Examples with KeyValue org.vcell.util.document.KeyValue used on opensource projects

Example 26 with KeyValue

use of org.vcell.util.document.KeyValue 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 27 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class ExportServiceImpl method fireExportCompleted.

/**
 * Insert the method's description here.
 * Creation date: (4/1/2001 11:20:45 AM)
 * @deprecated
 */
protected ExportEvent fireExportCompleted(long jobID, VCDataIdentifier vcdID, String format, String location, ExportSpecs exportSpecs) {
    User user = null;
    Object object = jobRequestIDs.get(new Long(jobID));
    if (object != null) {
        user = (User) object;
    }
    TimeSpecs timeSpecs = (exportSpecs != null) ? exportSpecs.getTimeSpecs() : (null);
    VariableSpecs varSpecs = (exportSpecs != null) ? exportSpecs.getVariableSpecs() : (null);
    final KeyValue dataKey;
    if (vcdID instanceof VCSimulationDataIdentifier) {
        dataKey = ((VCSimulationDataIdentifier) vcdID).getSimulationKey();
    } else if (vcdID instanceof ExternalDataIdentifier) {
        dataKey = ((ExternalDataIdentifier) vcdID).getSimulationKey();
    } else {
        throw new RuntimeException("unexpected VCDataIdentifier");
    }
    ExportEvent event = new ExportEvent(this, jobID, user, vcdID.getID(), dataKey, ExportEvent.EXPORT_COMPLETE, format, location, null, timeSpecs, varSpecs);
    fireExportEvent(event);
    return event;
}

Example 28 with KeyValue

use of org.vcell.util.document.KeyValue 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 29 with KeyValue

use of org.vcell.util.document.KeyValue 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());
    }
}

Example 30 with KeyValue

use of org.vcell.util.document.KeyValue in project vcell by virtualcell.

the class ClientDocumentManager method getMathModel.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 4:02:44 PM)
 * @return cbit.vcell.biomodel.BioModel
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public MathModel getMathModel(KeyValue mathModelKey) throws DataAccessException {
    XMLHolder<MathModel> mathModelXML = getMathModelXML(mathModelKey);
    MathModel mathModel = getMathModelFromDatabaseXML(mathModelXML);
    // 
    // preload SimulationJobStatus for all simulations if any missing from hash.
    // 
    Simulation[] simulations = mathModel.getSimulations();
    KeyValue[] simKeys = new KeyValue[simulations.length];
    for (int i = 0; i < simulations.length; i++) {
        VCSimulationIdentifier vcSimulationIdentifier = simulations[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
        simKeys[i] = vcSimulationIdentifier.getSimulationKey();
    }
    preloadSimulationStatus(simKeys);
    return mathModel;
}