/**
* Constructs a <code>StudyDef Tree item root</code> to bind other items to.
*
* @param xDef <code>StudyDef</code> for whom to create root.
* @return Constructed <code>Tree Item.</code>
*/
private static TreeItem constructTreeItem(StudyDef xDef) {
TreeItem root = new CompositeTreeItem(new TreeItemWidget(images.note(), xDef.getName(), popup));
if (root.getUserObject() != null) {
if (!root.getUserObject().equals(xDef)) {
root.setUserObject(xDef);
tree.addItem(root);
}
} else {
root.setUserObject(xDef);
tree.addItem(root);
}
return root;
}
/**
* Constructs a tree item for generic ("Advanced") component blocks for component types that
* appear in form.
*
* @param form only component types that appear in this Form will be included
* @return tree item for this form
*/
public TreeItem getGenericComponentsTree(MockForm form) {
Map<String, String> typesAndIcons = Maps.newHashMap();
form.collectTypesAndIcons(typesAndIcons);
TreeItem advanced = new TreeItem(new HTML("<span>" + MESSAGES.anyComponentLabel() + "</span>"));
List<String> typeList = new ArrayList<String>(typesAndIcons.keySet());
Collections.sort(typeList);
for (final String typeName : typeList) {
TreeItem itemNode =
new TreeItem(
new HTML(
"<span>"
+ typesAndIcons.get(typeName)
+ MESSAGES.textAnyComponentLabel()
+ TranslationDesignerPallete.getCorrespondingString(typeName)
+ "</span>"));
SourceStructureExplorerItem sourceItem =
new BlockSelectorItem() {
@Override
public void onSelected() {
fireGenericDrawerSelected(typeName);
}
};
itemNode.setUserObject(sourceItem);
advanced.addItem(itemNode);
}
return advanced;
}
public TreeItem buildTreeItem(final CategoryItem category) {
final TreeItem it = new TreeItem();
it.setHTML(
AbstractImagePrototype.create(ImageResources.INSTANCE.categorySmall()).getHTML()
+ h(category.getName()));
it.setUserObject(category);
return it;
}
/**
* Adds a new Item according to selected item on the <tt>Tree View.</tt>
*
* <p>If a <Study</tt> is selected, a new <tt>Study</tt> will be added.
*
* <p>If a <tt>Form</tt> is selected, a new <tt>Form</tt> will be added.
*
* <p>If a <tt>Form Version</tt> is selected, a new <tt>Form Version</tt> will be added.
*/
public static void addNewItem(String xForm, Tree tree, List<StudyDef> studies, PopupPanel popup) {
TreeItem item = tree.getSelectedItem();
if (item == null || item.getUserObject() instanceof StudyDef) {
StudyDef studyDef = new StudyDef(0, "New Study" + (tree.getItemCount() + 1));
studyDef.setCreator(Context.getAuthenticatedUser());
studyDef.setDateCreated(new Date());
studyDef.setDirty(true);
TreeItem root =
new CompositeTreeItem(new TreeItemWidget(images.note(), studyDef.getName(), popup));
root.setUserObject(studyDef);
tree.addItem(root);
studies.add(studyDef);
tree.setSelectedItem(root);
// Automatically add a new form
addNewChildItem(tree, studies, popup);
} else if (item.getUserObject() instanceof FormDef) {
TreeItem parent = item.getParentItem();
FormDef formDef =
new FormDef(
0, "New Form" + (parent.getChildCount() + 1), (StudyDef) parent.getUserObject());
formDef.setCreator(Context.getAuthenticatedUser());
formDef.setDateCreated(new Date());
formDef.setDirty(true);
item = addImageItem(parent, formDef.getName(), images.drafts(), formDef, null, popup);
((StudyDef) parent.getUserObject()).addForm(formDef);
tree.setSelectedItem(item);
parent.setState(true);
// Automatically add a new form version
addNewChildItem(tree, studies, popup);
} else if (item.getUserObject() instanceof FormDefVersion) {
TreeItem parent = item.getParentItem();
FormDefVersion formDefVersion =
new FormDefVersion(
0, "v" + (parent.getChildCount() + 1), (FormDef) parent.getUserObject());
formDefVersion.setCreator(Context.getAuthenticatedUser());
formDefVersion.setDateCreated(new Date());
formDefVersion.getFormDef().turnOffOtherDefaults(formDefVersion);
formDefVersion.setDirty(true);
if (xForm != null) formDefVersion.setXform(xForm);
item =
addImageItem(
parent, formDefVersion.getName(), images.markRead(), formDefVersion, null, popup);
((FormDef) parent.getUserObject()).addVersion(formDefVersion);
tree.setSelectedItem(item);
parent.setState(true);
}
}
/** Initialize the menu */
private void intiMenu() {
removeAll();
// Item 1 sub-tree
TreeItem item1 = new TreeItem();
item1.setText(SafeHtmlUtils.htmlEscape(CATEGORY_MENU));
item1.setUserObject(CATEGORY_MENU);
addItem(item1);
}
/**
* Loads a study and its contents in this view.
