Examples with ExecutableException org.vcell.util.exe.ExecutableException used on opensource projects

Example 11 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class VisitSupport method launchVisTool.

public static void launchVisTool(File visitExecutable, SimulationDataSetRef simulationDataSetRef) throws IOException, ExecutableException, URISyntaxException, InterruptedException {
    if (OperatingSystemInfo.getInstance().isMac()) {
        launchVisToolMac(visitExecutable);
        return;
    } else if (OperatingSystemInfo.getInstance().isLinux()) {
        launchVisToolLinux(visitExecutable);
        return;
    }
    // MSWindows
    if (visitExecutable == null) {
        visitExecutable = ResourceUtil.getExecutable(VISIT_EXEC_NAME, false);
        if (visitExecutable == null || !visitExecutable.exists() || !visitExecutable.isFile()) {
            throw new IOException("visit executable not found, " + visitExecutable.getAbsolutePath());
        }
    }
    VCellConfiguration.setFileProperty(PropertyLoader.visitExe, visitExecutable);
    File visMainCLI = getVisToolPythonScript();
    if (!visMainCLI.exists() || !visMainCLI.isFile()) {
        throw new IOException("vcell/visit main python file not found, " + visMainCLI.getAbsolutePath());
    }
    if (lg.isInfoEnabled()) {
        lg.info("Starting VCellVisIt as a sub-process");
    }
    // 
    // get existing environment variables and add visit command and python script to it.
    // 
    Map<String, String> envVariables = System.getenv();
    ArrayList<String> envVarList = new ArrayList<String>();
    for (String varname : envVariables.keySet()) {
        String value = envVariables.get(varname);
        envVarList.add(varname + "=" + value);
    }
    String siteName = ResourceUtil.getSiteName();
    File vcellHomeVisFolder = new File(new File(ResourceUtil.getVcellHome(), "Vis"), siteName);
    if (!vcellHomeVisFolder.exists()) {
        if (!vcellHomeVisFolder.mkdirs()) {
            throw new IOException("Cannot create directory " + vcellHomeVisFolder.getCanonicalPath());
        }
    }
    // FileUtils.copyDirectoryShallow(visMainCLI.getParentFile(), vcellHomeVisFolder);
    FileUtils.copyDirectory(visMainCLI.getParentFile(), vcellHomeVisFolder, true, new VisitFolderFileFilter());
    File vcellHomeVisMainCLI = new File(vcellHomeVisFolder, visMainCLI.getName());
    vcellHomeVisMainCLI.setExecutable(true);
    envVarList.add("visitcmd=" + /*"\""+*/
    visitExecutable.getPath());
    envVarList.add("pythonscript=" + vcellHomeVisMainCLI.getPath().replace("\\", "/"));
    // envVarList.add("pythonscript="+visMainCLI.toURI().toASCIIString());
    final String[] cmdStringArray = new String[] { "cmd", "/K", "start", "\"\"", visitExecutable.getPath(), "-cli", "-uifile", vcellHomeVisMainCLI.getPath().replace("\\", "/") };
    if (simulationDataSetRef != null) {
        File simDataSetRefFile = new File(ResourceUtil.getLocalVisDataDir(), "SimID_" + simulationDataSetRef.getSimId() + "_" + simulationDataSetRef.getJobIndex() + "_.simref");
        VisMeshUtils.writeSimulationDataSetRef(simDataSetRefFile, simulationDataSetRef);
        envVarList.add("INITIALSIMDATAREFFILE=" + simDataSetRefFile.getPath().replace("\\", "/"));
    }
    // @SuppressWarnings("unused")
    new Thread(new Runnable() {

        @Override
        public void run() {
            try {
                Executable exec = new Executable(cmdStringArray);
                // Executable exec = new Executable(new String[] {st});
                for (String var : envVarList) {
                    StringTokenizer st2 = new StringTokenizer(var, "=");
                    exec.addEnvironmentVariable(st2.nextToken(), st2.nextToken());
                }
                exec.start();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }).start();
    if (lg.isInfoEnabled()) {
        lg.info("Started VCellVisIt");
    }
/*
			List<String> cmds = new ArrayList<String>();
			cmds.add(visitExecutable.getAbsolutePath());
			cmds.add("-cli");
			cmds.add("-ufile");
			cmds.add(script.getAbsolutePath());
			ProcessBuilder pb = new ProcessBuilder(cmds);
			final Process p = pb.start();
			Runnable mon = new Runnable() {
				
				@Override
				public void run() {
					try {
						System.err.println("waiting for visit");
						p.waitFor();
						int rcode = p.exitValue();
						System.err.println("visit exit code " + rcode);
					} catch (Exception e) {
						e.printStackTrace();
					}
				}
			};
			new Thread(mon).start();
			*/
}

Example 12 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class SBMLStandaloneImporter method attemptImport.

