private static SetInfo parseSet(Node parent) throws XmlParserException {
String id = "";
String type = "";
String measurementids = null;
NodeList nodes = parent.getChildNodes();
Vector<SetInfo> sets = new Vector<SetInfo>();
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("id")) id = element.getTextContent();
else if (element.getTagName().equals("set")) sets.add(parseSet(element));
else if (element.getTagName().equals("type")) type = element.getTextContent();
else if (element.getTagName().equals("measurementids"))
measurementids = element.getTextContent();
}
// create the set
SetInfo set = new SetInfo(id, Integer.parseInt(type));
if (measurementids != null) {
int mids[] = ByteArray.toIntArray(Base64.decode(measurementids), ByteArray.ENDIAN_LITTLE, 32);
for (int mid : mids) set.addMeasurementID(mid);
}
// add the children
for (SetInfo s : sets) set.addChild(s);
return set;
}
private static MeasurementInfo parseMeasurement(Node parent) throws XmlParserException {
String id = "";
String label = "";
String sampleid = "";
Vector<FileInfo> files = null;
Vector<ScanInfo> scans = null;
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("id")) id = element.getTextContent();
else if (element.getTagName().equals("label")) label = element.getTextContent();
else if (element.getTagName().equals("sampleid")) sampleid = element.getTextContent();
else if (element.getTagName().equals("scans")) scans = parseScans(node);
else if (element.getTagName().equals("files")) files = parseFiles(node);
}
MeasurementInfo measurement = new MeasurementInfo(Integer.parseInt(id), sampleid);
measurement.setLabel(label);
measurement.addFileInfos(files);
if (scans != null) measurement.addScanInfos(scans);
return measurement;
}
private static Header parseHeader(Node parent) throws XmlParserException {
Header header = new Header();
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;
try {
if (element.getTagName().equals("nrpeaks"))
header.setNrPeaks(Integer.parseInt(element.getTextContent()));
else if (element.getTagName().equals("date")) header.setDate(element.getTextContent());
else if (element.getTagName().equals("owner")) header.setOwner(element.getTextContent());
else if (element.getTagName().equals("description"))
header.setDescription(element.getTextContent());
else if (element.getTagName().equals("sets")) header.addSetInfos(parseSets(element));
else if (element.getTagName().equals("measurements"))
header.addMeasurementInfos(parseMeasurements(element));
else if (element.getTagName().equals("annotations")) {
Vector<Annotation> annotations = parseAnnotations(element);
if (annotations != null)
for (Annotation annotation : annotations) header.addAnnotation(annotation);
}
} catch (Exception e) {
throw new XmlParserException(
"Invalid value in header (" + element.getTagName() + "): '" + e.getMessage() + "'.");
}
}
return header;
}
/**
* WhiteboardObjectTextJabberImpl constructor.
*
* @param xml the XML string object to parse.
