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

Example 41 with BioModelInfo

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

the class ClientDocumentManager method setGroupPrivate.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
public BioModelInfo setGroupPrivate(BioModelInfo bioModelInfo) throws DataAccessException {
    try {
        // 
        // unpublish from database
        // 
        BioModelInfo newBioModelInfo = (BioModelInfo) setGroupPrivate0(bioModelInfo, VersionableType.BioModelMetaData, bioModelInfoHash);
        // 
        // delete BioModelMetaData from cache
        // 
        xmlHash.remove(bioModelInfo.getVersion().getVersionKey());
        fireDatabaseUpdate(new DatabaseEvent(this, DatabaseEvent.UPDATE, bioModelInfo, newBioModelInfo));
        return newBioModelInfo;
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException(e.getMessage());
    }
}

Example 42 with BioModelInfo

use of org.vcell.util.document.BioModelInfo 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 43 with BioModelInfo

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

the class ClientDocumentManager method reloadBioModelInfos.

/**
 * Insert the method's description here.
 * Creation date: (11/14/00 5:33:21 PM)
 * @return cbit.vcell.biomodel.BioModelInfo[]
 */
private void reloadBioModelInfos() throws DataAccessException {
    try {
        System.out.println("ClientDocumentManager.reloadBioModelInfos()");
        BioModelInfo[] bioModelInfos = sessionManager.getUserMetaDbServer().getBioModelInfos(true);
        if (bioModelInfos != null) {
            bioModelInfoHash.clear();
            for (int i = 0; i < bioModelInfos.length; i++) {
                bioModelInfoHash.put(bioModelInfos[i].getVersion().getVersionKey(), bioModelInfos[i]);
            }
        }
    } catch (RemoteProxyException e) {
        handleRemoteProxyException(e);
        throw new DataAccessException("RemoteProxyException: " + e.getMessage());
    }
}

Example 44 with BioModelInfo

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

the class DatabaseWindowManager method comparePreviousEdition.

/**
 * Comment
 */
public void comparePreviousEdition() {
    // 
    if (getPanelSelection() == null) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : No first document selected");
        return;
    }
    VCDocumentInfo thisDocumentInfo = getPanelSelection();
    // 
    // Get the previous version of the documentInfo
    // 
    VCDocumentInfo[] documentVersionsList = null;
    try {
        documentVersionsList = getDocumentVersionDates(thisDocumentInfo);
    } catch (DataAccessException e) {
        PopupGenerator.showErrorDialog(this, "Error accessing second document!");
    }
    if (documentVersionsList == null || documentVersionsList.length == 0) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : Not Enough Versions to Compare!");
        return;
    }
    // 
    // Obtaining the previous version of the current biomodel. Set the previousBioModelInfo to
    // the first version in the bioModelVersionList. Then compare all the versions in the list
    // with the previousBioModelInfo to see if any of them are before previousBioModelInfo
    // datewise. If so, update previousBioModelInfo. The biomodelinfo stored in previousBioModelInfo
    // when it comes out of the loop is the previous version of the biomodel.
    // 
    VCDocumentInfo previousDocumentInfo = documentVersionsList[0];
    boolean bPrevious = false;
    for (int i = 0; i < documentVersionsList.length; i++) {
        if (documentVersionsList[i].getVersion().getDate().before(thisDocumentInfo.getVersion().getDate())) {
            bPrevious = true;
            previousDocumentInfo = documentVersionsList[i];
        } else {
            break;
        }
    }
    if (previousDocumentInfo.equals(documentVersionsList[0]) && !bPrevious) {
        PopupGenerator.showErrorDialog(this, "Current Version is the oldest! Choose another Version or Model to compare!");
        return;
    }
    // Check if both document types are of the same kind. If not, throw an error.
    if (((thisDocumentInfo instanceof BioModelInfo) && !(previousDocumentInfo instanceof BioModelInfo)) || ((thisDocumentInfo instanceof MathModelInfo) && !(previousDocumentInfo instanceof MathModelInfo)) || ((thisDocumentInfo instanceof GeometryInfo) && !(previousDocumentInfo instanceof GeometryInfo))) {
        PopupGenerator.showErrorDialog(this, "Error Comparing documents : The two documents are not of the same type!");
        return;
    }
    // Now that we have both the document versions to be compared, do the comparison and display the result
    compareWithOther(previousDocumentInfo, thisDocumentInfo);
}

Example 45 with BioModelInfo

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

the class DatabaseWindowManager method getDocumentVersionDates.

/**
 * Insert the method's description here.
 * Creation date: (10/3/2002 10:34:00 AM)
 */
private VCDocumentInfo[] getDocumentVersionDates(VCDocumentInfo thisDocumentInfo) throws DataAccessException {
    // 
    if (thisDocumentInfo == null) {
        return new VCDocumentInfo[0];
    }
    VCDocumentInfo[] vcDocumentInfos = null;
    if (thisDocumentInfo instanceof BioModelInfo) {
        vcDocumentInfos = getRequestManager().getDocumentManager().getBioModelInfos();
    } else if (thisDocumentInfo instanceof MathModelInfo) {
        vcDocumentInfos = getRequestManager().getDocumentManager().getMathModelInfos();
    } else if (thisDocumentInfo instanceof GeometryInfo) {
        vcDocumentInfos = getRequestManager().getDocumentManager().getGeometryInfos();
    }
    // 
    // From the list of biomodels in the workspace, get list of biomodels with the same branch ID.
    // This is the list of different versions of the same biomodel.
    // 
    Vector<VCDocumentInfo> documentBranchList = new Vector<VCDocumentInfo>();
    for (int i = 0; i < vcDocumentInfos.length; i++) {
        VCDocumentInfo vcDocumentInfo = vcDocumentInfos[i];
        if (vcDocumentInfo.getVersion().getBranchID().equals(thisDocumentInfo.getVersion().getBranchID())) {
            documentBranchList.add(vcDocumentInfo);
        }
    }
    if (documentBranchList.size() == 0) {
        PopupGenerator.showErrorDialog(this, "Error comparing BioModels : No Versions of document ");
        return new VCDocumentInfo[0];
    }
    VCDocumentInfo[] vcDocumentInfosInBranch = new VCDocumentInfo[documentBranchList.size()];
    documentBranchList.copyInto(vcDocumentInfosInBranch);
    // 
    // From the versions list, remove the currently selected version and return the remaining list of
    // versions for the biomodel
    // 
    VCDocumentInfo[] revisedDocInfosInBranch = new VCDocumentInfo[vcDocumentInfosInBranch.length - 1];
    int j = 0;
    for (int i = 0; i < vcDocumentInfosInBranch.length; i++) {
        if (!thisDocumentInfo.getVersion().getDate().equals(vcDocumentInfosInBranch[i].getVersion().getDate())) {
            revisedDocInfosInBranch[j] = vcDocumentInfosInBranch[i];
            j++;
        }
    }
    return revisedDocInfosInBranch;
}