From 0ddf418d7540e715e6f0d112e2375fb1d7f1f294 Mon Sep 17 00:00:00 2001
From: soares <bsoares@dundee.ac.uk>
Date: Tue, 12 Nov 2019 20:10:08 +0000
Subject: [PATCH] JAL-3210 multiple core templates.

---
 build.gradle      |   43 ++++++++++++++++++++++++-------------------
 gradle.properties |    3 +--
 2 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/build.gradle b/build.gradle
index fc4d9ca..4080744 100644
--- a/build.gradle
+++ b/build.gradle
@@ -293,7 +293,6 @@ ext {
   jalviewjsTransferSiteCoreDir = string("${jalviewjsBuildDir}/tmp/${jalviewjs_site_dir}_core")
   jalviewjsJalviewCoreHtmlFile = string("")
   jalviewjsJalviewCoreName = string(jalviewjs_core_name)
-  jalviewjsDefaultCoreName = string(jalviewjs_default_core)
   jalviewjsCoreClasslists = []
   jalviewjsJalviewTemplateName = string(jalviewjs_name)
 
@@ -1439,6 +1438,9 @@ task jalviewjsSetEclipseWorkspace {
       props.store(bytes, null)
       def propertiesString = bytes.toString()
       propsFile.text = propertiesString
+      print("NEW ")
+    } else {
+      print("EXISTING ")
     }
 
     println("ECLIPSE WORKSPACE: "+eclipseWorkspace.getPath())
@@ -1893,6 +1895,8 @@ task jalviewjsBuildAllCores {
   dependsOn jalviewjsTransferUnzipSwingJs
 
   def j2sDir = "${jalviewDir}/${jalviewjsTransferSiteJsDir}/${jalviewjs_j2s_subdir}"
+  def swingJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_j2s_subdir}"
+  def libJ2sDir = "${jalviewDir}/${jalviewjsTransferSiteLibDir}/${jalviewjs_j2s_subdir}"
   def jsDir = "${jalviewDir}/${jalviewjsTransferSiteSwingJsDir}/${jalviewjs_js_subdir}"
   def outputDir = "${jalviewDir}/${jalviewjsTransferSiteCoreDir}/${jalviewjs_j2s_subdir}/core"
   def prefixFile = "${jsDir}/core/coretop2.js"
@@ -1969,10 +1973,13 @@ task jalviewjsBuildAllCores {
 
   // _all core
   def allClasslistName = "_all"
+  def allJsFiles = fileTree(dir: j2sDir, include: "**/*.js")
+  //allJsFiles += fileTree(dir: libJ2sDir, include: "**/*.js")
+  //allJsFiles += fileTree(dir: swingJ2sDir, include: "**/*.js")
   def allClasslist = [
     'jsfile': "${outputDir}/core${allClasslistName}.js",
     'zjsfile': "${outputDir}/core${allClasslistName}.z.js",
-    'list': fileTree(dir: j2sDir, include: "**/*.js"),
+    'list': allJsFiles,
     'name': allClasslistName
   ]
   jalviewjsCoreClasslists += allClasslist
@@ -2155,36 +2162,34 @@ task jalviewjsServer {
     def start = port
     def running = false
     def url
+    def jalviewjsServer
     while(port < start+1000 && !running) {
       try {
         def doc_root = new File("${jalviewDirAbsolutePath}/${jalviewjsSiteDir}")
-        def jalviewjsServer = factory.start(doc_root, port)
+        jalviewjsServer = factory.start(doc_root, port)
         running = true
         url = jalviewjsServer.getResourceUrl(jalviewjs_server_resource)
         println("SERVER STARTED with document root ${doc_root}.")
         println("Go to "+url+" . Run  gradle --stop  to stop (kills all gradle daemons).")
         println("For debug: "+url+"?j2sdebug")
-        println("For core: "+urlcore)
-
-        htmlText = """
-        <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
-        <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
-        """
-        jalviewjsCoreClasslists.each { cl ->
-          urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
-          htmlText += """
-          <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
-          """
-        }
-
-        file(htmlFile).text = htmlText
-
+        println("For verbose: "+url+"?j2sverbose")
       } catch (Exception e) {
-        e.printStackTrace()
         port++;
       }
     }
+    def htmlText = """
+      <p><a href="${url}">JalviewJS Test. &lt;${url}&gt;</a></p>
+      <p><a href="${url}?j2sdebug">JalviewJS Test with debug. &lt;${url}?j2sdebug&lt;</a></p>
+      """
+    jalviewjsCoreClasslists.each { cl ->
+      def urlcore = jalviewjsServer.getResourceUrl(file(cl.outputfile).getName())
+      htmlText += """
+      <p><a href="${urlcore}">${jalviewjsJalviewTemplateName} [core ${cl.name}]. &lt;${urlcore}&gt;</a></p>
+      """
+      println("For core ${cl.name}: "+urlcore)
+    }
 
+    file(htmlFile).text = htmlText
   }
 
   outputs.file(htmlFile)
diff --git a/gradle.properties b/gradle.properties
index aaf403d..d268369 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -173,11 +173,10 @@ jalviewjs_eclipse_build_arg = cleanBuild
 jalviewjs_server_port = 9001
 jalviewjs_server_wait = 30
 jalviewjs_server_resource = /jalview_bin_Jalview.html
-jalviewjs_core_name = _all
+jalviewjs_core_name = _jalview
 jalviewjs_name = JalviewJS
 #jalviewjs_core_key = core
 jalviewjs_core_key = preloadCore
-jalviewjs_default_core = all
 
 j2s.compiler.status = enable
 #j2s.site.directory = null ## site defined from buildDir+'/jalviewjs/'+jalviewjs_site_dir
-- 
1.7.10.2