@Override
protected void onReset() {
super.onReset();
Console.MODULES.getHeader().highlight(NameTokens.DomainRuntimePresenter);
String currentToken = placeManager.getCurrentPlaceRequest().getNameToken();
if (!currentToken.equals(getProxy().getNameToken())) {
lastSubPlace = currentToken;
} else if (lastSubPlace != null) {
placeManager.revealPlace(new PlaceRequest(lastSubPlace));
}
// first request, select default contents
if (!hasBeenRevealed
&& NameTokens.DomainRuntimePresenter.equals(
placeManager.getCurrentPlaceRequest().getNameToken())) {
placeManager.revealPlace(new PlaceRequest(NameTokens.InstancesPresenter));
hasBeenRevealed = true;
} else if (!NameTokens.DomainRuntimePresenter.equals(
placeManager.getCurrentPlaceRequest().getNameToken())) {
Scheduler.get()
.scheduleDeferred(
new Scheduler.ScheduledCommand() {
@Override
public void execute() {
loadHostData();
}
});
}
}
@Override
protected void onReset() {
super.onReset();
PlaceRequest currentPlace = placeManager.getCurrentPlaceRequest();
if (phenotype != null) {
getView().showPhenotypeInfo(phenotype);
if (currentPlace.getParameterNames().size() == 1) {
phenotypeOverviewPresenter.setData(phenotype, mRNAHistogramDataTable, bsHistogramDataTable);
setInSlot(TYPE_SetMainContent, phenotypeOverviewPresenter);
getView().setActiveLink(NAV_ITEMS.Overview, SUB_NAV_ITEMS.mRNA);
} else {
Dataset dataset =
phenotype.getDatasetFromName(
Dataset.TYPE.valueOf(currentPlace.getParameter("dataset", "")));
String env = currentPlace.getParameter("env", "");
if (env.equals("GxE")) {
gxeDetailPresenter.setData(phenotype, dataset);
setInSlot(TYPE_SetMainContent, gxeDetailPresenter);
} else {
phenotypeDetailPresenter.setData(
phenotype,
dataset.getEnvironmentFromName(env),
getSingleHistogramDataTable(env, dataset.getType()));
setInSlot(TYPE_SetMainContent, phenotypeDetailPresenter);
}
getView().setActiveLink(NAV_ITEMS.valueOf(env), SUB_NAV_ITEMS.mRNA);
}
}
}
@Override
protected void onReset() {
super.onReset();
String nameToken = placeManager.getCurrentPlaceRequest().getNameToken();
getView().selectProduct(nameToken);
}
@Override
public void prepareFromRequest(PlaceRequest request) {
super.prepareFromRequest(request);
PlaceRequest currentPlace = placeManager.getCurrentPlaceRequest();
String phenotype_id = currentPlace.getParameter("id", "");
if (phenotype_id.equals("")) getProxy().manualReveal(PhenotypePresenter.this);
else {
dispatch.execute(
new GetPhenotypeDataAction(phenotype_id, phenotypeReader),
new CustomCallback<GetPhenotypeDataActionResult>(getEventBus()) {
@Override
public void onSuccess(GetPhenotypeDataActionResult result) {
PhenotypePresenter.this.phenotype = result.getPhenotype();
PhenotypePresenter.this.mRNAHistogramDataTable = result.getmRNAHistogramDataTable();
PhenotypePresenter.this.bsHistogramDataTable = result.getBsHistogramDataTable();
getProxy().manualReveal(PhenotypePresenter.this);
}
@Override
public void onFailure(Throwable caught) {
getProxy().manualReveal(PhenotypePresenter.this);
super.onFailure(caught);
// getProxy().manualRevealFailed();
}
});
}
}
@Override
public void onBootstrap() {
if (appConfig.isUseCookieDomainNone()) {
analytics.create().cookieDomain("none");
} else {
analytics.create();
}
placeManager.revealPlace(new PlaceRequest.Builder().nameToken(NameTokens.visualizer).build());
}
@Override
protected void onReset() {
header.highlight(getProxy().getNameToken());
if (getProxy().getNameToken().equals(placeManager.getCurrentPlaceRequest().getNameToken()))
loadServer();
if (!hasBeenLoaded) hasBeenLoaded = true;
}
private void initUserSession() {
String username = requestCredentials.getUsername();
if (!requestCredentials.hasCredentials()) {
placeManager.revealUnauthorizedPlace(Places.LOGIN);
} else if (Strings.isNullOrEmpty(username) || "undefined".equals(username)) {
initUsernameFromSession();
} else {
revealCurrentPlace();
}
}
@Override
public void openCard(boolean addContent) {
cachingService.putCachedObject(
StorySummary.class,
CachedObjectKeys.OPENED_STORY,
editedStorySummary == null ? storySummary : editedStorySummary);
PlaceRequest place = getStoryDetailsPlaceRequestBuilder(addContent, true).build();
placeManager.revealRelativePlace(place);
}
@Override
public void onSearchTag(String tag) {
PlaceRequest placeRequest =
new PlaceRequest.Builder()
.nameToken(NameTokens.stories)
.with(ParameterTokens.search, "tag:(" + tag + ")")
.build();
placeManager.revealPlace(placeRequest);
}
public void requestHostIndex(int hostIndex) {
// TODO Use the in-memory model of the topology for paging
