public void onDocument(Document document, String xpath) throws XmlParserException {
if (xpath.equals(XPATH_IPEAK)) {
Node node = document.getFirstChild();
// check whether we're getting the correct ipeak
Node typeattribute = node.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null)
throw new XmlParserException("Failed to locate the type attribute.");
if (!typeattribute.getNodeValue().equals(PeakMLWriter.TYPE_BACKGROUNDION))
throw new XmlParserException(
"IPeak ("
+ typeattribute.getNodeValue()
+ ") is not of type: '"
+ PeakMLWriter.TYPE_BACKGROUNDION
+ "'");
// parse this node as a mass chromatogram
BackgroundIon<? extends Peak> backgroundion = parseBackgroundIon(node);
if (backgroundion != null) peaks.add(backgroundion);
//
if (_listener != null && result.header != null && result.header.getNrPeaks() != 0)
_listener.update((100. * index++) / result.header.getNrPeaks());
} else if (xpath.equals(XPATH_HEADER)) {
result.header = parseHeader(document.getFirstChild());
}
}
/**
* Handle text node during validation.
*
* @param received
* @param source
*/
private void doText(Node received, Node source) {
if (log.isDebugEnabled()) {
log.debug("Validating node value for element: " + received.getParentNode());
}
if (received.getNodeValue() != null) {
Assert.isTrue(
source.getNodeValue() != null,
ValidationUtils.buildValueMismatchErrorMessage(
"Node value not equal for element '" + received.getParentNode().getLocalName() + "'",
null,
received.getNodeValue().trim()));
Assert.isTrue(
received.getNodeValue().trim().equals(source.getNodeValue().trim()),
ValidationUtils.buildValueMismatchErrorMessage(
"Node value not equal for element '" + received.getParentNode().getLocalName() + "'",
source.getNodeValue().trim(),
received.getNodeValue().trim()));
} else {
Assert.isTrue(
source.getNodeValue() == null,
ValidationUtils.buildValueMismatchErrorMessage(
"Node value not equal for element '" + received.getParentNode().getLocalName() + "'",
source.getNodeValue().trim(),
null));
}
if (log.isDebugEnabled()) {
log.debug("Node value '" + received.getNodeValue().trim() + "': OK");
}
}
private static IPeak parseIPeak(Node parent) throws XmlParserException {
Node type = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (type == null) return null;
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_PEAKSET)) return parsePeakSet(parent);
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_BACKGROUNDION))
return parseBackgroundIon(parent);
else if (type.getNodeValue().equals(PeakMLWriter.TYPE_MASSCHROMATOGRAM))
return parseMassChromatogram(parent);
else return null;
}
/**
* Perform validation on namespace qualified attribute values if present. This includes the
* validation of namespace presence and equality.
