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

Example 1 with IExecutable

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

the class CopasiServicePython method runCopasiPython.

public static void runCopasiPython(File copasiOptProblemFile, File copasiResultsFile) throws IOException {
    // It's 2015 -- forward slash works for all operating systems
    File PYTHON = PythonSupport.getPythonExe();
    InstallStatus copasiInstallStatus = PythonSupport.getPythonPackageStatus(PythonPackage.COPASI);
    if (copasiInstallStatus == InstallStatus.FAILED) {
        throw new RuntimeException("failed to install COPASI python package, consider re-installing VCell-managed python\n ...see Preferences->Python->Re-install");
    }
    if (copasiInstallStatus == InstallStatus.INITIALIZING) {
        throw new RuntimeException("VCell is currently installing or verifying the COPASI python package ... please try again in a minute");
    }
    File vcellOptDir = ResourceUtil.getVCellOptPythonDir();
    File optServicePythonFile = new File(vcellOptDir, "optService.py");
    if (PYTHON == null || !PYTHON.exists()) {
        throw new RuntimeException("python executable not specified, set python location in VCell menu File->Preferences...->Python Properties");
    }
    String[] cmd = new String[] { PYTHON.getAbsolutePath(), optServicePythonFile.getAbsolutePath(), copasiOptProblemFile.getAbsolutePath(), copasiResultsFile.getAbsolutePath() };
    IExecutable exe = prepareExecutable(cmd);
    try {
        exe.start(new int[] { 0 });
        if (exe.getExitValue() != 0) {
            throw new RuntimeException("copasi python solver (optService.py) failed with return code " + exe.getExitValue() + ": " + exe.getStderrString());
        }
    } catch (ExecutableException e) {
        e.printStackTrace();
        throw new RuntimeException("optService.py invocation failed: " + e.getMessage(), e);
    }
}

Example 2 with IExecutable

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

the class VtkServicePython method writeVtkGridAndIndexData.

private void writeVtkGridAndIndexData(String visMeshType, VisMesh visMesh, String domainName, File vtkFile, File indexFile) throws IOException {
    if (lg.isDebugEnabled()) {
        lg.debug("writeVtkGridAndIndexData (python) for domain " + domainName);
    }
    File PYTHON = PythonSupport.getPythonExe();
    InstallStatus copasiInstallStatus = PythonSupport.getPythonPackageStatus(PythonPackage.VTK);
    if (copasiInstallStatus == InstallStatus.FAILED) {
        throw new RuntimeException("failed to install VTK python package, consider re-installing VCell-managed python\n ...see Preferences->Python->Re-install");
    }
    if (copasiInstallStatus == InstallStatus.INITIALIZING) {
        throw new RuntimeException("VCell is currently installing or verifying the VTK python package ... please try again in a minute");
    }
    String baseFilename = vtkFile.getName().replace(".vtu", ".visMesh");
    File visMeshFile = new File(vtkFile.getParentFile(), baseFilename);
    VisMeshUtils.writeVisMesh(visMeshFile, visMesh);
    File vtkServiceFile = new File(ResourceUtil.getVCellVTKPythonDir(), "vtkService.py");
    // It's 2015 -- forward slash works for all operating systems
    String[] cmd = new String[] { PYTHON.getAbsolutePath(), vtkServiceFile.getAbsolutePath(), visMeshType, domainName, visMeshFile.getAbsolutePath(), vtkFile.getAbsolutePath(), indexFile.getAbsolutePath() };
    IExecutable exe = prepareExecutable(cmd);
    try {
        exe.start(new int[] { 0 });
        if (exe.getExitValue() != 0) {
            throw new RuntimeException("mesh generation script for domain " + domainName + " failed with return code " + exe.getExitValue() + ": " + exe.getStderrString());
        }
    } catch (ExecutableException e) {
        e.printStackTrace();
        throw new RuntimeException("vtkService.py invocation failed: " + e.getMessage(), e);
    }
}

Example 3 with IExecutable

use of org.vcell.util.exe.IExecutable 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 4 with IExecutable

use of org.vcell.util.exe.IExecutable 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;
    }
}