When running a remote command with a Local connection from a Linux host a new 
LocalHostShell is created.
At this time, a new LocalHostThread is launched, along side with two 
LocalShellOutputReaders (output and error). The constructors for the 
OutputReaders will receive a reference to the reader created by the 
LocalHostThread.

When calling runCommandRemote, the newly created IHostShell is returned, making 
it possible to create an adapter(IHostShellProcessAdapter) that  will then be 
used to read all available output from the readers.
When the LocalShellThread finishes running its run() method, it will perform a 
cleanup causing both readers (output and error) to be closed.
If at this point, there are any readers, or handlers to the readers that are 
still trying to read data (read using handlers readers), an error will be 
thrown saying that the the pipe to the stream is closed ("Ensure open stream"/ 
"Pipe closed" errors).
After inspecting the internalReadLine, it seems that it expects a null 
reference of the reader in order to consider that the reading is done.
In order to ensure that this will happen once the LocalShellThread closes the 
stream(s), we will make sure that the reference to the readers is set to null, 
and that LocalShellOutputReader(s) use the same reference of the reader as the 
LocalShellThread. For this to happen, a reference of the thread must be kept in 
the reader, in order to retrieve the correct reference of the underlying reader.
Since there can still be race conditions in this solution, all operations that 
involve the reference to now the only reader, must be performed under mutual 
exclusion using a shared lock between the LocalShellOutputReader and 
LocalShellThread.

[update] : there is no need to protect internalReadLine with locks as long as 
we do it when reading.

Signed-off-by: Ioana Grigoropol <ioanax.grigoro...@intel.com>
---
 .../dstore/shells/DStoreShellOutputReader.java     |   12 ++++++++
 .../services/local/shells/LocalHostShell.java      |    5 ++--
 .../local/shells/LocalShellOutputReader.java       |   29 +++++++++++++-------
 .../services/local/shells/LocalShellThread.java    |   18 ++++++++++++
 .../.settings/.api_filters                         |   22 +++++++++++++++
 .../shells/TerminalServiceShellOutputReader.java   |   14 ++++++++++
 .../services/shells/IHostShellOutputReader.java    |   13 ++++++++-
 7 files changed, 100 insertions(+), 13 deletions(-)

diff --git 
a/rse/plugins/org.eclipse.rse.services.dstore/src/org/eclipse/rse/internal/services/dstore/shells/DStoreShellOutputReader.java
 
b/rse/plugins/org.eclipse.rse.services.dstore/src/org/eclipse/rse/internal/services/dstore/shells/DStoreShellOutputReader.java
index 84c9bb9..35dbea4 100644
--- 
a/rse/plugins/org.eclipse.rse.services.dstore/src/org/eclipse/rse/internal/services/dstore/shells/DStoreShellOutputReader.java
+++ 
b/rse/plugins/org.eclipse.rse.services.dstore/src/org/eclipse/rse/internal/services/dstore/shells/DStoreShellOutputReader.java
@@ -13,10 +13,13 @@
  * 
  * Contributors:
  * David McKnight (IBM) - [286671] return null when status is null
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
*******************************************************************************/
 
 package org.eclipse.rse.internal.services.dstore.shells;
 
+import java.io.BufferedReader;
+import java.util.concurrent.locks.Lock;
 import org.eclipse.dstore.core.model.DataElement;
 import org.eclipse.dstore.extra.DomainEvent;
 import org.eclipse.dstore.extra.IDomainListener;
@@ -168,6 +171,15 @@ public class DStoreShellOutputReader extends 
AbstractHostShellOutputReader imple
                notifyResponse();
        }
        