private BioModel attemptImport(File sbmlFile) throws ExecutableException, IOException, ClassNotFoundException, XmlParseException {
    if (subProcess == null || subProcess.getStatus() != LiveProcessStatus.RUNNING) {
        subProcess = createProcess();
    }
    toChildProcess.writeObject(sbmlFile);
    Object back = fromChildProcess.readObject();
    if (back instanceof String) {
        String xml = (String) back;
        if (lg.isDebugEnabled()) {
            try (FileWriter fw = new FileWriter(sbmlFile.getAbsolutePath() + ".dump")) {
                fw.append(xml);
            }
        }
        XMLSource source = new XMLSource(xml);
        return XmlHelper.XMLToBioModel(source);
    }
    if (back instanceof Exception) {
        try {
            throw (Exception) back;
        } catch (SBMLImportException sie) {
            throw sie;
        } catch (Exception e) {
            throw new ExecutableException("child process exception", e);
        }
    }
    throw new ExecutableException("unexpected object from child process:  " + back.getClass().getName() + " " + back.toString());
}

Example 13 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class SBMLStandaloneImporter method createProcess.

private LiveProcess<ClosedInput, InheritOutput, InheritOutput> createProcess() throws ExecutableException, IOException {
    @SuppressWarnings("resource") ServerSocket ss = new ServerSocket(0);
    InetSocketAddress isa = (InetSocketAddress) ss.getLocalSocketAddress();
    String home = System.getProperty("java.home");
    String exe = home + "/bin/java";
    String classpath = System.getProperty("java.class.path");
    String us = getClass().getName();
    ArrayList<String> cmdArgs = new ArrayList<String>();
    cmdArgs.add(exe);
    cmdArgs.addAll(jvmArgs());
    String[] invokeArgs = { "-classpath", classpath, us };
    cmdArgs.addAll(Arrays.asList(invokeArgs));
    InheritOutput i = new InheritOutput();
    LiveProcess<ClosedInput, InheritOutput, InheritOutput> lp = new LiveProcess<ClosedInput, InheritOutput, InheritOutput>(new ClosedInput(), i, i, cmdArgs.toArray(new String[cmdArgs.size()]));
    lp.setEnvironment(PORT_KEY, Integer.toString(isa.getPort()));
    lp.setEnvironment(HOST_KEY, isa.getHostName());
    lp.begin(OUR_LABEL);
    ss.setSoTimeout(START_TIMEOUT_SECONDS * 1000);
    try {
        channel = ss.accept();
    } catch (SocketTimeoutException sto) {
        throw new ExecutableException("Standalone client failed to communicate in " + START_TIMEOUT_SECONDS + " seconds");
    }
    toChildProcess = new ObjectOutputStream(channel.getOutputStream());
    fromChildProcess = new ObjectInputStream(channel.getInputStream());
    return lp;
}

Example 14 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class NFSimSolver method main.

