Fixes bug where logs do not properly get updated in significant size simulations.

vcell-cli/src/main/java/org/vcell/cli/CLIPythonManager.java

@@ -35,7 +35,7 @@ public class CLIPythonManager {
     private static final String PYTHON_EXE_NAME = OperatingSystemInfo.getInstance().isWindows() ? "python" : "python3";
 
     private static CLIPythonManager instance = null;
-    private static final int DEFAULT_TIMEOUT = 7000; // was 600 seconds (10 minutes), now 5 seconds
+    private static final int DEFAULT_TIMEOUT = 15000; // was 600 seconds (10 minutes), now 15 seconds
 
     private static final boolean USE_SHARED_SHELL = true;
 
@@ -101,6 +101,9 @@ public void closePythonProcess() throws IOException {
         // Exit the living Python Process
         lg.debug("Closing Python Instance");
         if (this.pythonOSW != null && this.pythonISB != null) this.sendNewCommand("exit()"); // Sends kill command ("exit()") to python.exe instance;
+        try {
+            for (int i = 1; i <= 5; i++) if (this.pythonProcess != null && this.pythonProcess.isAlive()) Thread.sleep(1000 * i);
+        } catch (InterruptedException ignored) {} // Just want to try and give the process a chance to close gracefully
         if (this.pythonProcess != null && this.pythonProcess.isAlive()) this.pythonProcess.destroyForcibly(); // Making sure it's quite dead
 
         // Making sure we clean up
@@ -191,6 +194,16 @@ private String callPython(String command) throws PythonStreamException, TimeoutE
                 }
             } catch (IOException | InterruptedException e4){
                 throw new PythonStreamException("Python process encountered an exception:\n" + e4.getMessage(), e4);
+            } finally { // Let's make sure our buffer isn't clogged; for now, we'll log, but discard any extra output
+                StringBuilder remainder = new StringBuilder("Leftovers in buffer: \n");
+                try {
+                    while (this.pythonISB.ready()){
+                        remainder.append(this.getResultsOfLastCommand()).append("\n");
+                    }
+                } catch (IOException | InterruptedException cleaningException){
+                    lg.warn("Received exception while trying to clear buffer:", cleaningException);
+                }
+                lg.debug(remainder.toString());
             }
         }
     }

vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java

@@ -96,7 +96,7 @@ public Integer call() {
             try {
                 CLIPythonManager.getInstance().instantiatePythonProcess();
                 ExecuteImpl.singleMode(ARCHIVE, tmpDir, cliRecorder, true);
-                FileUtils.copyDirectoryContents(tmpDir, OUT_DIR, true, null);
+                CLIPythonManager.getInstance().closePythonProcess(); // Give the process time to finish
                 if (!Tracer.hasErrors()) return 0;
                 if (!bQuiet) {
                     logger.error("Errors occurred during execution");
@@ -110,6 +110,7 @@ public Integer call() {
                     logger.error(e.getMessage(), e);
                 }
                 logger.debug("Finished all execution.");
+                FileUtils.copyDirectoryContents(tmpDir, OUT_DIR, true, null);
             }
         } catch (Exception e) {
             if (!bQuiet) {

vcell-cli/src/main/java/org/vcell/cli/run/ExecuteCommand.java

@@ -129,9 +129,9 @@ public Integer call() {
                             bEncapsulateOutput, bSmallMeshOverride);
                 }
             }
-            FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null);
             CLIPythonManager.getInstance().closePythonProcess();
             // WARNING: Python needs re-instantiation once the above line is called!
+            FileUtils.copyDirectoryContents(tmpDir, outputFilePath, true, null);
             return 0;
         } catch (Exception e) { ///TODO: Break apart into specific exceptions to maximize logging.
             org.apache.logging.log4j.LogManager.getLogger(this.getClass()).error(e.getMessage(), e);

vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java

@@ -191,6 +191,7 @@ public void postProcessessArchive() throws InterruptedException, PythonStreamExc
 
         }
         PythonCalls.setOutputMessage("null", "null", outputDir, "omex", logOmexMessage.toString());
+
         logger.debug("Finished Execution of Archive: " + bioModelBaseName);
     }
 

vcell-cli/src/main/java/org/vcell/cli/run/PythonCalls.java

@@ -148,22 +148,16 @@ public static void genPlotsPseudoSedml(String sedmlPath, String resultOutDir) th
         CLIPythonManager cliPythonManager = CLIPythonManager.getInstance();
         String results = cliPythonManager.callPython("genPlotsPseudoSedml", sedmlPath, resultOutDir);
         cliPythonManager.parsePythonReturn(results);
-        /**
-         * replace with the following once the leak is fixed
-         */
-//        CLIPythonManager cliPythonManager = CLIPythonManager.getInstance();
-//        String results = cliPythonManager.callPython("genPlotsPseudoSedml", sedmlPath, resultOutDir);
-//        cliPythonManager.printPythonErrors(results);
     }
 
     private static String stripIllegalChars(String s){
-        String fStr = "";
+        StringBuilder fStr = new StringBuilder();
         for (char c : s.toCharArray()){
             char cAppend = ((int)c) < 16 ? ' ' : c;
             if (cAppend == '"') 
             	cAppend = '\'';
-            fStr += cAppend;
+            fStr.append(cAppend);
         }
-        return fStr;
+        return fStr.toString();
     }
 }