*
* @param studyDef the study definition object.
*/
public static void loadStudy(StudyDef studyDef) {
TreeItem studyRoot =
new CompositeTreeItem(new TreeItemWidget(images.note(), studyDef.getName(), popup));
studyRoot.setUserObject(studyDef);
tree.addItem(studyRoot);
if (studyDef.getForms() != null) {
for (FormDef def : studyDef.getForms()) loadForm(def, studyRoot, false);
}
Utilities.selectFirstItemOnTreeView(tree);
}
/**
* A helper method to simplify adding tree items that have attached images. {@link
* #addImageItem(TreeItem, String) code}
*
* @param root the tree item to which the new item will be added.
* @param title the text associated with this item.
*/
private static TreeItem addImageItem(
TreeItem root,
String title,
ImageResource imageProto,
Object userObj,
String helpText,
PopupPanel popup) {
TreeItem item = new CompositeTreeItem(new TreeItemWidget(imageProto, title, popup));
item.setUserObject(userObj);
item.setTitle(helpText);
root.addItem(item);
return item;
}
private void loadItem(VariableSerializable[] vars) {
for (int j = 0; j < vars.length; j++) {
// Do not include variables with subset_variable="true" used to denote "selector"
// variables in in-situ data sets like SOCAT
// TODO and for now no variables with character string values
// if ( Util.keep(vars[j].getDSID(), vars[j].getName()) && Util.keep(vars[j].getDSID(),
// vars[j].getAttributes()) ) {
TreeItem item = new TreeItem();
item.setText(vars[j].getName());
item.setUserObject(vars[j]);
currentlySelected.addItem(item);
// }
}
}
public void onSuccess(GWTFolder result) {
// Only executes on initalization and the actualItem is root
// element on initialization
// We put the id on root
actualItem.setUserObject(result);
evaluesFolderIcon(actualItem);
actualItem.setState(true);
actualItem.setSelected(true);
// Enables or disables move button ( evalues security to move to folder with permissions )
evaluateSecurityToAction(actualItem);
getChilds(result.getPath());
}
private void addTreeItem(JSONObject jsonObject, int index) {
Node node =
new Node(
jsonObject.get("id").isString().stringValue(),
jsonObject.get("leaf").isBoolean().booleanValue(),
jsonObject.get("text").isString().stringValue());
if (node.getText() != null) {
TreeItem item = new TreeItem();
item.setText(node.getText());
item.setUserObject(node);
if (!node.isLeaf()) item.addItem(""); // Temporarily add an item so we can expand this node
treeItem.addItem(item);
}
}
/**
* Bind <tt>StudyDef</tt> contents.
*
* @param tree <tt>Tree View</tt> to bind <tt>StudyDef</tt> to.
* @param popup <tt>Popup</tt> to bind to the <tt>Tree View.</tt>
* @param editable <tt>Editable</tt> we are checking contents for.
