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

Example 6 with Executable

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

the class VCellSBMLSolver method solveVCell.

public File solveVCell(String filePrefix, File outDir, String sbmlFileName, SimSpec testSpec) throws IOException, SolverException, SbmlException {
    try {
        cbit.util.xml.VCLogger logger = new LocalLogger();
        // 
        // Instantiate an SBMLImporter to get the speciesUnitsHash - to compute the conversion factor from VC->SB species units.
        // and import SBML  (sbml->bioModel)
        org.vcell.sbml.vcell.SBMLImporter sbmlImporter = new org.vcell.sbml.vcell.SBMLImporter(sbmlFileName, logger, false);
        BioModel bioModel = sbmlImporter.getBioModel();
        if (bRoundTrip) {
            // Round trip the bioModel (bioModel->sbml->bioModel).
            // export bioModel as sbml and save
            String vcml_sbml = cbit.vcell.xml.XmlHelper.exportSBML(bioModel, 2, 1, 0, false, bioModel.getSimulationContext(0), null);
            // re-import bioModel from exported sbml
            XMLSource vcml_sbml_Src = new XMLSource(vcml_sbml);
            BioModel newBioModel = (BioModel) XmlHelper.importSBML(logger, vcml_sbml_Src, false);
            // have rest of code use the round-tripped biomodel
            bioModel = newBioModel;
        }
        // 
        // select only Application, generate math, and create a single Simulation.
        // 
        SimulationContext simContext = bioModel.getSimulationContext(0);
        MathMapping mathMapping = simContext.createNewMathMapping();
        MathDescription mathDesc = mathMapping.getMathDescription();
        simContext.setMathDescription(mathDesc);
        SimulationVersion simVersion = new SimulationVersion(new KeyValue("100"), "unnamed", null, null, null, null, null, null, null, null);
        Simulation sim = new Simulation(simVersion, mathDesc);
        sim.setName("unnamed");
        // if time factor from SBML is not 1 (i.e., it is not in secs but in minutes or hours), convert endTime to min/hr as : endTime*timeFactor
        // double endTime = testSpec.getEndTime()*timeFactor;
        double endTime = testSpec.getEndTime();
        sim.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
        TimeStep timeStep = new TimeStep();
        sim.getSolverTaskDescription().setTimeStep(new TimeStep(timeStep.getMinimumTimeStep(), timeStep.getDefaultTimeStep(), endTime / 10000));
        sim.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec((endTime - 0) / testSpec.getNumTimeSteps()));
        sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(testSpec.getAbsTolerance(), testSpec.getRelTolerance()));
        // sim.getSolverTaskDescription().setErrorTolerance(new ErrorTolerance(1e-10, 1e-12));
        // Generate .idaInput string
        File idaInputFile = new File(outDir, filePrefix + SimDataConstants.IDAINPUT_DATA_EXTENSION);
        PrintWriter idaPW = new java.io.PrintWriter(idaInputFile);
        SimulationJob simJob = new SimulationJob(sim, 0, null);
        SimulationTask simTask = new SimulationTask(simJob, 0);
        IDAFileWriter idaFileWriter = new IDAFileWriter(idaPW, simTask);
        idaFileWriter.write();
        idaPW.close();
        // use the idastandalone solver
        File idaOutputFile = new File(outDir, filePrefix + SimDataConstants.IDA_DATA_EXTENSION);
        // String sundialsSolverExecutable = "C:\\Developer\\Eclipse\\workspace\\VCell 4.8\\SundialsSolverStandalone_NoMessaging.exe";
        String executableName = null;
        try {
            executableName = SolverUtilities.getExes(SolverDescription.IDA)[0].getAbsolutePath();
        } catch (IOException e) {
            throw new RuntimeException("failed to get executable for solver " + SolverDescription.IDA.getDisplayLabel() + ": " + e.getMessage(), e);
        }
        Executable executable = new Executable(new String[] { executableName, idaInputFile.getAbsolutePath(), idaOutputFile.getAbsolutePath() });
        executable.start();
        /*			// Generate .cvodeInput string
			File cvodeFile = new File(outDir,filePrefix+SimDataConstants.CVODEINPUT_DATA_EXTENSION);
			PrintWriter cvodePW = new java.io.PrintWriter(cvodeFile);
			SimulationJob simJob = new SimulationJob(sim, 0, null);
		    CVodeFileWriter cvodeFileWriter = new CVodeFileWriter(cvodePW, simJob);
			cvodeFileWriter.write();
			cvodePW.close();

