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

Example 1 with VCellSoftwareVersion

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

the class BioModelTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con, DatabaseSyntax dbSyntax) throws SQLException, org.vcell.util.DataAccessException {
    KeyValue modelRef = new KeyValue(rset.getBigDecimal(table.modelRef.toString()));
    BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    VCellSoftwareVersion vcSoftwareVersion = VCellSoftwareVersion.fromString(softwareVersion);
    String serialDbChildSummary = DbDriver.varchar2_CLOB_get(rset, BioModelTable.table.childSummarySmall, BioModelTable.table.childSummaryLarge, dbSyntax);
    return new org.vcell.util.document.BioModelInfo(version, modelRef, serialDbChildSummary, vcSoftwareVersion);
}

Example 2 with VCellSoftwareVersion

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

the class MathVisitor method filterMathModel.

@Override
public boolean filterMathModel(MathModelInfo mathModelInfo) {
    VCellSoftwareVersion vers = mathModelInfo.getSoftwareVersion();
    boolean current = vers.getMajorVersion() >= 5;
    return current;
}

Example 3 with VCellSoftwareVersion

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

the class MicroscopyXmlproducer method getXML.

/**
 * This method returns a XML representation for a Biomodel object.
 * Creation date: (2/14/2001 3:41:13 PM)
 * @param param cbit.vcell.biomodel.BioModel
 * @return Element
 * @throws XmlParseException
 * @throws cbit.vcell.parser.ExpressionException
 */
private static Element getXML(FRAPStudy param, Xmlproducer vcellXMLProducer, ClientTaskStatusSupport progressListener, boolean bSaveCompressed) throws XmlParseException, cbit.vcell.parser.ExpressionException {
    Element frapStudyNode = new Element(MicroscopyXMLTags.FRAPStudyTag);
    // name
    if (param.getName() != null) {
        String name = param.getName();
        frapStudyNode.setAttribute(XMLTags.NameAttrTag, name);
    }
    VCellSoftwareVersion vCellSoftwareVersion = VCellSoftwareVersion.fromSystemProperty();
    if (vCellSoftwareVersion != null && vCellSoftwareVersion.getSoftwareVersionString() != null) {
        frapStudyNode.setAttribute(XMLTags.SoftwareVersionAttrTag, vCellSoftwareVersion.getSoftwareVersionString());
    }
    // originalImageFilePath
    if (param.getOriginalImageFilePath() != null && param.getOriginalImageFilePath().length() > 0) {
        String name = param.getOriginalImageFilePath();
        frapStudyNode.setAttribute(MicroscopyXMLTags.OriginalImagePathAttrTag, name);
    }
    // Description
    if (param.getDescription() != null && param.getDescription().length() > 0) {
        Element annotationElem = new Element(XMLTags.AnnotationTag);
        annotationElem.setText(mangle(param.getDescription()));
        frapStudyNode.addContent(annotationElem);
    }
    // starting index for recovery
    if (param.getStartingIndexForRecovery() != null) {
        Element indexElem = new Element(MicroscopyXMLTags.StartingIndexForRecoveryTag);
        indexElem.setText(mangle(param.getStartingIndexForRecovery().toString()));
        frapStudyNode.addContent(indexElem);
    }
    // Get frap best model index
    if (param.getBestModelIndex() != null) {
        Element bestModelIdxElem = new Element(MicroscopyXMLTags.BestModelIndexTag);
        bestModelIdxElem.setText(mangle(param.getBestModelIndex().toString()));
        frapStudyNode.addContent(bestModelIdxElem);
    }
    // Get selected ROIs
    if (param.getSelectedROIsForErrorCalculation() != null && param.getSelectedROIsForErrorCalculation().length > 0) {
        Element selectedROIsNode = new Element(MicroscopyXMLTags.SelectedROIsTag);
        boolean[] selectedROIs = param.getSelectedROIsForErrorCalculation();
        String rowText = "";
        for (int i = 0; i < selectedROIs.length; i++) {
            if (i > 0) {
                rowText += " ";
            }
            rowText += selectedROIs[i];
        }
        selectedROIsNode.addContent(rowText);
        frapStudyNode.addContent(selectedROIsNode);
    }
    // Get frap models
    if (param.getModels() != null && param.getModels().length > 0) {
        Element frapModelsNode = new Element(MicroscopyXMLTags.FrapModelsTag);
        if (param.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null) {
            frapModelsNode.addContent(getXML(param.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT]));
        }
        if (param.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] != null) {
            frapModelsNode.addContent(getXML(param.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS]));
        }
        if (param.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] != null) {
            frapModelsNode.addContent(getXML(param.getModels()[FRAPModel.IDX_MODEL_REACTION_OFF_RATE]));
        }
        if (param.getModels()[FRAPModel.IDX_MODEL_DIFF_BINDING] != null) {
            frapModelsNode.addContent(getXML(param.getModels()[FRAPModel.IDX_MODEL_DIFF_BINDING]));
        }
        frapStudyNode.addContent(frapModelsNode);
    }
    // Get ExternalDataIdentifier (for timeseries)
    if (param.getFrapDataExternalDataInfo() != null) {
        Element imageDatasetEDINode = new Element(MicroscopyXMLTags.ImageDatasetExternalDataInfoTag);
        imageDatasetEDINode.setAttribute(MicroscopyXMLTags.FilenameAttrTag, param.getFrapDataExternalDataInfo().getFilename());
        imageDatasetEDINode.addContent(getXML(param.getFrapDataExternalDataInfo().getExternalDataIdentifier()));
        frapStudyNode.addContent(imageDatasetEDINode);
    }
    // Get ExternalDataIdentifier (for ROIs)
    if (param.getRoiExternalDataInfo() != null) {
        Element roiEDINode = new Element(MicroscopyXMLTags.ROIExternalDataInfoTag);
        roiEDINode.setAttribute(MicroscopyXMLTags.FilenameAttrTag, param.getRoiExternalDataInfo().getFilename());
        roiEDINode.addContent(getXML(param.getRoiExternalDataInfo().getExternalDataIdentifier()));
        frapStudyNode.addContent(roiEDINode);
    }
    // Get Reference Data (for reference data)
    if (param.getStoredRefData() != null) {
        frapStudyNode.addContent(getXML(param.getStoredRefData(), MicroscopyXMLTags.ReferenceDataTag));
    }
    // Get profile data for one diffusing component (list of profile data, one for each parameter)
    if (param.getProfileData_oneDiffComponent() != null) {
        frapStudyNode.addContent(getXML(param.getProfileData_oneDiffComponent(), MicroscopyXMLTags.ListOfProfileData_OneDiffTag));
    }
    if (param.getProfileData_twoDiffComponents() != null) {
        frapStudyNode.addContent(getXML(param.getProfileData_twoDiffComponents(), MicroscopyXMLTags.ListOfProfileData_TwoDiffTag));
    }
    if (param.getProfileData_reactionOffRate() != null) {
        frapStudyNode.addContent(getXML(param.getProfileData_reactionOffRate(), MicroscopyXMLTags.ListOfProfileData_ReacOffRateTag));
    }
    // Get BioModel
    if (param.getBioModel() != null) {
        frapStudyNode.addContent(vcellXMLProducer.getXML(param.getBioModel()));
    }
    // Get FrapData
    if (param.getFrapData() != null) {
        frapStudyNode.addContent(getXML(param.getFrapData(), vcellXMLProducer, progressListener, bSaveCompressed));
    }
    return frapStudyNode;
}