*/
private static void setStudyContent(final Tree tree, final PopupPanel popup, Editable editable) {
StudyDef studyDef = (StudyDef) editable;
studyDef.setCreator(Context.getAuthenticatedUser());
studyDef.setDateCreated(new Date());
studyDef.setDirty(true);
TreeItem root =
new CompositeTreeItem(new TreeItemWidget(images.note(), studyDef.getName(), popup));
root.setUserObject(studyDef);
tree.addItem(root);
Context.getStudies().add(studyDef);
tree.setSelectedItem(root);
List<FormDef> forms = studyDef.getForms();
if (forms != null) {
for (FormDef formDef : forms) importForm(tree, root, formDef, popup);
}
}
/** Folder Tree */
public FolderSelectTree() {
tree = new Tree();
rootItem.setStyleName("okm-TreeItem");
rootItem.setUserObject(new GWTFolder());
rootItem.setSelected(true);
rootItem.setState(true);
tree.setStyleName("okm-Tree");
tree.addItem(rootItem);
tree.addSelectionHandler(
new SelectionHandler<TreeItem>() {
@Override
public void onSelection(SelectionEvent<TreeItem> event) {
boolean refresh = true;
TreeItem item = event.getSelectedItem();
// Enables or disables move button ( evalues security to move to folder with permissions
// )
evaluateSecurityToAction(item);
// Case that not refreshing tree and file browser ( right click )
if (actualItem.equals(item)) {
refresh = false;
} else {
// Disables actual item because on changing active node by
// application this it's not changed automatically
if (!actualItem.equals(item)) {
actualItem.setSelected(false);
actualItem = item;
} else {
refresh = false;
}
}
if (refresh) {
refresh(true);
}
}
});
actualItem = tree.getItem(0);
initWidget(tree);
}
public void setFullyQualifiedClassNames(final List<String> fullyQualifiedClassNames) {
if (tree.getItem(0) != null) {
tree.clear();
}
if (fullyQualifiedClassNames != null) {
for (String type : fullyQualifiedClassNames) {
final TreeItem it = new TreeItem();
it.setHTML(
AbstractImagePrototype.create(DRLTextEditorResources.INSTANCE.images().classImage())
.getHTML()
+ "<small>"
+ type
+ "</small>");
it.setUserObject(new ClassUserObject(type + "( )", type));
tree.addItem(it);
it.addItem(Util.toSafeHtml(LAZY_LOAD));
}
}
}
private void setupPackageNode(final TreeItem packageRootNode) {
packageRootNode.setState(true);
packageRootNode.setUserObject(new String("rootNode"));
RepositoryServiceFactory.getService()
.listPackages(
new GenericCallback<PackageConfigData[]>() {
public void onSuccess(PackageConfigData[] packageConfigDatas) {
PackageHierarchy packageHierarchy = new PackageHierarchy();
for (PackageConfigData packageConfigData : packageConfigDatas) {
packageHierarchy.addPackage(packageConfigData);
}
for (PackageHierarchy.Folder folder : packageHierarchy.getRoot().getChildren()) {
buildPkgTree(packageRootNode, folder);
}
}
});
}
public void onSuccess(List<GWTFolder> result) {
boolean directAdd = true;
// If has no childs directly add values is permited
if (actualItem.getChildCount() > 0) {
directAdd = false;
// to prevent remote folder remove it disables all tree branch
// items and after sequentially activate
hideAllBranch(actualItem);
}
// On refreshing not refreshed the actual item values but must
// ensure that has childs value is consistent
if (result.isEmpty()) {
((GWTFolder) actualItem.getUserObject()).setHasChildren(false);
} else {
((GWTFolder) actualItem.getUserObject()).setHasChildren(true);
}
// Ads folders childs if exists
for (Iterator<GWTFolder> it = result.iterator(); it.hasNext(); ) {
GWTFolder folder = it.next();
TreeItem folderItem = new TreeItem(folder.getName());
folderItem.setUserObject(folder);
folderItem.setStyleName("okm-TreeItem");
// If has no childs directly add values is permited, else
// evalues each node to refresh, remove or add
if (directAdd) {
evaluesFolderIcon(folderItem);
actualItem.addItem(folderItem);
} else {
// sequentially activate items and refreshes values
addFolder(actualItem, folderItem);
}
}
actualItem.setState(true);
evaluesFolderIcon(actualItem);
}
/**
* Constructs a tree item for built-in blocks.