+       public BufferedReader getReader() {
+               // TODO Auto-generated method stub
+               return null;
+       }
+
+       public Lock getReaderLock() {
+               return null;
+       }
+
        /*
        private void handleInput()
        {
diff --git 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalHostShell.java
 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalHostShell.java
index 250a904..213bf2e 100644
--- 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalHostShell.java
+++ 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalHostShell.java
@@ -13,6 +13,7 @@
  * 
  * Contributors:
  * Martin Oberhuber (Wind River) - [161838] local shell reports isActive() 
wrong
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
*******************************************************************************/
 
 package org.eclipse.rse.internal.services.local.shells;
@@ -37,8 +38,8 @@ public class LocalHostShell extends AbstractHostShell 
implements IHostShell
        public LocalHostShell(String initialWorkingDirectory, String 
invocation, String encoding, String[] environment)
        {
                _shellThread = new LocalShellThread(initialWorkingDirectory, 
invocation, encoding, environment);        
-               _stdoutHandler = new LocalShellOutputReader(this, 
_shellThread.getOutputStream(), false);
-               _stderrHandler = new LocalShellOutputReader(this, 
_shellThread.getErrorStream(),true);
+               _stdoutHandler = new LocalShellOutputReader(this, _shellThread, 
false);
+               _stderrHandler = new LocalShellOutputReader(this, _shellThread, 
true);
        }
        
        protected void run(IProgressMonitor monitor)
diff --git 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellOutputReader.java
 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellOutputReader.java
index ab8ff5c..fd7096c 100644
--- 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellOutputReader.java
+++ 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellOutputReader.java
@@ -12,13 +12,14 @@
  * Emily Bruner, Mazen Faraj, Adrian Storisteanu, Li Ding, and Kent Hawley.
  * 
  * Contributors:
- * {Name} (company) - description of contribution.
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
*******************************************************************************/
 
 package org.eclipse.rse.internal.services.local.shells;
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.util.concurrent.locks.Lock;
 
 import org.eclipse.rse.internal.services.local.Activator;
 import org.eclipse.rse.services.shells.AbstractHostShellOutputReader;
@@ -33,14 +34,14 @@ import org.eclipse.rse.services.shells.SimpleHostOutput;
  */
 public class LocalShellOutputReader extends AbstractHostShellOutputReader 
implements IHostShellOutputReader
 {
-       protected BufferedReader _reader;
+       private LocalShellThread _shellThread;
        private String fPromptChars = ">$%#]"; //Characters we accept as the 
end of a prompt //$NON-NLS-1$;
 
        
-       public LocalShellOutputReader(IHostShell hostShell, BufferedReader 
reader, boolean isErrorReader)
+       public LocalShellOutputReader(IHostShell hostShell, LocalShellThread 
shellThread, boolean isErrorReader)
        {
                super(hostShell, isErrorReader);
-               _reader = reader;
+               _shellThread = shellThread;
        }
        /*
        protected Object internalReadLine()
@@ -137,7 +138,7 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
        }
 */
        protected IHostOutput internalReadLine() {
-               if (_reader == null) {
+               if (getReader() == null) {
                        //Our workaround sets the stderr reader to null, so we 
never give any stderr output.
                        //TODO Check if ssh supports some method of having 
separate stdout and stderr streams
                        return null;
@@ -149,7 +150,7 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
                boolean done = false;
                while (!done && !isFinished()) {
                        try {
-                               ch = _reader.read();
+                               ch = getReader().read();
                                switch (ch) {
                                case -1:
                                case 65535:
@@ -185,13 +186,13 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
                                                theLine.append(tch); // Any 
other character
                                        } else if (ch == 27) {
                                                // Escape: ignore next char too
-                                               int nch = _reader.read();
+                                               int nch = getReader().read();
                                                if (theDebugLine!=null) 
theDebugLine.append((char)nch);
                                                if (nch == 91) {
                                                        //vt100 escape 
sequence: read until end-of-command (skip digits and semicolon)
                                                        //e.g. \x1b;13;m --> 
ignore the entire command, including the trailing m
                                                        do {
-                                                               nch = 
_reader.read();
+                                                               nch = 
getReader().read();
                                                                if 
(theDebugLine!=null) theDebugLine.append((char)nch);
                                                        } while 
(Character.isDigit((char)nch) || nch == ';');
                                                }
@@ -202,7 +203,7 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
                                // there are more characters
                                // in the Buffer...If not, then we assume it is 
waiting for
                                // input.
-                               if (!done && !_reader.ready()) {
+                               if (!done && !getReader().ready()) {
                                        // wait to make sure -- max. 500 msec 
to wait for new chars 
                                        // if we are not at a CRLF seems to be 
appropriate for the 
                                        // Pipes and Threads in ssh.
@@ -219,7 +220,7 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
                                                Thread.sleep(waitIncrement);
                                        } catch (InterruptedException e) {
                                        }
-                                       if (!_reader.ready()) {
+                                       if (!getReader().ready()) {
                                                done = true;
                                        }
                                }
@@ -237,6 +238,14 @@ public class LocalShellOutputReader extends 
AbstractHostShellOutputReader implem
                }
                return new SimpleHostOutput(theLine.toString());
        }
+       public BufferedReader getReader() {
+               if (isErrorReader())
+                       return _shellThread.getErrorStream();
+               return _shellThread.getOutputStream();
+       }
+       public Lock getReaderLock() {
+               return _shellThread.getLock();
+       }
 