*/
public WhiteboardObjectTextJabberImpl(String xml) {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder;
try {
builder = factory.newDocumentBuilder();
InputStream in = new ByteArrayInputStream(xml.getBytes());
Document doc = builder.parse(in);
Element e = doc.getDocumentElement();
String elementName = e.getNodeName();
if (elementName.equals("text")) {
// we have a text
String id = e.getAttribute("id");
double x = Double.parseDouble(e.getAttribute("x"));
double y = Double.parseDouble(e.getAttribute("y"));
String fill = e.getAttribute("fill");
String fontFamily = e.getAttribute("font-family");
int fontSize = Integer.parseInt(e.getAttribute("font-size"));
String text = e.getTextContent();
this.setID(id);
this.setWhiteboardPoint(new WhiteboardPoint(x, y));
this.setFontName(fontFamily);
this.setFontSize(fontSize);
this.setText(text);
this.setColor(Color.decode(fill).getRGB());
}
} catch (ParserConfigurationException ex) {
if (logger.isDebugEnabled()) logger.debug("Problem WhiteboardObject : " + xml);
} catch (IOException ex) {
if (logger.isDebugEnabled()) logger.debug("Problem WhiteboardObject : " + xml);
} catch (Exception ex) {
if (logger.isDebugEnabled()) logger.debug("Problem WhiteboardObject : " + xml);
}
}
private static Vector<Annotation> parseAnnotations(Node parent) throws XmlParserException {
Vector<Annotation> annotations = new Vector<Annotation>();
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("annotation")) {
String label = null, value = null, valuetype = null, unit = null;
NodeList annotation_nodes = element.getChildNodes();
for (int annotationid = 0; annotationid < annotation_nodes.getLength(); ++annotationid) {
Node annotation_node = annotation_nodes.item(annotationid);
if (annotation_node.getNodeType() != Node.ELEMENT_NODE) continue;
Element annotation_element = (Element) annotation_node;
if (annotation_element.getTagName().equals("label"))
label = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("value"))
value = annotation_element.getTextContent();
else if (annotation_element.getTagName().equals("valuetype"))
valuetype = annotation_element.getTextContent();
}
if (label == null || value == null || valuetype == null)
throw new XmlParserException("Annotation is missing either: label, value or valuetype");
Annotation annotation =
new Annotation(label, value, Annotation.ValueType.valueOf(valuetype));
annotation.setUnit(unit);
if (annotation.getValueType() == Annotation.ValueType.ONTOLOGY)
annotation.setOntologyRef(element.getAttribute("ontologyref"));
if (element.getAttribute("unit") != null) annotation.setUnit(element.getAttribute("unit"));
annotations.add(annotation);
}
}
return annotations;
}
private static FileInfo parseFile(Node parent) throws XmlParserException {
String label = "";
String name = "";
String location = "";
Vector<Annotation> annotations = null;
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("label")) label = element.getTextContent();
else if (element.getTagName().equals("name")) name = element.getTextContent();
else if (element.getTagName().equals("location")) location = element.getTextContent();
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(node);
}
FileInfo file = new FileInfo(label, name, location);
if (annotations != null) file.addAnnotations(annotations);
return file;
}
private static ScanInfo parseScan(Node parent) throws XmlParserException {
double retentiontime = 0;
Polarity polarity = Polarity.NEUTRAL;
Vector<Annotation> annotations = null;
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("polarity"))
polarity = Polarity.valueOf(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
}
ScanInfo scan = new ScanInfo(retentiontime, polarity);
if (annotations != null) scan.addAnnotations(annotations);
return scan;
}
/**
* Method that reads a XML-file, and returns a Model that contains the information
*
* @param file
* @return
* @return
*/
public static Model readXML(String file) {
// initialize table to be filled with content of XML file
Model t = new Model();
try {
// Create file to be parsed by document parser
File xmlfile = new File(file);
// create parser