*
* @param receivedElement
* @param receivedAttribute
* @param sourceElement
* @param sourceAttribute
*/
private void doNamespaceQualifiedAttributeValidation(
Node receivedElement, Node receivedAttribute, Node sourceElement, Node sourceAttribute) {
String receivedValue = receivedAttribute.getNodeValue();
String sourceValue = sourceAttribute.getNodeValue();
if (receivedValue.contains(":") && sourceValue.contains(":")) {
// value has namespace prefix set, do special QName validation
String receivedPrefix = receivedValue.substring(0, receivedValue.indexOf(':'));
String sourcePrefix = sourceValue.substring(0, sourceValue.indexOf(':'));
Map<String, String> receivedNamespaces =
XMLUtils.lookupNamespaces(receivedAttribute.getOwnerDocument());
receivedNamespaces.putAll(XMLUtils.lookupNamespaces(receivedElement));
if (receivedNamespaces.containsKey(receivedPrefix)) {
Map<String, String> sourceNamespaces =
XMLUtils.lookupNamespaces(sourceAttribute.getOwnerDocument());
sourceNamespaces.putAll(XMLUtils.lookupNamespaces(sourceElement));
if (sourceNamespaces.containsKey(sourcePrefix)) {
Assert.isTrue(
sourceNamespaces.get(sourcePrefix).equals(receivedNamespaces.get(receivedPrefix)),
ValidationUtils.buildValueMismatchErrorMessage(
"Values not equal for attribute value namespace '" + receivedValue + "'",
sourceNamespaces.get(sourcePrefix),
receivedNamespaces.get(receivedPrefix)));
// remove namespace prefixes as they must not form equality
receivedValue = receivedValue.substring((receivedPrefix + ":").length());
sourceValue = sourceValue.substring((sourcePrefix + ":").length());
} else {
throw new ValidationException(
"Received attribute value '"
+ receivedAttribute.getLocalName()
+ "' describes namespace qualified attribute value,"
+ " control value '"
+ sourceValue
+ "' does not");
}
}
}
Assert.isTrue(
receivedValue.equals(sourceValue),
ValidationUtils.buildValueMismatchErrorMessage(
"Values not equal for attribute '" + receivedAttribute.getLocalName() + "'",
sourceValue,
receivedValue));
}
private Node[] processIndexNode(
final Node theNode,
final Document theTargetDocument,
final IndexEntryFoundListener theIndexEntryFoundListener) {
theNode.normalize();
boolean ditastyle = false;
String textNode = null;
final NodeList childNodes = theNode.getChildNodes();
final StringBuilder textBuf = new StringBuilder();
final List<Node> contents = new ArrayList<Node>();
for (int i = 0; i < childNodes.getLength(); i++) {
final Node child = childNodes.item(i);
if (checkElementName(child)) {
ditastyle = true;
break;
} else if (child.getNodeType() == Node.ELEMENT_NODE) {
textBuf.append(XMLUtils.getStringValue((Element) child));
contents.add(child);
} else if (child.getNodeType() == Node.TEXT_NODE) {
textBuf.append(child.getNodeValue());
contents.add(child);
}
}
textNode = IndexStringProcessor.normalizeTextValue(textBuf.toString());
if (textNode.length() == 0) {
textNode = null;
}
if (theNode.getAttributes().getNamedItem(elIndexRangeStartName) != null
|| theNode.getAttributes().getNamedItem(elIndexRangeEndName) != null) {
ditastyle = true;
}
final ArrayList<Node> res = new ArrayList<Node>();
if ((ditastyle)) {
final IndexEntry[] indexEntries = indexDitaProcessor.processIndexDitaNode(theNode, "");
for (final IndexEntry indexEntrie : indexEntries) {
theIndexEntryFoundListener.foundEntry(indexEntrie);
}
final Node[] nodes = transformToNodes(indexEntries, theTargetDocument, null);
for (final Node node : nodes) {
res.add(node);
}
} else if (textNode != null) {
final Node[] nodes =
processIndexString(textNode, contents, theTargetDocument, theIndexEntryFoundListener);
for (final Node node : nodes) {
res.add(node);
}
} else {
return new Node[0];
}
return (Node[]) res.toArray(new Node[res.size()]);
}
/**
* Checks whether the given node contains a validation matcher
*
* @param node
* @return true if node value contains validation matcher, false if not
*/
private boolean isValidationMatcherExpression(Node node) {
switch (node.getNodeType()) {
case Node.ELEMENT_NODE:
return node.getFirstChild() != null
&& StringUtils.hasText(node.getFirstChild().getNodeValue())
&& ValidationMatcherUtils.isValidationMatcherExpression(
node.getFirstChild().getNodeValue().trim());
case Node.ATTRIBUTE_NODE:
return StringUtils.hasText(node.getNodeValue())
&& ValidationMatcherUtils.isValidationMatcherExpression(node.getNodeValue().trim());
default:
return false; // validation matchers makes no sense
}
}
private void extractAttribute(
Set<String> pReadAttributes, Set<String> pWriteAttributes, Node pParam) {
Node mode = pParam.getAttributes().getNamedItem("mode");
pReadAttributes.add(pParam.getTextContent().trim());
if (mode == null || !mode.getNodeValue().equalsIgnoreCase("read")) {
pWriteAttributes.add(pParam.getTextContent().trim());
}
}
/**
* Handle processing instruction during validation.
