// Gets the specified XML Schema doc if one is mentioned in the file
public static File getSchemaFile(Document xmlDoc) {
/** @todo Must be an easier way of doing this... */
logger.logComment("Getting schema file for: " + xmlDoc.getDocumentURI());
NodeList nl = xmlDoc.getChildNodes();
for (int j = 0; j < nl.getLength(); j++) {
Node node = nl.item(j);
logger.logComment("Type: " + node.getNodeType() + "Name: " + node.getNodeName());
if (node.getNodeName().equals(XML_STYLESHEET_NODE)) {
String nodeVal = node.getNodeValue();
logger.logComment("Looking at: " + nodeVal);
String xslFileName =
nodeVal.substring(nodeVal.indexOf("href=\"") + 6, nodeVal.length() - 1);
File xslFile = new File(xslFileName);
return xslFile;
}
if (node.getAttributes().getLength() > 0) {
logger.logComment("Attributes: " + node.getAttributes());
if (node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR) != null) {
String locString = node.getAttributes().getNamedItem(XML_SCHEMA_LOC_ATTR).getNodeValue();
logger.logComment("Loc string: " + locString);
String file = locString.split("\\s")[1];
return new File(file);
}
}
}
logger.logError("No node found with name: " + XML_STYLESHEET_NODE);
return null;
}
public static final Map parseFrame(Node node) {
NodeList bones = node.getChildNodes();
Map bone_infos = new HashMap();
for (int i = 0; i < bones.getLength(); i++) {
Node bone = bones.item(i);
if (bone.getNodeName().equals("transform")) {
String name = bone.getAttributes().getNamedItem("name").getNodeValue();
float[] matrix = new float[16];
matrix[0 * 4 + 0] = getAttrFloat(bone, "m00");
matrix[0 * 4 + 1] = getAttrFloat(bone, "m01");
matrix[0 * 4 + 2] = getAttrFloat(bone, "m02");
matrix[0 * 4 + 3] = getAttrFloat(bone, "m03");
matrix[1 * 4 + 0] = getAttrFloat(bone, "m10");
matrix[1 * 4 + 1] = getAttrFloat(bone, "m11");
matrix[1 * 4 + 2] = getAttrFloat(bone, "m12");
matrix[1 * 4 + 3] = getAttrFloat(bone, "m13");
matrix[2 * 4 + 0] = getAttrFloat(bone, "m20");
matrix[2 * 4 + 1] = getAttrFloat(bone, "m21");
matrix[2 * 4 + 2] = getAttrFloat(bone, "m22");
matrix[2 * 4 + 3] = getAttrFloat(bone, "m23");
matrix[3 * 4 + 0] = getAttrFloat(bone, "m30");
matrix[3 * 4 + 1] = getAttrFloat(bone, "m31");
matrix[3 * 4 + 2] = getAttrFloat(bone, "m32");
matrix[3 * 4 + 3] = getAttrFloat(bone, "m33");
bone_infos.put(name, matrix);
}
}
return bone_infos;
}
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());
}
}
/**
* Get a list of the names for all of the attributes for this node.
