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

Example 56 with XMLSource

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

the class NagiosVCellCheck method checkVCell.

private static String checkVCell(VCELL_CHECK_LEVEL checkLevel, String rmiHostName, int rmiPort, String rmiBootstrapStubName, String vcellNagiosPassword, int warningTimeout, int criticalTimeout) throws Exception {
    long startTime = System.currentTimeMillis();
    SimulationStatusPersistent lastSimStatus = null;
    if (rmiHostName == null || rmiPort == -1) {
        throw new UnexpectedTestStateException("Host name/ip and rmiPort required for testing, rmihostname=" + rmiHostName + " rmiport=" + rmiPort);
    }
    String rmiUrl = "//" + rmiHostName + ":" + rmiPort + "/" + rmiBootstrapStubName;
    VCellBootstrap vcellBootstrap = null;
    try {
        vcellBootstrap = (VCellBootstrap) Naming.lookup(rmiUrl);
    } catch (Exception e) {
        throw new UnexpectedTestStateException("Error during bootstrap lookup, " + e.getClass().getSimpleName() + " " + e.getMessage());
    }
    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.CONNECT_1.ordinal()) {
        if (vcellNagiosPassword == null) {
            throw new UnexpectedTestStateException("vcellNagios Password required for " + VCELL_CHECK_LEVEL.CONNECT_1.toString() + " and above");
        }
        VCellConnection vcellConnection = vcellBootstrap.getVCellConnection(new UserLoginInfo("vcellNagios", new DigestedPassword(vcellNagiosPassword)));
        if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.INFOS_2.ordinal()) {
            VCInfoContainer vcInfoContainer = vcellConnection.getUserMetaDbServer().getVCInfoContainer();
            if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.LOAD_3.ordinal()) {
                KeyValue bioModelKey = null;
                final String testModelName = "Solver Suite 5.1 (BETA only ode)";
                for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                    if (bioModelInfo.getVersion().getName().equals(testModelName)) {
                        bioModelKey = bioModelInfo.getVersion().getVersionKey();
                        break;
                    }
                }
                BigString bioModelXML = vcellConnection.getUserMetaDbServer().getBioModelXML(bioModelKey);
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                bioModel.refreshDependencies();
                if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.DATA_4.ordinal()) {
                    final String testSimContextName = "non-spatial ODE";
                    SimulationContext simulationContext = bioModel.getSimulationContext(testSimContextName);
                    final String testSimName = "Copy of combined ida/cvode";
                    Simulation simulation = simulationContext.getSimulation(testSimName);
                    if (simulation == null) {
                        throw new UnexpectedTestStateException("Couldn't find sim '" + testSimName + "' for " + checkLevel.toString());
                    }
                    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), 0);
                    ArrayList<AnnotatedFunction> outputFunctionsList = simulationContext.getOutputFunctionContext().getOutputFunctionsList();
                    OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
                    double[] times = vcellConnection.getDataSetController().getDataSetTimes(vcSimulationDataIdentifier);
                    ODESimData odeSimData = vcellConnection.getDataSetController().getODEData(vcSimulationDataIdentifier);
                    // SimDataBlock simDataBlock = vcellConnection.getDataSetController().getSimDataBlock(outputContext, vcSimulationDataIdentifier, "RanC_cyt",times[times.length-1]);
                    if (checkLevel.ordinal() >= VCELL_CHECK_LEVEL.RUN_5.ordinal()) {
                        KeyValue copy1Key = null;
                        KeyValue copy2Key = null;
                        try {
                            if (simulationContext.getSimulations().length != 1) {
                                throw new UnexpectedTestStateException("Expecting only 1 sim to be copied for " + checkLevel.toString());
                            }
                            SimulationStatusPersistent simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(simulation.getVersion().getVersionKey());
                            if (!simulationStatus.isCompleted()) {
                                throw new UnexpectedTestStateException("Expecting completed sim to copy for " + checkLevel.toString());
                            }
                            String copyModelName = testModelName + "_" + rmiHostName + "_" + rmiPort;
                            for (BioModelInfo bioModelInfo : vcInfoContainer.getBioModelInfos()) {
                                if (bioModelInfo.getVersion().getName().equals(copyModelName)) {
                                    throw new UnexpectedTestStateException("Messy test environment, not expecting " + copyModelName + " to exist at this point");
                                }
                            }
                            BigString copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModelAs(bioModelXML, copyModelName, null);
                            BioModel copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy1Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation copySim = copyBioModel.getSimulationContext(testSimContextName).copySimulation(copyBioModel.getSimulationContext(testSimContextName).getSimulation(testSimName));
                            final String copyTestSimName = "test";
                            copySim.setName(copyTestSimName);
                            copyBioModel.refreshDependencies();
                            copyBioModelXMLStr = new BigString(XmlHelper.bioModelToXML(copyBioModel));
                            copyBioModelXMLStr = vcellConnection.getUserMetaDbServer().saveBioModel(copyBioModelXMLStr, null);
                            copyBioModel = XmlHelper.XMLToBioModel(new XMLSource(copyBioModelXMLStr.toString()));
                            copy2Key = copyBioModel.getVersion().getVersionKey();
                            copyBioModel.refreshDependencies();
                            Simulation newSimulation = copyBioModel.getSimulationContext(testSimContextName).getSimulation(copyTestSimName);
                            simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                            if (simulationStatus != null && !simulationStatus.isNeverRan()) {
                                throw new UnexpectedTestStateException("Expecting new sim to have 'never ran' status for " + checkLevel.toString());
                            }
                            VCSimulationIdentifier newSimID = new VCSimulationIdentifier(newSimulation.getVersion().getVersionKey(), copyBioModel.getVersion().getOwner());
                            vcellConnection.getSimulationController().startSimulation(newSimID, 1);
                            lastSimStatus = simulationStatus;
                            MessageEvent[] messageEvents = null;
                            while (simulationStatus == null || (!simulationStatus.isStopped() && !simulationStatus.isCompleted() && !simulationStatus.isFailed())) {
                                Thread.sleep(200);
                                if (((System.currentTimeMillis() - startTime) / 1000) > criticalTimeout) {
                                    vcellConnection.getSimulationController().stopSimulation(newSimID);
                                    vcellConnection.getMessageEvents();
                                    break;
                                }
                                simulationStatus = vcellConnection.getUserMetaDbServer().getSimulationStatus(newSimulation.getVersion().getVersionKey());
                                if (simulationStatus != null && !simulationStatus.toString().equals((lastSimStatus == null ? null : lastSimStatus.toString()))) {
                                    lastSimStatus = simulationStatus;
                                }
                                messageEvents = vcellConnection.getMessageEvents();
                            }
                        } finally {
                            try {
                                if (copy1Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy1Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                            try {
                                if (copy2Key != null) {
                                    vcellConnection.getUserMetaDbServer().deleteBioModel(copy2Key);
                                }
                            } catch (Exception e) {
                                e.printStackTrace();
                            }
                        }
                    }
                }
            }
        }
    }
    long endTime = System.currentTimeMillis();
    if (criticalTimeout != -1 && ((endTime - startTime) / 1000) > criticalTimeout) {
        throw new Exception(checkLevel.toString() + " test exceeded criticalTimeout=" + criticalTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    if (warningTimeout != -1 && ((endTime - startTime) / 1000) > warningTimeout) {
        throw new WarningTestConditionException(checkLevel.toString() + " test exceeded warningTimeout=" + warningTimeout + " seconds lastSimStatus=" + lastSimStatus);
    }
    return vcellBootstrap.getVCellSoftwareVersion();
}

