/**
* Process a single session element node.
*
* @param session
* @param element
*/
private void process(Session session, Node element, HashMap additionalInformation) {
if ((element == null) || (session == null)) {
return;
}
String nodeName = element.getNodeName();
if (nodeName.equalsIgnoreCase(SessionElement.RESOURCES.getText())
|| nodeName.equalsIgnoreCase(SessionElement.FILES.getText())) {
processResources(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.RESOURCE.getText())
|| nodeName.equalsIgnoreCase(SessionElement.DATA_FILE.getText())) {
processResource(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.REGIONS.getText())) {
processRegions(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.REGION.getText())) {
processRegion(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.GENE_LIST.getText())) {
processGeneList(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.FILTER.getText())) {
processFilter(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.FILTER_ELEMENT.getText())) {
processFilterElement(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALES.getText())) {
processColorScales(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALE.getText())) {
processColorScale(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.PREFERENCES.getText())) {
processPreferences(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.DATA_TRACKS.getText())
|| nodeName.equalsIgnoreCase(SessionElement.FEATURE_TRACKS.getText())
|| nodeName.equalsIgnoreCase(SessionElement.PANEL.getText())) {
processPanel(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.PANEL_LAYOUT.getText())) {
processPanelLayout(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.HIDDEN_ATTRIBUTES.getText())) {
processHiddenAttributes(session, (Element) element, additionalInformation);
} else if (nodeName.equalsIgnoreCase(SessionElement.VISIBLE_ATTRIBUTES.getText())) {
processVisibleAttributes(session, (Element) element, additionalInformation);
}
}
private void processResource(Session session, Element element, HashMap additionalInformation) {
String nodeName = element.getNodeName();
boolean oldSession = nodeName.equals(SessionElement.DATA_FILE.getText());
String label = getAttribute(element, SessionAttribute.LABEL.getText());
String name = getAttribute(element, SessionAttribute.NAME.getText());
String sampleId = getAttribute(element, SessionAttribute.SAMPLE_ID.getText());
String description = getAttribute(element, SessionAttribute.DESCRIPTION.getText());
String type = getAttribute(element, SessionAttribute.TYPE.getText());
String coverage = getAttribute(element, SessionAttribute.COVERAGE.getText());
String trackLine = getAttribute(element, SessionAttribute.TRACK_LINE.getText());
String colorString = getAttribute(element, SessionAttribute.COLOR.getText());
String relPathValue = getAttribute(element, SessionAttribute.RELATIVE_PATH.getText());
boolean isRelativePath = ((relPathValue != null) && relPathValue.equalsIgnoreCase("true"));
String serverURL = getAttribute(element, SessionAttribute.SERVER_URL.getText());
// Older sessions used the "name" attribute for the path.
String path = getAttribute(element, SessionAttribute.PATH.getText());
if (oldSession && name != null) {
path = name;
int idx = name.lastIndexOf("/");
if (idx > 0 && idx + 1 < name.length()) {
name = name.substring(idx + 1);
}
}
ResourceLocator resourceLocator;
if (isRelativePath) {
final String sessionPath = session.getPath();
String absolutePath;
if (sessionPath == null) {
log.error("Null session path -- this is not expected");
MessageUtils.showMessage("Unexpected error loading session: null session path");
return;
}
absolutePath = FileUtils.getAbsolutePath(path, sessionPath);
fullToRelPathMap.put(absolutePath, path);
resourceLocator = new ResourceLocator(serverURL, absolutePath);
// If the resourceLocator is relative, we assume coverage is as well
if (coverage != null) {
String absoluteCoveragePath = FileUtils.getAbsolutePath(coverage, sessionPath);
resourceLocator.setCoverage(absoluteCoveragePath);
}
} else {
resourceLocator = new ResourceLocator(serverURL, path);
resourceLocator.setCoverage(coverage);
}
String url = getAttribute(element, SessionAttribute.URL.getText());
if (url == null) {
url = getAttribute(element, SessionAttribute.FEATURE_URL.getText());
}
resourceLocator.setUrl(url);
String infolink = getAttribute(element, SessionAttribute.HYPERLINK.getText());
if (infolink == null) {
infolink = getAttribute(element, SessionAttribute.INFOLINK.getText());
}
resourceLocator.setInfolink(infolink);
// Label is deprecated in favor of name.
if (name != null) {
resourceLocator.setName(name);
} else {
resourceLocator.setName(label);
}
resourceLocator.setSampleId(sampleId);
resourceLocator.setDescription(description);
// This test added to get around earlier bug in the writer
if (type != null && !type.equals("local")) {
resourceLocator.setType(type);
}
resourceLocator.setCoverage(coverage);
resourceLocator.setTrackLine(trackLine);
if (colorString != null) {
try {
Color c = ColorUtilities.stringToColor(colorString);
resourceLocator.setColor(c);
} catch (Exception e) {
log.error("Error setting color: ", e);
}
}
dataFiles.add(resourceLocator);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
}