*
* @param received
*/
private void doPI(Node received) {
log.info(
"Ignored processing instruction ("
+ received.getLocalName()
+ "="
+ received.getNodeValue()
+ ")");
}
/* return the value of the XML text node (never null) */
protected static String GetNodeText(Node root) {
StringBuffer sb = new StringBuffer();
if (root != null) {
NodeList list = root.getChildNodes();
for (int i = 0; i < list.getLength(); i++) {
Node n = list.item(i);
if (n.getNodeType() == Node.CDATA_SECTION_NODE) { // CDATA Section
sb.append(n.getNodeValue());
} else if (n.getNodeType() == Node.TEXT_NODE) {
sb.append(n.getNodeValue());
} else {
// Print.logWarn("Unrecognized node type: " + n.getNodeType());
}
}
}
return sb.toString();
}
public static String text(Node node) {
if (node.getNodeType() == Node.TEXT_NODE) {
return node.getNodeValue();
}
if (node.hasChildNodes()) {
return text(node.getChildNodes());
}
return "";
}
/** 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();
}
/** @deprecated use allText(Element elem, boolean trim) */
public static String allTextFromElement(Element elem, boolean trim) throws DOMException {
StringBuffer textBuf = new StringBuffer();
NodeList nl = elem.getChildNodes();
for (int j = 0, len = nl.getLength(); j < len; ++j) {
Node node = nl.item(j);
if (node instanceof Text) // includes Text and CDATA!
textBuf.append(node.getNodeValue());
}
String out = textBuf.toString();
return (trim ? out.trim() : out);
}
private static String getValue(Node node) {
String textValue = "";
Node child = null;
if (node != null)
for (child = node.getFirstChild(); child != null; child = child.getNextSibling()) {
if (child.getNodeType() == Node.TEXT_NODE) {
textValue = child.getNodeValue();
break;
}
}
return textValue.trim();
}
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;
}
private static String getTextContent(Node n) {
NodeList nodeList = n.getChildNodes();
String textContent = "";
for (int j = 0; j < nodeList.getLength(); j++) {
Node k = nodeList.item(j);
if (k.getNodeType() == Node.TEXT_NODE) {
textContent = k.getNodeValue();
break;
}
}
return textContent;
}
public void onDocument(Document document, String xpath) throws XmlParserException {
if (xpath.equals(XPATH_IPEAK)) {
Node node = document.getChildNodes().item(0);
// check whether we're getting the correct ipeak
Node typeattribute = node.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null
|| !typeattribute.getNodeValue().equals(PeakMLWriter.TYPE_PEAKSET))
throw new XmlParserException("Failed to locate a type attribute.");
// parse this node as a mass chromatogram
IPeakSet<? extends IPeak> peakset = parsePeakSet(node);
if (peakset != null) peaks.add(peakset);
//
if (_listener != null && result.header != null && result.header.getNrPeaks() != 0)
_listener.update((100. * index++) / result.header.getNrPeaks());
} else if (xpath.equals(XPATH_HEADER)) {
result.header = parseHeader(document.getFirstChild());
}
}
private static NodeList getChildElements(Element self, String elementName) {
List result = new ArrayList();
NodeList nodeList = self.getChildNodes();
for (int i = 0; i < nodeList.getLength(); i++) {
Node node = nodeList.item(i);
if (node.getNodeType() == Node.ELEMENT_NODE) {
Element child = (Element) node;
if ("*".equals(elementName) || child.getTagName().equals(elementName)) {
result.add(child);
}
} else if (node.getNodeType() == Node.TEXT_NODE) {
String value = node.getNodeValue();
if (trimWhitespace) {
value = value.trim();
}
if ("*".equals(elementName) && value.length() > 0) {
node.setNodeValue(value);
result.add(node);
}
}
}
return new NodesHolder(result);
}
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);
}
}
}
}
public static String getFirstTextNodeVal(Node node) {
node = getFirstTextNode(node);
if (node != null) return node.getNodeValue();
return null;
}
/**
* Handle attribute node during validation.