			// use the cvodeStandalone solver
			File cvodeOutputFile = new File(outDir,filePrefix+SimDataConstants.IDA_DATA_EXTENSION);
			String sundialsSolverExecutable = PropertyLoader.getRequiredProperty(PropertyLoader.sundialsSolverExecutableProperty);
			Executable executable = new Executable(new String[]{sundialsSolverExecutable, cvodeFile.getAbsolutePath(), cvodeOutputFile.getAbsolutePath()});
			executable.start();
*/
        // get the result
        ODESolverResultSet odeSolverResultSet = getODESolverResultSet(simJob, idaOutputFile.getPath());
        // remove CVOde input and output files ??
        idaInputFile.delete();
        idaOutputFile.delete();
        // 
        // print header
        // 
        File outputFile = new File(outDir, "results" + filePrefix + ".csv");
        java.io.PrintStream outputStream = new java.io.PrintStream(new java.io.BufferedOutputStream(new java.io.FileOutputStream(outputFile)));
        outputStream.print("time");
        for (int i = 0; i < testSpec.getVarsList().length; i++) {
            outputStream.print("," + testSpec.getVarsList()[i]);
        }
        outputStream.println();
        // 
        // extract data for time and species
        // 
        double[][] data = new double[testSpec.getVarsList().length + 1][];
        int column = odeSolverResultSet.findColumn("t");
        data[0] = odeSolverResultSet.extractColumn(column);
        int origDataLength = data[0].length;
        for (int i = 0; i < testSpec.getVarsList().length; i++) {
            column = odeSolverResultSet.findColumn(testSpec.getVarsList()[i]);
            if (column == -1) {
                Variable var = simJob.getSimulationSymbolTable().getVariable(testSpec.getVarsList()[i]);
                data[i + 1] = new double[data[0].length];
                if (var instanceof cbit.vcell.math.Constant) {
                    double value = ((cbit.vcell.math.Constant) var).getExpression().evaluateConstant();
                    for (int j = 0; j < data[i + 1].length; j++) {
                        data[i + 1][j] = value;
                    }
                } else {
                    throw new RuntimeException("Did not find " + testSpec.getVarsList()[i] + " in simulation");
                }
            } else {
                data[i + 1] = odeSolverResultSet.extractColumn(column);
            }
        }
        // 
        // for each time, print row
        // 
        int index = 0;
        double[] sampleTimes = new double[testSpec.getNumTimeSteps() + 1];
        for (int i = 0; i <= testSpec.getNumTimeSteps(); i++) {
            sampleTimes[i] = endTime * i / testSpec.getNumTimeSteps();
        }
        Model vcModel = bioModel.getModel();
        ReservedSymbol kMole = vcModel.getKMOLE();
        for (int i = 0; i < sampleTimes.length; i++) {
            // 
            while (true) {
                // 
                if (index == odeSolverResultSet.getRowCount() - 1) {
                    if (data[0][index] == sampleTimes[i]) {
                        break;
                    } else {
                        throw new RuntimeException("sampleTime does not match at last time point");
                    }
                }
                // 
                if (data[0][index + 1] > sampleTimes[i]) {
                    break;
                }
                // 
                // sampleTime must be later in our data list.
                // 
                index++;
            }
            // if data[0][index] == sampleTime no need to interpolate
            if (data[0][index] == sampleTimes[i]) {
                // if timeFactor is not 1.0, time is not in seconds (mins or hrs); if timeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                // if (timeFactor != 1.0) {
                // outputStream.print(data[0][index]/timeFactor);
                // } else {
                outputStream.print(data[0][index]);
                // }
                for (int j = 0; j < testSpec.getVarsList().length; j++) {
                    // SBMLImporter.SBVCConcentrationUnits spConcUnits = speciesUnitsHash.get(testSpec.getVarsList()[j]);
                    // if (spConcUnits != null) {