*
* @webref xml:method
* @brief Returns a list of names of all attributes as an array
*/
public String[] listAttributes() {
NamedNodeMap nnm = node.getAttributes();
String[] outgoing = new String[nnm.getLength()];
for (int i = 0; i < outgoing.length; i++) {
outgoing[i] = nnm.item(i).getNodeName();
}
return outgoing;
}
public static void traverseAMLforObjectNames(
HashMap partialMap, Node currentNode, HashMap ObjDef_LinkId, HashMap ModelId_ModelType) {
if (currentNode.hasChildNodes()) {
for (int i = 0; i < currentNode.getChildNodes().getLength(); i++) {
Node currentChild = currentNode.getChildNodes().item(i);
if (currentChild.getNodeName().equals("Group")) {
traverseAMLforObjectNames(partialMap, currentChild, ObjDef_LinkId, ModelId_ModelType);
}
if (currentChild.getNodeName().equals("Model")) {
if (currentChild.hasAttributes()) {
String mid = currentChild.getAttributes().getNamedItem("Model.ID").getNodeValue();
String type = currentChild.getAttributes().getNamedItem("Model.Type").getNodeValue();
ModelId_ModelType.put(mid, type);
}
// traverseAMLforObjectNames(partialMap, currentChild,
// ObjDef_LinkId);
}
if (currentChild.getNodeName().equals("ObjDef")) {
String id = currentChild.getAttributes().getNamedItem("ObjDef.ID").getNodeValue();
NodeList currentChildren = currentChild.getChildNodes();
String ObjName = "";
for (int k = 0; k < currentChildren.getLength(); k++) {
Node Child = currentChildren.item(k);
if (!Child.getNodeName().equals("AttrDef")) {
continue;
} else if (!Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
continue;
} else if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
ObjName = getTextContent(Child.getChildNodes().item(l));
ObjName = ObjName.replaceAll("\n", "\\\\n");
break;
}
}
}
}
partialMap.put(id, ObjName);
for (int j = 0; j < currentChild.getAttributes().getLength(); j++) {
if (currentChild.getAttributes().item(j).getNodeName().equals("LinkedModels.IdRefs")) {
String links =
currentChild.getAttributes().getNamedItem("LinkedModels.IdRefs").getNodeValue();
/*
* if (links.indexOf(" ") > -1) {
* Message.add("yes, yes, yes"); links =
* links.substring(0, links.indexOf(" ")); }
*/
ObjDef_LinkId.put(id, links);
}
}
}
}
}
}
public String getAtributo(Node nodo, String nombreAtributo) {
NamedNodeMap atts;
atts = nodo.getAttributes();
if (atts == null) return null;
for (int i = 0; i < atts.getLength(); i++) {
Node atributo = atts.item(i);
if (atributo.getNodeName().equalsIgnoreCase(nombreAtributo)) return atributo.getNodeValue();
}
return null;
}
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;
}
public String getString(String name, String defaultValue) {
NamedNodeMap attrs = node.getAttributes();
if (attrs != null) {
Node attr = attrs.getNamedItem(name);
if (attr != null) {
return attr.getNodeValue();
}
}
return defaultValue;
}
private static final Skeleton parseSkeleton(Node skel_node) {
Map name_to_bone_map = new HashMap();
Map initial_pose =
AnimationLoader.parseFrame(ConvertToBinary.getNodeByName("init_pose", skel_node));
NodeList bone_list = ConvertToBinary.getNodeByName("bones", skel_node).getChildNodes();
Map bone_parent_map = new HashMap();
for (int i = 0; i < bone_list.getLength(); i++) {
Node bone_node = bone_list.item(i);
if (bone_node.getNodeName().equals("bone")) {
String bone_name = bone_node.getAttributes().getNamedItem("name").getNodeValue();
String bone_parent_name = bone_node.getAttributes().getNamedItem("parent").getNodeValue();
// System.out.println("bone name = " + bone_name + " parent name = " + bone_parent_name);
bone_parent_map.put(bone_name, bone_parent_name);
}
}
Map bone_children_map = new HashMap();
Iterator it = bone_parent_map.keySet().iterator();
String root = null;
while (it.hasNext()) {
String name = (String) it.next();
String parent = (String) bone_parent_map.get(name);
if (bone_parent_map.get(parent) == null) {
if (root != null) {
System.out.println(
"WARNING: Multiple roots in skeleton, root = "
+ root
+ ", additional root = "
+ name);
parent = root;
bone_parent_map.put(name, parent);
} else root = name;
}
List parent_children = (List) bone_children_map.get(parent);
if (parent_children == null) {
parent_children = new ArrayList();
bone_children_map.put(parent, parent_children);
}
parent_children.add(name);
}
Bone bone_root = buildBone((byte) 0, bone_children_map, root, name_to_bone_map);
return new Skeleton(bone_root, initial_pose, name_to_bone_map);
}
/** 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();
}
/**
* 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 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)
throw new XmlParserException("Failed to locate a type attribute.");
// ...
