/**
* Convert the contents of a ProfileManager to XML and write the XML to the given writer.
*
* @param profileManager the ProfileManager
* @param writer the XMLStreamWriter to write to
*/
public static void marshal(ProfileManager profileManager, XMLStreamWriter writer) {
try {
writer.writeStartElement("userprofiles");
String profileVersion = getProfileVersion(profileManager.getProfileObjectStoreWriter());
writer.writeAttribute(MetadataManager.PROFILE_FORMAT_VERSION, profileVersion);
List<?> usernames = profileManager.getProfileUserNames();
for (Object userName : usernames) {
Profile profile = profileManager.getProfile((String) userName);
LOG.info("Writing profile: " + profile.getUsername());
long startTime = System.currentTimeMillis();
ProfileBinding.marshal(
profile,
profileManager.getProductionObjectStore(),
writer,
profileManager.getVersion(),
getClassKeys(profileManager.getProductionObjectStore()));
long totalTime = System.currentTimeMillis() - startTime;
LOG.info(
"Finished writing profile: " + profile.getUsername() + " took " + totalTime + "ms.");
}
TrackManagerBinding.marshal(profileManager.getProfileObjectStoreWriter(), writer);
writer.writeEndElement();
} catch (XMLStreamException e) {
throw new RuntimeException(e);
}
}
/** {@inheritDoc} */
@Override
public void startElement(String uri, String localName, String qName, Attributes attrs)
throws SAXException {
if ("userprofile".equals(qName)) {
if (attrs.getValue("username") != null) {
username = attrs.getValue("username");
}
if (attrs.getValue("password") != null) {
password = attrs.getValue("password");
}
if (attrs.getValue("apikey") != null) {
apiKey = attrs.getValue("apikey");
}
if (attrs.getValue("localAccount") != null) {
isLocal = Boolean.parseBoolean(attrs.getValue("localAccount"));
}
if (attrs.getValue("superUser") != null) {
isSuperUser = Boolean.parseBoolean(attrs.getValue("superUser"));
}
}
if ("bags".equals(qName)) {
savedBags = new LinkedHashMap();
invalidBags = new LinkedHashMap();
bagsValues = new LinkedHashMap();
subHandler =
new InterMineBagHandler(
profileManager.getProfileObjectStoreWriter(),
osw,
savedBags,
invalidBags,
bagsValues);
}
if ("shared-bags".equals(qName)) {
sharedBags = new ArrayList<Map<String, String>>();
subHandler = new SharedBagHandler(sharedBags);
}
if ("template-queries".equals(qName)) {
savedTemplates = new LinkedHashMap();
subHandler = new TemplateQueryHandler(savedTemplates, version);
}
if ("queries".equals(qName)) {
savedQueries = new LinkedHashMap();
subHandler = new SavedQueryHandler(savedQueries, savedBags, version);
}
if ("tags".equals(qName)) {
subHandler = new TagHandler(username, tags);
}
if ("preferences".equals(qName)) {
subHandler = new PreferencesHandler(preferences);
}
if ("invitations".equals(qName)) {
subHandler = invitationHandler;
}
if (subHandler != null) {
subHandler.startElement(uri, localName, qName, attrs);
}
}
/**
* Method called when user has finished updating a constraint.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @return an ActionForward object defining where control goes next
* @exception Exception if the application business logic throws an exception
*/
@Override
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
ProfileManager pm = im.getProfileManager();
String username = ((CreateAccountForm) form).getUsername();
String password = ((CreateAccountForm) form).getPassword();
pm.createNewProfile(username, password);
Properties webProperties = SessionMethods.getWebProperties(session.getServletContext());
try {
MailUtils.email(username, webProperties);
if (((CreateAccountForm) form).getMailinglist()
&& webProperties.getProperty("mail.mailing-list") != null
&& webProperties.getProperty("mail.mailing-list").length() > 0) {
MailUtils.subscribe(username, webProperties);
}
SessionMethods.recordMessage(
"You have successfully created an account, and logged in.", session);
} catch (Exception e) {
SessionMethods.recordError("Failed to send confirmation email", session);
}
/*
* This code generates an MD5 key for the given username which is then
* encoded in Hexadecimal. This could later be used for account
* activation.