                    // VCUnitDefinition sbunits = spConcUnits.getSBConcentrationUnits();
                    // VCUnitDefinition vcunits = spConcUnits.getVCConcentrationUnits();
                    // SBMLUnitParameter unitFactor = SBMLUtils.getConcUnitFactor("spConcParam", vcunits, sbunits, kMole);
                    // outputStream.print("," + data[j + 1][index] * unitFactor.getExpression().evaluateConstant()); 		//earlier, hack unitfactor = 0.000001
                    // earlier, hack unitfactor = 0.000001
                    outputStream.print("," + data[j + 1][index]);
                // }
                }
                // System.out.println("No interpolation needed!");
                outputStream.println();
            } else {
                // if data[0][index] < sampleTime, must interpolate
                double fraction = (sampleTimes[i] - data[0][index]) / (data[0][index + 1] - data[0][index]);
                // if timeFactor is not 1.0, time is not in seconds (mins or hrs); if timeFactor is 60, divide sampleTime/60; if it is 3600, divide sampleTime/3600.
                // if (timeFactor != 1.0) {
                // outputStream.print(sampleTimes[i]/timeFactor);
                // } else {
                outputStream.print(sampleTimes[i]);
                // }
                for (int j = 0; j < testSpec.getVarsList().length; j++) {
                    double interpolatedValue = 0.0;
                    double[] speciesVals = null;
                    double[] times = null;
                    // Currently using 2nd order interpolation
                    if (index == 0) {
                        // can only do 1st order interpolation
                        times = new double[] { data[0][index], data[0][index + 1] };
                        speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1] };
                        interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                    } else if (index >= 1 && index <= origDataLength - 3) {
                        double val_1 = Math.abs(sampleTimes[i] - data[0][index - 1]);
                        double val_2 = Math.abs(sampleTimes[i] - data[0][index + 2]);
                        if (val_1 < val_2) {
                            times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                            speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                        } else {
                            times = new double[] { data[0][index], data[0][index + 1], data[0][index + 2] };
                            speciesVals = new double[] { data[j + 1][index], data[j + 1][index + 1], data[j + 1][index + 2] };
                        }
                        interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                    } else {
                        times = new double[] { data[0][index - 1], data[0][index], data[0][index + 1] };
                        speciesVals = new double[] { data[j + 1][index - 1], data[j + 1][index], data[j + 1][index + 1] };
                        interpolatedValue = MathTestingUtilities.taylorInterpolation(sampleTimes[i], times, speciesVals);
                    }
                    // // Currently using 1st order interpolation
                    // times = new double[] { data[0][index], data[0][index+1] };
                    // speciesVals = new double[] { data[j+1][index], data[j+1][index+1] };
                    // interpolatedValue = taylorInterpolation(sampleTimes[i], times, speciesVals);
                    // interpolatedValue = interpolatedValue * unitFactor.getExpression().evaluateConstant(); 		//earlier, hack unitfactor = 0.000001
                    // System.out.println("Sample time: " + sampleTimes[i] + ", between time[" + index + "]=" + data[0][index]+" and time["+(index+1)+"]="+(data[0][index+1])+", interpolated = "+interpolatedValue);
                    outputStream.print("," + interpolatedValue);
                }
                outputStream.println();
            }
        }
        outputStream.close();
        return outputFile;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        // File outputFile = new File(outDir,"results" + filePrefix + ".csv");
        throw new SolverException(e.getMessage());
    }
}

