@Override
public VPackage parse() {
logger.debug("Starting parsing package: " + xmlFile.getAbsolutePath());
long startParsing = System.currentTimeMillis();
try {
Document document = getDocument();
Element root = document.getDocumentElement();
_package = new VPackage(xmlFile);
Node name = root.getElementsByTagName(EL_NAME).item(0);
_package.setName(name.getTextContent());
Node descr = root.getElementsByTagName(EL_DESCRIPTION).item(0);
_package.setDescription(descr.getTextContent());
NodeList list = root.getElementsByTagName(EL_CLASS);
boolean initPainters = false;
for (int i = 0; i < list.getLength(); i++) {
PackageClass pc = parseClass((Element) list.item(i));
if (pc.getPainterName() != null) {
initPainters = true;
}
}
if (initPainters) {
_package.initPainters();
}
logger.info(
"Parsing the package '{}' finished in {}ms.\n",
_package.getName(),
(System.currentTimeMillis() - startParsing));
} catch (Exception e) {
collector.collectDiagnostic(e.getMessage(), true);
if (RuntimeProperties.isLogDebugEnabled()) {
e.printStackTrace();
}
}
try {
checkProblems("Error parsing package file " + xmlFile.getName());
} catch (Exception e) {
return null;
}
return _package;
}
public double getDoubleContent(double defaultValue) {
String c = node.getTextContent();
if (c != null) {
try {
return Double.parseDouble(c);
} catch (NumberFormatException nfe) {
}
}
return defaultValue;
}
public long getLongContent(long defaultValue) {
String c = node.getTextContent();
if (c != null) {
try {
return Long.parseLong(c);
} catch (NumberFormatException nfe) {
}
}
return defaultValue;
}
private void call(Node operation)
throws ParserConfigurationException, TransformerConfigurationException {
String opName = operation.getNodeName();
if (opName.equals("call")) {
String script =
Utils.combine(Utils.getParentDir(this.currentScript), operation.getTextContent());
call(script);
} else if (opName.equals("apply")) processApply(operation);
else if (opName.equals("xml")) processXml(operation);
else if (opName.equals("txt")) processTxt(operation);
else if (opName.equals("copy")) processCopy(operation);
else if (opName.equals("delete")) processDelete(operation);
}
private void processDelete(Node operation) {
String path = absolutePath(operation.getTextContent());
File target = new File(path);
if (!target.exists()) {
Utils.onError(new Error.FileNotFound(target.getPath()));
return;
}
try {
if (target.isDirectory()) {
FileUtils.deleteDirectory(target);
} else {
FileUtils.forceDelete(target);
}
} catch (IOException ex) {
Utils.onError(new Error.FileDelete(target.getPath()));
}
}
/**
* @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 defaultValue the default value of the attribute */
public float getFloatContent(float defaultValue) {
return PApplet.parseFloat(node.getTextContent(), defaultValue);
}
/** @param defaultValue the default value of the attribute */
public int getIntContent(int defaultValue) {
return PApplet.parseInt(node.getTextContent(), defaultValue);
}
public String getContent(String defaultValue) {
String s = node.getTextContent();
return (s != null) ? s : defaultValue;
}
/**
* Return the #PCDATA content of the element. If the element has a combination of #PCDATA content
* and child elements, the #PCDATA sections can be retrieved as unnamed child objects. In this
* case, this method returns null.
*
* @webref xml:method
* @brief Gets the content of an element
* @return the content.
* @see XML#getIntContent()
* @see XML#getFloatContent()
*/
public String getContent() {
return node.getTextContent();
}
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()));
}
}
}
