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

Example 21 with XmlParseException

use of cbit.vcell.xml.XmlParseException 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 22 with XmlParseException

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

the class ClientDocumentManager method isChanged.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 */
public boolean isChanged(MathModel mathModel, String mathModelXML) throws DataAccessException {
    if (mathModel.getVersion() == null) {
        // 
        return true;
    } else {
        // 
        if (!mathModel.getVersion().getName().equals(mathModel.getName())) {
            return true;
        }
        // 
        if (!mathModel.getVersion().getAnnot().equals(mathModel.getDescription())) {
            return true;
        }
        // 
        // check for same number of simulations as saved version
        // 
        MathModelInfo savedMathModelInfo = getMathModelInfo(mathModel.getVersion().getVersionKey());
        if (savedMathModelInfo == null) {
            // 
            // if savedMathModelInfo is null, then the record was deleted
            // while it was loaded in client (changed is true)
            // 
            System.out.println("MathModel(" + mathModel.getVersion().getVersionKey() + ") must have been deleted, therefore isChanged() is true");
            return true;
        }
        // MathModelMetaData savedMathModelMetaData = getMathModelMetaData(savedMathModelInfo);
        // if (savedMathModelMetaData.getNumSimulations() != mathModel.getNumSimulations()){
        // return true;
        // }
        // 
        // compare saved and this bioModel
        // 
        XMLHolder<MathModel> savedMathModelXML = getMathModelXML(mathModel.getVersion().getVersionKey());
        if (savedMathModelXML == null) {
            // must have been deleted
            return true;
        }
        try {
            if (mathModelXML == null) {
                mathModelXML = XmlHelper.mathModelToXML(mathModel);
            }
            return !VCMLComparator.compareEquals(savedMathModelXML.getXmlString(), mathModelXML, true);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
}

Example 23 with XmlParseException

use of cbit.vcell.xml.XmlParseException 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 24 with XmlParseException

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

the class ClientDocumentManager method saveAsNew.

/**
 * Insert the method's description here.
 * Creation date: (1/19/01 11:27:52 AM)
 */
public BioModel saveAsNew(BioModel bioModel, java.lang.String newName, String[] independentSims) throws DataAccessException {
    try {
        String bioModelXML = null;
        try {
            bioModel.getVCMetaData().cleanupMetadata();
            bioModelXML = XmlHelper.bioModelToXML(bioModel);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedBioModelXML = sessionManager.getUserMetaDbServer().saveBioModelAs(new BigString(bioModelXML), newName, independentSims).toString();
        BioModel savedBioModel = getBioModelFromDatabaseXML(new XMLHolder<BioModel>(savedBioModelXML));
        KeyValue savedKey = savedBioModel.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedBioModelXML);
        }
        BioModelInfo savedBioModelInfo = new BioModelInfo(savedBioModel.getVersion(), savedBioModel.getModel().getKey(), savedBioModel.createBioModelChildSummary(), VCellSoftwareVersion.fromSystemProperty());
        bioModelInfoHash.put(savedKey, savedBioModelInfo);
        SimulationContext[] scArr = savedBioModel.getSimulationContexts();
        for (int i = 0; i < scArr.length; i++) {
            updateGeometryRelatedHashes(scArr[i].getGeometry());
        }
        fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedBioModelInfo));
        return savedBioModel;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}

Example 25 with XmlParseException

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

the class ClientDocumentManager method save.

/**
 * Insert the method's description here.
 * Creation date: (10/28/00 12:08:30 AM)
 */
public BioModel save(BioModel bioModel, String[] independentSims) throws DataAccessException {
    try {
        String bioModelXML = null;
        try {
            bioModel.getVCMetaData().cleanupMetadata();
            bioModelXML = XmlHelper.bioModelToXML(bioModel);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedBioModelXML = sessionManager.getUserMetaDbServer().saveBioModel(new BigString(bioModelXML), independentSims).toString();
        BioModel savedBioModel = getBioModelFromDatabaseXML(new XMLHolder<BioModel>(savedBioModelXML));
        KeyValue savedKey = savedBioModel.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedBioModelXML);
        }
        BioModelInfo savedBioModelInfo = new BioModelInfo(savedBioModel.getVersion(), savedBioModel.getModel().getKey(), savedBioModel.createBioModelChildSummary(), VCellSoftwareVersion.fromSystemProperty());
        bioModelInfoHash.put(savedKey, savedBioModelInfo);
        SimulationContext[] scArr = savedBioModel.getSimulationContexts();
        for (int i = 0; i < scArr.length; i++) {
            updateGeometryRelatedHashes(scArr[i].getGeometry());
        }
        // copy some transient info from the old model to the new one
        for (SimulationContext newsc : scArr) {
            SimulationContext oldsc = bioModel.getSimulationContext(newsc.getName());
            newsc.getTaskCallbackProcessor().initialize((oldsc.getTaskCallbackProcessor()));
            newsc.setMostRecentlyCreatedOutputSpec(oldsc.getMostRecentlyCreatedOutputSpec());
            newsc.setMd5hash(oldsc.getMd5hash());
        }
        fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedBioModelInfo));
        return savedBioModel;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}