Add strings to indicate when the process is done

Author: ThomasHickman

cwltool/cwlNodeEngine.js

@@ -5,9 +5,16 @@ process.stdin.on("data", function(chunk) {
   incoming += chunk;
   var i = incoming.indexOf("\n");
   if (i > -1) {
-    var fn = JSON.parse(incoming.substr(0, i));
-    incoming = incoming.substr(i+1);
-    process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {})) + "\n");
+    try{
+      var fn = JSON.parse(incoming.substr(0, i));
+      incoming = incoming.substr(i+1);
+      process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {})) + "\n");
+    }
+    finally{
+      /*strings to indicate the process has finished*/
+      console.log("r1cepzbhUTxtykz5XTC4"); 
+      console.error("r1cepzbhUTxtykz5XTC4");
+    }
   }
 });
 process.stdin.on("end", process.exit);

cwltool/cwlNodeEngineJSConsole.js

@@ -11,14 +11,21 @@ process.stdin.on("data", function(chunk) {
   incoming += chunk;
   var i = incoming.indexOf("\n");
   if (i > -1) {
-    var fn = JSON.parse(incoming.substr(0, i));
-    incoming = incoming.substr(i+1);
-    process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {
-	console: {
-	    log: js_console_log, 
-	    error: js_console_err
-	}
-    })) + "\n");
+      try{
+        var fn = JSON.parse(incoming.substr(0, i));
+        incoming = incoming.substr(i+1);
+        process.stdout.write(JSON.stringify(require("vm").runInNewContext(fn, {
+        console: {
+            log: js_console_log, 
+            error: js_console_err
+        }
+        })) + "\n");
+    }
+    finally{
+        /*strings to indicate the process has finished*/
+        console.log("r1cepzbhUTxtykz5XTC4");
+        console.error("r1cepzbhUTxtykz5XTC4");
+    }
   }
 });
 process.stdin.on("end", process.exit);

cwltool/sandboxjs.py

@@ -164,6 +164,12 @@ def terminate():
     rselect = [nodejs.stdout, nodejs.stderr]  # type: List[BytesIO]
     wselect = [nodejs.stdin]  # type: List[BytesIO]
 
+    PROCESS_FINISHED_STR = "r1cepzbhUTxtykz5XTC4\n"
+
+    def process_finished():
+        return stdout_buf.getvalue().decode().endswith(PROCESS_FINISHED_STR) and \
+            stderr_buf.getvalue().decode().endswith(PROCESS_FINISHED_STR)
+
     # On windows system standard input/output are not handled properly by select module
     # (modules like  pywin32, msvcrt, gevent don't work either)
     if sys.platform=='win32':
@@ -214,7 +220,9 @@ def get_error(error_queue):
         error_thread.daemon=True
         error_thread.start()
 
-        while (len(wselect) + len(rselect)) > 0:
+        finished = False
+
+        while not finished and tm.isAlive():
             try:
                 if nodejs.stdin in wselect:
                     if not input_queue.empty():
@@ -227,41 +235,35 @@ def get_error(error_queue):
 
                 if nodejs.stderr in rselect:
                     if not error_queue.empty():
-                        stderr_buf.write(error_queue.get())
+                        stderr_buf.write(error_queue.get())                
 
-                if stdout_buf.getvalue().endswith("\n".encode()):
-                    rselect = []
+                if process_finished() and error_queue.empty() and output_queue.empty():
+                    finished = True
                     no_more_output.release()
                     no_more_error.release()
             except OSError as e:
                 break
 
     else:
-        while (len(wselect) + len(rselect)) > 0:
+        while not (process_finished() or not tm.isAlive()):
             rready, wready, _ = select.select(rselect, wselect, [])
             try:
                 if nodejs.stdin in wready:
                     b = stdin_buf.read(select.PIPE_BUF)
                     if b:
                         os.write(nodejs.stdin.fileno(), b)
-                    else:
-                        wselect = []
                 for pipes in ((nodejs.stdout, stdout_buf), (nodejs.stderr, stderr_buf)):
                     if pipes[0] in rready:
                         b = os.read(pipes[0].fileno(), select.PIPE_BUF)
                         if b:
                             pipes[1].write(b)
-                        else:
-                            rselect.remove(pipes[0])
-                if stdout_buf.getvalue().endswith("\n".encode()):
-                    rselect = []
             except OSError as e:
                 break
     tm.cancel()
 
     stdin_buf.close()
-    stdoutdata = stdout_buf.getvalue()
-    stderrdata = stderr_buf.getvalue()
+    stdoutdata = stdout_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
+    stderrdata = stderr_buf.getvalue()[:-len(PROCESS_FINISHED_STR) - 1]
 
     def fn_linenum():  # type: () -> Text
         lines = fn.splitlines()