public static void main(String[] args) {
    String baseName = "SimID_";
    String workingDir = "C:\\Users\\jmasison\\.vcell\\simdata\\user\\sub\\";
    String executable = "C:\\Users\\jmasison\\workspace\\VCell_trunk\\localsolvers\\win64\\NFsim_x64.exe";
    String blankDelimiters = " \t";
    String debugfile = "C:\\Users\\jmasison\\.vcell\\simdata\\user\\sub\\debug.txt";
    int seed = 1807259453;
    int steps = 100;
    // unit system is in sec
    double duration = 0.1;
    Map<Integer, Double> timestepMap = new HashMap<>();
    BufferedReader br = null;
    PrintWriter writer = null;
    try {
        writer = new PrintWriter(debugfile, "UTF-8");
        for (int i = 1; i < steps + 1; i++) {
            // print				writer.println("\t\t\t\tentering i loop");
            // C:\\TEMP\\eee\\SimID_000.nfsimInput
            String input = workingDir + baseName + "000" + ".nfsimInput";
            String output = workingDir + baseName + i + ".gdat";
            String species = workingDir + baseName + i + ".species";
            double interval = duration / steps;
            // we start at timepoint 0
            double dur = interval * (i - 1);
            String sdur = "" + dur;
            if (sdur.length() > 6) {
                sdur = sdur.substring(0, 6);
            }
            // average length of patterns at this timepoint, over many simulations
            double averageOfAverage = 0;
            int numSimulations = 50;
            for (int ii = 0; ii < numSimulations; ii++) {
                // print					writer.println("\t\t\t\t\tentering ii loop");
                // calculate a new seed for this simulation (same start seeds will be used for each time point)
                int curSeed = seed + ii * 538297;
                // String command = executable + " -seed " + curSeed + " -vcell -xml " + input + " -o " + output + " -sim " + sdur + " -ss " + species + " -oSteps 1" + " -notf -cb";
                // Process p = Runtime.getRuntime().exec(command);
                // p.waitFor();
                String curspecies = species + "_sim_" + ii;
                String[] commands = new String[] { executable, "-seed", Integer.toString(curSeed), "-vcell", "-xml", input, "-o", output, "-sim", sdur, "-ss", curspecies, "-oSteps", "1", "-notf", "-cb" };
                MathExecutable mathExe = new MathExecutable(commands, new File(workingDir));
                try {
                    mathExe.start();
                } catch (ExecutableException e) {
                    e.printStackTrace();
                    System.out.println("exe failed, exitValue=" + mathExe.getExitValue() + ", \nstderr=" + mathExe.getStderrString() + ", \nstdout=" + mathExe.getStdoutString());
                }
                // command = "cmd.exe /c del " + workingDir + "*.gdat";
                // p = Runtime.getRuntime().exec(command);
                // p.waitFor();
                // delete the intermediate .gdat files
                // MathExecutable mathExeDel = new MathExecutable(new String[] {"cmd.exe", "/c", "del", workingDir, "*.gdat"}, new File(workingDir));
                // try {
                // mathExeDel.start();
                // } catch (ExecutableException e) {
                // e.printStackTrace();
                // }
                Map<Integer, Integer> occurencesMap = new HashMap<>();
                br = new BufferedReader(new FileReader(curspecies));
                // ex: A(s!1,t!2).B(u!1).B(u!2)  5
                String line;
                while ((line = br.readLine()) != null) {
                    if (line.startsWith("#")) {
                        continue;
                    }
                    // how many molecules in the above pattern => 3
                    int numMolecules = 1;
                    // how many instances of this pattern => 5
                    int number;
                    StringTokenizer nextLine = new StringTokenizer(line, blankDelimiters);
                    // A(s!1,t!2).B(u!1).B(u!2)
                    String pattern = nextLine.nextToken();
                    for (int j = 0; j < pattern.length(); j++) {
                        if (pattern.charAt(j) == '.') {
                            // numMolecules equals the number of 'dot' characters in string + 1
                            numMolecules++;
                        }
                    }
                    // 5
                    String s = nextLine.nextToken();
                    number = Integer.parseInt(s);
                    if (occurencesMap.containsKey(numMolecules)) {
                        int currentNumber = occurencesMap.get(numMolecules);
                        currentNumber += number;
                        occurencesMap.put(numMolecules, currentNumber);
                    } else {
                        occurencesMap.put(numMolecules, number);
                    }
                }
                double up = 0;
                double down = 0;
                for (Map.Entry<Integer, Integer> entry : occurencesMap.entrySet()) {
                    Integer key = entry.getKey();
                    if (key == 1) {
                        continue;
                    }
                    Integer value = entry.getValue();
                    up += key * value;
                    down += value;
                // print						writer.println(curspecies+"_"+i+" : "+ up + ", " + down);
                }
                double average;
                if (down > 0) {
                    average = up / down;
                } else {
                    average = 0;
                }
                // print					writer.println("average: "+average);; writer.println();
                averageOfAverage += average;
                // print					writer.println("Avergae_of_average_for_sim_"+ii+"_time_"+i+" : "+average);; writer.println();
                br.close();
            // if uncimmented make sure to use mathexecutable
            // command = "cmd.exe /c del " + workingDir + "*.species";
            // p = Runtime.getRuntime().exec(command);
            // p.waitFor();
            }
            averageOfAverage = averageOfAverage / numSimulations;
            // print				writer.println("Final_average_for_time_"+i+" : "+averageOfAverage); writer.println();
            // save average for time step (i) to map
            timestepMap.put(i, averageOfAverage);
        }
        // exited both loops
        // print		writer.println();
        writer.println("Time\tAverageCLusterSize");
        for (int j = 1; j < steps + 1; j++) {
            writer.println((j - 1) + "\t" + timestepMap.get(j));
        }
        writer.println();
        writer.println("Done");
        writer.close();
        System.out.println("\n\n\n\nDone\n\n");
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        try {
            if (br != null) {
                br.close();
            }
        } catch (IOException ex) {
            ex.printStackTrace();
        }
    }
}

Example 15 with ExecutableException

use of org.vcell.util.exe.ExecutableException in project vcell by virtualcell.

the class CommandServiceSshNativeTest method test_install_secret_keyfile.

@Test
public void test_install_secret_keyfile() throws IOException, ExecutableException {
    CommandServiceSshNative cmd = null;
    try {
        cmd = new CommandServiceSshNative("vcell-service.cam.uchc.edu", "vcell", new File("/Users/schaff/.ssh/schaff_rsa"), new File("/Users/schaff"));
        System.out.println("after created cmdService");
        CommandOutput output = cmd.command(new String[] { "ls -al | head -4" });
        System.out.println("ls output is: " + output.getStandardOutput());
        output = cmd.command(new String[] { "ls -al | head -9" });
        System.out.println("ls output is: " + output.getStandardOutput());
        output = cmd.command(new String[] { "ls -al | head -4" });
        System.out.println("ls output is: " + output.getStandardOutput());
    } catch (Exception e) {
        e.printStackTrace();
        fail("exception thrown: " + e.getMessage());
    } finally {
        if (cmd != null) {
            cmd.close();
        }
    }
}