// IPeak peak = (_loadall ? parseIPeak(node) : parseCentroid(node));
IPeak peak = parseIPeak(node);
if (peak != null) _listener.onIPeak(peak);
} else if (xpath.equals(XPATH_HEADER)) {
Header header = parseHeader(document.getFirstChild());
_listener.onHeader(header);
}
}
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());
}
}
/**
* @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 final float getAttrFloat(Node node, String name) {
return Float.parseFloat(node.getAttributes().getNamedItem(name).getNodeValue());
}
/**
* @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();
}
}
}
/**
* @param list
* @param document
* @param parent
*/
void addAttributesFromListToNode(AttributeList list, Document document, Node parent) {
DicomDictionary dictionary = list.getDictionary();
Iterator i = list.values().iterator();
while (i.hasNext()) {
Attribute attribute = (Attribute) i.next();
AttributeTag tag = attribute.getTag();
String elementName = dictionary.getNameFromTag(tag);
if (elementName == null) {
elementName = makeElementNameFromHexadecimalGroupElementValues(tag);
}
Node node = document.createElement(elementName);
parent.appendChild(node);
{
Attr attr = document.createAttribute("group");
attr.setValue(HexDump.shortToPaddedHexString(tag.getGroup()));
node.getAttributes().setNamedItem(attr);
}
{
Attr attr = document.createAttribute("element");
attr.setValue(HexDump.shortToPaddedHexString(tag.getElement()));
node.getAttributes().setNamedItem(attr);
}
{
Attr attr = document.createAttribute("vr");
attr.setValue(ValueRepresentation.getAsString(attribute.getVR()));
node.getAttributes().setNamedItem(attr);
}
if (attribute instanceof SequenceAttribute) {
int count = 0;
Iterator si = ((SequenceAttribute) attribute).iterator();
while (si.hasNext()) {
SequenceItem item = (SequenceItem) si.next();
Node itemNode = document.createElement("Item");
Attr numberAttr = document.createAttribute("number");
numberAttr.setValue(Integer.toString(++count));
itemNode.getAttributes().setNamedItem(numberAttr);
node.appendChild(itemNode);
addAttributesFromListToNode(item.getAttributeList(), document, itemNode);
}
} else {
// Attr attr = document.createAttribute("value");
// attr.setValue(attribute.getDelimitedStringValuesOrEmptyString());
// node.getAttributes().setNamedItem(attr);
// node.appendChild(document.createTextNode(attribute.getDelimitedStringValuesOrEmptyString()));
String values[] = null;
try {
values = attribute.getStringValues();
} catch (DicomException e) {
// e.printStackTrace(System.err);
}
if (values != null) {
for (int j = 0; j < values.length; ++j) {
Node valueNode = document.createElement("value");
Attr numberAttr = document.createAttribute("number");
numberAttr.setValue(Integer.toString(j + 1));
valueNode.getAttributes().setNamedItem(numberAttr);
valueNode.appendChild(document.createTextNode(values[j]));
node.appendChild(valueNode);
}
}
}
}
}
/**
* Returns whether an attribute exists.