*
* try { MessageDigest md5 = MessageDigest.getInstance("MD5"); byte[]
* buffer = username.getBytes(); md5.update(buffer); byte[] array =
* md5.digest(); String encoded = HexBin.encode(array); } catch
* (NoSuchAlgorithmException e) { }
*/
doLogin(request, username, password);
return new ActionForward("/begin.do");
}
/** {@inheritDoc} */
@Override
public void startElement(String uri, String localName, String qName, Attributes attrs)
throws SAXException {
if ("userprofiles".equals(qName)) {
String value = attrs.getValue(MetadataManager.PROFILE_FORMAT_VERSION);
if (value == null) {
version = 0;
} else {
version = Integer.parseInt(value);
}
ObjectStoreWriter userprofileOsw = profileManager.getProfileObjectStoreWriter();
Connection con = null;
try {
con = ((ObjectStoreInterMineImpl) userprofileOsw).getConnection();
if (!DatabaseUtil.tableExists(con, "bagvalues")) {
DatabaseUtil.createBagValuesTables(con);
}
} catch (SQLException sqle) {
LOG.error("Problem retrieving connection", sqle);
} finally {
((ObjectStoreInterMineImpl) userprofileOsw).releaseConnection(con);
}
sharedBagsByUsers = new HashedMap();
}
if ("userprofile".equals(qName)) {
startTime = System.currentTimeMillis();
profileHandler = new ProfileHandler(profileManager, osw, version, sharedBagsByUsers);
}
if (profileHandler != null) {
profileHandler.startElement(uri, localName, qName, attrs);
}
if ("tracks".equals(qName)) {
trackHandler = new TrackManagerHandler(profileManager.getProfileObjectStoreWriter());
}
if (trackHandler != null) {
trackHandler.startElement(uri, localName, qName, attrs);
}
}
/** {@inheritDoc} */
@Override
public void endElement(String uri, String localName, String qName) throws SAXException {
super.endElement(uri, localName, qName);
if ("userprofile".equals(qName)) {
Profile profile;
profile = profileHandler.getProfile();
profileManager.createProfileWithoutBags(profile);
try {
Map<String, Set<BagValue>> bagValues = profileHandler.getBagsValues();
for (StorableBag bag : profile.getAllBags().values()) {
bag.saveWithBagValues(profile.getUserId(), bagValues.get(bag.getName()));
}
} catch (ObjectStoreException ose) {
throw new SAXException(ose);
}
// Must come after the bags themselves have been stored.
try {
SharedBagManager.getInstance(profileManager);
profileHandler.getInvitationHandler().storeInvites(profile);
} catch (SQLException e) {
LOG.error("Cannot store invitations", e);
if (abortOnError) {
throw new SAXException(e);
}
}
Set<Tag> tags = profileHandler.getTags();
TagManager tagManager = new TagManagerFactory(profile.getProfileManager()).getTagManager();
for (Tag tag : tags) {
try {
tagManager.addTag(tag.getTagName(), tag.getObjectIdentifier(), tag.getType(), profile);
} catch (TagManager.TagException e) {
LOG.error("Cannot add tag: " + tag.toString(), e);
if (abortOnError) {
throw new SAXException(e);
}
} catch (RuntimeException e) {
LOG.error("Error adding tag: " + tag.toString(), e);
if (abortOnError) {
throw new SAXException(e);
}
}
}
profile.getSearchRepository().receiveEvent(new MassTaggingEvent());
profileHandler = null;
long totalTime = System.currentTimeMillis() - startTime;
LOG.info("Finished profile: " + profile.getUsername() + " took " + totalTime + "ms.");
}
if ("userprofiles".equals(qName)) {
if (!sharedBagsByUsers.isEmpty()) {
SharedBagManager sharedBagManager = SharedBagManager.getInstance(profileManager);
String bagName, dateCreated;
for (String user : sharedBagsByUsers.keySet()) {
List<Map<String, String>> sharedBags = sharedBagsByUsers.get(user);
if (!sharedBags.isEmpty()) {
for (Map<String, String> sharedBag : sharedBags) {
bagName = sharedBag.get("name");
dateCreated = sharedBag.get("dateCreated");
sharedBagManager.shareBagWithUser(bagName, dateCreated, user);
}
}
}
}
}
if (profileHandler != null) {
profileHandler.endElement(uri, localName, qName);
}
if (trackHandler != null) {
trackHandler.endElement(uri, localName, qName);
}
}