Examples with BigString org.vcell.util.BigString used on opensource projects

Example 31 with BigString

use of org.vcell.util.BigString 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 32 with BigString

use of org.vcell.util.BigString 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);
    }
}

Example 33 with BigString

use of org.vcell.util.BigString 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 34 with BigString

use of org.vcell.util.BigString 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());
    }
}

Example 35 with BigString

use of org.vcell.util.BigString in project vcell by virtualcell.

the class ClientDocumentManager method save.

/**
 * Insert the method's description here.
 * Creation date: (2/5/01 4:58:40 PM)
 */
public VCImage save(VCImage vcImage) throws DataAccessException {
    try {
        String vcImageXML = null;
        try {
            vcImageXML = XmlHelper.imageToXML(vcImage);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedVCImageXML = sessionManager.getUserMetaDbServer().saveVCImage(new BigString(vcImageXML)).toString();
        VCImage savedVCImage = null;
        try {
            savedVCImage = XmlHelper.XMLToImage(savedVCImageXML);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        savedVCImage.refreshDependencies();
        KeyValue savedKey = savedVCImage.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedVCImageXML);
        }
        try {
            ISize size = new ISize(savedVCImage.getNumX(), savedVCImage.getNumY(), savedVCImage.getNumZ());
            GIFImage browseData = BrowseImage.makeBrowseGIFImage(savedVCImage);
            VCImageInfo savedVCImageInfo = new VCImageInfo(savedVCImage.getVersion(), size, savedVCImage.getExtent(), browseData, VCellSoftwareVersion.fromSystemProperty());
            imgInfoHash.put(savedKey, savedVCImageInfo);
            fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedVCImageInfo));
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
        return savedVCImage;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}