From ef1d19d74a85425a99ed463d638545c46297ef0e Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 11 Feb 2022 18:44:19 +0000
Subject: [PATCH] =?utf8?q?JAL-3949=20ensure=20Jalview=20command=20line=20ops?=
 =?utf8?q?=20setup=20actually=20quits=20after=20SETUP=5FTIME=20milliseconds=20?=
 =?utf8?q?-=20seems=20there=E2=80=99s=20less=20stderr=20noise=20than=20befor?=
 =?utf8?q?e=20!?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 test/jalview/bin/CommandLineOperations.java |   51 ++++++++++++++++++++++-----
 1 file changed, 43 insertions(+), 8 deletions(-)

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 4323699..2ccb5dd 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -246,18 +246,53 @@ public class CommandLineOperations
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
-    Worker worker = getJalviewDesktopRunner(false, cmds, SETUP_TIMEOUT);
-    String ln = null;
-    int count = 0;
-    while ((ln = worker.getErrorReader().readLine()) != null)
+    final Worker worker = getJalviewDesktopRunner(false, cmds,
+            SETUP_TIMEOUT);
+    
+    
+    // number of lines expected on STDERR when Jalview starts up normally
+    // may need to adjust this if Jalview is excessively noisy ?
+    final int STDERR_SETUPLINES=50;
+    
+    // thread monitors stderr - bails after SETUP_TIMEOUT or when
+    // STDERR_SETUPLINES have been read
+    Thread runner = new Thread(new Runnable()
     {
-      System.out.println(ln);
-      successfulCMDs.add(ln);
-      if (++count > 50)
+      public void run()
+      {
+        String ln = null;
+        int count = 0;
+        try
+        {
+          while ((ln = worker.getErrorReader().readLine()) != null)
+          {
+            System.out.println(ln);
+            successfulCMDs.add(ln);
+            if (++count > STDERR_SETUPLINES)
+            {
+              break;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err.println(
+                  "Unexpected Exception reading stderr from the Jalview process");
+          e.printStackTrace();
+        }
+      }
+    });
+    long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+    runner.start();
+    while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
       {
-        break;
       }
     }
+    runner.interrupt();
     if (worker != null && worker.exit == null)
     {
       worker.interrupt();
-- 
1.7.10.2