From 439d89cfdb49de11de73e31b2604672edcc5a45d Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Tue, 21 Apr 2020 01:11:04 +0100
Subject: [PATCH] JAL-3602 Added configuration for enforced use of UTF-8 for
 creating the core js files and also in the
 closure-compiler.

---
 build.gradle      |   31 ++++++++++++++++++++-----------
 gradle.properties |    4 +++-
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/build.gradle b/build.gradle
index d955de3..985cc87 100644
--- a/build.gradle
+++ b/build.gradle
@@ -804,11 +804,12 @@ task cleanClover {
 
 
 compileJava {
-
+	
+  sourceCompatibility = compile_source_compatibility
+  targetCompatibility = compile_target_compatibility
+  options.compilerArgs = additional_compiler_args
+  options.encoding = "UTF-8"
   doFirst {
-    sourceCompatibility = compile_source_compatibility
-    targetCompatibility = compile_target_compatibility
-    options.compilerArgs = additional_compiler_args
     print ("Setting target compatibility to "+targetCompatibility+"\n")
   }
 
@@ -1423,6 +1424,11 @@ task getdown() {
 }
 
 
+tasks.withType(JavaCompile) {
+	options.encoding = 'UTF-8'
+}
+
+
 clean {
   doFirst {
     delete getdownWebsiteDir
@@ -1818,13 +1824,14 @@ task jalviewjsEclipsePaths {
     eclipseProduct = "${eclipseRoot}/Contents/Eclipse/.eclipseproduct"
   } else if (OperatingSystem.current().isWindows()) { // check these paths!!
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
-      eclipseRoot += "/eclipse.exe"
+      eclipseRoot += "/eclipse"
     }
-    eclipseBinary = "${eclipseRoot}/eclipse"
+    eclipseBinary = "${eclipseRoot}/eclipse.exe"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
   } else { // linux or unix
     if (file("${eclipseRoot}/eclipse").isDirectory() && file("${eclipseRoot}/eclipse/.eclipseproduct").exists()) {
       eclipseRoot += "/eclipse"
+println("eclipseDir exists")
     }
     eclipseBinary = "${eclipseRoot}/eclipse"
     eclipseProduct = "${eclipseRoot}/.eclipseproduct"
@@ -2203,11 +2210,11 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
   def coreBottom = file(suffixFile)
   coreFile.getParentFile().mkdirs()
   coreFile.createNewFile()
-  coreFile.write( coreTop.text )
+  coreFile.write( coreTop.getText("UTF-8") )
   list.each {
     f ->
     if (f.exists()) {
-      def t = f.text
+      def t = f.getText("UTF-8")
       t.replaceAll("Clazz\\.([^_])","Clazz_${1}")
       coreFile.append( t )
     } else {
@@ -2216,7 +2223,7 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
       logOutFile.append(msg+"\n")
     }
   }
-  coreFile.append( coreBottom.text )
+  coreFile.append( coreBottom.getText("UTF-8") )
 
   msg = "Generating ${zjsfile}"
   println(msg)
@@ -2225,8 +2232,10 @@ def jalviewjsCallCore(String name, FileCollection list, String prefixFile, Strin
   def logErrFOS = logOutFOS
 
   javaexec {
-    classpath = files(["${jalviewDir}/tools/closure_compiler.jar"])
-    args = [ "--js", jsfile, "--js_output_file", zjsfile ]
+    classpath = files(["${jalviewDir}/${jalviewjs_closure_compiler}"])
+    main = "com.google.javascript.jscomp.CommandLineRunner"
+    jvmArgs = [ "-Dfile.encoding=UTF-8" ]
+    args = [ "--compilation_level", "SIMPLE_OPTIMIZATIONS", "--warning_level", "QUIET", "--charset", "UTF-8", "--js", jsfile, "--js_output_file", zjsfile ]
     maxHeapSize = "2g"
 
     msg = "\nRunning '"+commandLine.join(' ')+"'\n"
diff --git a/gradle.properties b/gradle.properties
index 1507117..59699e3 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,4 +1,5 @@
-org.gradle.jvmargs=-Xmx1536m -Xms512m
+org.gradle.jvmargs=-Xmx1536m -Xms512m -Dfile.encoding=UTF-8
+#systemProp.file.encoding=UTF-8
 
 jalviewDir = .
 
@@ -213,6 +214,7 @@ j2s_coretemplate_html = utils/jalviewjs/coretemplate.html
 jalviewjs_j2s_transpile_stdout = j2s-transpile.out
 #jalviewjs_j2s_stderr = j2s-transpile.err # all going into out
 jalviewjs_j2s_to_console = true
+jalviewjs_closure_compiler = tools/closure_compiler.jar
 jalviewjs_j2s_closure_stdout = j2s-closure.out
 
 
-- 
1.7.10.2