Example 7 with Executable

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

the class BioformatsImageDatasetReader method launchServer.

private void launchServer(int port) {
    synchronized (BioformatsImageDatasetReader.class) {
        if (serverThread != null) {
            return;
        }
        Runnable runnable = new Runnable() {

            @Override
            public void run() {
                Executable executable = new Executable(new String[] { "java", "-jar", bioformatsExecutableJarFile.getAbsolutePath(), Integer.toString(port) });
                try {
                    executable.start();
                } catch (ExecutableException e) {
                    e.printStackTrace();
                    serverThread = null;
                }
            }
        };
        serverThread = new Thread(runnable, "bioformatsServerThread");
        serverThread.setDaemon(true);
        serverThread.start();
        try {
            // give some time for the service to start listening
            Thread.sleep(2000);
        } catch (InterruptedException e) {
        }
    }
}

Example 8 with Executable

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

the class PythonSupport method checkPackage.

private static boolean checkPackage(File pythonExe, PythonPackage pythonPackage) {
    String[] cmd;
    if (OperatingSystemInfo.getInstance().isWindows()) {
        // cmd = new String[] { "cmd", "/C", condaExe.getAbsolutePath(), "-c", "'import "+pythonPackage.pythonModuleName+"'"};
        cmd = new String[] { pythonExe.getAbsolutePath(), "-c", "\"import " + pythonPackage.pythonModuleName + "\"" };
    } else {
        cmd = new String[] { "bash", "-c", pythonExe.getAbsolutePath() + " -c  'import " + pythonPackage.pythonModuleName + "'" };
    }
    System.out.println(Arrays.asList(cmd).toString());
    IExecutable exe = new Executable(cmd);
    try {
        System.out.println("checking package " + pythonPackage.condaName);
        exe.start(new int[] { 0 });
        System.out.println("Exit value: " + exe.getExitValue());
        System.out.println(exe.getStdoutString());
        System.out.println(exe.getStderrString());
        return true;
    } catch (ExecutableException e) {
        // e.printStackTrace();
        System.out.println("Exit value: " + exe.getExitValue());
        System.out.println(exe.getStdoutString());
        System.out.println(exe.getStderrString());
        return false;
    }
}

Example 9 with Executable

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

the class PythonSupport method checkPython.

private static boolean checkPython(File pythonExe) {
    String[] cmd;
    if (OperatingSystemInfo.getInstance().isWindows()) {
        // cmd = new String[] {"cmd", "/C", managedMiniconda.pythonExe.getAbsolutePath(), "--version"};
        cmd = new String[] { pythonExe.getAbsolutePath(), "--version" };
    } else {
        cmd = new String[] { pythonExe.getAbsolutePath(), "--version" };
    }
    IExecutable exe = new Executable(cmd);
    try {
        exe.start(new int[] { 0 });
        System.out.println("Exit value: " + exe.getExitValue());
        System.out.println("stdout=\"" + exe.getStdoutString() + "\"");
        System.out.println("stderr=\"" + exe.getStderrString() + "\"");
        if (exe.getExitValue() != 0) {
            throw new RuntimeException("Python test failed with return code " + exe.getExitValue() + ": " + exe.getStderrString());
        }
        // }
        return true;
    } catch (ExecutableException e) {
        e.printStackTrace();
        throw new RuntimeException("Python test invocation failed: " + e.getMessage(), e);
    }
}

Example 10 with Executable

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

the class VisitSupport method launchVisToolLinux.

