Examples with XMLSource cbit.vcell.xml.XMLSource used on opensource projects

Example 46 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientDocumentManager method getGeometryFromDatabaseXML.

/**
 * Insert the method's description here.
 * Creation date: (9/22/2004 5:22:40 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param mathModelXML java.lang.String
 */
private Geometry getGeometryFromDatabaseXML(String geometryXML) throws DataAccessException {
    try {
        Geometry geometry = XmlHelper.XMLToGeometry(new XMLSource(geometryXML));
        geometry.refreshDependencies();
        try {
            if (geometry.getDimension() > 0) {
                geometry.getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new DataAccessException("Geometric surface generation error:\n" + e.getMessage());
        }
        return geometry;
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new DataAccessException(e.getClass().getName() + ": " + e.getMessage());
    }
}

Example 47 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientDocumentManager method getMathModelXML.

/**
 * Insert the method's description here.
 * Creation date: (3/29/2004 4:04:16 PM)
 * @return java.lang.String
 * @param vType cbit.sql.VersionableType
 * @param vKey cbit.sql.KeyValue
 */
private XMLHolder<MathModel> getMathModelXML(KeyValue vKey) throws DataAccessException {
    try {
        String xmlString = (String) xmlHash.get(vKey);
        if (xmlString == null) {
            xmlString = sessionManager.getUserMetaDbServer().getMathModelXML(vKey).toString();
            if (xmlString != null) {
                MathModel mathModel = XmlHelper.XMLToMathModel(new XMLSource(xmlString));
                String newXmlString = XmlHelper.mathModelToXML(mathModel);
                xmlHash.put(vKey, newXmlString);
                return new XMLHolder<MathModel>(newXmlString, mathModel);
            } else {
                throw new RuntimeException("unexpected: UserMetaDbServer.getMathModelXML() returned null");
            }
        } else {
            return new XMLHolder<MathModel>(xmlString);
        }
    } catch (ObjectNotFoundException e) {
        throw new DataAccessException("MathModel (id=" + vKey + ") does not exist. It either " + "has been deleted or its reference is outdated. Please use menu 'Server->Reconnect' to update document references.");
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw FailToLoadDocumentExc.createException(e, vKey, this);
    }
}

Example 48 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientDocumentManager method getGeometry.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public Geometry getGeometry(GeometryInfo geometryInfo) throws DataAccessException {
    Geometry geometry = null;
    try {
        XMLSource geomSource = new XMLSource(getGeometryXML(geometryInfo.getVersion().getVersionKey()));
        geometry = XmlHelper.XMLToGeometry(geomSource);
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
    try {
        if (geometry.getDimension() > 0 && geometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
            geometry.getGeometrySurfaceDescription().updateAll();
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    // throw new DataAccessException("Geometric surface generation error:\n"+e.getMessage());
    }
    return geometry;
}

Example 49 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class ClientDocumentManager method getMathModelFromDatabaseXML.

/**
 * Insert the method's description here.
 * Creation date: (9/22/2004 5:22:40 PM)
 * @return cbit.vcell.mathmodel.MathModel
 * @param mathModelXML java.lang.String
 */
private MathModel getMathModelFromDatabaseXML(XMLHolder<MathModel> mathModelXML) throws DataAccessException {
    try {
        MathModel mm = mathModelXML.getDocument();
        if (mm == null) {
            mm = XmlHelper.XMLToMathModel(new XMLSource(mathModelXML.getXmlString()));
        }
        cacheSimulations(mm.getSimulations());
        mm.refreshDependencies();
        try {
            if (mm.getMathDescription().getGeometry().getDimension() > 0 && mm.getMathDescription().getGeometry().getGeometrySurfaceDescription().getGeometricRegions() == null) {
                mm.getMathDescription().getGeometry().getGeometrySurfaceDescription().updateAll();
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new DataAccessException("Geometric surface generation error:\n" + e.getMessage());
        }
        return mm;
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new DataAccessException(e.getClass().getName() + ": " + e.getMessage());
    }
}

