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

Example 6 with KeyValue

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

the class XmlReader method getVersion.

/**
 * This method returns a Version object from an XML representation.
 * Creation date: (3/16/2001 3:41:24 PM)
 * @return cbit.sql.Version
 * @param param org.jdom.Element
 */
private Version getVersion(Element xmlVersion) throws XmlParseException {
    if (xmlVersion == null) {
        return null;
    }
    // determine if it should be processed using the 'fromVersionable'
    if (xmlVersion.getAttributeValue(XMLTags.FromVersionableTag) == null || Boolean.valueOf(xmlVersion.getAttributeValue(XMLTags.FromVersionableTag)).booleanValue() || this.readKeysFlag == false) {
        // this came from a versionable object, so skip! Or it should not explicitly import the information inside the Version
        return null;
    }
    // Read all the attributes
    // *name
    String name = unMangle(xmlVersion.getAttributeValue(XMLTags.NameAttrTag));
    // *key
    String temp = xmlVersion.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(temp);
    // *owner
    Element tempElement = xmlVersion.getChild(XMLTags.OwnerTag, vcNamespace);
    User owner = new User(unMangle(tempElement.getAttributeValue(XMLTags.NameAttrTag)), new KeyValue(tempElement.getAttributeValue(XMLTags.IdentifierAttrTag)));
    // *access
    GroupAccess groupAccess = getGroupAccess(xmlVersion.getChild(XMLTags.GroupAccessTag, vcNamespace));
    // *Branchpointref
    temp = xmlVersion.getAttributeValue(XMLTags.BranchPointRefTag);
    KeyValue branchpointref = null;
    if (temp != null) {
        branchpointref = new KeyValue(temp);
    }
    // *BranchID
    java.math.BigDecimal branchId = new java.math.BigDecimal(xmlVersion.getAttributeValue(XMLTags.BranchIdAttrTag));
    // *Flag
    temp = xmlVersion.getAttributeValue(XMLTags.FlagAttrTag);
    VersionFlag flag = VersionFlag.fromInt(Integer.parseInt(temp));
    // *Date
    java.util.Date date = null;
    temp = xmlVersion.getAttributeValue(XMLTags.DateAttrTag);
    if (temp != null) {
        try {
            SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
            date = simpleDateFormat.parse(temp);
        } catch (java.text.ParseException e) {
            e.printStackTrace();
            throw new XmlParseException("Invalid date:" + temp, e);
        }
    }
    // *Annotation
    String annotation = null;
    String annotationText = xmlVersion.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        annotation = unMangle(annotationText);
    }
    // Create and return the version object
    return new Version(key, name, owner, groupAccess, branchpointref, branchId, date, flag, annotation);
}

Example 7 with KeyValue

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

the class XmlReader method getMembrane.

/**
 * This method returns a Membrane object from a XML element.
 * Creation date: (4/4/2001 4:17:32 PM)
 * @return cbit.vcell.model.Membrane
 * @param param org.jdom.Element
 */
private Membrane getMembrane(Model model, Element param, List<Structure> featureList) throws XmlParseException {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    Membrane newmembrane = null;
    // retrieve the key if there is one
    KeyValue key = null;
    String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (stringkey != null && stringkey.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(stringkey);
    }
    // try to create new Membrane named "name"
    try {
        newmembrane = new Membrane(key, name);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("An error occurred while trying to create the Membrane object " + name, e);
    }
    // set inside feature
    String infeaturename = unMangle(param.getAttributeValue(XMLTags.InsideFeatureTag));
    String outfeaturename = unMangle(param.getAttributeValue(XMLTags.OutsideFeatureTag));
    String posFeatureName = unMangle(param.getAttributeValue(XMLTags.PositiveFeatureTag));
    String negFeatureName = unMangle(param.getAttributeValue(XMLTags.NegativeFeatureTag));
    Feature infeatureref = null;
    Feature outfeatureref = null;
    Feature posFeature = null;
    Feature negFeature = null;
    for (Structure s : featureList) {
        String sname = s.getName();
        if (sname.equals(infeaturename)) {
            infeatureref = (Feature) s;
        }
        if (sname.equals(outfeaturename)) {
            outfeatureref = (Feature) s;
        }
        if (sname.equals(posFeatureName)) {
            posFeature = (Feature) s;
        }
        if (sname.equals(negFeatureName)) {
            negFeature = (Feature) s;
        }
    }
    // set inside and outside features
    if (infeatureref != null) {
        model.getStructureTopology().setInsideFeature(newmembrane, infeatureref);
    }
    if (outfeatureref != null) {
        model.getStructureTopology().setOutsideFeature(newmembrane, outfeatureref);
    }
    // set positive & negative features
    if (posFeature != null) {
        model.getElectricalTopology().setPositiveFeature(newmembrane, posFeature);
    }
    if (negFeature != null) {
        model.getElectricalTopology().setNegativeFeature(newmembrane, negFeature);
    }
    // set MemVoltName
    if (param.getAttribute(XMLTags.MemVoltNameTag) == null) {
        throw new XmlParseException("Error reading membrane Voltage Name!");
    }
    String memvoltName = unMangle(param.getAttributeValue(XMLTags.MemVoltNameTag));
    try {
        newmembrane.getMembraneVoltage().setName(memvoltName);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("Error setting the membrane Voltage Name", e);
    }
    return newmembrane;
}

Example 8 with KeyValue

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

the class XmlReader method getPixelClass.

