/**
* @param inputStream
* @param session
* @param sessionName @return
* @throws RuntimeException
*/
public void loadSession(InputStream inputStream, Session session, String sessionName) {
log.debug("Load session");
Document document = null;
try {
document = Utilities.createDOMDocumentFromXmlStream(inputStream);
} catch (Exception e) {
log.error("Load session error", e);
throw new RuntimeException(e);
}
NodeList tracks = document.getElementsByTagName("Track");
hasTrackElments = tracks.getLength() > 0;
HashMap additionalInformation = new HashMap();
additionalInformation.put(INPUT_FILE_KEY, sessionName);
NodeList nodes = document.getElementsByTagName(SessionElement.GLOBAL.getText());
if (nodes == null || nodes.getLength() == 0) {
nodes = document.getElementsByTagName(SessionElement.SESSION.getText());
}
processRootNode(session, nodes.item(0), additionalInformation);
// Add tracks not explicitly allocated to panels. It is legal to define sessions with the
// Resources
// section only (no Panel or Track elements).
addLeftoverTracks(trackDictionary.values());
if (session.getGroupTracksBy() != null && session.getGroupTracksBy().length() > 0) {
igv.setGroupByAttribute(session.getGroupTracksBy());
}
if (session.isRemoveEmptyPanels()) {
igv.getMainPanel().removeEmptyDataPanels();
}
igv.resetOverlayTracks();
}
private void processRootNode(Session session, Node node, HashMap additionalInformation) {
if ((node == null) || (session == null)) {
MessageUtils.showMessage("Invalid session file: root node not found");
return;
}
String nodeName = node.getNodeName();
if (!(nodeName.equalsIgnoreCase(SessionElement.GLOBAL.getText())
|| nodeName.equalsIgnoreCase(SessionElement.SESSION.getText()))) {
MessageUtils.showMessage(
"Session files must begin with a \"Global\" or \"Session\" element. Found: " + nodeName);
}
process(session, node, additionalInformation);
Element element = (Element) node;
// Load the genome, which can be an ID, or a path or URL to a .genome or indexed fasta file.
String genomeId = getAttribute(element, SessionAttribute.GENOME.getText());
if (genomeId != null && genomeId.length() > 0) {
if (genomeId.equals(GenomeManager.getInstance().getGenomeId())) {
// We don't have to reload the genome, but the gene track for the current genome should be
// restored.
Genome genome = GenomeManager.getInstance().getCurrentGenome();
IGV.getInstance().setGenomeTracks(genome.getGeneTrack());
} else {
// Selecting a genome will actually "reset" the session so we have to
// save the path and restore it.
String sessionPath = session.getPath();
if (IGV.getInstance().getGenomeIds().contains(genomeId)) {
IGV.getInstance().selectGenomeFromList(genomeId);
} else {
String genomePath = genomeId;
if (!ParsingUtils.pathExists(genomePath)) {
genomePath = FileUtils.getAbsolutePath(genomeId, session.getPath());
}
if (ParsingUtils.pathExists(genomePath)) {
try {
IGV.getInstance().loadGenome(genomePath, null);
} catch (IOException e) {
throw new RuntimeException("Error loading genome: " + genomeId);
}
} else {
MessageUtils.showMessage("Warning: Could not locate genome: " + genomeId);
}
}
session.setPath(sessionPath);
}
}
session.setLocus(getAttribute(element, SessionAttribute.LOCUS.getText()));
session.setGroupTracksBy(getAttribute(element, SessionAttribute.GROUP_TRACKS_BY.getText()));
String removeEmptyTracks = getAttribute(element, "removeEmptyTracks");
if (removeEmptyTracks != null) {
try {
Boolean b = Boolean.parseBoolean(removeEmptyTracks);
session.setRemoveEmptyPanels(b);
} catch (Exception e) {
log.error("Error parsing removeEmptyTracks string: " + removeEmptyTracks, e);
}
}
String versionString = getAttribute(element, SessionAttribute.VERSION.getText());
try {
version = Integer.parseInt(versionString);
} catch (NumberFormatException e) {
log.error("Non integer version number in session file: " + versionString);
}
session.setVersion(version);
NodeList elements = element.getChildNodes();
process(session, elements, additionalInformation);
// ReferenceFrame.getInstance().invalidateLocationScale();
}