DocumentBuilder parser = DocumentBuilderFactory.newInstance().newDocumentBuilder();
// parse the file
Document parsedfile = parser.parse(xmlfile);
// normalize the parsed file (make it more user-friendly)
parsedfile.getDocumentElement().normalize();
NodeList cells = parsedfile.getElementsByTagName("CELL");
for (int i = 0; i < cells.getLength(); i++) {
// Get cell at list index i
Node currentcell = cells.item(i);
// read the elements "location" attributes row/column
if (Node.ELEMENT_NODE == currentcell.getNodeType()) {
Element cellinfo = (Element) currentcell;
// get the row number from node attribute
int row = Integer.parseInt(cellinfo.getAttribute("row")) - 1;
// get the column number from the node attribute
int col = Integer.parseInt(cellinfo.getAttribute("column")) - 1;
// get content from node
String content = cellinfo.getTextContent();
if (content != null) {
content = content.replace("\n", "");
}
// Make the content an Integer (if it is a number), easier
// for
// using it later on
// put content in table, with row/column inserted as x/y
t.setContent(row, col, (String) content);
}
}
} catch (ParserConfigurationException e) {
System.out.println("Fileparser could not be made");
} catch (IOException f) {
System.out.println("File could not be parsed, did you enter the correct file name?");
} catch (SAXException g) {
System.out.println("Something went wrong in parsing the file");
}
return t;
}
private static void parseIPeak(Node parent, IPeak peak) throws XmlParserException {
// retrieve all the properties
int scan = -1;
double retentiontime = -1;
double mass = -1;
double intensity = -1;
int patternid = -1;
int measurementid = -1;
// String sha1 = null;
Vector<Annotation> annotations = null;
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("patternid"))
patternid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("measurementid"))
measurementid = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("annotations")) annotations = parseAnnotations(element);
else if (element.getTagName().equals("scan"))
scan = Integer.parseInt(element.getTextContent());
else if (element.getTagName().equals("retentiontime"))
retentiontime = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("mass"))
mass = Double.parseDouble(element.getTextContent());
else if (element.getTagName().equals("intensity"))
intensity = Double.parseDouble(element.getTextContent());
// else if (element.getTagName().equals("sha1sum"))
// sha1 = element.getTextContent();
}
// check whether obligatory values are missing
if (mass == -1 || intensity == -1)
throw new XmlParserException("Mass and/or intensity information is missing for IPeak.");
peak.setScanID(scan);
peak.setRetentionTime(retentiontime);
peak.setMass(mass);
peak.setIntensity(intensity);
peak.setPatternID(patternid);
peak.setMeasurementID(measurementid);
if (annotations != null)
for (Annotation annotation : annotations) peak.addAnnotation(annotation);
// check whether
// if (sha1!=null && !sha1.equals(peak.sha1()))
// throw new XmlParserException("SHA1-sum for individual ipeak element does not match.");
}
public String getFolderName(String pageCode) {
String usefulSection =
pageCode.substring(
pageCode.indexOf("<h3 id=\"breadcrumb\">"),
pageCode.indexOf("<div id=\"list-view\" class=\"view\""));
String folderName;
try {
DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(usefulSection));
Document doc = db.parse(is);
NodeList divs = doc.getElementsByTagName("h3");
for (int i = 0; i < divs.getLength(); i++) {
Element div = (Element) divs.item(i);
String a = div.getTextContent();
folderName = a.substring(a.indexOf("/>") + 2).trim();
return folderName;
}
} catch (Exception e) {
debug(e.toString());
}
return "Error!";
}
public boolean runTest(Test test) throws Exception {
String filename = test.file.toString();
if (this.verbose) {
System.out.println(
"Running "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
this.document = parseDocument(filename);
if (this.baseUrl == null) {
NodeList links = this.document.getElementsByTagName("link");
if (links.getLength() != 0) {
Element link = (Element) links.item(0);