*
* @webref xml:method
* @brief Checks whether or not an element has the specified attribute
*/
public boolean hasAttribute(String name) {
return (node.getAttributes().getNamedItem(name) != null);
}
public void serializeNode(Node node, Writer writer, String indentLevel) throws IOException {
// Determine action based on node type
switch (node.getNodeType()) {
case Node.DOCUMENT_NODE:
writer.write("<?xml version = '1.0'?>"); // "<xml version=\"1.0\">");
writer.write(lineSeparator);
// recurse on each child
NodeList nodes = node.getChildNodes();
if (nodes != null) {
for (int i = 0; i < nodes.getLength(); i++) {
serializeNode(nodes.item(i), writer, "");
}
}
/*
* Document doc = (Document)node;
* serializeNode(doc.getDocumentElement( ), writer, " ");
*/
break;
case Node.ELEMENT_NODE:
String name = node.getNodeName();
writer.write(indentLevel + "<" + name);
NamedNodeMap attributes = node.getAttributes();
for (int i = 0; i < attributes.getLength(); i++) {
Node current = attributes.item(i);
writer.write(" " + current.getNodeName() + "=\"" + current.getNodeValue() + "\"");
}
writer.write(">");
// recurse on each child
NodeList children = node.getChildNodes();
if (children != null) {
if ((children.item(0) != null) && (children.item(0).getNodeType() == Node.ELEMENT_NODE)) {
writer.write(lineSeparator);
}
for (int i = 0; i < children.getLength(); i++) {
serializeNode(children.item(i), writer, indentLevel + indent);
}
if ((children.item(0) != null)
&& (children.item(children.getLength() - 1).getNodeType() == Node.ELEMENT_NODE)) {
writer.write(indentLevel);
}
}
writer.write("</" + name + ">");
writer.write(lineSeparator);
break;
case Node.TEXT_NODE:
writer.write(node.getNodeValue());
break;
case Node.CDATA_SECTION_NODE:
writer.write("<![CDATA[" + node.getNodeValue() + "]]>");
break;
case Node.COMMENT_NODE:
writer.write(indentLevel + "<!-- " + node.getNodeValue() + " -->");
writer.write(lineSeparator);
break;
case Node.PROCESSING_INSTRUCTION_NODE:
writer.write("<?" + node.getNodeName() + " " + node.getNodeValue() + "?>");
writer.write(lineSeparator);
break;
case Node.ENTITY_REFERENCE_NODE:
writer.write("&" + node.getNodeName() + ";");
break;
case Node.DOCUMENT_TYPE_NODE:
DocumentType docType = (DocumentType) node;
writer.write("<!DOCTYPE " + docType.getName());
if (docType.getPublicId() != null) {
System.out.print(" PUBLIC \"" + docType.getPublicId() + "\" ");
} else {
writer.write(" SYSTEM ");
}
writer.write("\"" + docType.getSystemId() + "\">");
writer.write(lineSeparator);
break;
}
}
/**
* Returns the number of attributes.
*
* @webref xml:method
* @brief Counts the specified element's number of attributes
*/
public int getAttributeCount() {
return node.getAttributes().getLength();
}
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;
}
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()));
}
}
}
/** Prints the specified node, recursively. */
public String print(Node node) {
// is there anything to do?
if (node == null) {
return sb.toString();
}
int type = node.getNodeType();
switch (type) {
// print document
case Node.DOCUMENT_NODE:
{
return print(((Document) node).getDocumentElement());
// out.flush();
// break;
}
// print element with attributes
case Node.ELEMENT_NODE:
{
sb.append('<');
sb.append(node.getNodeName());
Attr attrs[] = sortAttributes(node.getAttributes());
for (int i = 0; i < attrs.length; i++) {
Attr attr = attrs[i];
sb.append(' ');
sb.append(attr.getNodeName());
sb.append("=\"");
sb.append(normalize(attr.getNodeValue()));
sb.append('"');
}
sb.append('>');
NodeList children = node.getChildNodes();
if (children != null) {
int len = children.getLength();
for (int i = 0; i < len; i++) {
