public static ClientUser buildUserFromProfile(NativeDocument profile, String username) {
NativeElement root = profile.getDocumentElement();
ClientUser currentUser = new ClientUser();
currentUser.setUsername(username);
// backwards compatibility for the moment...
if (root.getElementsByTagName("creds").getLength() != 0) {
Debug.println("Profile detected Old version...");
currentUser.setFirstName(root.getElementByTagName("first").getTextContent());
currentUser.setLastName(root.getElementByTagName("last").getTextContent());
currentUser.setAffiliation(root.getElementByTagName("affiliation").getTextContent());
} else {
Debug.println("Profile detected New shiny version!");
NativeNodeList nodes = root.getChildNodes();
for (int i = 0; i < nodes.getLength(); i++) {
NativeNode curNode = nodes.item(i);
if (curNode.getNodeType() != NativeNode.ELEMENT_NODE) continue;
String name = curNode.getNodeName();
if (name.equals(NewAccountPanel.EMAIL_KEY)) currentUser.setEmail(curNode.getTextContent());
else if (name.equals(NewAccountPanel.FIRSTNAME_KEY))
currentUser.setFirstName(curNode.getTextContent());
else if (name.equals(NewAccountPanel.LASTNAME_KEY))
currentUser.setLastName(curNode.getTextContent());
else if (name.equals(NewAccountPanel.AFFILIATION_KEY))
currentUser.setAffiliation(curNode.getTextContent());
else currentUser.setProperty(name, curNode.getTextContent());
}
if (root.getElementByTagName("quickGroup") == null)
currentUser.setProperty("quickGroup", "rlu");
}
return currentUser;
}
public void parse(NativeElement rootTag) {
NativeNodeList orgs = rootTag.getElementsByTagName("organization");
for (int i = 0; i < orgs.getLength(); i++) {
NativeElement curTag = orgs.elementAt(i);
Organization organization =
new Organization(
curTag.getAttribute("title"), curTag.getAttribute("shortTitle"), curTag, true);
organizations.add(organization);
}
}
public void fillTable() {
table.removeAll();
String fetchList = "";
for (int i = start; i < start + NUMBER_OF_RESULTS && i < currentResults.getLength(); i++)
fetchList += ((NativeElement) currentResults.item(i)).getAttribute("id") + ",";
if (fetchList.length() > 0)
TaxonomyCache.impl.fetchList(
fetchList,
new GenericCallback<String>() {
public void onFailure(Throwable arg0) {
WindowUtils.hideLoadingAlert();
WindowUtils.errorAlert("Error loading results. Inconsistency in index table.");
}
public void onSuccess(String arg0) {
List<String> assessmentList = new ArrayList<String>();
final String[][] x = new String[20][7];
for (int i = start;
i < start + NUMBER_OF_RESULTS && i < currentResults.getLength();
i++) {
TaxonNode currentNode =
TaxonomyCache.impl.getNode(
((NativeElement) currentResults.item(i)).getAttribute("id"));
x[i - start][0] = currentNode.getFullName();
if (currentNode.getCommonNames().size() > 0)
x[i - start][1] = (currentNode.getCommonNames().get(0)).getName().toLowerCase();
else x[i - start][1] = "";
x[i - start][2] = TaxonNode.getDisplayableLevel(currentNode.getLevel());
x[i - start][4] = String.valueOf(currentNode.getId());
if (currentNode.getAssessments().size() > 0) {
x[i - start][3] = String.valueOf(currentNode.getAssessments().get(0));
assessmentList.add(
currentNode.getAssessments().get(0)
+ "_"
+ BaseAssessment.PUBLISHED_ASSESSMENT_STATUS);
} else x[i - start][3] = "N/A";
if (currentNode.getFootprint().length >= 5)
x[i - start][5] = currentNode.getFootprint()[4];
else x[i - start][5] = "N/A";
if (currentNode.getFootprint().length >= 6)
x[i - start][6] = currentNode.getFootprint()[5];
else x[i - start][5] = "N/A";
}
AssessmentCache.impl.fetchAssessments(
new AssessmentFetchRequest(assessmentList, null),
new GenericCallback<String>() {
public void onFailure(Throwable caught) {
for (int i = start;
i < start + NUMBER_OF_RESULTS && i < currentResults.getLength();
i++) {
x[i - start][3] = "N/A";
TableItem tItem = new TableItem(x[i - start]);
table.add(tItem);
}
// x[i-start][3] = "N/A";
// SysDebugger.getInstance().println("FAILURES!");
SysDebugger.getInstance().println(caught.getMessage());
layout();
}
public void onSuccess(String result) {
for (int i = start;
i < start + NUMBER_OF_RESULTS && i < currentResults.getLength();
i++) {
AssessmentData aData =
AssessmentCache.impl.getPublishedAssessment(x[i - start][3], false);
if (aData == null) x[i - start][3] = "N/A";
else x[i - start][3] = aData.getProperCategoryAbbreviation();
TableItem tItem = new TableItem(x[i - start]);
table.add(tItem);
}
layout();
}
});
}
});
}
private String batchCreate(Request request, String username) {
NativeDocument doc = NativeDocumentFactory.newNativeDocument();
