Examples with OptRun org.vcell.optimization.thrift.OptRun used on opensource projects

Example 1 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptServerImplTest method main.

public static void main(String[] args) {
    try {
        System.setProperty(PropertyLoader.installationRoot, "/Users/schaff/Documents/workspace-modular/vcell");
        System.setProperty(PropertyLoader.pythonExe, "/Users/schaff/anaconda/bin/python");
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.COPASI, PythonPackage.LIBSBML, PythonPackage.THRIFT });
        try {
            Thread.sleep(2000);
        } catch (InterruptedException e) {
        }
        File optProbFile = new File(ResourceUtil.getVCellOptPythonDir(), "optprob.bin");
        System.out.println("using optProblem: " + optProbFile.getAbsolutePath());
        OptServerImpl optServerImpl = new OptServerImpl();
        OptProblem optProblem = CopasiServicePython.readOptProblem(optProbFile);
        ArrayList<String> jobIDs = new ArrayList<String>();
        jobIDs.add(optServerImpl.submit(optProblem));
        jobIDs.add(optServerImpl.submit(optProblem));
        optServerImpl.start();
        jobIDs.add(optServerImpl.submit(optProblem));
        jobIDs.add(optServerImpl.submit(optProblem));
        boolean done = false;
        while (!done) {
            done = true;
            for (String jobID : jobIDs) {
                OptRunContext optRunContext = optServerImpl.getOptRunContextByOptimizationId(jobID);
                if (optRunContext == null) {
                    throw new RuntimeException("optRunContext was null for id = " + jobID);
                }
                OptRunStatus status = optRunContext.getStatus();
                if (status != OptRunStatus.Complete && status != OptRunStatus.Failed) {
                    done = false;
                }
                if (status == OptRunStatus.Complete) {
                    OptRun optRun = CopasiServicePython.readOptRun(optRunContext.getOptRunBinaryFile());
                    System.out.println("job " + jobID + ": status " + status + " " + optRun.getOptResultSet().toString());
                } else {
                    System.out.println("job " + jobID + ": status " + status);
                }
            }
            try {
                Thread.sleep(1000);
            } catch (InterruptedException e) {
            }
        }
        System.out.println("done with all jobs");
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class CopasiServicePython method readOptRun.

public static OptRun readOptRun(File optRunFile) throws IOException {
    TDeserializer deserializer = new TDeserializer(new TBinaryProtocol.Factory());
    try {
        OptRun optJob = new OptRun();
        byte[] bytes = FileUtils.readFileToByteArray(optRunFile);
        deserializer.deserialize(optJob, bytes);
        return optJob;
    } catch (TException e) {
        e.printStackTrace();
        throw new IOException("error reading optRun from file " + optRunFile.getPath() + ": " + e.getMessage(), e);
    }
}

Example 3 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class OptimizationApiTest method main.

public static void main(String[] args) {
    try {
        boolean bIgnoreCertProblems = true;
        boolean bIgnoreHostMismatch = true;
        VCellApiClient apiClient = new VCellApiClient(host, port, bIgnoreCertProblems, bIgnoreHostMismatch);
        File optProbFile = new File("../pythonScripts/VCell_Opt/optprob.bin");
        System.out.println("using optProblem: " + optProbFile.getAbsolutePath());
        OptProblem optProblem = readOptProblem(optProbFile);
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optProblemJson = serializer.toString(optProblem);
        ArrayList<String> jobIDs = new ArrayList<String>();
        jobIDs.add(apiClient.submitOptimization(optProblemJson));
        jobIDs.add(apiClient.submitOptimization(optProblemJson));
        jobIDs.add(apiClient.submitOptimization(optProblemJson));
        jobIDs.add(apiClient.submitOptimization(optProblemJson));
        boolean done = false;
        while (!done) {
            done = true;
            for (String jobID : jobIDs) {
                String optRunJson = apiClient.getOptRunJson(jobID);
                TDeserializer deserializer = new TDeserializer(new TJSONProtocol.Factory());
                OptRun optRun = new OptRun();
                deserializer.deserialize(optRun, optRunJson.getBytes());
                OptRunStatus status = optRun.status;
                if (status != OptRunStatus.Complete && status != OptRunStatus.Failed) {
                    done = false;
                }
                if (status == OptRunStatus.Complete) {
                    System.out.println("job " + jobID + ": status " + status + " " + optRun.getOptResultSet().toString());
                } else {
                    System.out.println("job " + jobID + ": status " + status);
                }
            }
            try {
                Thread.sleep(1000);
            } catch (InterruptedException e) {
            }
        }
        System.out.println("done with all jobs");
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 4 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class CopasiOptimizationSolver method solveRemoteApi.