print(children.item(i));
}
}
break;
}
// handle entity reference nodes
case Node.ENTITY_REFERENCE_NODE:
{
if (canonical) {
NodeList children = node.getChildNodes();
if (children != null) {
int len = children.getLength();
for (int i = 0; i < len; i++) {
print(children.item(i));
}
}
} else {
sb.append('&');
sb.append(node.getNodeName());
sb.append(';');
}
break;
}
// print cdata sections
case Node.CDATA_SECTION_NODE:
{
if (canonical) {
sb.append(normalize(node.getNodeValue()));
} else {
sb.append("<![CDATA[");
sb.append(node.getNodeValue());
sb.append("]]>");
}
break;
}
// print text
case Node.TEXT_NODE:
{
sb.append(normalize(node.getNodeValue()));
break;
}
// print processing instruction
case Node.PROCESSING_INSTRUCTION_NODE:
{
sb.append("<?");
sb.append(node.getNodeName());
String data = node.getNodeValue();
if (data != null && data.length() > 0) {
sb.append(' ');
sb.append(data);
}
sb.append("?>");
break;
}
// handle entity reference nodes
case Node.DOCUMENT_FRAGMENT_NODE:
{
NodeList children = node.getChildNodes();
if (children != null) {
int len = children.getLength();
for (int i = 0; i < len; i++) {
print(children.item(i));
}
}
break;
}
}
if (type == Node.ELEMENT_NODE) {
sb.append("</");
sb.append(node.getNodeName());
sb.append('>');
}
return sb.toString();
} // print(Node)
private static void parseNet(
Node node,
EPC net,
HashMap ObjDef_Name,
HashMap ObjDef_LinkId,
HashMap function_LinkId,
String ModelName)
throws Exception {
HashMap mapping = new HashMap();
// read all nodes
NodeList nodes = node.getChildNodes();
net.setIdentifier(ModelName);
// Message.add("here I am still happy");
for (int i = 0; i < nodes.getLength(); i++) {
Node n = nodes.item(i);
if (!n.getNodeName().equals("ObjOcc")) {
continue;
}
if (n.getAttributes().getNamedItem("SymbolNum") == null) {
continue;
}
String symbolnum = n.getAttributes().getNamedItem("SymbolNum").getNodeValue();
if (!(symbolnum.equals("ST_FUNC")
|| symbolnum.equals("ST_EV")
|| symbolnum.equals("ST_OPR_AND_1")
|| symbolnum.equals("ST_OPR_OR_1")
|| symbolnum.equals("ST_OPR_XOR_1"))) {
continue;
}
String ObjDef = n.getAttributes().getNamedItem("ObjDef.IdRef").getNodeValue();
String ownName = (String) ObjDef_Name.get(ObjDef);
// Message.add("YES " +
// n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue());
String id = n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue();
// Message.add(id + " " + ownName);
if (ownName == null || ownName == "") {
ownName = id.substring(7, 11);
}
if (symbolnum.equals("ST_FUNC")) {
if (ObjDef_LinkId.containsKey(ObjDef)) {
EPCSubstFunction sf =
(EPCSubstFunction)
net.addFunction(
new EPCSubstFunction(new LogEvent(ownName, "unknown:normal"), net, null));
sf.setIdentifier(ownName);
mapping.put(id, sf);
function_LinkId.put(sf, ObjDef_LinkId.get(ObjDef));
} else {
EPCFunction f =
net.addFunction(new EPCFunction(new LogEvent(ownName, "unknown:normal"), net));
f.setIdentifier(ownName);
mapping.put(id, f);
}
} else if (symbolnum.equals("ST_EV")) {
EPCEvent e = net.addEvent(new EPCEvent(ownName, net));
e.setIdentifier(ownName);
mapping.put(id, e);
} else if (symbolnum.equals("ST_OPR_AND_1")) {
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.AND, net));
mapping.put(id, c);
} else if (symbolnum.equals("ST_OPR_OR_1")) {
// EPCConnector c = net.addConnector(new
// EPCConnector(EPCConnector.OR, net));
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.AND, net));
mapping.put(id, c);
} else if (symbolnum.equals("ST_OPR_XOR_1")) {
EPCConnector c = net.addConnector(new EPCConnector(EPCConnector.XOR, net));
mapping.put(id, c);
}
}
for (int i = 0; i < nodes.getLength(); i++) {
Node n = nodes.item(i);
