void removeNamespace(Namespace namespace) {
Namespace current = getNodeNamespace();
// Do not remove in-use namespace
if (namespace.is(current)) return;
NamedNodeMap attrs = this.dom.getAttributes();
for (int i = 0; i < attrs.getLength(); i++) {
XmlNode attr = XmlNode.createImpl(attrs.item(i));
if (namespace.is(attr.getNodeNamespace())) return;
}
// TODO I must confess I am not sure I understand the spec fully. See ECMA357 13.4.4.31
String existingPrefix = getExistingPrefixFor(namespace);
if (existingPrefix != null) {
if (namespace.isUnspecifiedPrefix()) {
// we should remove any namespace with this URI from scope; we do this by declaring a
// namespace with the same
// prefix as the existing prefix and setting its URI to the default namespace
declareNamespace(existingPrefix, getDefaultNamespace().getUri());
} else {
if (existingPrefix.equals(namespace.getPrefix())) {
declareNamespace(existingPrefix, getDefaultNamespace().getUri());
}
}
} else {
// the argument namespace is not declared in this scope, so do nothing.
}
}
XmlNode[] getAttributes() {
NamedNodeMap attrs = this.dom.getAttributes();
// TODO Or could make callers handle null?
if (attrs == null) throw new IllegalStateException("Must be element.");
XmlNode[] rv = new XmlNode[attrs.getLength()];
for (int i = 0; i < attrs.getLength(); i++) {
rv[i] = createImpl(attrs.item(i));
}
return rv;
}
private static Command parseCommand(Node n) {
NamedNodeMap atts = n.getAttributes();
String name = atts.getNamedItem("name").getNodeValue();
String desc = atts.getNamedItem("description").getNodeValue();
String command = atts.getNamedItem("command").getNodeValue();
Command com = new Command(name, desc, command);
NodeList children = n.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
Node child = children.item(i);
if (!child.getNodeName().equals("Argument")) continue;
NamedNodeMap childAtts = child.getAttributes();
String childName = childAtts.getNamedItem("name").getNodeValue();
String childDesc = childAtts.getNamedItem("description").getNodeValue();
String childVal = "";
if (childAtts.getNamedItem("default") != null)
childVal = childAtts.getNamedItem("default").getNodeValue();
Argument arg = new Argument(childName, childDesc, childVal);
com.addArgument(arg);
}
return com;
}
/**
* Counts the attributenode for an element (xmlns attributes ignored)
*
* @param attributesR attributesMap
* @return number of attributes
*/
private int countAttributes(NamedNodeMap attributesR) {
int cntAttributes = 0;
for (int i = 0; i < attributesR.getLength(); i++) {
if (!attributesR.item(i).getNodeName().startsWith(XMLConstants.XMLNS_ATTRIBUTE)) {
cntAttributes++;
}
}
return cntAttributes;
}
/** Возвращает имя метода. */
public String getName() {
/** Получаем атрибуты узла метода. */
NamedNodeMap attributes = node.getAttributes();
/** Получаем узел аттрибута. */
Node nameAttrib = attributes.getNamedItem("name");
/** Возвращаем значение атрибута. */
return nameAttrib.getNodeValue();
}
protected Element copyElementToName(Element element, String tagName) {
Element newElement = element.getOwnerDocument().createElement(tagName);
NamedNodeMap attrs = element.getAttributes();
for (int i = 0; i < attrs.getLength(); i++) {
Node attribute = attrs.item(i);
newElement.setAttribute(attribute.getNodeName(), attribute.getNodeValue());
}
for (int i = 0; i < element.getChildNodes().getLength(); i++) {
newElement.appendChild(element.getChildNodes().item(i).cloneNode(true));
}
return newElement;
}
public static Map<String, String> getAttrList(Node node) {
Map<String, String> map = new HashMap<String, String>();
NamedNodeMap list = node.getAttributes();
if (list != null)
for (int i = 0; i < list.getLength(); i++) {
Attr attr = (Attr) list.item(i);
map.put(attr.getName(), attr.getValue());
}
return map;
}
private static Category parseCategory(Node n) {
NamedNodeMap atts = n.getAttributes();
String name = atts.getNamedItem("name").getNodeValue();
String desc = atts.getNamedItem("description").getNodeValue();
Category cat = new Category(name, desc);
NodeList children = n.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
parseNode(children.item(i), cat);
}
return cat;
}
/**
* Retrieves default values from xml.
*
* @param list the configuration list
*/
private static void parseDefaults(NodeList list) {
for (int i = 0; i < list.getLength(); ++i) {
NamedNodeMap mapping = list.item(i).getAttributes();
String attribute = mapping.getNamedItem("attribute").getNodeValue();
String value = mapping.getNamedItem("value").getNodeValue();
try {
Default field = Default.fromString(attribute);
DEFAULTS.put(field, value);
} catch (IllegalArgumentException exc) {
logger.warn("Unrecognized default attribute: " + attribute);
}
}
}
/**
* Populates LOCALES list with contents of xml.
