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

Example 21 with XMLSource

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

the class ServerDocumentManager method getBioModelXML.

/**
 * 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 getBioModelXML(QueryHashtable dbc, User user, KeyValue bioModelKey, boolean bRegenerateXML) throws DataAccessException {
    String bioModelXML = null;
    try {
        bioModelXML = dbServer.getDBTopLevel().getBioModelXML(user, bioModelKey, true);
        if (bioModelXML != null) {
            if (bRegenerateXML) {
                try {
                    BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(bioModelXML));
                    return cbit.vcell.xml.XmlHelper.bioModelToXML(bioModel);
                } catch (XmlParseException e) {
                    e.printStackTrace();
                    throw new DataAccessException(e.getMessage(), e);
                }
            } else {
                return bioModelXML;
            }
        }
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (ObjectNotFoundException e) {
    // 
    // not stored as XML currently, retrieve traditional way.
    // 
    }
    try {
        bioModelXML = getBioModelUnresolved(dbc, user, bioModelKey);
        dbServer.insertVersionableXML(user, VersionableType.BioModelMetaData, bioModelKey, bioModelXML);
        return bioModelXML;
    } catch (java.sql.SQLException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    } catch (cbit.vcell.xml.XmlParseException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
}

Example 22 with XMLSource

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

the class VCDatabaseScanner method scanMathModels.

public void scanMathModels(VCDatabaseVisitor databaseVisitor, PrintStream logFilePrintStream, User[] users, KeyValue singleMathmodelKey, HashSet<KeyValue> includeHash, HashSet<KeyValue> excludeHash, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    BadMathVisitor badMathVisitor = null;
    if (databaseVisitor instanceof BadMathVisitor) {
        badMathVisitor = (BadMathVisitor) databaseVisitor;
    }
    final boolean isBadMathVisitor = badMathVisitor != null;
    if (users == null) {
        users = getAllUsers();
    }
    try {
        // start visiting models and writing log
        logFilePrintStream.println("Start scanning mathmodels ......");
        logFilePrintStream.println("\n");
        for (int i = 0; i < users.length; i++) {
            User user = users[i];
            MathModelInfo[] mathInfos = dbServerImpl.getMathModelInfos(user, false);
            for (int j = 0; j < mathInfos.length; j++) {
                if (singleMathmodelKey != null && !mathInfos[j].getVersion().getVersionKey().compareEqual(singleMathmodelKey)) {
                    System.out.println("skipping geometry, not the single one that we wanted");
                    continue;
                }
                if (excludeHash != null && excludeHash.contains(mathInfos[j].getVersion().getVersionKey())) {
                    System.out.println("skipping geometry with key '" + mathInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (includeHash != null && !includeHash.contains(mathInfos[j].getVersion().getVersionKey())) {
                    System.out.println("not including geometry with key '" + mathInfos[j].getVersion().getVersionKey() + "'");
                    continue;
                }
                if (!databaseVisitor.filterMathModel(mathInfos[j])) {
                    continue;
                }
                KeyValue vk = null;
                try {
                    vk = mathInfos[j].getVersion().getVersionKey();
                    BigString mathModelXML = dbServerImpl.getMathModelXML(user, mathInfos[j].getVersion().getVersionKey());
                    MathModel mathModel = cbit.vcell.xml.XmlHelper.XMLToMathModel(new XMLSource(mathModelXML.toString()));
                    mathModel.refreshDependencies();
                    databaseVisitor.visitMathModel(mathModel, logFilePrintStream);
                } catch (Exception e2) {
                    if (isBadMathVisitor) {
                        badMathVisitor.unableToLoad(vk, e2);
                    }
                    lg.error(e2.getMessage(), e2);
                    if (bAbortOnDataAccessException) {
                        throw e2;
                    }
                }
            }
        }
        logFilePrintStream.close();
    } catch (Exception e) {
        System.err.println("error writing to log file.");
    }
}

Example 23 with XMLSource

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

the class VCDatabaseScanner method scanBioModels.

public void scanBioModels(BioModelVisitor databaseVisitor, Logger logger, User[] users, boolean bAbortOnDataAccessException) throws DataAccessException, XmlParseException {
    if (users == null) {
        users = getAllUsers();
    }
    // start visiting models and writing log
    logger.info("Start scanning bio-models......");
    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, bioModelInfos[j].getVersion().getVersionKey());
                BioModel bioModel = cbit.vcell.xml.XmlHelper.XMLToBioModel(new XMLSource(bioModelXML.toString()));
                bioModel.refreshDependencies();
                if (logger.isDebugEnabled()) {
                    // + bioModelInfos[j].getVersion().getName() + " -----> ");
                    logger.debug("---- " + (j + 1) + " ----> " + bioModel.getName());
                }
                databaseVisitor.visitBioModel(bioModel);
            } catch (Exception e2) {
                logger.warn("exception biomodel " + bmi.getModelKey(), e2);
                if (bAbortOnDataAccessException) {
                    throw e2;
                }
            }
        }
    }
}

Example 24 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 25 with XMLSource

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

the class ClientDocumentManager method getBioModelXML.

/**
 * 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<BioModel> getBioModelXML(KeyValue vKey) throws DataAccessException {
    try {
        String xmlString = (String) xmlHash.get(vKey);
        if (xmlString == null) {
            BigString xmlBS = sessionManager.getUserMetaDbServer().getBioModelXML(vKey);
            xmlString = (xmlBS != null ? xmlBS.toString() : null);
            if (xmlString != null) {
                BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(xmlString));
                String newXmlString = XmlHelper.bioModelToXML(bioModel);
                xmlHash.put(vKey, newXmlString);
                return new XMLHolder<BioModel>(newXmlString, bioModel);
            } else {
                throw new RuntimeException("unexpected: UserMetaDbServer.getBioModelXML() returned null");
            }
        } else {
            return new XMLHolder<BioModel>(xmlString);
        }
    } catch (ObjectNotFoundException e) {
        throw new DataAccessException("BioModel (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);
    }
}