From dfa39e09cf3ffa44cc1e764bfa72900bab96136d Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 23 Mar 2017 18:47:41 +0000
Subject: [PATCH] JAL-2314 Tweaks to stop thread sync issues

---
 src/jalview/gui/Desktop.java                      |    2 ++
 src/jalview/ws/jws2/Jws2Discoverer.java           |   27 +++++++++++++++++++++
 test/jalview/ws/jabaws/RNAStructExportImport.java |    6 +++++
 3 files changed, 35 insertions(+)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 7d0eb7f..32e5f64 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2875,6 +2875,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                 || (t2 != null && t2.isAlive())
                 || (t3 != null && t3.isAlive())
                 || (t0 != null && t0.isAlive());
+        // could just as easily ask discoverer if it is still running instead of
+        // holding ref to thread
       }
     }
   }
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index adca0fa..12a08a0 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -172,6 +172,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
         {
         }
       }
+      aborted = false;
       Cache.log.debug("Old discovery thread has finished.");
     }
     running = true;
@@ -765,6 +766,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
     return true;
   }
 
+  public boolean restart()
+  {
+    synchronized (this)
+    {
+      if (running)
+      {
+        aborted = true;
+      }
+      else
+      {
+        running = true;
+      }
+      return aborted;
+    }
+  }
+
   /**
    * Start a fresh discovery thread and notify the given object when we're
    * finished. Any known existing threads will be killed before this one is
@@ -775,6 +792,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
    */
   public Thread startDiscoverer(PropertyChangeListener changeSupport2)
   {
+    /*    if (restart())
+        {
+          return;
+        }
+        else
+        {
+          Thread thr = new Thread(this);
+          thr.start();
+        }
+       */
     if (isRunning())
     {
       setAborted(true);
diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 6cd32c7..23c7751 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -89,6 +89,12 @@ public class RNAStructExportImport
     Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+
     for (Jws2Instance svc : disc.getServices())
     {
 
-- 
1.7.10.2