 
 }
diff --git 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellThread.java
 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellThread.java
index 0a33ad4..28e8ad9 100644
--- 
a/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellThread.java
+++ 
b/rse/plugins/org.eclipse.rse.services.local/src/org/eclipse/rse/internal/services/local/shells/LocalShellThread.java
@@ -17,6 +17,7 @@
  * David McKnight       (IBM)    - [189387] Use specified encoding for shell 
output
  * Martin Oberhuber (Wind River) - [161838] local shell reports isActive() 
wrong
  * Anna Dushistova  (MontaVsita) - [249354] Incorrect behaviour of local 
shells subsystem runCommand method 
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
*******************************************************************************/
 
 package org.eclipse.rse.internal.services.local.shells;
@@ -29,6 +30,8 @@ import java.io.InputStreamReader;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.net.URL;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.eclipse.core.runtime.FileLocator;
 
@@ -62,6 +65,7 @@ public class LocalShellThread extends Thread
        private BufferedReader _stdInput;
        private BufferedReader _stdError;
 
+       private Lock _lock;
        /**
         * constructor for local command shell monitor
         * 
@@ -260,6 +264,7 @@ public class LocalShellThread extends Thread
 
                        _stdError = new BufferedReader(new 
InputStreamReader(_theProcess.getErrorStream()));
 
+                       _lock = new ReentrantLock();
                }
                catch (IOException e)
                {
@@ -438,9 +443,14 @@ public class LocalShellThread extends Thread
                _isDone = true;
                try
                {
+                       _lock.lock();
                        _stdInput.close();
                        _stdError.close();
 
+                       _stdInput = null;
+                       _stdError = null;
+
+                       _lock.unlock();
                        if (_theProcess != null)
                        {
 
@@ -511,4 +521,12 @@ public class LocalShellThread extends Thread
        }
 
 
+       public Lock getLock() {
+               return _lock;
+       }
+
+       public void setLock(Lock _lock) {
+               this._lock = _lock;
+       }
+
 }
diff --git a/rse/plugins/org.eclipse.rse.services/.settings/.api_filters 
b/rse/plugins/org.eclipse.rse.services/.settings/.api_filters
index 19273c2..da67bc9 100644
--- a/rse/plugins/org.eclipse.rse.services/.settings/.api_filters
+++ b/rse/plugins/org.eclipse.rse.services/.settings/.api_filters
@@ -1,5 +1,13 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.rse.services" version="2">
+    <resource path="META-INF/MANIFEST.MF">
+        <filter id="923795461">
+            <message_arguments>
+                <message_argument value="3.2.200"/>
+                <message_argument value="3.2.200"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="META-INF/MANIFEST.MF" 
type="org.eclipse.rse.internal.services.terminals.AbstractTerminalService">
         <filter id="305324134">
             <message_arguments>
@@ -119,4 +127,18 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource 
path="src/org/eclipse/rse/services/shells/IHostShellOutputReader.java" 
type="org.eclipse.rse.services.shells.IHostShellOutputReader">
+        <filter id="403804204">
+            <message_arguments>
+                <message_argument 
value="org.eclipse.rse.services.shells.IHostShellOutputReader"/>
+                <message_argument value="getReader()"/>
+            </message_arguments>
+        </filter>
+        <filter id="403804204">
+            <message_arguments>
+                <message_argument 
value="org.eclipse.rse.services.shells.IHostShellOutputReader"/>
+                <message_argument value="getReaderLock()"/>
+            </message_arguments>
+        </filter>
+    </resource>
 </component>
diff --git 
a/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/internal/services/shells/TerminalServiceShellOutputReader.java
 