*
* @param list the configuration list
*/
private static void parseLocales(NodeList list) {
for (int i = 0; i < list.getLength(); ++i) {
Node node = list.item(i);
NamedNodeMap attributes = node.getAttributes();
String label = ((Attr) attributes.getNamedItem("label")).getValue();
String code = ((Attr) attributes.getNamedItem("isoCode")).getValue();
String dictLocation = ((Attr) attributes.getNamedItem("dictionaryUrl")).getValue();
try {
LOCALES.add(new Locale(label, code, new URL(dictLocation)));
} catch (MalformedURLException exc) {
logger.warn(
"Unable to parse dictionary location of " + label + " (" + dictLocation + ")", exc);
}
}
}
public void validateContent(IProgressMonitor monitor) {
Element element = getDocumentRoot();
if (element == null) return;
String elementName = element.getNodeName();
if (!"plugin".equals(elementName)
&& !"fragment".equals(elementName)) { // $NON-NLS-1$ //$NON-NLS-2$
reportIllegalElement(element, CompilerFlags.ERROR);
} else {
int severity = CompilerFlags.getFlag(fProject, CompilerFlags.P_DEPRECATED);
if (severity != CompilerFlags.IGNORE) {
NamedNodeMap attrs = element.getAttributes();
for (int i = 0; i < attrs.getLength(); i++) {
reportUnusedAttribute(element, attrs.item(i).getNodeName(), severity);
}
}
NodeList children = element.getChildNodes();
for (int i = 0; i < children.getLength(); i++) {
if (monitor.isCanceled()) break;
Element child = (Element) children.item(i);
String name = child.getNodeName();
if (name.equals("extension")) { // $NON-NLS-1$
validateExtension(child);
} else if (name.equals("extension-point")) { // $NON-NLS-1$
validateExtensionPoint(child);
} else {
if (!name.equals("runtime") && !name.equals("requires")) { // $NON-NLS-1$ //$NON-NLS-2$
severity = CompilerFlags.getFlag(fProject, CompilerFlags.P_UNKNOWN_ELEMENT);
if (severity != CompilerFlags.IGNORE) reportIllegalElement(child, severity);
} else {
severity = CompilerFlags.getFlag(fProject, CompilerFlags.P_DEPRECATED);
if (severity != CompilerFlags.IGNORE) reportUnusedElement(child, severity);
}
}
}
IExtensions extensions = fModel.getExtensions();
if (extensions != null
&& extensions.getExtensions().length == 0
&& extensions.getExtensionPoints().length == 0)
report(
MDECoreMessages.Builders_Manifest_useless_file,
-1,
IMarker.SEVERITY_WARNING,
MDEMarkerFactory.P_USELESS_FILE,
MDEMarkerFactory.CAT_OTHER);
}
}
protected static XmlConfigurator parse(Element root_element) throws java.io.IOException {
XmlConfigurator configurator = null;
final LinkedList<ProtocolConfiguration> prot_data = new LinkedList<ProtocolConfiguration>();
/**
* CAUTION: crappy code ahead ! I (bela) am not an XML expert, so the code below is pretty
* amateurish... But it seems to work, and it is executed only on startup, so no perf loss on
* the critical path. If somebody wants to improve this, please be my guest.
*/
try {
String root_name = root_element.getNodeName();
if (!"config".equals(root_name.trim().toLowerCase()))
throw new IOException("the configuration does not start with a <config> element");
NodeList prots = root_element.getChildNodes();
for (int i = 0; i < prots.getLength(); i++) {
Node node = prots.item(i);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element tag = (Element) node;
String protocol = tag.getTagName();
Map<String, String> params = new HashMap<String, String>();
NamedNodeMap attrs = tag.getAttributes();
int attrLength = attrs.getLength();
for (int a = 0; a < attrLength; a++) {
Attr attr = (Attr) attrs.item(a);
String name = attr.getName();
String value = attr.getValue();
params.put(name, value);
}
ProtocolConfiguration cfg = new ProtocolConfiguration(protocol, params);
prot_data.add(cfg);
}
configurator = new XmlConfigurator(prot_data);
} catch (Exception x) {
if (x instanceof java.io.IOException) throw (java.io.IOException) x;
else {
IOException tmp = new IOException();
tmp.initCause(x);
throw tmp;
}
}
return configurator;
}
// DOM input
public void declareNamespace(Element element) {
NamedNodeMap attrs = element.getAttributes();
int size = attrs.getLength();
for (int i = 0; i < size; i++) {
Attr attr = (Attr) attrs.item(i);
String qName = attr.getName();
if (qName.startsWith("xmlns:")) {
String uri = attr.getValue();
String prefix = qName.substring("xmlns:".length());
declareNamespace(prefix, uri);
} else if (qName.startsWith("xmlns")) {
String uri = attr.getValue();
declareNamespace("", uri);
}
}
}
private void addNamespaces(Namespaces rv, Element element) {
if (element == null) throw new RuntimeException("element must not be null");
String myDefaultNamespace = toUri(element.lookupNamespaceURI(null));
String parentDefaultNamespace = "";
if (element.getParentNode() != null) {
parentDefaultNamespace = toUri(element.getParentNode().lookupNamespaceURI(null));
}
if (!myDefaultNamespace.equals(parentDefaultNamespace)
|| !(element.getParentNode() instanceof Element)) {
rv.declare(Namespace.create("", myDefaultNamespace));
}
NamedNodeMap attributes = element.getAttributes();
for (int i = 0; i < attributes.getLength(); i++) {
Attr attr = (Attr) attributes.item(i);
if (attr.getPrefix() != null && attr.getPrefix().equals("xmlns")) {
rv.declare(Namespace.create(attr.getLocalName(), attr.getValue()));
}
}
}
@Test
public void testgetAttributesWithNamedNodeMap() throws Exception {
// builderFactory = DocumentBuilderFactory.newInstance();
builderFactory.setNamespaceAware(true);
File f = new File(System.getProperty("user.dir"), "src/test/resources/sample-springbeans.xml");
