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

Example 6 with BigString

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

the class LocalUserMetaDbServerMessaging method getBioModelXML.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString getBioModelXML(KeyValue bioModelKey) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.getBioModelXML(key=" + bioModelKey + ")");
        BigString bioModelXML = dbServerProxy.getBioModelXML(bioModelKey);
        return bioModelXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 7 with BigString

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

the class LocalUserMetaDbServerMessaging method saveGeometryAs.

/**
 * getVersionInfo method comment.
 * @throws RemoteException
 */
public BigString saveGeometryAs(BigString geometryXML, String newName) throws DataAccessException {
    try {
        log.print("LocalUserMetaDbServerMessaging.saveGeometryAs(newName=" + newName + ")");
        BigString savedGeometryXML = dbServerProxy.saveGeometryAs(geometryXML, newName);
        return savedGeometryXML;
    } catch (DataAccessException e) {
        log.exception(e);
        throw e;
    } catch (Throwable e) {
        log.exception(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 8 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 MathModel saveAsNew(MathModel mathModel, java.lang.String newName, String[] independentSims) throws DataAccessException {
    try {
        String mathModelXML = null;
        try {
            mathModelXML = XmlHelper.mathModelToXML(mathModel);
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        // System.out.println(mathModelXML);
        String savedMathModelXML = sessionManager.getUserMetaDbServer().saveMathModelAs(new BigString(mathModelXML), newName, independentSims).toString();
        MathModel savedMathModel = getMathModelFromDatabaseXML(new XMLHolder<MathModel>(savedMathModelXML));
        KeyValue savedKey = savedMathModel.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedMathModelXML);
        }
        MathModelInfo savedMathModelInfo = new MathModelInfo(savedMathModel.getVersion(), savedMathModel.getMathDescription().getKey(), savedMathModel.createMathModelChildSummary(), VCellSoftwareVersion.fromSystemProperty());
        mathModelInfoHash.put(savedKey, savedMathModelInfo);
        updateGeometryRelatedHashes(savedMathModel.getMathDescription().getGeometry());
        fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedMathModelInfo));
        return savedMathModel;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}

Example 9 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 MathModel save(MathModel mathModel, String[] independentSims) throws DataAccessException {
    try {
        String mathModelXML = null;
        try {
            mathModelXML = XmlHelper.mathModelToXML(mathModel);
            if (LG.isInfoEnabled()) {
                LG.info(XmlUtil.beautify(mathModelXML));
            }
        } catch (XmlParseException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
        String savedMathModelXML = sessionManager.getUserMetaDbServer().saveMathModel(new BigString(mathModelXML), independentSims).toString();
        MathModel savedMathModel = getMathModelFromDatabaseXML(new XMLHolder<MathModel>(savedMathModelXML));
        if (LG.isInfoEnabled()) {
            LG.info(XmlUtil.beautify(savedMathModelXML));
        }
        KeyValue savedKey = savedMathModel.getVersion().getVersionKey();
        if (xmlHash.get(savedKey) == null) {
            xmlHash.put(savedKey, savedMathModelXML);
        }
        MathModelInfo savedMathModelInfo = new MathModelInfo(savedMathModel.getVersion(), savedMathModel.getMathDescription().getKey(), savedMathModel.createMathModelChildSummary(), VCellSoftwareVersion.fromSystemProperty());
        mathModelInfoHash.put(savedKey, savedMathModelInfo);
        updateGeometryRelatedHashes(savedMathModel.getMathDescription().getGeometry());
        fireDatabaseInsert(new DatabaseEvent(this, DatabaseEvent.INSERT, null, savedMathModelInfo));
        return savedMathModel;
    } catch (RemoteProxyException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(VCellErrorMessages.FAIL_SAVE_MESSAGE + "\n\n" + e.getMessage());
    }
}

Example 10 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: (2/5/01 4:58:40 PM)
 */
public VCImage saveAsNew(VCImage vcImage, java.lang.String newName) 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().saveVCImageAs(new BigString(vcImageXML), newName).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());
    }
}