/**
* Can annotate SVG heatmap.plus charts made by R. Reads and writes using StAX, adding row and col
* attributes to <path> elements corresponding to data points in the heatmap. All indexes can be
* calculated using nRow, nCol, nRowAnnotations and nColAnnotations.
*
* @param chart
* @throws FactoryConfigurationError
* @throws XMLStreamException
* @throws FileNotFoundException
*/
public void annotateHeatMap(HeatMapChart chart)
throws XMLStreamException, FactoryConfigurationError, FileNotFoundException {
XMLEventReader reader =
XMLInputFactory.newInstance().createXMLEventReader(new FileInputStream(inFile));
OutputStream os = new FileOutputStream(outFile);
XMLEventWriter writer = XMLOutputFactory.newInstance().createXMLEventWriter(os);
// get values from HeatMapChart
int nRow = chart.getData().getRowTargets().size();
int nCol = chart.getData().getColumnTargets().size();
// TODO get from HeatMapChart:
int nRowAnnotations = 0;
int nColAnnotations = 0;
// skip the headers and <def> bit until we reach <g id="">
while (true) {
XMLEvent event = (XMLEvent) reader.next();
if (event.isStartElement()) {
StartElement se = event.asStartElement();
if (se.getName().getLocalPart().equals(G) && se.getAttributeByName(ID) != null) {
LOG.info("<g id=\"\"> reached");
writer.add(event);
break;
}
}
writer.add(event);
}
// annotation begins here
// ROW ANNOTATIONS
if (nRowAnnotations > 0) {
LOG.info("parsing " + nRowAnnotations + " row annotations");
annotateHeatMapBlock(nRow, nRowAnnotations, "rowAnnotation", writer, reader);
}
// COLUMN ANNOTATIONS
if (nColAnnotations > 0) {
LOG.info("parsing " + nColAnnotations + " col annotations");
annotateHeatMapBlock(nColAnnotations, nCol, "colAnnotatation", writer, reader);
}
// MATRIX ANNOTATIONS
LOG.info("parsing " + (nRow * nCol) + " matrix values");
annotateHeatMapBlock(nRow, nCol, "matrix", writer, reader);
// COLUMN NAMES
LOG.info("parsing " + nCol + " column names");
int counter = 0;
while (counter < nCol) {
XMLEvent event = (XMLEvent) reader.next();
if (event.isStartElement() && event.asStartElement().getName().getLocalPart().equals(G)) {
@SuppressWarnings("unchecked")
Iterator<Attribute> attributes = event.asStartElement().getAttributes();
StartElement newSe = eventFactory.createStartElement(new QName(G), attributes, null);
writer.add(newSe);
writer.add(eventFactory.createAttribute(ID, "colName"));
writer.add(eventFactory.createAttribute(new QName("col"), Integer.toString(counter + 1)));
counter++;
} else {
writer.add(event);
}
}
// ROW NAMES
LOG.info("parsing " + nRow + " row names");
counter = 0;
while (counter < nRow) {
XMLEvent event = (XMLEvent) reader.next();
if (event.isStartElement() && event.asStartElement().getName().getLocalPart().equals(G)) {
@SuppressWarnings("unchecked")
Iterator<Attribute> attributes = event.asStartElement().getAttributes();
StartElement newSe = eventFactory.createStartElement(new QName(G), attributes, null);
writer.add(newSe);
writer.add(eventFactory.createAttribute(ID, "rowName"));
writer.add(
eventFactory.createAttribute(new QName("row"), Integer.toString(nRow - counter)));
counter++;
} else {
writer.add(event);
}
}
// finish rest of file
while (reader.hasNext()) {
XMLEvent event = (XMLEvent) reader.next();
if (event.isEndElement()) {
// close the <g id=""> tag, right before the </svg> end element
if (event.asEndElement().getName().getLocalPart().equals("svg")) {
EndElement newEe = eventFactory.createEndElement(new QName(G), null);
writer.add(newEe);
}
}
writer.add(event);
}
writer.close();
}
public void doFilter(
ServletRequest servletRequest, ServletResponse servletResponse, FilterChain chain)
throws IOException, ServletException {
HttpServletRequest request = (HttpServletRequest) servletRequest;
RequestURIParts parts = parseParts(request);
if (parts != null) {
String realBaseAddress = parts.getBaseAddress();
String idlPath = parts.getFilePath();
InputStream idl = this.servletContext.getResourceAsStream(idlPath);
if (idl != null) {
servletResponse.setContentType("text/xml");
String assumedBaseAddress = null;
try {
XMLEventReader eventReader = this.inputFactory.createXMLEventReader(idl);
XMLEventWriter eventWriter =
this.outputFactory.createXMLEventWriter(servletResponse.getWriter());
while (eventReader.hasNext()) {
XMLEvent event = eventReader.nextEvent();
if (event.isProcessingInstruction()) {
String target = ((ProcessingInstruction) event).getTarget();
if ("enunciate-assumed-base-uri".equals(target)) {
assumedBaseAddress = ((ProcessingInstruction) event).getData();
if (assumedBaseAddress.endsWith("/")) {
assumedBaseAddress =
assumedBaseAddress.substring(0, assumedBaseAddress.length() - 1);
}
}
continue;
} else if (event.getEventType() == XMLStreamConstants.CDATA
|| event.getEventType() == XMLStreamConstants.CHARACTERS) {
String data = ((Characters) event).getData();
if (assumedBaseAddress != null && data.contains(assumedBaseAddress)) {
data = data.replace(assumedBaseAddress, realBaseAddress);
event = new DelegatingCharacters(((Characters) event), data);
}
} else if (event.getEventType() == XMLStreamConstants.START_ELEMENT) {
List<Attribute> attributes = new ArrayList<Attribute>();
Iterator attributesIt = ((StartElement) event).getAttributes();
while (attributesIt.hasNext()) {
Attribute attribute = (Attribute) attributesIt.next();
String value = attribute.getValue();
if (assumedBaseAddress != null && value.contains(assumedBaseAddress)) {
value = value.replace(assumedBaseAddress, realBaseAddress);
attribute = new DelegatingAttribute(attribute, value);
event = new DelegatingStartElement(((StartElement) event), attributes);
}
attributes.add(attribute);
}
}
eventWriter.add(event);
}
eventReader.close();
eventWriter.flush();
eventWriter.close();
return;
} catch (XMLStreamException e) {
throw new ServletException(e);
}
}
}
chain.doFilter(servletRequest, servletResponse);
}