DocumentBuilder builder = builderFactory.newDocumentBuilder();
Document doc = builder.parse(f);
Element root = doc.getDocumentElement();
// System.out.println("* current impl: " + doc.getClass().getName());
// id, class
Map<String, String> actualMap = new HashMap<String, String>();
NodeList list = root.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
if (node instanceof Element) {
Element elem = (Element) node;
if (elem.getTagName().equals("beans:bean")) {
// System.out.println("bean[" + elem.getAttribute("id") + "]");
NamedNodeMap map = elem.getAttributes();
String valueId = null;
String valueClass = null;
for (int x = 0; x < map.getLength(); x++) {
Node attr = map.item(x);
if (attr.getNodeName().equals("id")) valueId = attr.getNodeValue();
if (attr.getNodeName().equals("class")) valueClass = attr.getNodeValue();
}
if (valueId != null && valueClass != null) actualMap.put(valueId, valueClass);
}
}
}
Map<String, String> expected = new HashMap<String, String>();
expected.put("authenticationManager", "org.springframework.security.providers.ProviderManager");
expected.put(
"daoAuthenticationProvider",
"org.springframework.security.providers.dao.DaoAuthenticationProvider");
expected.put(
"loggerListener", "org.springframework.security.event.authentication.LoggerListener");
Assert.assertEquals("Attributes with NamedNodeMap", expected, actualMap);
}
private void validateExistingExtensionAttributes(
Element element, NamedNodeMap attrs, ISchemaElement schemaElement) {
for (int i = 0; i < attrs.getLength(); i++) {
Attr attr = (Attr) attrs.item(i);
ISchemaAttribute attInfo = schemaElement.getAttribute(attr.getName());
if (attInfo == null) {
HashSet allowedElements = new HashSet();
computeAllowedElements(schemaElement.getType(), allowedElements);
if (allowedElements.contains(attr.getName())) {
validateJavaAttribute(element, attr);
} else {
int flag = CompilerFlags.getFlag(fProject, CompilerFlags.P_UNKNOWN_ATTRIBUTE);
if (flag != CompilerFlags.IGNORE) reportUnknownAttribute(element, attr.getName(), flag);
}
} else {
validateExtensionAttribute(element, attr, attInfo);
}
}
}
@Override
protected AbstractBeanDefinition parseInternal(Element element, ParserContext parserContext) {
BeanDefinitionBuilder builder =
BeanDefinitionBuilder.genericBeanDefinition(SpringJolokiaConfigHolder.class);
Map<String, String> config = new HashMap<String, String>();
NamedNodeMap attrs = element.getAttributes();
for (int i = 0; i < attrs.getLength(); i++) {
Attr attr = (Attr) attrs.item(i);
String name = attr.getName();
if (skipMap.contains(name)) {
continue;
}
config.put(name, attr.getValue());
}
builder.addPropertyValue("config", config);
String order = element.getAttribute("order");
if (StringUtils.hasText(order)) {
builder.addPropertyValue("order", Integer.parseInt(order));
}
return builder.getBeanDefinition();
}
/**
* @param node
* @param indent
*/
public static String toString(Node node, int indent) {
StringBuffer str = new StringBuffer();
for (int i = 0; i < indent; ++i) str.append(" ");
str.append(node);
if (node.hasAttributes()) {
NamedNodeMap attrs = node.getAttributes();
for (int j = 0; j < attrs.getLength(); ++j) {
Node attr = attrs.item(j);
// str.append(toString(attr,indent+2));
str.append(" ");
str.append(attr);
}
}
str.append("\n");
++indent;
for (Node child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
str.append(toString(child, indent));
// str.append("\n");
}
return str.toString();
}
private static void parseXML() {
try {
Document doc =
DocumentBuilderFactory.newInstance()
.newDocumentBuilder()
.parse(CommandBuilder.class.getResourceAsStream("/CommandMap.xml"));
NodeList nodes = doc.getElementsByTagName("CommandMap");
for (int i = 0; i < nodes.getLength(); i++) {
Node n = nodes.item(i);
NamedNodeMap atts = n.getAttributes();
String rootCommand = atts.getNamedItem("rootCommand").getNodeValue();
rootNode = new Category(rootCommand, "");
NodeList children = n.getChildNodes();
for (int p = 0; p < children.getLength(); p++) {
parseNode(children.item(p), rootNode);
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
private void processPanelLayout(Session session, Element element, HashMap additionalInformation) {
String nodeName = element.getNodeName();
String panelName = nodeName;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String name = node.getNodeName();
if (name.equals("dividerFractions")) {
String value = node.getNodeValue();
String[] tokens = value.split(",");
double[] divs = new double[tokens.length];
try {
for (int j = 0; j < tokens.length; j++) {
divs[j] = Double.parseDouble(tokens[j]);
}
session.setDividerFractions(divs);
} catch (NumberFormatException e) {
log.error("Error parsing divider locations", e);
}
}
}
}
void invalidateNamespacePrefix() {
if (!(dom instanceof Element)) throw new IllegalStateException();
String prefix = this.dom.getPrefix();
QName after = QName.create(this.dom.getNamespaceURI(), this.dom.getLocalName(), null);
renameNode(after);
NamedNodeMap attrs = this.dom.getAttributes();
for (int i = 0; i < attrs.getLength(); i++) {
if (attrs.item(i).getPrefix().equals(prefix)) {
createImpl(attrs.item(i))
.renameNode(
QName.create(attrs.item(i).getNamespaceURI(), attrs.item(i).getLocalName(), null));
}
}
}
public static int size(NamedNodeMap namedNodeMap) {
return namedNodeMap.getLength();
}
/**
* Constructs an attribute element from an existing XML block.