*
* @return tree item
*/
public TreeItem getBuiltInBlocksTree() {
initBundledImages();
TreeItem builtinNode =
new TreeItem(new HTML("<span>" + MESSAGES.builtinBlocksLabel() + "</span>"));
for (final String drawerName : BUILTIN_DRAWER_NAMES) {
Image drawerImage = new Image(bundledImages.get(drawerName));
TreeItem itemNode =
new TreeItem(
new HTML("<span>" + drawerImage + getBuiltinDrawerNames(drawerName) + "</span>"));
SourceStructureExplorerItem sourceItem =
new BlockSelectorItem() {
@Override
public void onSelected() {
fireBuiltinDrawerSelected(drawerName);
}
};
itemNode.setUserObject(sourceItem);
builtinNode.addItem(itemNode);
}
builtinNode.setState(true);
return builtinNode;
}
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);
}
}
private TreeItem loadPackage(String name, PackageConfigData conf) {
TreeItem pn = ExplorerNodeConfig.getPackageItemStructure(name, conf.uuid, itemWidgets);
pn.setUserObject(conf);
return pn;
}
public void onSuccess(Object result) {
CategorySerializable[] cats = (CategorySerializable[]) result;
if (cats != null && cats.length > 0) {
if (currentlySelected == null) {
for (int i = 0; i < cats.length; i++) {
CategorySerializable cat = cats[i];
String children = cat.getAttributes().get("children");
boolean empty = false;
if (children != null && children.equals("none")) empty = true;
if (applyFilters(cat) && !empty) {
TreeItem item = new TreeItem();
item.addItem(
new SafeHtmlBuilder().appendEscaped(DatasetWidget.LOADING).toSafeHtml());
InnerItem inner = new InnerItem(cat);
item.setWidget(inner);
item.setUserObject(cat);
addItem(item);
}
}
} else {
for (int i = 0; i < cats.length; i++) {
CategorySerializable cat = cats[i];
if (cat.isCategoryChildren()) {
String name = cat.getName();
TreeItem item;
if (i == 0) {
item = currentlySelected.getChild(0);
} else {
item = new TreeItem();
}
item.addItem(
new SafeHtmlBuilder().appendEscaped(DatasetWidget.LOADING).toSafeHtml());
InnerItem inner = new InnerItem(cat);
item.setWidget(inner);
item.setUserObject(cat);
if (i > 0) {
currentlySelected.addItem(item);
}
} else if (cat.isVariableChildren()) {
// Must have variable children...
TreeItem item = currentlySelected.getChild(0);
if (cat.hasMultipleDatasets()) {
DatasetSerializable[] dses = cat.getDatasetSerializableArray();
DatasetSerializable ds = dses[0];
VariableSerializable[] vars = ds.getVariablesSerializable();
currentlySelected.removeItems();
for (int j = 0; j < dses.length; j++) {
ds = dses[j];
vars = ds.getVariablesSerializable();
loadItem(vars);
}
} else {
DatasetSerializable ds = cat.getDatasetSerializable();
VariableSerializable[] vars = ds.getVariablesSerializable();
currentlySelected.removeItems();
loadItem(vars);
}
}
}
}
} else {
// A category was selected, but it came back empty...
if (currentlySelected != null) {
TreeItem item = currentlySelected.getChild(0);
item.setText("No data sets found.");
}
}
if (saveSelection != null) {
currentlySelected = saveSelection;
saveSelection = null;
}
}
private TreeItem loadPackage(String name, PackageConfigData config) {
TreeItem treeItem = ExplorerNodeConfig.getPackageItemStructure(name, config.uuid, itemWidgets);
treeItem.setUserObject(config);
return treeItem;
}