StringBuffer successfulIDs = new StringBuffer();
StringBuffer extantIDs = new StringBuffer();
StringBuffer unsuccessfulIDs = new StringBuffer();
try {
String text = request.getEntity().getText();
doc.parse(text);
AssessmentFilter filter =
AssessmentFilter.parseXML(
doc.getDocumentElement()
.getElementsByTagName(AssessmentFilter.HEAD_TAG)
.elementAt(0));
NativeNodeList nodes = doc.getDocumentElement().getElementsByTagName("taxon");
boolean useTemplate =
Boolean.parseBoolean(
doc.getDocumentElement()
.getElementsByTagName("useTemplate")
.elementAt(0)
.getTextContent());
System.out.println("Using template? " + useTemplate);
for (int i = 0; i < nodes.getLength(); i++) {
TaxonNode taxon = TaxaIO.readNode(nodes.elementAt(i).getTextContent(), vfs);
AssessmentData curAss = null;
curAss =
doCreateAssessmentForBatch(
request.getChallengeResponse().getIdentifier(), filter, useTemplate, taxon);
try {
AssessmentIOWriteResult result = assignIDAndSave(curAss, username);
if (result.status.isSuccess())
successfulIDs.append(
curAss.getSpeciesName() + (i == nodes.getLength() - 1 ? "" : ", "));
else
unsuccessfulIDs.append(
curAss.getSpeciesName() + (i == nodes.getLength() - 1 ? "" : ", "));
} catch (RegionConflictException e) {
extantIDs.append(curAss.getSpeciesName() + (i == nodes.getLength() - 1 ? "" : ", "));
}
}
StringBuilder ret = new StringBuilder();
if (unsuccessfulIDs.length() > 0)
ret.append(
"<div>Unable to create an assessment for the following species: "
+ unsuccessfulIDs
+ "</div>\r\n");
if (extantIDs.length() > 0)
ret.append(
"<div>The following species already have draft assessments with the specific locality: "
+ extantIDs
+ "</div>\r\n");
if (successfulIDs.length() > 0)
ret.append(
"<div>Successfully created an assessment for the following species: "
+ successfulIDs
+ "</div>\r\n");
return ret.toString();
} catch (IOException e) {
e.printStackTrace();
return null;
} catch (NullPointerException e) {
e.printStackTrace();
return null;
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
/**
* Assumes that: - Users have already been converted - Working Sets have already been converted -
* Working Set IDs have remained the same.
*/
protected void run() throws Exception {
userIO = new UserIO(session);
relationshipIO = new RelationshipIO(session);
taxonIO = new TaxonIO(session);
if (isTestMode()) print("### RUNNING IN TEST MODE ###");
final WorkingSetIO wsIO = new WorkingSetIO(session);
for (VFSPathToken token : data.getOldVFS().list(new VFSPath("/users"))) {
final User user = userIO.getUserFromUsername(token.toString());
if (user == null) printf("## No user exists for data directory %s ==", token);
else {
Hibernate.initialize(user.getSubscribedWorkingSets());
final VFSPath workingSetPath =
new VFSPath("/users/" + user.getUsername() + "/workingSet.xml");
final NativeDocument document = new JavaNativeDocument();
try {
document.parse(data.getOldVFS().getString(workingSetPath));
} catch (Exception e) {
continue;
}
printf("== Finding working sets for %s (%s) ==", user.getUsername(), user.getId());
final NativeNodeList nodes = document.getDocumentElement().getChildNodes();
for (int i = 0; i < nodes.getLength(); i++) {
NativeNode node = nodes.item(i);
if ("public".equals(node.getNodeName())) {
NativeNodeList children = node.getChildNodes();
for (int k = 0; k < children.getLength(); k++) {
NativeNode child = children.item(k);
if ("workingSet".equals(child.getNodeName())) {
NativeElement el = (NativeElement) child;
String id = el.getAttribute("id");
String creator = el.getAttribute("creator");
if (!user.getUsername().equals(creator)) {
boolean success = wsIO.subscribeToWorkingSet(Integer.valueOf(id), user);
if (!success) printf("# Failed to subscribe to ws %s", id);
else {
printf("Subscribed to ws %s", id);
/*if (count.incrementAndGet() % 50 == 0) {
printf("Converted %s working set subscriptions...", count.get());
commitAndStartTransaction();
}*/
}
}
}
}
} else if ("private".equals(node.getNodeName())) {
NativeNodeList children = node.getChildNodes();
for (int k = 0; k < children.getLength(); k++) {
NativeNode child = children.item(k);
if ("workingSet".equals(child.getNodeName())) {
WorkingSetData data =
new WorkingSetParser().parseSingleWorkingSet((NativeElement) node);
if ("".equals(data.getId())) {
continue;
}
WorkingSet privateWS =
WorkingSetConverter.convertWorkingSetData(
data, session, relationshipIO, userIO, taxonIO, user);
if (privateWS != null) {
printf("Created private working set %s", privateWS.getName());
session.save(privateWS);
}
}
}
}
}
}
commitAndStartTransaction();
}
// commitAndStartTransaction();
}