Example 57 with XMLSource

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

the class VCDatabaseScanner method scanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void scanBioModels(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleModelKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning bio-models......");
        logFilePrintStream.println("\n");
        // adapter for verifyMathDescriptionsUnchanged
        PrintWriter logFilePrintWriter = new PrintWriter(logFilePrintStream);
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (int j = 0; j < bioModelInfos.length; j++) {
                if (singleModelKey != null && !bioModelInfos[j].getVersion().getVersionKey().compareEqual(singleModelKey)) {
                    System.out.println("skipping biomodel, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(bioModelInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping bioModel with key '" + bioModelInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(bioModelInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including bioModel with key '" + bioModelInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterBioModel(bioModelInfos[j])) {
                    continue;
                }
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bioModelInfos[j].getVersion().getVersionKey());
                    BioModel bioModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    bioModel.refreshDependencies();
                    // + bioModelInfos[j].getVersion().getName() + " -----> ");
                    logFilePrintStream.println("---- " + (j + 1) + " ----> " + bioModel.getName());
                    databaseVisitor.visitBioModel(bioModel, logFilePrintStream);
                // verifyMathDescriptionsUnchanged(bioModel, logFilePrintWriter);
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    logFilePrintStream.println("======= " + e2.getMessage());
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("error writing to log file.");
    }
}