public static void launchVisToolLinux(File visitExecutable) throws ExecutableException, IOException {
    File mpirun = null;
    if (visitExecutable == null) {
        File userDir = new File(System.getProperty("user.home"));
        System.out.println(userDir.getAbsolutePath() + " " + userDir.exists());
        // find -L ~/ -name 'visit' -executable -type f -print
        // 'find -L /home/frm -name 'visit' -executable -type f -print'
        Executable exec = new Executable(new String[] { "/bin/sh", "-c", "find -L " + userDir.getAbsolutePath() + " -maxdepth 4 -name 'visit' -executable -type f -print" });
        // exec.setWorkingDir(userDir);
        exec.start();
        System.out.println(exec.getExitValue());
        System.out.println(exec.getStdoutString());
        // System.out.println(exec.getStderrString());
        if (exec.getExitValue() == 0) {
            visitExecutable = new File(exec.getStdoutString().trim());
        }
        // look for mpirun starting 2 levels above visit executable dir location
        exec = new Executable(new String[] { "/bin/sh", "-c", "find -L " + visitExecutable.getParentFile().getParent() + " -maxdepth 6 -name 'mpirun' -executable -type f -print" });
        exec.start();
        System.out.println(exec.getExitValue());
        System.out.println(exec.getStdoutString());
        System.err.println(exec.getStderrString());
        // System.out.println(exec.getStderrString());
        if (exec.getExitValue() == 0) {
            String mpiStr = exec.getStdoutString();
            if (mpiStr != null) {
                mpiStr = mpiStr.trim();
            }
            if (mpiStr != null && mpiStr.length() != 0) {
                mpirun = new File(mpiStr);
            } else {
                mpirun = null;
            }
        }
        if (mpirun == null) {
            // See if any mpi run installed
            exec = new Executable(new String[] { "/bin/sh", "-c", "which mpirun" });
            exec.start();
            System.out.println(exec.getExitValue());
            System.out.println(exec.getStdoutString());
            System.out.println(exec.getStderrString());
            if (exec.getExitValue() == 0) {
                String mpiStr = exec.getStdoutString();
                if (mpiStr != null) {
                    mpiStr = mpiStr.trim();
                }
                if (mpiStr != null && mpiStr.length() != 0) {
                    mpirun = new File(mpiStr);
                } else {
                    mpirun = null;
                }
            }
        }
    }
    System.out.println(visitExecutable.getAbsolutePath());
    if (visitExecutable == null || !visitExecutable.exists() || !visitExecutable.isFile()) {
        throw new IOException("visit executable not found");
    }
    VCellConfiguration.setFileProperty(PropertyLoader.visitExe, visitExecutable);
    System.out.println(mpirun.getAbsolutePath());
    if (mpirun == null || !mpirun.exists() || !mpirun.isFile()) {
        throw new IOException("mpirun executable not found");
    }
    File visMainCLI = getVisToolPythonScript();
    if (!visMainCLI.exists() || !visMainCLI.isFile()) {
        throw new IOException("vcell/visit main python file not found, " + visMainCLI.getAbsolutePath());
    }
    File scriptFile = File.createTempFile("VCellVisitLaunch", ".command");
    System.out.println("Launch script location=" + scriptFile.getAbsolutePath());
    Executable exec = new Executable(new String[] { /*"/bin/sh","-c",*/
    scriptFile.getAbsolutePath() });
    // 
    // 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);
        if (varname.equals("PATH")) {
            value = value + ":" + visitExecutable.getParent();
        }
        // envVarList.add(varname+"="+value);
        exec.addEnvironmentVariable(varname, value);
        System.out.println(varname + "=" + value);
    }
    String visitCommandString = visitExecutable.getPath().replace("\"", "");
    System.out.println("Visit Command String = " + visitCommandString);
    // envVarList.add(visitCommandString);
    if (lg.isInfoEnabled()) {
        lg.info("visitcmd=" + visitExecutable.getPath().replace("\"", ""));
    }
    // envVarList.add("pythonscript="+visMainCLI.getPath());
    String pythonScriptString = visMainCLI.getPath();
    System.out.println("Python script = " + pythonScriptString);
    scriptFile.setExecutable(true);
    BufferedWriter writer = new BufferedWriter(new FileWriter(scriptFile));
    // export PATH="$HOME/opt/bin:$PATH"
    System.out.println("export PATH=\"$PATH:" + mpirun.getParent() + "\"\n");
    writer.append("export PATH=\"$PATH:" + mpirun.getParent() + "\"\n");
    System.out.println(visitCommandString + " -cli -uifile " + pythonScriptString + "\n");
    writer.append(visitCommandString + " -cli -uifile " + pythonScriptString + "\n");
    writer.close();
    // cli
    // mdserver
    // engine_ser
    new Thread(new Runnable() {

        @Override
        public void run() {
            try {
                exec.start();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }).start();
    // envVarList.toArray(new String[0]));
    if (lg.isInfoEnabled()) {
        lg.info("Started VCellVisIt");
    }
}