b/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/internal/services/shells/TerminalServiceShellOutputReader.java
index 16364e1..9b01c10 100644
--- 
a/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/internal/services/shells/TerminalServiceShellOutputReader.java
+++ 
b/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/internal/services/shells/TerminalServiceShellOutputReader.java
@@ -17,12 +17,15 @@
  * Anna Dushistova  (MontaVista) - adapted from SshShellOutputReader
  * Anna Dushistova  (MontaVista) - [240523] [rseterminals] Provide a generic 
adapter factory that adapts any ITerminalService to an IShellService
  * Rob Stryker (JBoss) - [335059] TerminalServiceShellOutputReader logs error 
when hostShell.exit() is called
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
*******************************************************************************/
 
 package org.eclipse.rse.internal.services.shells;
 
 import java.io.BufferedReader;
 import java.io.IOException;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.eclipse.rse.internal.services.Activator;
 import org.eclipse.rse.services.shells.AbstractHostShellOutputReader;
@@ -36,6 +39,7 @@ import org.eclipse.rse.services.shells.SimpleHostOutput;
 public class TerminalServiceShellOutputReader extends
                AbstractHostShellOutputReader {
        protected BufferedReader fReader;
+       protected Lock lock;
        private volatile Thread fReaderThread = null;
        private volatile boolean isCanceled = false;
        private String fPromptChars = ">$%#]"; //Characters we accept as the 
end of a prompt //$NON-NLS-1$;
@@ -174,4 +178,14 @@ public class TerminalServiceShellOutputReader extends
                        fReaderThread.interrupt();
                }
        }
+
+       public BufferedReader getReader() {
+               return fReader;
+       }
+
+       public Lock getReaderLock() {
+               if (lock == null)
+                       lock = new ReentrantLock();
+               return lock;
+       }
 }
diff --git 
a/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/services/shells/IHostShellOutputReader.java
 
b/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/services/shells/IHostShellOutputReader.java
index 103c31f..b70b3db 100644
--- 
a/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/services/shells/IHostShellOutputReader.java
+++ 
b/rse/plugins/org.eclipse.rse.services/src/org/eclipse/rse/services/shells/IHostShellOutputReader.java
@@ -11,11 +11,14 @@
  * Emily Bruner, Mazen Faraj, Adrian Storisteanu, Li Ding, and Kent Hawley.
  * 
  * Contributors:
- * {Name} (company) - description of contribution.
+ * Ioana Grigoropol (Intel) - [399231] Race conditions occur when trying to 
read from local processes using LocalShellOutputReader
  
********************************************************************************/
 
 package org.eclipse.rse.services.shells;
 
+import java.io.BufferedReader;
+import java.util.concurrent.locks.Lock;
+
 public interface IHostShellOutputReader extends IHostShellOutputNotifier
 {
        public IHostOutput readLine();
@@ -23,4 +26,12 @@ public interface IHostShellOutputReader extends 
IHostShellOutputNotifier
        public void addOutputListener(IHostShellOutputListener listener);
        public boolean isErrorReader();
        public void finish();
+       /**
+        * @since 3.2
+        */
+       public BufferedReader getReader();
+       /**
+        * @since 3.2
+        */
+       public Lock getReaderLock();
 }
\ No newline at end of file
-- 
1.7.9.5

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