setBaseUrl(link.getAttribute("href"));
}
}
if (this.verbose) {
System.out.println("Base URL=" + this.baseUrl);
}
Node body = this.document.getElementsByTagName("body").item(0);
Element resultContainer = document.createElement("div");
resultContainer.setTextContent("Result: ");
Element resultElt = document.createElement("span");
resultElt.setAttribute("id", "result");
resultElt.setIdAttribute("id", true);
resultContainer.appendChild(resultElt);
body.insertBefore(resultContainer, body.getFirstChild());
Element executionLogContainer = document.createElement("div");
executionLogContainer.setTextContent("Execution Log:");
Element executionLog = document.createElement("div");
executionLog.setAttribute("id", "log");
executionLog.setIdAttribute("id", true);
executionLog.setAttribute("style", "white-space: pre;");
executionLogContainer.appendChild(executionLog);
body.appendChild(executionLogContainer);
NodeList tableRows = document.getElementsByTagName("tr");
Element theadRow = (Element) tableRows.item(0);
test.name = theadRow.getTextContent();
appendCellToRow(theadRow, "Result");
this.commandProcessor =
new HtmlCommandProcessor(this.host, this.port, this.browser, this.baseUrl);
String resultState;
String resultLog;
test.result = true;
try {
this.commandProcessor.start();
test.commands = new Command[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element stepRow = (Element) tableRows.item(i);
Command command = executeStep(stepRow);
appendCellToRow(stepRow, command.result);
test.commands[i - 1] = command;
if (command.error) {
test.result = false;
}
if (command.failure) {
test.result = false;
// break;
}
}
resultState = test.result ? "PASSED" : "FAILED";
resultLog = (test.result ? "Test Complete" : "Error");
this.commandProcessor.stop();
} catch (Exception e) {
test.result = false;
resultState = "ERROR";
resultLog = "Failed to initialize session\n" + e;
e.printStackTrace();
}
document.getElementById("result").setTextContent(resultState);
Element log = document.getElementById("log");
log.setTextContent(log.getTextContent() + resultLog + "\n");
return test.result;
}
public boolean runSuite(String filename) throws Exception {
if (this.verbose) {
System.out.println(
"Running test suite "
+ filename
+ " against "
+ this.host
+ ":"
+ this.port
+ " with "
+ this.browser);
}
TestSuite suite = new TestSuite();
long start = System.currentTimeMillis();
suite.numTestPasses = 0;
suite.file = new File(filename);
File suiteDirectory = suite.file.getParentFile();
this.document = parseDocument(filename);
Element table = (Element) this.document.getElementsByTagName("table").item(0);
NodeList tableRows = table.getElementsByTagName("tr");
Element tableNameRow = (Element) tableRows.item(0);
suite.name = tableNameRow.getTextContent();
suite.result = true;
suite.tests = new Test[tableRows.getLength() - 1];
for (int i = 1; i < tableRows.getLength(); i++) {
Element tableRow = (Element) tableRows.item(i);
Element cell = (Element) tableRow.getElementsByTagName("td").item(0);
Element link = (Element) cell.getElementsByTagName("a").item(0);
Test test = new Test();
test.label = link.getTextContent();
test.file = new File(suiteDirectory, link.getAttribute("href"));
SeleniumHtmlClient subclient = new SeleniumHtmlClient();
subclient.setHost(this.host);
subclient.setPort(this.port);
subclient.setBrowser(this.browser);
// subclient.setResultsWriter(this.resultsWriter);
subclient.setBaseUrl(this.baseUrl);
subclient.setVerbose(this.verbose);
subclient.runTest(test);
if (test.result) {
suite.numTestPasses++;
}
suite.result &= test.result;
suite.tests[i - 1] = test;
}
long end = System.currentTimeMillis();
suite.totalTime = (end - start) / 1000;
if (this.resultsWriter != null) {
this.resultsWriter.write("<html><head>\n");
this.resultsWriter.write("<style type='text/css'>\n");
this.resultsWriter.write(
"body, table {font-family: Verdana, Arial, sans-serif;font-size: 12;}\n");
this.resultsWriter.write("table {border-collapse: collapse;border: 1px solid #ccc;}\n");
this.resultsWriter.write("th, td {padding-left: 0.3em;padding-right: 0.3em;}\n");