Example 50 with XMLSource

use of cbit.vcell.xml.XMLSource in project vcell by virtualcell.

the class HybridSolverTester method runHybridTest.

public void runHybridTest(String site) {
    try {
        double[] timePoints = null;
        File mathModelFile = new File(mathModelVCMLFileName);
        XMLSource vcmlSource = new XMLSource(mathModelFile);
        MathModel mathModel = XmlHelper.XMLToMathModel(vcmlSource);
        File simDataDir = mathModelFile.getParentFile();
        Simulation sim = mathModel.getSimulations()[0];
        // run multiple trials and each run will have a simID = origSimID + i
        for (int i = 0; i < numRuns; i++) {
            System.out.println("--------------Trial No: " + (startTrialNo + i) + "----------------");
            // replace random seed
            sim.getSolverTaskDescription().getSmoldynSimulationOptions().setRandomSeed(new Integer(startTrialNo + i));
            // create sim job
            int jobIndex = startTrialNo + i;
            SimulationTask simTask = new SimulationTask(new SimulationJob(sim, jobIndex, null), 0);
            /*
				 * When you want to run the multiple trials on local uncomment the line below.
				 */
            // ResourceUtil.prepareSolverExecutable(sim.getSolverTaskDescription().getSolverDescription());
            /*
				 * When you want to run the multiple trials on server (without VCell user interface), use the next line of code 
				 * Corresponding changes should be made in the shell script runhybridtest for the location of executable on server
				 */
            FVSolverStandalone fvSolver = new FVSolverStandalone(simTask, simDataDir, false);
            fvSolver.startSolver();
            SolverStatus status = fvSolver.getSolverStatus();
            while (status.getStatus() != SolverStatus.SOLVER_FINISHED && status.getStatus() != SolverStatus.SOLVER_ABORTED) {
                System.out.println("progress: " + (int) (fvSolver.getProgress() * 100) + "%");
                // ask status every 2 seconds
                Thread.sleep(2000);
                status = fvSolver.getSolverStatus();
            }
            if (status.getStatus() == SolverStatus.SOLVER_FINISHED) {
                // get data
                VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(sim.getVersion().getVersionKey(), sim.getVersion().getOwner());
                VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
                File hdf5File = new File(simDataDir, vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
                DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimDataID, false, null), hdf5File);
                if (i == 0) {
                    // do only one time
                    timePoints = dataProcessingOutputInfo.getVariableTimePoints();
                    for (int j = 0; j < varNames.length; j++) {
                        // row: numTimePoints, col:first col time + numRuns
                        double[][] data = new double[numRuns + 1][timePoints.length];
                        data[0] = timePoints;
                        results.add(data);
                    }
                }
                // write into results after each run
                for (int j = 0; j < varNames.length; j++) {
                    results.get(j)[i + 1] = dataProcessingOutputInfo.getVariableStatValues().get(varNames[j]);
                }
                // delete the file generated for this run
                deleteSimFiles(simDataDir, vcSimDataID);
            } else {
                throw new Exception("Sover did not finish normally." + status);
            }
        }
        // write to output file, tab delimited
        if (results != null && results.size() > 0) {
            for (int j = 0; j < varNames.length; j++) {
                File file = new File(simDataDir, "SimID_" + sim.getVersion().getVersionKey().toString() + "_" + varNames[j] + "_" + startTrialNo + ".txt");
                PrintWriter pw = new PrintWriter(file);
                double[][] data = results.get(j);
                if (data != null) {
                    for (int k = 0; k < data.length; k++) {
                        if (!bPrintTime && k == 0) {
                            continue;
                        }
                        String rowStr = (k == 0) ? "Time\t" : ("trialNo_" + (startTrialNo + k - 1) + "\t");
                        double[] rowData = data[k];
                        for (int q = 0; q < rowData.length; q++) {
                            rowStr += rowData[q] + "\t";
                        }
                        pw.println(rowStr);
                    }
                }
                pw.close();
            }
        }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}