*
* @param element representing a DOM tree element.
* @exception SAMLException if there is an error in the sender or in the element definition.
*/
public Attribute(Element element) throws SAMLException {
// make sure that the input xml block is not null
if (element == null) {
SAMLUtilsCommon.debug.message("Attribute: Input is null.");
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
// Make sure this is an Attribute.
String tag = null;
tag = element.getLocalName();
if ((tag == null) || (!tag.equals("Attribute"))) {
SAMLUtilsCommon.debug.message("Attribute: wrong input");
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("wrongInput"));
}
int i = 0;
// handle attributes
NamedNodeMap atts = element.getAttributes();
int attrCount = atts.getLength();
for (i = 0; i < attrCount; i++) {
Node att = atts.item(i);
if (att.getNodeType() == Node.ATTRIBUTE_NODE) {
String attName = att.getLocalName();
if (attName == null) {
attName = att.getNodeName();
}
if (attName == null || attName.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("Attribute:" + "Attribute Name is either null or empty.");
}
continue;
// throw new SAMLRequesterException(
// SAMLUtilsCommon.bundle.getString("nullInput"));
}
if (attName.equals("AttributeName")) {
this._attributeName = ((Attr) att).getValue().trim();
} else if (attName.equals("AttributeNamespace")) {
this._attributeNameSpace = ((Attr) att).getValue().trim();
}
}
}
// AttributeName is required
if (_attributeName == null || _attributeName.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("Attribute: " + "AttributeName is required attribute");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("missingAttribute"));
}
// AttributeNamespace is required
if (_attributeNameSpace == null || _attributeNameSpace.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("Attribute: " + "AttributeNamespace is required attribute");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("missingAttribute"));
}
// handle the children of Attribute element
NodeList nodes = element.getChildNodes();
int nodeCount = nodes.getLength();
if (nodeCount > 0) {
for (i = 0; i < nodeCount; i++) {
Node currentNode = nodes.item(i);
if (currentNode.getNodeType() == Node.ELEMENT_NODE) {
String tagName = currentNode.getLocalName();
String tagNS = currentNode.getNamespaceURI();
if ((tagName == null) || tagName.length() == 0 || tagNS == null || tagNS.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"Attribute:"
+ " The tag name or tag namespace of child"
+ " element is either null or empty.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
if (tagName.equals("AttributeValue")
&& tagNS.equals(SAMLConstants.assertionSAMLNameSpaceURI)) {
if (_attributeValue == null) {
_attributeValue = new ArrayList();
}
if (!(_attributeValue.add((Element) currentNode))) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"Attribute: failed to " + "add to the attribute value list.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("addListError"));
}
} else {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("Attribute:" + "wrong element:" + tagName);
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("wrongInput"));
}
} // end of if (currentNode.getNodeType() == Node.ELEMENT_NODE)
} // end of for loop
} // end of if (nodeCount > 0)
if (_attributeValue == null || _attributeValue.isEmpty()) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"Attribute: " + "should contain at least one AttributeValue.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("missingElement"));
}
}
/** updates the XMl with hashcode for the files */
protected BudgetSubAwards updateXML(
byte xmlContents[], Map fileMap, BudgetSubAwards budgetSubAwardBean, Budget budget)
throws Exception {
javax.xml.parsers.DocumentBuilderFactory domParserFactory =
javax.xml.parsers.DocumentBuilderFactory.newInstance();
javax.xml.parsers.DocumentBuilder domParser = domParserFactory.newDocumentBuilder();
ByteArrayInputStream byteArrayInputStream = new ByteArrayInputStream(xmlContents);
org.w3c.dom.Document document = domParser.parse(byteArrayInputStream);
byteArrayInputStream.close();
String namespace = null;
String formName = null;
if (document != null) {
Node node;
Element element = document.getDocumentElement();
NamedNodeMap map = element.getAttributes();
String namespaceHolder =
element.getNodeName().substring(0, element.getNodeName().indexOf(':'));
node = map.getNamedItem("xmlns:" + namespaceHolder);
namespace = node.getNodeValue();
FormMappingInfo formMappingInfo = new FormMappingLoader().getFormInfo(namespace);
formName = formMappingInfo.getFormName();
budgetSubAwardBean.setNamespace(namespace);
budgetSubAwardBean.setFormName(formName);
}
String xpathEmptyNodes =
"//*[not(node()) and local-name(.) != 'FileLocation' and local-name(.) != 'HashValue']";
String xpathOtherPers =
"//*[local-name(.)='ProjectRole' and local-name(../../.)='OtherPersonnel' and count(../NumberOfPersonnel)=0]";
removeAllEmptyNodes(document, xpathEmptyNodes, 0);
removeAllEmptyNodes(document, xpathOtherPers, 1);
removeAllEmptyNodes(document, xpathEmptyNodes, 0);
changeDataTypeForNumberOfOtherPersons(document);
List<String> fedNonFedSubAwardForms = getFedNonFedSubawardForms();