this.resultsWriter.write("a {text-decoration: none;}\n");
this.resultsWriter.write(".title {font-style: italic;}");
this.resultsWriter.write(".selected {background-color: #ffffcc;}\n");
this.resultsWriter.write(".status_done {background-color: #eeffee;}\n");
this.resultsWriter.write(".status_passed {background-color: #ccffcc;}\n");
this.resultsWriter.write(".status_failed {background-color: #ffcccc;}\n");
this.resultsWriter.write(
".breakpoint {background-color: #cccccc;border: 1px solid black;}\n");
this.resultsWriter.write("</style>\n");
this.resultsWriter.write("<title>" + suite.name + "</title>\n");
this.resultsWriter.write("</head><body>\n");
this.resultsWriter.write("<h1>Test suite results </h1>\n\n");
this.resultsWriter.write("<table>\n");
this.resultsWriter.write(
"<tr>\n<td>result:</td>\n<td>" + (suite.result ? "passed" : "failed") + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>totalTime:</td>\n<td>" + suite.totalTime + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestTotal:</td>\n<td>" + suite.tests.length + "</td>\n</tr>\n");
this.resultsWriter.write(
"<tr>\n<td>numTestPasses:</td>\n<td>" + suite.numTestPasses + "</td>\n</tr>\n");
int numTestFailures = suite.tests.length - suite.numTestPasses;
this.resultsWriter.write(
"<tr>\n<td>numTestFailures:</td>\n<td>" + numTestFailures + "</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandPasses:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandFailures:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>numCommandErrors:</td>\n<td>0</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Version:</td>\n<td>2.24</td>\n</tr>\n");
this.resultsWriter.write("<tr>\n<td>Selenium Revision:</td>\n<td>.1</td>\n</tr>\n");
// test suite
this.resultsWriter.write("<tr>\n<td>\n");
this.resultsWriter.write(
"<table id=\"suiteTable\" class=\"selenium\" border=\"1\" cellpadding=\"1\" cellspacing=\"1\"><tbody>\n");
this.resultsWriter.write(
"<tr class=\"title "
+ (suite.result ? "status_passed" : "status_failed")
+ "\"><td><b>Test Suite</b></td></tr>\n");
int i = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr class=\""
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td><a href=\"#testresult"
+ i
+ "\">"
+ test.name
+ "</a></td></tr>");
i++;
}
this.resultsWriter.write(
"</tbody></table>\n</td>\n<td> </td>\n</tr>\n</table>\n<table>");
int j = 0;
for (Test test : suite.tests) {
this.resultsWriter.write(
"<tr><td><a name=\"testresult" + j + "\">" + test.file + "</a><br/><div>\n");
this.resultsWriter.write("<table border=\"1\" cellpadding=\"1\" cellspacing=\"1\">\n");
this.resultsWriter.write(
"<thead>\n<tr class=\"title "
+ (test.result ? "status_passed" : "status_failed")
+ "\"><td rowspan=\"1\" colspan=\"3\">"
+ test.name
+ "</td></tr>");
this.resultsWriter.write("</thead><tbody>\n");
for (Command command : test.commands) {
boolean result = command.result.startsWith("OK");
boolean isAssert = command.cmd.startsWith("assert") || command.cmd.startsWith("verify");
;
if (!isAssert) {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_done" : "") + "\">\n<td>\n");
} else {
this.resultsWriter.write(
"<tr class=\"" + (result ? "status_passed" : "status_failed") + "\">\n<td>\n");
}
this.resultsWriter.write(command.cmd);
this.resultsWriter.write("</td>\n");
if (command.args != null) {
for (String arg : Arrays.asList(command.args)) {
this.resultsWriter.write("<td>" + arg + "</td>\n");
}
}
}
this.resultsWriter.write("</tr>\n");
this.resultsWriter.write("</tbody></table>\n");
this.resultsWriter.write("</div></td>\n<td> </td>\n</tr>");
j++;
}
int k = 0;
for (Test test : suite.tests) {
k++;
}
this.resultsWriter.write("</tbody></table>\n</td><td> </td>\n</tr>\n</table>\n");
this.resultsWriter.write("</body></html>");
}
return suite.result;
}
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;
}
public void addPackageClass(PackageClass pClass) {
Document doc;
try {
doc = getDocument();
} catch (Exception e) {
e.printStackTrace();
return;
}
String name = pClass.getName();
// check if such class exists and remove duplicates
Element rootEl = doc.getDocumentElement();
NodeList classEls = rootEl.getElementsByTagName(EL_CLASS);