*
* @param receivedElement
* @param receivedAttribute
* @param sourceElement
* @param validationContext
*/
private void doAttribute(
Node receivedElement,
Node receivedAttribute,
Node sourceElement,
XmlMessageValidationContext validationContext,
NamespaceContext namespaceContext,
TestContext context) {
if (receivedAttribute.getNodeName().startsWith(XMLConstants.XMLNS_ATTRIBUTE)) {
return;
}
String receivedAttributeName = receivedAttribute.getLocalName();
if (log.isDebugEnabled()) {
log.debug(
"Validating attribute: "
+ receivedAttributeName
+ " ("
+ receivedAttribute.getNamespaceURI()
+ ")");
}
NamedNodeMap sourceAttributes = sourceElement.getAttributes();
Node sourceAttribute =
sourceAttributes.getNamedItemNS(receivedAttribute.getNamespaceURI(), receivedAttributeName);
Assert.isTrue(
sourceAttribute != null,
"Attribute validation failed for element '"
+ receivedElement.getLocalName()
+ "', unknown attribute "
+ receivedAttributeName
+ " ("
+ receivedAttribute.getNamespaceURI()
+ ")");
if (XmlValidationUtils.isAttributeIgnored(
receivedElement,
receivedAttribute,
sourceAttribute,
validationContext.getIgnoreExpressions(),
namespaceContext)) {
return;
}
String receivedValue = receivedAttribute.getNodeValue();
String sourceValue = sourceAttribute.getNodeValue();
if (isValidationMatcherExpression(sourceAttribute)) {
ValidationMatcherUtils.resolveValidationMatcher(
sourceAttribute.getNodeName(),
receivedAttribute.getNodeValue().trim(),
sourceAttribute.getNodeValue().trim(),
context);
} else if (receivedValue.contains(":") && sourceValue.contains(":")) {
doNamespaceQualifiedAttributeValidation(
receivedElement, receivedAttribute, sourceElement, sourceAttribute);
} else {
Assert.isTrue(
receivedValue.equals(sourceValue),
ValidationUtils.buildValueMismatchErrorMessage(
"Values not equal for attribute '" + receivedAttributeName + "'",
sourceValue,
receivedValue));
}
if (log.isDebugEnabled()) {
log.debug("Attribute '" + receivedAttributeName + "'='" + receivedValue + "': OK");
}
}
/**
* @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 void processTxt(Node operation) {
List<Node> targets = getChildNodes(operation, "target");
List<Node> optionNodes = getChildNodes(operation, "opt");
List<Node> separatorNode = getChildNodes(operation, "separator");
if (targets.isEmpty() || optionNodes.isEmpty()) {
return;
}
String defaultSeparator = "=";
String globalSeparator = defaultSeparator;
if (!separatorNode.isEmpty()) {
globalSeparator = separatorNode.get(0).getTextContent();
if (globalSeparator.length() != 1) {
globalSeparator = defaultSeparator;
}
}
Map<String, String> options = new HashMap<String, String>();
Map<String, String> processedOptions = new HashMap<String, String>();
for (int i = 0; i < optionNodes.size(); i++) {
Node option = optionNodes.get(i);
String name = option.getAttributes().getNamedItem("name").getNodeValue();
String value = option.getTextContent();
if (options.containsKey(name)) {
options.remove(name);
}
options.put(name, value);
}
for (int t = 0; t < targets.size(); t++) {
File target = new File(absolutePath(targets.get(t).getTextContent()));
File tmpFile = new File(Utils.timestamp());
BufferedWriter bw = null;
BufferedReader br = null;
try {
Node separatorAttr = targets.get(t).getAttributes().getNamedItem("separator");
String separator = (separatorAttr == null) ? globalSeparator : separatorAttr.getNodeValue();
if (separator.length() != 1) {
separator = globalSeparator;
}
bw = new BufferedWriter(new FileWriter(tmpFile));