PlaceRequest.Builder builder =
new PlaceRequest.Builder()
.nameToken(NameTokens.Topology)
.with("hostIndex", String.valueOf(hostIndex));
if (fake) {
builder.with("fake", "true");
}
placeManager.revealPlace(builder.build());
}
@Override
protected void onReveal() {
super.onReveal();
PlaceRequest currentPlaceRequest = placeManager.getCurrentPlaceRequest();
if (!hasBeenRevealed
&& NameTokens.ServerGroupMgmtPresenter.equals(currentPlaceRequest.getNameToken())) {
hasBeenRevealed = true;
// update LHS
serverGroupStore.loadServerGroups(
new SimpleCallback<List<ServerGroupRecord>>() {
@Override
public void onSuccess(List<ServerGroupRecord> result) {
getView().updateServerGroups(result);
}
});
// forward default to ServerGroupPresenter, this presenter doesn't have a default view
placeManager.revealRelativePlace(new PlaceRequest(NameTokens.ServerGroupPresenter));
}
}
@Override
public void onCloseTab(NavigationTab element) {
int index = elements.indexOf(element);
getView().removeTab(index);
elements.remove(index);
if (index >= elements.size()) {
index = (elements.size() - 1) >= 0 ? (elements.size() - 1) : 0;
}
if (index == 0 && elements.size() == 0) {
placeManager.revealPlace(new PlaceRequest.Builder().nameToken(NameTokens.getCars()).build());
} else {
onTabSelected(index);
}
}
@Override
public void render(Context context, CandidateGeneListProxy value, SafeHtmlBuilder sb) {
if (value == null) return;
placeRequest.with("id", value.getId().toString());
SafeUri link =
UriUtils.fromTrustedString("#" + placeManager.buildHistoryToken(placeRequest.build()));
SafeHtml name = SafeHtmlUtils.fromString(value.getName());
SafeHtmlBuilder builder = new SafeHtmlBuilder();
builder
.append(SafeHtmlUtils.fromSafeConstant("created on "))
.append(
SafeHtmlUtils.fromString(
DateTimeFormat.getFormat(DateTimeFormat.PredefinedFormat.DATE_SHORT)
.format(value.getCreated())))
.append(SafeHtmlUtils.fromSafeConstant(" by "))
.append(
SafeHtmlUtils.fromString(
value.getOwnerUser().getFirstname() + " " + value.getOwnerUser().getLastname()));
sb.append(templates.cell(link, name, builder.toSafeHtml()));
}
@Override
protected void onReset() {
super.onReset();
getView().setMessage("Loading...");
getView().setBackLinkHistoryToken(placeManager.buildRelativeHistoryToken(-1));
dispatcher.execute(
new GetProductAction(id),
new AsyncCallback<GetProductResult>() {
@Override
public void onFailure(Throwable caught) {
getView().setMessage("Unknown product");
}
@Override
public void onSuccess(GetProductResult result) {
getView().setProductDetails(result.getProduct());
}
});
}
@Override
public void execute() {
String initialToken = History.getToken();
if (!initialToken.isEmpty() && !isBlackListed(initialToken)) {
List<PlaceRequest> hierarchy = formatter.toPlaceRequestHierarchy(initialToken);
final PlaceRequest placeRequest = hierarchy.get(hierarchy.size() - 1);
Scheduler.get()
.scheduleDeferred(
new Scheduler.ScheduledCommand() {
@Override
public void execute() {
placeManager.revealPlace(placeRequest, true);
}
});
bootstrapContext.setInitialPlace(placeRequest.getNameToken());
} else {
placeManager.revealDefaultPlace();
}
}
@Override
protected void onReveal() {
super.onReveal();
if (isStoryDetails) {
tagsPresenter.setSearchTagHandler(this);
addVisibleHandler(CreateContentEvent.TYPE, this);
getView().setForStoryDetails();
} else {
tagsPresenter.setSearchTagHandler(null);
String historyToken =
placeManager.buildHistoryToken(getStoryDetailsPlaceRequestBuilder(false, false).build());
getView().setForStoryCard(historyToken);
}
if (isEditMode) {
StorySummary openedStoryData =
cachingService.getCachedObject(StorySummary.class, CachedObjectKeys.OPENED_STORY);
doEdit(openedStoryData);
}
}
@Override
public void onTabSelected(int index) {
placeManager.revealPlace(
new PlaceRequest.Builder().nameToken(elements.get(index).getToken()).build());
}
@Override
public void logout() {
securityUtils.clearCredentials();
placeManager.revealPlace(new PlaceRequest(NameTokens.getLogin()));
}
private void setHistoryTokens() {
getView()
.setTaxonomiesHistoryToken(
placeManager.buildRelativeHistoryToken(
new PlaceRequest.Builder().nameToken(Places.TAXONOMIES).build(), 1));
}
@UiHandler("contact")
public void onButtonClick2(final ClickEvent event) {
PlaceRequest myRequest = new PlaceRequest(NameTokens.CONTACT);
place.revealPlace(myRequest);
}
@Override
protected void onReset() {
super.onReset();
if (placeManager.getCurrentPlaceRequest().matchesNameToken(getProxy().getNameToken()))
refreshServerList();