for (int i = 0; i < classEls.getLength(); i++) {
Element nameEl = getElementByName((Element) classEls.item(i), EL_NAME);
if (name.equals(nameEl.getTextContent())) {
rootEl.removeChild(classEls.item(i));
}
}
Element classNode = doc.createElement(EL_CLASS);
doc.getDocumentElement().appendChild(classNode);
classNode.setAttribute(ATR_TYPE, PackageClass.ComponentType.SCHEME.getXmlName());
classNode.setAttribute(ATR_STATIC, "false");
Element className = doc.createElement(EL_NAME);
className.setTextContent(name);
classNode.appendChild(className);
Element desrc = doc.createElement(EL_DESCRIPTION);
desrc.setTextContent(pClass.getDescription());
classNode.appendChild(desrc);
Element icon = doc.createElement(EL_ICON);
icon.setTextContent(pClass.getIcon());
classNode.appendChild(icon);
// graphics
classNode.appendChild(generateGraphicsNode(doc, pClass.getGraphics()));
// ports
List<Port> ports = pClass.getPorts();
if (!ports.isEmpty()) {
Element portsEl = doc.createElement(EL_PORTS);
classNode.appendChild(portsEl);
for (Port port : ports) {
portsEl.appendChild(generatePortNode(doc, port));
}
}
// fields
Collection<ClassField> fields = pClass.getFields();
if (!fields.isEmpty()) {
Element fieldsEl = doc.createElement(EL_FIELDS);
classNode.appendChild(fieldsEl);
for (ClassField cf : fields) {
fieldsEl.appendChild(generateFieldNode(doc, cf));
}
}
// write
try {
writeDocument(doc, new FileOutputStream(xmlFile));
} catch (FileNotFoundException e) {
e.printStackTrace();
}
}
private PackageClass parseClass(Element classNode) {
PackageClass newClass = new PackageClass();
_package.getClasses().add(newClass);
newClass.setComponentType(PackageClass.ComponentType.getType(classNode.getAttribute(ATR_TYPE)));
newClass.setStatic(Boolean.parseBoolean(classNode.getAttribute(ATR_STATIC)));
newClass.setName(getElementByName(classNode, EL_NAME).getTextContent());
final String source = getElementStringByName(classNode, EL_FILE);
if (source != null) {
newClass.setSource(source);
}
newClass.setTarget(getElementStringByName(classNode, EL_EXTENDS));
newClass.setDescription(getElementByName(classNode, EL_DESCRIPTION).getTextContent());
newClass.setIcon(getElementByName(classNode, EL_ICON).getTextContent());
// parse all variables declared in the corresponding specification
if (newClass.getComponentType().hasSpec()) {
final String newClassName = newClass.getName();
try {
switch (RuntimeProperties.getSpecParserKind()) {
case REGEXP:
{
ClassList classList = new ClassList();
SpecParser.parseSpecClass(newClassName, getWorkingDir(), classList);
newClass.setSpecFields(classList.getType(newClassName).getFields());
break;
}
case ANTLR:
{
if (specificationLoader == null) {
specificationLoader =
new SpecificationLoader(new PackageSpecSourceProvider(_package), null);
}
final AnnotatedClass annotatedClass =
specificationLoader.getSpecification(newClassName);
newClass.setSpecFields(annotatedClass.getFields());
break;
}
default:
throw new IllegalStateException("Undefined specification language parser");
}
} catch (SpecParseException e) {
final String msg = "Unable to parse the specification of class " + newClassName;
logger.error(msg, e);
collector.collectDiagnostic(msg + "\nReason: " + e.getMessage() + "\nLine: " + e.getLine());
}
}
// Graphics
Element grNode = getElementByName(classNode, EL_GRAPHICS);
newClass.addGraphics(
getGraphicsParser().parse(grNode/*, newClass.getComponentType() == ComponentType.REL*/ ));
Element painter;
if ((painter = getElementByName(grNode, EL_PAINTER)) != null) {
newClass.setPainterName(painter.getTextContent());
}
// Ports
NodeList ports = classNode.getElementsByTagName(EL_PORT);
for (int i = 0; i < ports.getLength(); i++) {
parsePort(newClass, (Element) ports.item(i));
}
// Fields
NodeList fields = classNode.getElementsByTagName(EL_FIELD);
for (int i = 0; i < fields.getLength(); i++) {
parseField(newClass, (Element) fields.item(i));
}
return newClass;
}
private String getElementStringByName(Element root, String name) {
Element element;
return (element = getElementByName(root, name)) != null ? element.getTextContent() : null;
}