Example 58 with XMLSource

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

the class VCDatabaseScanner method multiScanBioModels.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void multiScanBioModels(VCMultiBioVisitor databaseVisitor, Writer writer, User[] users, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    assert users != null;
    try {
        PrintWriter printWriter = new PrintWriter(writer);
        // start visiting models and writing log
        printWriter.println("Start scanning bio-models......");
        printWriter.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            BioModelInfo[] bioModelInfos = dbServerImpl.getBioModelInfos(user, false);
            for (int j = 0; j < bioModelInfos.length; j++) {
                BioModelInfo bmi = bioModelInfos[j];
                if (!databaseVisitor.filterBioModel(bmi)) {
                    continue;
                }
                try {
                    BigString bioModelXML = dbServerImpl.getBioModelXML(user, bmi.getVersion().getVersionKey());
                    BioModel storedModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                    System.out.println(storedModel.getName());
                    if (databaseVisitor.filterBioModel(storedModel)) {
                        storedModel.refreshDependencies();
                        verifyMathDescriptionsUnchanged(storedModel, printWriter);
                        databaseVisitor.setBioModel(storedModel, printWriter);
                        // + bioModelInfos[j].getVersion().getName() + " -----> ");
                        printWriter.println("---- " + (j + 1) + " ----> " + storedModel.getName());
                        for (BioModel bioModel : databaseVisitor) {
                            SimulationContext[] simContexts = bioModel.getSimulationContexts();
                            for (SimulationContext sc : simContexts) {
                                try {
                                    sc.createNewMathMapping().getMathDescription();
                                } catch (Exception e) {
                                    printWriter.println("\t " + bioModel.getName() + " :: " + sc.getName() + " ----> math regeneration failed.s");
                                // e.printStackTrace();
                                }
                            }
                        }
                    }
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    printWriter.println("======= " + e2.getMessage());
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        printWriter.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 59 with XMLSource

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

the class VCDatabaseScanner method scanGeometries.

/**
 * Insert the method's description here.
 * Creation date: (2/2/01 3:40:29 PM)
 * @throws DataAccessException
 * @throws XmlParseException
 */
public void scanGeometries(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleGeometryKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning geometries......");
        logFilePrintStream.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            GeometryInfo[] geoInfos = dbServerImpl.getGeometryInfos(user, false);
            for (int j = 0; j < geoInfos.length; j++) {
                if (singleGeometryKey != null && !geoInfos[j].getVersion().getVersionKey().compareEqual(singleGeometryKey)) {
                    System.out.println("skipping geometry, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(geoInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including geometry with key '" + geoInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterGeometry(geoInfos[j])) {
                    continue;
                }
                try {
                    BigString geometryXML = dbServerImpl.getGeometryXML(user, geoInfos[j].getVersion().getVersionKey());
                    Geometry geometry = cbit.vcell.xml.XmlHelper.XMLToGeometry(new XMLSource(geometryXML.toString()));
                    geometry.refreshDependencies();
                    databaseVisitor.visitGeometry(geometry, logFilePrintStream);
                } catch (Exception e2) {
                    lg.error(e2.getMessage(), e2);
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        System.err.println("error writing to log file.");
    }
}

Example 60 with XMLSource

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

the class ServerDocumentManager 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
 */
public String getMathModelXML(QueryHashtable dbc, User user, KeyValue mathModelKey, boolean bRegenerateXML) throws DataAccessException {
    String mathModelXML = null;
    try {
        mathModelXML = dbServer.getDBTopLevel().getMathModelXML(user, mathModelKey, true);
        if (mathModelXML != null) {
            if (bRegenerateXML) {
                try {
                    MathModel mathModel = XmlHelper.XMLToMathModel(new XMLSource(mathModelXML));
                    return cbit.vcell.xml.XmlHelper.mathModelToXML(mathModel);
                } catch (XmlParseException e) {
                    e.printStackTrace();
                    throw new DataAccessException(e.getMessage(), e);
                }
            } else {
                return mathModelXML;
            }
        }
    } catch (java.sql.SQLException e) {
        lg.error(e.getLocalizedMessage(), e);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
    // 
    // not stored as XML currently, retrieve traditional way.
    // 
    }
    try {
        MathModel mathModel = getMathModelUnresolved(dbc, user, mathModelKey);
        mathModelXML = cbit.vcell.xml.XmlHelper.mathModelToXML(mathModel);
        dbServer.insertVersionableXML(user, VersionableType.MathModelMetaData, mathModelKey, mathModelXML);
        return mathModelXML;
    } catch (java.sql.SQLException e) {
        lg.error(e.getLocalizedMessage(), e);
        throw new DataAccessException(e.getMessage());
    } catch (cbit.vcell.xml.XmlParseException e) {
        lg.error(e.getLocalizedMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
}