Example 4 with VCellSoftwareVersion

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

the class DocumentWindowAboutBox method parseVCellVersion.

public static void parseVCellVersion() {
    try {
        VCellSoftwareVersion vcellSoftwareVersion = VCellSoftwareVersion.fromSystemProperty();
        EDITION = vcellSoftwareVersion.getSite().name().toUpperCase();
        VERSION_NO = vcellSoftwareVersion.getVersionNumber();
        BUILD_NO = vcellSoftwareVersion.getBuildNumber();
    } catch (Exception exc) {
        System.out.println("Failed to parse vcell.softwareVersion: " + exc.getMessage());
        exc.printStackTrace(System.out);
    }
}

Example 5 with VCellSoftwareVersion

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

the class ClientServerManager method checkClientServerSoftwareVersion.

private void checkClientServerSoftwareVersion(InteractiveContext requester, ClientServerInfo clientServerInfo) {
    String clientSoftwareVersion = System.getProperty(PropertyLoader.vcellSoftwareVersion);
    if (clientSoftwareVersion != null && clientSoftwareVersion.toLowerCase().contains("devel")) {
        return;
    }
    if (clientServerInfo.getServerType() == ServerType.SERVER_REMOTE) {
        String apihost = clientServerInfo.getApihost();
        Integer apiport = clientServerInfo.getApiport();
        String serverSoftwareVersion = RemoteProxyVCellConnectionFactory.getVCellSoftwareVersion(apihost, apiport);
        if (serverSoftwareVersion != null && !serverSoftwareVersion.equals(clientSoftwareVersion)) {
            VCellSoftwareVersion clientVersion = VCellSoftwareVersion.fromString(clientSoftwareVersion);
            VCellSoftwareVersion serverVersion = VCellSoftwareVersion.fromString(serverSoftwareVersion);
            if (clientVersion.getSite() == VCellSite.beta) {
                requester.showWarningDialog("VCell Public Beta program has been discontinued - please use our Release VCell version\n\n" + "We have adopted a Release Early, Release Often software development approach\n\n" + "\nPlease exit VCell and download the latest client from VCell Software page (http://vcell.org).");
            }
            if (clientVersion.getMajorVersion() != serverVersion.getMajorVersion() || clientVersion.getMinorVersion() != serverVersion.getMinorVersion() || clientVersion.getPatchVersion() != serverVersion.getPatchVersion()) {
                requester.showWarningDialog("software version mismatch between client and server:\n" + "client VCell version : " + clientSoftwareVersion + "\n" + "server VCell version : " + serverSoftwareVersion + "\n" + "\nPlease exit VCell and download the latest client from VCell Software page (http://vcell.org).");
            }
        }
    }
}