/**
 * This method returns a VCImageRegion from a XML Representation.
 * Creation date: (5/2/2001 12:17:05 PM)
 * @return cbit.image.VCImageRegion
 * @param param org.jdom.Element
 */
private VCPixelClass getPixelClass(Element param) {
    // Read attributes
    String pixelClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    int pixelvalue = Integer.parseInt(param.getAttributeValue(XMLTags.ImagePixelValueTag));
    // retrieve the key if there is one
    KeyValue key = null;
    String stringkey = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (stringkey != null && stringkey.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(stringkey);
    }
    return new VCPixelClass(key, pixelClassName, pixelvalue);
}

Example 9 with KeyValue

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

the class XmlReader method getDataSymbols.

private ArrayList<DataSymbol> getDataSymbols(Element dataContextElement, DataContext dataContext, ModelUnitSystem modelUnitSystem) {
    ArrayList<DataSymbol> dataSymbolsList = new ArrayList<DataSymbol>();
    // iterate over fieldDatasymbols. When other dataSymbol types are implemented, repeat this loop.
    Iterator dataSymbolsElementIter = dataContextElement.getChildren(XMLTags.FieldDataSymbolTag, vcNamespace).iterator();
    while (dataSymbolsElementIter.hasNext()) {
        Element dataSymbolElement = (Element) dataSymbolsElementIter.next();
        String dataSymbolName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolNameTag));
        DataSymbolType dataSymbolType = DataSymbolType.fromDatabaseName(unMangle(dataSymbolElement.getAttributeValue(XMLTags.DataSymbolTypeTag)));
        String symbol = dataSymbolElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
        VCUnitDefinition vcUnitDefinition = null;
        if (symbol != null) {
            vcUnitDefinition = modelUnitSystem.getInstance(symbol);
        }
        // ExternalDataIdentifier dataSetID in FieldDataSymbol
        Element dataSetIDElement = dataSymbolElement.getChild(XMLTags.ExternalDataIdentifierTag, vcNamespace);
        String name = unMangle(dataSetIDElement.getAttributeValue(XMLTags.NameAttrTag));
        String key = unMangle(dataSetIDElement.getAttributeValue(XMLTags.KeyValueAttrTag));
        String userID = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerNameAttrTag));
        String userKey = unMangle(dataSetIDElement.getAttributeValue(XMLTags.OwnerKeyAttrTag));
        User owner = new User(userID, new KeyValue(userKey));
        ExternalDataIdentifier edi = new ExternalDataIdentifier(new KeyValue(key), owner, name);
        // ---
        String fieldItemName = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemNameTag));
        String fieldItemType = unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTypeTag));
        double fieldItemTime = Double.parseDouble(unMangle(dataSymbolElement.getAttributeValue(XMLTags.FieldItemTimeTag)));
        FieldDataSymbol fds = new FieldDataSymbol(dataSymbolName, dataSymbolType, dataContext, vcUnitDefinition, edi, fieldItemName, fieldItemType, fieldItemTime);
        dataSymbolsList.add(fds);
    }
    return dataSymbolsList;
}

Example 10 with KeyValue

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

the class XmlReader method getCSGObject.

public CSGObject getCSGObject(Element param, KeyValue keyFromDB) throws XmlParseException {
    // retrieve the attributes
    String name = param.getAttributeValue(XMLTags.NameAttrTag);
    int handle = Integer.parseInt(param.getAttributeValue(XMLTags.HandleAttrTag));
    // process the key
    KeyValue key = null;
    String temp = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    if (temp != null && temp.length() > 0 && this.readKeysFlag) {
        key = new KeyValue(temp);
    }
    if (keyFromDB != null) {
        key = keyFromDB;
    }
    // Retrieve CSGObject CSGNode - CSGObject element should have one child (the root node of the CSGObject)
    Object[] elements = param.getChildren().toArray();
    if (elements.length > 1) {
        throw new XmlParseException("CSGObject subvolume element cannot have more than one child element");
    }
    CSGNode csgRootNode = getCSGNode((Element) elements[0]);
    // Create the CSGObject
    CSGObject newCSGObjectSubvol = new CSGObject(key, name, handle);
    newCSGObjectSubvol.setRoot(csgRootNode);
    return newCSGObjectSubvol;
}