public static OptimizationResultSet solveRemoteApi(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    try {
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        boolean bIgnoreCertProblems = true;
        boolean bIgnoreHostMismatch = true;
        // e.g. vcell.serverhost=vcellapi.cam.uchc.edu:8080
        String serverHost = PropertyLoader.getRequiredProperty(PropertyLoader.vcellServerHost);
        String[] parts = serverHost.split(":");
        String host = parts[0];
        int port = Integer.parseInt(parts[1]);
        VCellApiClient apiClient = new VCellApiClient(host, port, bIgnoreCertProblems, bIgnoreHostMismatch);
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optProblemJson = serializer.toString(optProblem);
        String optimizationId = apiClient.submitOptimization(optProblemJson);
        // 20 second minute timeout
        final long TIMEOUT_MS = 1000 * 20;
        long startTime = System.currentTimeMillis();
        OptRun optRun = null;
        while ((System.currentTimeMillis() - startTime) < TIMEOUT_MS) {
            if (optSolverCallbacks.getStopRequested()) {
                throw new RuntimeException(STOP_REQUESTED);
            }
            String optRunJson = apiClient.getOptRunJson(optimizationId);
            TDeserializer deserializer = new TDeserializer(new TJSONProtocol.Factory());
            optRun = new OptRun();
            deserializer.deserialize(optRun, optRunJson.getBytes());
            OptRunStatus status = optRun.status;
            if (status == OptRunStatus.Complete) {
                System.out.println("job " + optimizationId + ": status " + status + " " + optRun.getOptResultSet().toString());
                break;
            }
            if (status == OptRunStatus.Failed) {
                throw new RuntimeException("optimization failed, message=" + optRun.statusMessage);
            }
            System.out.println("job " + optimizationId + ": status " + status);
            try {
                Thread.sleep(1000);
            } catch (InterruptedException e) {
            }
        }
        System.out.println("done with optimization");
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM VCellAPI---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        if (e.getMessage() != null && e.getMessage().equals(STOP_REQUESTED)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    }
}

Example 5 with OptRun

use of org.vcell.optimization.thrift.OptRun in project vcell by virtualcell.

the class CopasiOptimizationSolver method solveLocalPython.

public static OptimizationResultSet solveLocalPython(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    File dir = Files.createTempDirectory("parest", new FileAttribute<?>[] {}).toFile();
    try {
        String prefix = "testing_" + Math.abs(new Random().nextInt(10000));
        File optProblemThriftFile = new File(dir, prefix + ".optprob.bin");
        File optRunFile = new File(dir, prefix + ".optrun.bin");
        // 
        // Setup Python COPASI opt problem and write to disk
        // 
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        CopasiServicePython.writeOptProblem(optProblemThriftFile, optProblem);
        // 
        // run Python COPASI opt problem
        // 
        CopasiServicePython.runCopasiPython(optProblemThriftFile, optRunFile);
        if (!optRunFile.exists()) {
            throw new RuntimeException("COPASI optimization output file not found:\n" + optRunFile.getAbsolutePath());
        }
        OptRun optRun = CopasiServicePython.readOptRun(optRunFile);
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM PYTHON---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    } finally {
        if (dir != null && dir.exists()) {
            FileUtils.deleteDirectory(dir);
        }
    }
}