NodeList budgetYearList =
XPathAPI.selectNodeList(document, "//*[local-name(.) = 'BudgetYear']");
for (int i = 0; i < budgetYearList.getLength(); i++) {
Node bgtYearNode = budgetYearList.item(i);
String period = getValue(XPathAPI.selectSingleNode(bgtYearNode, "BudgetPeriod"));
if (fedNonFedSubAwardForms.contains(namespace)) {
Element newBudgetYearElement =
copyElementToName((Element) bgtYearNode, bgtYearNode.getNodeName());
bgtYearNode.getParentNode().replaceChild(newBudgetYearElement, bgtYearNode);
} else {
Element newBudgetYearElement =
copyElementToName((Element) bgtYearNode, bgtYearNode.getNodeName() + period);
bgtYearNode.getParentNode().replaceChild(newBudgetYearElement, bgtYearNode);
}
}
Node oldroot = document.removeChild(document.getDocumentElement());
Node newroot = document.appendChild(document.createElement("Forms"));
newroot.appendChild(oldroot);
org.w3c.dom.NodeList lstFileName = document.getElementsByTagName("att:FileName");
org.w3c.dom.NodeList lstFileLocation = document.getElementsByTagName("att:FileLocation");
org.w3c.dom.NodeList lstMimeType = document.getElementsByTagName("att:MimeType");
org.w3c.dom.NodeList lstHashValue = document.getElementsByTagName("glob:HashValue");
if ((lstFileName.getLength() != lstFileLocation.getLength())
|| (lstFileLocation.getLength() != lstHashValue.getLength())) {
// throw new RuntimeException("Tag occurances mismatch in XML File");
}
org.w3c.dom.Node fileNode, hashNode, mimeTypeNode;
org.w3c.dom.NamedNodeMap fileNodeMap, hashNodeMap;
String fileName;
byte fileBytes[];
String contentId;
List attachmentList = new ArrayList();
for (int index = 0; index < lstFileName.getLength(); index++) {
fileNode = lstFileName.item(index);
Node fileNameNode = fileNode.getFirstChild();
fileName = fileNameNode.getNodeValue();
fileBytes = (byte[]) fileMap.get(fileName);
if (fileBytes == null) {
throw new RuntimeException("FileName mismatch in XML and PDF extracted file");
}
String hashVal = GrantApplicationHash.computeAttachmentHash(fileBytes);
hashNode = lstHashValue.item(index);
hashNodeMap = hashNode.getAttributes();
Node temp = document.createTextNode(hashVal);
hashNode.appendChild(temp);
hashNode = hashNodeMap.getNamedItem("glob:hashAlgorithm");
hashNode.setNodeValue(S2SConstants.HASH_ALGORITHM);
fileNode = lstFileLocation.item(index);
fileNodeMap = fileNode.getAttributes();
fileNode = fileNodeMap.getNamedItem("att:href");
contentId = fileNode.getNodeValue();
String encodedContentId = cleanContentId(contentId);
fileNode.setNodeValue(encodedContentId);
mimeTypeNode = lstMimeType.item(0);
String contentType = mimeTypeNode.getFirstChild().getNodeValue();
BudgetSubAwardAttachment budgetSubAwardAttachmentBean = new BudgetSubAwardAttachment();
budgetSubAwardAttachmentBean.setAttachment(fileBytes);
budgetSubAwardAttachmentBean.setContentId(encodedContentId);
budgetSubAwardAttachmentBean.setContentType(contentType);
budgetSubAwardAttachmentBean.setBudgetId(budgetSubAwardBean.getBudgetId());
budgetSubAwardAttachmentBean.setSubAwardNumber(budgetSubAwardBean.getSubAwardNumber());
attachmentList.add(budgetSubAwardAttachmentBean);
}
budgetSubAwardBean.setBudgetSubAwardAttachments(attachmentList);
javax.xml.transform.Transformer transformer =
javax.xml.transform.TransformerFactory.newInstance().newTransformer();
transformer.setOutputProperty(javax.xml.transform.OutputKeys.INDENT, "yes");
ByteArrayOutputStream bos = new ByteArrayOutputStream();
javax.xml.transform.stream.StreamResult result =
new javax.xml.transform.stream.StreamResult(bos);
javax.xml.transform.dom.DOMSource source = new javax.xml.transform.dom.DOMSource(document);
transformer.transform(source, result);
budgetSubAwardBean.setSubAwardXmlFileData(new String(bos.toByteArray()));
bos.close();
return budgetSubAwardBean;
}
private static String xgetAt(NamedNodeMap namedNodeMap, String elementName) {
Attr a = (Attr) namedNodeMap.getNamedItem(elementName);
return a.getValue();
}
/**
* @param list
* @param parent
* @exception NumberFormatException
* @exception DicomException
*/
void addAttributesFromNodeToList(AttributeList list, Node parent)
throws NumberFormatException, DicomException {
if (parent != null) {
Node node = parent.getFirstChild();
while (node != null) {
String elementName = node.getNodeName();
NamedNodeMap attributes = node.getAttributes();
if (attributes != null) {
Node vrNode = attributes.getNamedItem("vr");
Node groupNode = attributes.getNamedItem("group");
Node elementNode = attributes.getNamedItem("element");
if (vrNode != null && groupNode != null && elementNode != null) {
String vrString = vrNode.getNodeValue();
String groupString = groupNode.getNodeValue();
String elementString = elementNode.getNodeValue();
if (vrString != null && groupString != null && elementString != null) {
byte[] vr = vrString.getBytes();
int group = Integer.parseInt(groupString, 16);
int element = Integer.parseInt(elementString, 16);
AttributeTag tag = new AttributeTag(group, element);
if ((group % 2 == 0 && element == 0)
|| (group == 0x0008 && element == 0x0001)
|| (group == 0xfffc && element == 0xfffc)) {
// System.err.println("ignoring group length or length to end or dataset trailing