if (!n.getNodeName().equals("ObjOcc")) {
continue;
}
if (n.getAttributes().getNamedItem("SymbolNum") == null) {
continue;
}
String symbolnum = n.getAttributes().getNamedItem("SymbolNum").getNodeValue();
if (!(symbolnum.equals("ST_FUNC")
|| symbolnum.equals("ST_EV")
|| symbolnum.equals("ST_OPR_AND_1")
|| symbolnum.equals("ST_OPR_OR_1")
|| symbolnum.equals("ST_OPR_XOR_1"))) {
continue;
}
String source = n.getAttributes().getNamedItem("ObjOcc.ID").getNodeValue();
if (n.hasChildNodes()) {
for (int j = 0; j < n.getChildNodes().getLength(); j++) {
if (n.getChildNodes().item(j).getNodeName().equals("CxnOcc")) {
Node CxnOcc = n.getChildNodes().item(j);
String dest = CxnOcc.getAttributes().getNamedItem("ToObjOcc.IdRef").getNodeValue();
if (mapping.get(dest) == null) {
continue;
}
if (net.addEdge((EPCObject) mapping.get(source), (EPCObject) mapping.get(dest))
== null) {
throw (new Exception(
"<html>Structural properties of EPCs are violated in input file.<br>"
+ "The following edge could not be added:<br><br>"
+ mapping.get(source).toString()
+ " ==> "
+ mapping.get(dest).toString()
+ "<br><br>Import aborted.</html>"));
}
}
}
}
}
}
public static EPCResult traverseAML(
EPCResult partialResult,
Node currentNode,
Object parent,
HashMap ObjDef_Name,
HashMap ObjDef_LinkId,
HashMap modelid_net,
HashMap function_LinkId)
throws Exception {
if (currentNode.hasChildNodes()) {
for (int i = 0; i < currentNode.getChildNodes().getLength(); i++) {
Node currentChild = currentNode.getChildNodes().item(i);
if (currentChild.getNodeName().equals("Group")) {
String id = currentChild.getAttributes().getNamedItem("Group.ID").getNodeValue();
String GroupName = "";
if (currentChild.hasChildNodes()) {
NodeList currentChildren = currentChild.getChildNodes();
for (int j = 0; j < currentChildren.getLength(); j++) {
Node Child = currentChildren.item(j);
if (!(Child.getNodeName().equals("AttrDef"))) {
continue;
}
if (Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
GroupName = getTextContent(Child.getChildNodes().item(l));
}
}
break;
}
}
}
if (GroupName.equals("")) {
GroupName = id;
}
}
ModelHierarchyDirectory dir = new ModelHierarchyDirectory(id, GroupName);
partialResult.addInHierarchy(dir, parent, GroupName);
partialResult =
traverseAML(
partialResult,
currentChild,
dir,
ObjDef_Name,
ObjDef_LinkId,
modelid_net,
function_LinkId);
}
if (currentChild.getNodeName().equals("Model")
&& currentChild
.getAttributes()
.getNamedItem("Model.Type")
.getNodeValue()
.equals("MT_EEPC")) {
String ModelName = "gaga";
if (currentChild.hasChildNodes()) {
NodeList currentChildren = currentChild.getChildNodes();
for (int j = 0; j < currentChildren.getLength(); j++) {
Node Child = currentChildren.item(j);
if (!(Child.getNodeName().equals("AttrDef"))) {
continue;
}
if (Child.getAttributes()
.getNamedItem("AttrDef.Type")
.getNodeValue()
.equals("AT_NAME")) {
if (Child.hasChildNodes()) {
for (int l = 0; l < Child.getChildNodes().getLength(); l++) {
if (!(Child.getChildNodes().item(l).getNodeName().equals("AttrValue"))) {
continue;
} else {
ModelName = getTextContent(Child.getChildNodes().item(l));
}
}
}
break;
}
}
}
try {
ModelName = ModelName.replaceAll("\n", " ");
EPC net = read(currentChild, ObjDef_Name, ObjDef_LinkId, function_LinkId, ModelName);
partialResult.addInHierarchy(net, parent, ModelName);
modelid_net.put(
currentChild.getAttributes().getNamedItem("Model.ID").getNodeValue(), net);
} catch (Throwable x) {
Message.add(x.getClass().getName());
// throw new IOException(x.getMessage());
}
}
}
}
return partialResult;
}
private static final int getAttrInt(Node node, String name) {
return Integer.parseInt(node.getAttributes().getNamedItem(name).getNodeValue());
}