}
@Override
public void onPreviousVariable() {
placeManager.revealPlace(
ProjectPlacesHelper.getVariablePlace(
table.getDatasourceName(), table.getName(), previousVariable.getName()));
}
@UiHandler("menuBar")
void onMenuItemChanged(ValueChangeEvent<MenuItem> event) {
placeManager.revealPlace(
new PlaceRequest.Builder().nameToken(menuBar.getValue().getPlaceToken()).build());
}
public void editEmpDetails(Integer empId) {
PlaceRequest placerequest =
new PlaceRequest(NameTokens.editdetails).with("Param", empId.toString());
placemanager.revealPlace(placerequest);
}
private void initTree() {
String section_key = "section";
String subsection_key = "subsection";
TreeItem root = new TreeItem("Help");
PlaceRequest rootPlace = new PlaceRequest(NameTokens.helpPage);
tree.addItem(
new Hyperlink(
"Introduction",
placeManager.buildHistoryToken(rootPlace.with(section_key, "introduction"))))
.setUserObject("introduction");
// Phenotypes
TreeItem phenotypes_item =
new TreeItem(
new Hyperlink(
"Phenotypes",
placeManager.buildHistoryToken(rootPlace.with(section_key, "phenotypes"))));
phenotypes_item.setUserObject("phenotypes");
phenotypes_item
.addItem(
new Hyperlink(
"Uploading Phenotypes",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "phenotypes").with(subsection_key, "upload"))))
.setUserObject("phenotypes_upload");
phenotypes_item
.addItem(
new Hyperlink(
"Phenotype Format",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "phenotypes").with(subsection_key, "format"))))
.setUserObject("phenotypes_format");
tree.addItem(phenotypes_item);
// Accessions
TreeItem accession_item =
new TreeItem(
new Hyperlink(
"Accessions",
placeManager.buildHistoryToken(rootPlace.with(section_key, "accessions"))));
accession_item.setUserObject("accessions");
tree.addItem(accession_item);
// Analysis
TreeItem analysis_item =
new TreeItem(
new Hyperlink(
"Analysis",
placeManager.buildHistoryToken(rootPlace.with(section_key, "analysis"))));
analysis_item.setUserObject("analysis");
analysis_item
.addItem(
new Hyperlink(
"Navigation",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "analysis").with(subsection_key, "navigation"))))
.setUserObject("analysis_navigation");
analysis_item
.addItem(
new Hyperlink(
"Phenotypes",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "analysis").with(subsection_key, "phenotypes"))))
.setUserObject("analysis_phenotypes");
analysis_item
.addItem(
new Hyperlink(
"Datasets",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "analysis").with(subsection_key, "datasets"))))
.setUserObject("analysis_datasets");
analysis_item
.addItem(
new Hyperlink(
"Transformations",
placeManager.buildHistoryToken(
rootPlace
.with(section_key, "analysis")
.with(subsection_key, "transformations"))))
.setUserObject("analysis_transformations");
analysis_item
.addItem(
new Hyperlink(
"Results",
placeManager.buildHistoryToken(
rootPlace.with(section_key, "analysis").with(subsection_key, "results"))))
.setUserObject("analysis_results");
tree.addItem(analysis_item);
// Tutorial
/*TreeItem tutorial_item = new TreeItem(new Hyperlink("Tutorial",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial"))));
tutorial_item.setUserObject("tutorial");
tutorial_item.addItem(new Hyperlink("1.) Uploading Phenotypes",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "uploading")))).setUserObject("tutorial_uploading");
tutorial_item.addItem(new Hyperlink("2.) Creating subset",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "subset")))).setUserObject("tutorial_subset");
tutorial_item.addItem(new Hyperlink("3.) Changing transformation",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "transformation")))).setUserObject("tutorial_transformation");
tutorial_item.addItem(new Hyperlink("4.) Running GWAS",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "gwas")))).setUserObject("tutorial_gwas");
tutorial_item.addItem(new Hyperlink("5.) Viewing Results",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "results")))).setUserObject("tutorial_results");
tutorial_item.addItem(new Hyperlink("6.) Running Step-Wise GWAS",placeManager.buildHistoryToken(rootPlace.with(section_key, "tutorial").with(subsection_key, "gwas_step")))).setUserObject("tutorial_gwas_step");
tree.addItem(tutorial_item);*/
Iterator<TreeItem> iterator = tree.treeItemIterator();
while (iterator.hasNext()) {
iterator.next().setState(true, false);
}
}
@Override
public void onGoBack(GoBackEvent event) {
placeManager.revealPlace(new Builder().nameToken(NameTokens.getRating()).build());
}