// padding "+tag);
} else {
if (vrString.equals("SQ")) {
SequenceAttribute a = new SequenceAttribute(tag);
// System.err.println("Created "+a);
if (node.hasChildNodes()) {
Node childNode = node.getFirstChild();
while (childNode != null) {
String childNodeName = childNode.getNodeName();
// System.err.println("childNodeName = "+childNodeName);
if (childNodeName != null && childNodeName.equals("Item")) {
// should check item number, but ignore for now :(
// System.err.println("Adding item to sequence");
AttributeList itemList = new AttributeList();
addAttributesFromNodeToList(itemList, childNode);
a.addItem(itemList);
}
// else may be a #text element in between
childNode = childNode.getNextSibling();
}
}
// System.err.println("Sequence Attribute is "+a);
list.put(tag, a);
} else {
Attribute a = AttributeFactory.newAttribute(tag, vr);
// System.err.println("Created "+a);
if (node.hasChildNodes()) {
Node childNode = node.getFirstChild();
while (childNode != null) {
String childNodeName = childNode.getNodeName();
// System.err.println("childNodeName = "+childNodeName);
if (childNodeName != null && childNodeName.equals("value")) {
// should check value number, but ignore for now :(
String value = childNode.getTextContent();
// System.err.println("Value value = "+value);
if (value != null) {
value =
StringUtilities.removeLeadingOrTrailingWhitespaceOrISOControl(
value); // just in case
a.addValue(value);
}
}
// else may be a #text element in between
childNode = childNode.getNextSibling();
}
}
// System.err.println("Attribute is "+a);
list.put(tag, a);
}
}
}
}
}
node = node.getNextSibling();
}
}
}
private Object deserialize(Node node, boolean setProperty, boolean popBean) throws Exception {
Object object = null;
currentType = null;
currentNode = node;
currentName = node.getNodeName();
boolean isNull = false;
NamedNodeMap attrs = node.getAttributes();
String arrayType = null;
for (int i = 0; i < attrs.getLength(); i++) {
String nodeName = attrs.item(i).getNodeName();
String nodeValue = attrs.item(i).getNodeValue();
if (nodeName.equals(NamespaceConstants.NSPREFIX_SCHEMA_XSI + ":" + Constants.ATTR_TYPE))
currentType = new StringBuffer(nodeValue).delete(0, nodeValue.indexOf(':') + 1).toString();
else if (nodeName.equals(
NamespaceConstants.NSPREFIX_SOAP_ENCODING + ":" + Constants.ATTR_ARRAY_TYPE))
arrayType = new StringBuffer(nodeValue).delete(0, nodeValue.indexOf(':') + 1).toString();
else if (nodeName.equals(NamespaceConstants.NSPREFIX_SCHEMA_XSI + ":null"))
isNull = nodeValue.equals("true");
}
Class cls = null;
if (currentType != null) cls = getXsdTypeClass(currentType);
// Handle array, Vector, ArrayList, LinkedList, Hashtable,
// Properties, and HashMap data types
if ((cls != null)
&& ((cls == java.lang.reflect.Array.class)
|| (cls == Vector.class)
|| (cls == ArrayList.class)
|| (cls == LinkedList.class)
|| (cls == Hashtable.class)
|| (cls == Properties.class)
|| (cls == HashMap.class)
|| (cls == SortedMap.class))) {
parentNode = currentNode;
String name = node.getNodeName();
// Handle arrays
if (cls == java.lang.reflect.Array.class) {
int a = arrayType.indexOf("[");
int b = arrayType.indexOf("]");
String s = arrayType.substring(a + 1, b);
int arrayLen = Integer.valueOf(s).intValue();
arrayType = arrayType.substring(0, a);
// check if the array element is a standard Java class
Class arrayClass = getXsdTypeClass(arrayType);
// otherwise try to get the class of the bean
if (arrayClass == null)
arrayClass = getClassOfBean((ClassLoader) classLoaderStrategy, arrayType);
object = java.lang.reflect.Array.newInstance(arrayClass, arrayLen);
} else {
// Construct the list or map type
Constructor ct = cls.getConstructor((Class[]) null);
object = ct.newInstance((Object[]) null);
}
// deserialize the elements of the array, list, or map
NodeList childNodes = node.getChildNodes();
int arrayIndex = -1;
Node childNode = null;
Object nodeObj = null;
for (int i = 0; i < childNodes.getLength(); i++) {
childNode = childNodes.item(i);
if (childNode.getNodeType() == Node.ELEMENT_NODE) {
if ((cls == java.lang.reflect.Array.class)
|| (cls == Vector.class)
|| (cls == ArrayList.class)
|| (cls == LinkedList.class)) {
nodeObj = deserialize(childNode, false, true);
if (nodeObj != null) {
if (cls == java.lang.reflect.Array.class)
java.lang.reflect.Array.set(object, ++arrayIndex, nodeObj);
else ((List) object).add(nodeObj);
}
} else if ((cls == Hashtable.class)
|| (cls == Properties.class)
|| (cls == HashMap.class)
|| (cls == SortedMap.class)) {
if (childNode.getLocalName().equals("item")) {
NodeList htNodes = childNode.getChildNodes();
if (htNodes.getLength() == 2) {
Object hashKey = deserialize(htNodes.item(0), false, false);
Object hashValue = deserialize(htNodes.item(1), false, true);
((Map) object).put(hashKey, hashValue);
}
}
}
}
}
setBeanProperty(name, object);
// Handle everything else (primitives & POJOs)
} else {
// recurse on each of the child nodes
NodeList childNodes = node.getChildNodes();
if ((childNodes != null) && (childNodes.getLength() > 0)) {
for (int i = 0; i < childNodes.getLength(); i++) {
Node childNode = childNodes.item(i);
if (childNode.getNodeType() == Node.ELEMENT_NODE) {