if (target.exists()) {
br = new BufferedReader(new FileReader(target));
for (String line; (line = br.readLine()) != null; ) {
String[] parts = line.split(separator);
if (parts.length < 2) {
bw.write(line);
bw.newLine();
continue;
}
String optName = parts[0].trim();
if (options.containsKey(optName)) {
String optValue = options.get(optName);
bw.write(optName + " " + separator + " " + optValue);
bw.newLine();
processedOptions.put(optName, optValue);
options.remove(optName);
} else if (processedOptions.containsKey(optName)) {
bw.write(optName + " " + separator + " " + processedOptions.get(optName));
bw.newLine();
} else {
bw.write(line);
bw.newLine();
}
}
br.close();
}
for (Map.Entry<String, String> entry : options.entrySet()) {
bw.write(entry.getKey() + " " + separator + " " + entry.getValue());
bw.newLine();
}
bw.close();
FileUtils.copyFile(tmpFile, target);
FileUtils.forceDelete(tmpFile);
} catch (IOException ex) {
Utils.onError(new Error.WriteTxtConfig(target.getPath()));
}
}
}
/**
* 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;
}
// -----------------------------------------------------
// Description: Get the value from the node.
// YUUGAMEE!
// -----------------------------------------------------
String getTagValue(String sTag, Element eElement) {
NodeList nlList = eElement.getElementsByTagName(sTag).item(0).getChildNodes();
Node nValue = (Node) nlList.item(0);
return nValue.getNodeValue();
}
/** 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;
}
/**
* Handle comment node during validation.
*
* @param received
*/
private void doComment(Node received) {
log.info("Ignored comment node (" + received.getNodeValue() + ")");
}
private static PeakData<? extends Peak> parsePeakData(Node parent) throws XmlParserException {
// get the attributes
Node typeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.TYPE);
if (typeattribute == null) throw new XmlParserException("Failed to locate a type attribute.");
Node sizeattribute = parent.getAttributes().getNamedItem(PeakMLWriter.SIZE);
if (sizeattribute == null) throw new XmlParserException("Failed to locate a size attribute.");
int size = Integer.parseInt(sizeattribute.getNodeValue());
String type = typeattribute.getNodeValue();
// create the arrays
int scanids[] = null;
int patternids[] = null;
int measurementids[] = null;
double masses[] = null;
double intensities[] = null;
double retentiontimes[] = null;
// retrieve all the data
NodeList nodes = parent.getChildNodes();
for (int nodeid = 0; nodeid < nodes.getLength(); ++nodeid) {
Node node = nodes.item(nodeid);
if (node.getNodeType() != Node.ELEMENT_NODE) continue;
Element element = (Element) node;
if (element.getTagName().equals("scanids"))
scanids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("patternids"))
patternids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("measurementids"))
measurementids =
ByteArray.toIntArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("masses"))
masses =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("intensities"))
intensities =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
else if (element.getTagName().equals("retentiontimes"))
retentiontimes =
ByteArray.toDoubleArray(
Base64.decode(element.getTextContent()), ByteArray.ENDIAN_LITTLE, 32);
}
// create the PeakData instance
if (type.equals("centroid"))
return new PeakData<Centroid>(
Centroid.factory,
size,
scanids,
patternids,
measurementids,
masses,
intensities,
retentiontimes);
return null;
}