc_root = new File(jalviewDirAbsolutePath +"/"+ jalviewjsSiteDir)
+          jalviewjsServer = factory.start(doc_root, port)
           running = true
-          println("SERVER STARTED. Go to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run  gradle jalviewjsServerStop  to stop.")
+          println("SERVER STARTED with document root ${doc_root}.\nGo to "+jalviewjsServer.getResourceUrl(jalviewjs_server_resource)+" . Run  gradle jalviewjsServerStop  to stop.")
           //println("Ctrl-c to stop.");java.lang.Thread.sleep(Integer.valueOf(jalviewjs_server_wait)*1000);
         } catch (Exception e) {
           port++;

diff --git a/gradle.properties b/gradle.properties
index d2c5394..bab2570 100644 (file)
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,7 +1,7 @@
 jalviewDir = .
 
-JAVA_VERSION = 1.8
-#JAVA_VERSION = 11
+#JAVA_VERSION = 1.8
+JAVA_VERSION = 11
 JALVIEW_VERSION = DEVELOPMENT
 INSTALLATION = Source
 
@@ -40,7 +40,6 @@ dev = false
 jalviewjs_eclipse_root = ~/buildtools/eclipse/eclipse-jee-2019-06
 
 jalviewjs_utils_dir = utils/jalviewjs
-jalviewjs_eclipse_plugins_dir = eclipse/plugins
 jalviewjs_eclipse_dropins_dir = eclipse/dropins
 jalviewjs_swingjs_zip = SwingJS-site.zip
 jalviewjs_libjs_dir = libjs
@@ -66,7 +65,7 @@ j2s.excluded.paths = test;testng;util
 #j2s.testing = null
 #j2s.compiler.nonqualified.packages = null
 #j2s.compiler.nonqualified.classes = null
-#j2s.compiler.mode = null
+j2s.compiler.mode = debug
 #a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made 
 j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
 #j2s.template.html = null
@@ -79,7 +78,11 @@ j2s.class.replacements = org.apache.log4j.->jalview.javascript.log4j.
 #output will be comma-separated: called method,caller class 
 #j2s.prop.j2s.log.all.calls=true
 
+jalviewjs_j2s_stdout = j2s-transpile.out
+jalviewjs_j2s_stderr = j2s-transpile.err
+
 spotless_eclipse_version = 4.12.0
-goomph_eclipse_version = 4.13
+goomph_eclipse_version = 4.12
 goomph_repo_buildship = https://download.eclipse.org/buildship/updates/e47/releases/3.x/
 goomph_feature_buildship = org.eclipse.buildship
+goomph_workspace = ../tmp/goomph-workspace

diff --git a/utils/jalviewjs/SwingJS-site.zip b/utils/jalviewjs/SwingJS-site.zip
index c8c7341..40feffa 100644 (file)
Binary files a/utils/jalviewjs/SwingJS-site.zip and b/utils/jalviewjs/SwingJS-site.zip differ

diff --git a/utils/jalviewjs/eclipse/plugins/com.seeq.eclipse.importprojects_1.4.0.jar b/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects_1.4.0.jar
similarity index 100%
rename from utils/jalviewjs/eclipse/plugins/com.seeq.eclipse.importprojects_1.4.0.jar
rename to utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects_1.4.0.jar

diff --git a/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core.jar b/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core.jar
index 87df1d9..e8288a9 100644 (file)
Binary files a/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core.jar and b/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core.jar differ