if (currentType != null)
createObject(
node,
currentName,
currentPackage,
currentType,
childNode.getNodeValue(),
setProperty);
parentNode = node;
object = deserialize(childNode, true, true);
} else if ((childNode.getNodeType() == Node.TEXT_NODE) && (currentType != null)) {
object =
createObject(
node,
currentName,
currentPackage,
currentType,
childNode.getNodeValue(),
setProperty);
}
currentType = null;
}
} else {
if (!isNull)
object = createObject(node, currentName, currentPackage, currentType, null, setProperty);
}
if (node.getParentNode() != parentNode) {
parentNode = node.getParentNode();
if (popBean) {
Object bean = popBeanOffStack();
if (bean != null) object = bean;
}
}
}
return object;
}
private Object createObject(
Node node, String name, String classPackage, String type, String value, boolean setProperty) {
Bean parentBean = null;
if (beansStack.size() > 0) parentBean = (Bean) beansStack.peek();
Object object = null;
// param is either an XSD type or a bean,
// check if it can be converted to an XSD type
XSDatatype dt = null;
try {
dt = DatatypeFactory.getTypeByName(type);
} catch (DatatypeException dte) {
// the type is not a valid XSD data type
}
// convert null value to default
if ((dt != null) && (value == null)) {
Class objType = dt.getJavaObjectType();
if (objType == String.class) value = "";
else if ((objType == java.math.BigInteger.class)
|| (objType == Long.class)
|| (objType == Integer.class)
|| (objType == Short.class)
|| (objType == Byte.class)) value = "0";
else if ((objType == java.math.BigDecimal.class)
|| (objType == Double.class)
|| (objType == Float.class)) value = "0.0";
else if (objType == Boolean.class) value = "false";
else if (objType == java.util.Date.class) value = DateUtils.getCurrentDate();
else if (objType == java.util.Calendar.class) value = DateUtils.getCurrentDateTime();
}
// check whether the type was converted to an XSD datatype
if ((dt != null) && dt.isValid(value, null)) {
// create and return an XSD Java object (e.g. String, Integer, Boolean, etc)
object = dt.createJavaObject(value, null);
if (object instanceof java.util.Calendar) {
// check that the object is truly a Calendar
// because DatatypeFactory converts xsd:date
// types to GregorianCalendar instead of Date.
if (type.equals("date")) {
java.text.DateFormat df = new java.text.SimpleDateFormat("yyyy-MM-dd");
try {
object = df.parse(value);
} catch (java.text.ParseException pe) {
object = new java.util.Date();
}
}
}
} else {
// Create a bean object
if (topLevelBean == null) topLevelBean = parentBean;
object = pushBeanOnStack(classPackage, type);
// Check fields to see if this property is the 'value' for the object
Field[] fields = object.getClass().getDeclaredFields();
for (int i = 0; i < fields.length; i++) {
if (fields[i].isAnnotationPresent(ObjectXmlAsValue.class)) {
try {
StringBuffer fieldName = new StringBuffer(fields[i].getName());
char c = fieldName.charAt(0);
if (c >= 'a' && c <= 'z') {
c += 'A' - 'a';
}
fieldName.setCharAt(0, c);
fieldName.insert(0, "set");
Method method =
object
.getClass()
.getMethod(fieldName.toString(), new Class[] {fields[i].getType()});
method.invoke(object, value);
break;
} catch (Exception e) {
System.err.println(e.getMessage());
}
}
}
NamedNodeMap nodeAttrs = node.getAttributes();
// iterate attributes and set field values for property attributes
for (int i = 0; i < nodeAttrs.getLength(); i++) {
String nodePrefix = nodeAttrs.item(i).getPrefix();
if (nodePrefix.equals(nsPrefix)) {
String nodeName = nodeAttrs.item(i).getLocalName();
String nodeValue = nodeAttrs.item(i).getNodeValue();
try {
Field field = object.getClass().getDeclaredField(nodeName);
if (field.isAnnotationPresent(ObjectXmlAsAttribute.class)) {
StringBuffer fieldName = new StringBuffer(field.getName());
char c = fieldName.charAt(0);
if (c >= 'a' && c <= 'z') {
c += 'A' - 'a';
}
fieldName.setCharAt(0, c);
fieldName.insert(0, "set");
Method method =
object.getClass().getMethod(fieldName.toString(), new Class[] {field.getType()});
if (field.getType() == String.class) method.invoke(object, nodeValue);
else if (field.getType() == Boolean.TYPE)
method.invoke(object, StringUtils.strToBool(nodeValue, "true"));
else if (field.getType() == Byte.TYPE)
method.invoke(object, Byte.valueOf(nodeValue).byteValue());
else if (field.getType() == Character.TYPE)
method.invoke(object, Character.valueOf(nodeValue.charAt(0)));
else if (field.getType() == Double.TYPE)
method.invoke(object, Double.valueOf(nodeValue).doubleValue());
else if (field.getType() == Float.TYPE)
method.invoke(object, Float.valueOf(nodeValue).floatValue());
else if (field.getType() == Integer.TYPE)
method.invoke(object, Integer.valueOf(nodeValue).intValue());
else if (field.getType() == Long.TYPE)
method.invoke(object, Long.valueOf(nodeValue).longValue());
else if (field.getType() == Short.TYPE)
method.invoke(object, Short.valueOf(nodeValue).shortValue());
}
} catch (Exception e) {
System.err.println(e.getMessage());
}
}
}
}
if ((parentBean != null) && (setProperty)) {
parentBean.setProperty(name, object);
}
return object;
}
/**
* Constructs an attribute designator element from an existing XML block.
