From 7b4179c8760e3c7e797ad2cecc3150cbd7608259 Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 14 Nov 2019 10:35:11 +0000
Subject: [PATCH] JAL-3210 Auto copy j2s plugin to Eclipse IDE dropins dir.
 Off by default

---
 build.gradle      |   46 ++++++++++++++++++++++++++++++++++++----------
 gradle.properties |    3 +++
 2 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/build.gradle b/build.gradle
index 7cdadc1..0117ffc 100644
--- a/build.gradle
+++ b/build.gradle
@@ -431,6 +431,9 @@ eclipse {
         def removeTheseToo = []
         HashMap<String, Boolean> alreadyAddedSrcPath = new HashMap<>();
         cp.entries.each { entry ->
+          // This conditional removes all src classpathentries that a) have already been added or b) aren't "src" or "test".
+          // e.g. this removes the resources dir being copied into bin/main, bin/test AND bin/clover
+          // we add the resources and help/help dirs in as libs afterwards (see below)
           if (entry.kind == 'src') {
             if (alreadyAddedSrcPath.getAt(entry.path) || !(entry.path == bareSourceDir || entry.path == bareTestSourceDir)) {
               removeTheseToo += entry
@@ -438,10 +441,11 @@ eclipse {
               alreadyAddedSrcPath.putAt(entry.path, true)
             }
           }
+
         }
         cp.entries.removeAll(removeTheseToo)
 
-        cp.entries += new Output("${eclipse_bin_dir}/main")
+        //cp.entries += new Output("${eclipse_bin_dir}/main")
         if (file(helpSourceDir).isDirectory()) {
           cp.entries += new Library(fileReference(helpSourceDir))
         }
@@ -454,8 +458,8 @@ eclipse {
         sourceSets.main.compileClasspath.findAll { it.name.endsWith(".jar") }.each {
           //don't want to add outputDir as eclipse is using its own output dir in bin/main
           if (it.isDirectory() || ! it.exists()) {
-            // don't add dirs to classpath
-            return
+            // don't add dirs to classpath, especially if they don't exist
+            return false // groovy "continue" in .any closure
           }
           def itPath = it.toString()
           if (itPath.startsWith("${jalviewDirAbsolutePath}/")) {
@@ -528,6 +532,7 @@ eclipse {
     // Don't want these to be activated if in headless build
     synchronizationTasks "eclipseSynchronizationTask"
     autoBuildTasks "eclipseAutoBuildTask"
+
   }
 }
 
@@ -2260,12 +2265,14 @@ task cleanJalviewjsAll {
 
 task jalviewjsIDE_checkJ2sPlugin {
   group "00 JalviewJS in Eclipse"
-  description "Compare the swingjs/net.sf.j2s.core.jar file with the Eclipse pluing version"
+  description "Compare the swingjs/net.sf.j2s.core.jar file with the Eclipse IDE's plugin version (found in the 'dropins' dir)"
 
   doFirst {
     def j2sPlugin = string("${jalviewDir}/${jalviewjs_j2s_plugin}")
     def j2sPluginFile = file(j2sPlugin)
     def eclipseHome = System.properties["eclipse.home.location"]
+    def copyPlugin = jalviewjs_eclipseIDE_auto_copy_j2s_plugin == "true"
+    def doCopy = false
     if (eclipseHome == null || ! IN_ECLIPSE) {
       throw new StopExecutionException("Cannot find running Eclipse home from System.properties['eclipse.home.location']. Skipping J2S Plugin Check.")
     }
@@ -2274,7 +2281,10 @@ task jalviewjsIDE_checkJ2sPlugin {
     if (!eclipseJ2sPluginFile.exists()) {
       def msg = "Eclipse J2S Plugin is not installed"
       println(msg)
-      throw new GradleException(msg)
+      if (! copyPlugin) {
+        throw new GradleException(msg)
+      }
+      doCopy = true
     }
 
     def digest = MessageDigest.getInstance("MD5")
@@ -2286,12 +2296,26 @@ task jalviewjsIDE_checkJ2sPlugin {
     def eclipseJ2sPluginMd5 = new BigInteger(1, digest.digest()).toString(16).padLeft(32, '0')
      
     if (j2sPluginMd5 != eclipseJ2sPluginMd5) {
-      def msg = "Eclipse J2S Plugin is different to '${j2sPlugin}'"
+      def msg = "WARNING! Eclipse J2S Plugin '${eclipseJ2sPlugin}' is different to this commit's version '${j2sPlugin}'"
       println(msg)
-      throw new GradleException(msg)
+      if (! copyPlugin) {
+        throw new StopExecutionException(msg)
+      }
+      doCopy = true
     }
 
-    println("Eclipse J2S Plugin is same as '${j2sPlugin}'")
+    if (doCopy) {
+      def msg = "WARNING! Auto-copying this commit's j2s plugin version '${j2sPlugin}' to Eclipse J2S Plugin '${eclipseJ2sPlugin}'\n         May require an Eclipse restart"
+      println(msg)
+      copy {
+        from j2sPlugin
+        eclipseJ2sPluginFile.getParentFile().mkdirs()
+        into eclipseJ2sPluginFile.getParent()
+      }
+    } else {
+      def msg = "Eclipse J2S Plugin is the same as '${j2sPlugin}'"
+      println(msg)
+    }
   }
 }
 
@@ -2341,15 +2365,17 @@ task jalviewjsIDE_Server {
 }
 
 
-// buildship runs this at import
+// buildship runs this at import or gradle refresh
 task eclipseSynchronizationTask {
   //dependsOn eclipseSetup
   dependsOn jalviewjsIDE_j2sFile
+  dependsOn jalviewjsIDE_checkJ2sPlugin
 }
 
 
-// buildship runs this at build time
+// buildship runs this at build time or project refresh
 task eclipseAutoBuildTask {
+  //dependsOn jalviewjsIDE_checkJ2sPlugin
   dependsOn jalviewjsIDE_PrepareSite
 }
 
diff --git a/gradle.properties b/gradle.properties
index 7389cbe..b64eb11 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -147,6 +147,9 @@ eclipse_project_name = jalview
 eclipse_bin_dir = bin
 eclipse_debug = false
 
+# for developing in Eclipse as IDE, set this to automatically copy current swingjs/net.sf.j2s.core.jar to your dropins dir
+jalviewjs_eclipseIDE_auto_copy_j2s_plugin = false
+# Override this in a local.properties file
 jalviewjs_eclipse_root = ~/buildtools/eclipse/jee-2019-09
 
 jalviewjs_eclipse_dropins_dir = utils/jalviewjs/eclipse/dropins
-- 
1.7.10.2