Examples with TSerializer org.apache.thrift.TSerializer used on opensource projects

Example 21 with TSerializer

use of org.apache.thrift.TSerializer 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 22 with TSerializer

use of org.apache.thrift.TSerializer in project vcell by virtualcell.

the class OptimizationServerResource method get_html.

@Override
public Representation get_html() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    OptRun optRun = getOptRun(vcellUser);
    if (optRun == null) {
        throw new RuntimeException("optimization not found");
    }
    try {
        Map<String, Object> dataModel = new HashMap<String, Object>();
        // +"?"+VCellApiApplication.REDIRECTURL_FORMNAME+"="+getRequest().getResourceRef().toUrl());
        dataModel.put("loginurl", "/" + VCellApiApplication.LOGINFORM);
        dataModel.put("logouturl", "/" + VCellApiApplication.LOGOUT + "?" + VCellApiApplication.REDIRECTURL_FORMNAME + "=" + Reference.encode(getRequest().getResourceRef().toUrl().toString()));
        if (vcellUser != null) {
            dataModel.put("userid", vcellUser.getName());
        }
        dataModel.put("optId", getQueryValue(VCellApiApplication.OPTIMIZATIONID));
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optRunJson = new String(serializer.serialize(optRun));
        dataModel.put("optimization", new JSONObject(optRunJson));
        dataModel.put("jsonResponse", optRunJson);
        Configuration templateConfiguration = application.getTemplateConfiguration();
        Representation formFtl = new ClientResource(LocalReference.createClapReference("/optimization.ftl")).get();
        TemplateRepresentation templateRepresentation = new TemplateRepresentation(formFtl, templateConfiguration, dataModel, MediaType.TEXT_HTML);
        return templateRepresentation;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

Example 23 with TSerializer

use of org.apache.thrift.TSerializer in project hive by apache.

the class DBSerializer method writeTo.

@Override
public void writeTo(JsonWriter writer, ReplicationSpec additionalPropertiesProvider) throws SemanticException, IOException {
    dbObject.putToParameters(ReplicationSpec.KEY.CURR_STATE_ID_SOURCE.toString(), additionalPropertiesProvider.getCurrentReplicationState());
    try {
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String value = serializer.toString(dbObject);
        writer.jsonGenerator.writeStringField(FIELD_NAME, value);
    } catch (TException e) {
        throw new SemanticException(ErrorMsg.ERROR_SERIALIZE_METASTORE.getMsg(), e);
    }
}

Example 24 with TSerializer

use of org.apache.thrift.TSerializer in project hive by apache.

the class FunctionSerializer method writeTo.

@Override
public void writeTo(JsonWriter writer, ReplicationSpec additionalPropertiesProvider) throws SemanticException, IOException, MetaException {
    List<ResourceUri> resourceUris = new ArrayList<>();
    if (function.getResourceUris() != null) {
        for (ResourceUri uri : function.getResourceUris()) {
            Path inputPath = new Path(uri.getUri());
            if ("hdfs".equals(inputPath.toUri().getScheme())) {
                FileSystem fileSystem = inputPath.getFileSystem(hiveConf);
                Path qualifiedUri = PathBuilder.fullyQualifiedHDFSUri(inputPath, fileSystem);
                String checkSum = ReplChangeManager.checksumFor(qualifiedUri, fileSystem);
                String encodedSrcUri = ReplChangeManager.getInstance(hiveConf).encodeFileUri(qualifiedUri.toString(), checkSum, null);
                if (copyAtLoad) {
                    if (hiveConf.getBoolVar(HiveConf.ConfVars.REPL_HA_DATAPATH_REPLACE_REMOTE_NAMESERVICE)) {
                        encodedSrcUri = Utils.replaceNameserviceInEncodedURI(encodedSrcUri, hiveConf);
                    }
                    resourceUris.add(new ResourceUri(uri.getResourceType(), encodedSrcUri));
                } else {
                    Path newBinaryPath = new Path(functionDataRoot, qualifiedUri.getName());
                    resourceUris.add(new ResourceUri(uri.getResourceType(), newBinaryPath.toString()));
                    functionBinaryCopyPaths.add(new EximUtil.DataCopyPath(additionalPropertiesProvider, new Path(encodedSrcUri), newBinaryPath));
                }
            } else {
                resourceUris.add(uri);
            }
        }
    }
    Function copyObj = new Function(this.function);
    if (!resourceUris.isEmpty()) {
        assert resourceUris.size() == this.function.getResourceUris().size();
        copyObj.setResourceUris(resourceUris);
    }
    try {
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        // This is required otherwise correct work object on repl load wont be created.
        writer.jsonGenerator.writeStringField(ReplicationSpec.KEY.REPL_SCOPE.toString(), "all");
        writer.jsonGenerator.writeStringField(ReplicationSpec.KEY.CURR_STATE_ID_SOURCE.toString(), additionalPropertiesProvider.getCurrentReplicationState());
        writer.jsonGenerator.writeStringField(FIELD_NAME, serializer.toString(copyObj));
    } catch (TException e) {
        throw new SemanticException(ErrorMsg.ERROR_SERIALIZE_METASTORE.getMsg(), e);
    }
}

Example 25 with TSerializer

use of org.apache.thrift.TSerializer in project hive by apache.

the class TableSerializer method writeTo.

@Override
public void writeTo(JsonWriter writer, ReplicationSpec additionalPropertiesProvider) throws SemanticException, IOException {
    if (!Utils.shouldReplicate(additionalPropertiesProvider, tableHandle, false, null, null, hiveConf)) {
        return;
    }
    Table tTable = updatePropertiesInTable(tableHandle.getTTable(), additionalPropertiesProvider);
    try {
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        writer.jsonGenerator.writeStringField(FIELD_NAME, serializer.toString(tTable));
        writer.jsonGenerator.writeFieldName(PartitionSerializer.FIELD_NAME);
        writePartitions(writer, additionalPropertiesProvider);
    } catch (TException e) {
        throw new SemanticException(ErrorMsg.ERROR_SERIALIZE_METASTORE.getMsg(), e);
    }
}