*
* @param element representing a DOM tree element.
* @exception SAMLException if that there is an error in the sender or in the element definition.
*/
public AttributeDesignator(Element element) throws SAMLException {
// make sure that the input xml block is not null
if (element == null) {
SAMLUtilsCommon.debug.message("AttributeDesignator: Input is null.");
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
// Make sure this is an AttributeDesignator.
String tag = null;
tag = element.getLocalName();
if ((tag == null) || (!tag.equals("AttributeDesignator"))) {
SAMLUtilsCommon.debug.message("AttributeDesignator: wrong input");
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("wrongInput"));
}
// handle attributes
int i = 0;
NamedNodeMap atts = ((Node) element).getAttributes();
int attrCount = atts.getLength();
for (i = 0; i < attrCount; i++) {
Node att = atts.item(i);
if (att.getNodeType() == Node.ATTRIBUTE_NODE) {
String attName = att.getLocalName();
if (attName == null || attName.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"AttributeDesignator:" + "Attribute Name is either null or empty.");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("nullInput"));
}
if (attName.equals("AttributeName")) {
_attributeName = ((Attr) att).getValue().trim();
} else if (attName.equals("AttributeNamespace")) {
_attributeNameSpace = ((Attr) att).getValue().trim();
}
}
}
// AttributeName is required
if (_attributeName == null || _attributeName.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"AttributeDesignator: " + "AttributeName is required attribute");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("missingAttribute"));
}
// AttributeNamespace is required
if (_attributeNameSpace == null || _attributeNameSpace.length() == 0) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message(
"AttributeDesignator: " + "AttributeNamespace is required attribute");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("missingAttribute"));
}
// handle the children of AttributeDesignator element
// Since AttributeDesignator does not have any child element_node,
// we will throw exception if we found any such child.
NodeList nodes = element.getChildNodes();
int nodeCount = nodes.getLength();
if (nodeCount > 0) {
for (i = 0; i < nodeCount; i++) {
Node currentNode = nodes.item(i);
if (currentNode.getNodeType() == Node.ELEMENT_NODE) {
if (SAMLUtilsCommon.debug.messageEnabled()) {
SAMLUtilsCommon.debug.message("AttributeDesignator: illegal input!");
}
throw new SAMLRequesterException(SAMLUtilsCommon.bundle.getString("wrongInput"));
}
}
}
}
/**
* Process a track element. This should return a single track, but could return multiple tracks
* since the uniqueness of the track id is not enforced.
*
* @param session
* @param element
* @param additionalInformation
* @return
*/
private List<Track> processTrack(
Session session, Element element, HashMap additionalInformation) {
String id = getAttribute(element, SessionAttribute.ID.getText());
// TODo -- put in utility method, extacts attributes from element **Definitely need to do this
HashMap<String, String> tAttributes = new HashMap();
HashMap<String, String> drAttributes = null;
NamedNodeMap tNodeMap = element.getAttributes();
for (int i = 0; i < tNodeMap.getLength(); i++) {
Node node = tNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
tAttributes.put(node.getNodeName(), value);
}
}
if (element.hasChildNodes()) {
drAttributes = new HashMap();
Node childNode = element.getFirstChild();
Node sibNode = childNode.getNextSibling();
String sibName = sibNode.getNodeName();
if (sibName.equals(SessionElement.DATA_RANGE.getText())) {
NamedNodeMap drNodeMap = sibNode.getAttributes();
for (int i = 0; i < drNodeMap.getLength(); i++) {
Node node = drNodeMap.item(i);
String value = node.getNodeValue();
if (value != null && value.length() > 0) {
drAttributes.put(node.getNodeName(), value);
}
}
}
}
// Get matching tracks.
List<Track> matchedTracks = trackDictionary.get(id);
if (matchedTracks == null) {
log.info("Warning. No tracks were found with id: " + id + " in session file");
} else {
for (final Track track : matchedTracks) {
// Special case for sequence & gene tracks, they need to be removed before being placed.
if (version >= 4 && track == geneTrack || track == seqTrack) {
igv.removeTracks(Arrays.asList(track));
}
track.restorePersistentState(tAttributes);
if (drAttributes != null) {
DataRange dr = track.getDataRange();
dr.restorePersistentState(drAttributes);
track.setDataRange(dr);
}
}
trackDictionary.remove(id);
}
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
return matchedTracks;
}