/**
* Returns the collection of attachments.
*
* @return See above.
*/
List<FileAnnotationData> removeAttachedFiles() {
List<FileAnnotationData> list = new ArrayList<FileAnnotationData>();
if (filesDocList.size() == 0) {
docFlag = false;
return list;
}
List<FileAnnotationData> toKeep = new ArrayList<FileAnnotationData>();
FileAnnotationData data;
DocComponent doc;
Object object;
Iterator<DocComponent> i = filesDocList.iterator();
while (i.hasNext()) {
doc = i.next();
object = doc.getData();
if (doc.canUnlink()) {
if (object instanceof FileAnnotationData) {
data = (FileAnnotationData) object;
if (data.getId() > 0) list.add(data);
}
} else {
toKeep.add((FileAnnotationData) object);
}
}
handleObjectsSelection(FileAnnotationData.class, toKeep, false);
if (list.size() == 0) docFlag = false;
return list;
}
/**
* Starts an asynchronous call to save the passed file back to the server.
*
* @param file The file to save.
* @param asynch Pass <code>true</code> to save asynchronously, <code>false</code> otherwise.
*/
void fireFileSaving(File file, boolean asynch) {
boolean fileIsExp = browser.isModelExperiment();
int fileType = (fileIsExp ? FileSaver.EXPERIMENT : FileSaver.PROTOCOL);
saveFile(file);
FileAnnotationData data = null;
DataObject linkTo = parent;
if (fileAnnotation != null) data = fileAnnotation;
else data = new FileAnnotationData(file);
if (data.getId() > 0) linkTo = null;
String description = CPEsummaryExport.export(browser.getTreeModel());
if (description != null) data.setDescription(description);
if (asynch) {
currentLoader = new FileSaver(component, ctx, file, data, fileType, linkTo);
currentLoader.load();
state = Editor.SAVING;
} else {
OmeroMetadataService svc = EditorAgent.getRegistry().getMetadataService();
try {
svc.archivedFile(ctx, fileAnnotation, file, fileType, linkTo);
} catch (Exception e) {
LogMessage msg = new LogMessage();
msg.print("State: " + state);
msg.print("Cannot save file back to server");
msg.print(e);
EditorAgent.getRegistry().getLogger().error(this, msg);
}
}
}
/**
* Attaches the passed file. Returns <code>true</code> if the file does not already exist, <code>
* false</code> otherwise.
*
* @param files The files to attach.
* @return See above
*/
boolean attachFiles(File[] files) {
List<FileAnnotationData> list = getCurrentAttachmentsSelection();
DocComponent doc;
List<File> toAdd = new ArrayList<File>();
Object data = null;
if (filesDocList.size() > 0) {
Iterator<DocComponent> i = filesDocList.iterator();
FileAnnotationData fa;
while (i.hasNext()) {
doc = i.next();
data = doc.getData();
if (data instanceof FileAnnotationData) {
fa = (FileAnnotationData) data;
/*
for (int j = 0; j < files.length; j++) {
if (fa.getId() <= 0) {
if (!fa.getFilePath().equals(
files[j].getAbsolutePath()))
toAdd.add(files[j]);
list.add(fa);
} else {
if (fa.getFileName().equals(files[j].getName())) {
toReplace.add(fa);
} else toAdd.add(files[j]);
}
}
*/
for (int j = 0; j < files.length; j++) {
if (fa.getId() >= 0 && fa.getFileName().equals(files[j].getName())) {
toReplace.add(fa);
}
}
}
}
}
// if (data == null) {
for (int i = 0; i < files.length; i++) {
toAdd.add(files[i]);
}
// }
if (toAdd.size() > 0) {
data = null;
try {
docFlag = true;
Iterator<File> j = toAdd.iterator();
while (j.hasNext()) {
list.add(new FileAnnotationData(j.next()));
}
} catch (Exception e) {
}
firePropertyChange(
EditorControl.SAVE_PROPERTY, Boolean.valueOf(false), Boolean.valueOf(true));
}
layoutAttachments(list);
return toAdd.size() > 0;
}
/**
* Handles the selection of objects via the selection wizard.
*
* @param type The type of objects to handle.
* @param objects The objects to handle.
* @param fire Pass <code>true</code> to notify, <code>false</code> otherwise.
*/
void handleObjectsSelection(Class type, Collection objects, boolean fire) {
if (objects == null) return;
if (TagAnnotationData.class.equals(type)) {
layoutTags(objects);
List<Long> ids = new ArrayList<Long>();
Iterator i = objects.iterator();
TagAnnotationData tag;
tagFlag = false;
Collection tags = model.getTags();
if (tags == null || tags.size() != objects.size()) {
tagFlag = true;
} else {
while (i.hasNext()) {
tag = (TagAnnotationData) i.next();
if (tag != null && !model.isAnnotationUsedByUser(tag)) {
ids.add(tag.getId());
}
}
i = tags.iterator();
while (i.hasNext()) {
tag = (TagAnnotationData) i.next();
if (tag != null && !ids.contains(tag.getId())) {
tagFlag = true;
break;
}
}
}
} else if (FileAnnotationData.class.equals(type)) {
layoutAttachments(objects);
List<Long> ids = new ArrayList<Long>();
Iterator i = objects.iterator();
FileAnnotationData data;
docFlag = false;
Collection attachments = model.getAttachments();
if (attachments == null || attachments.size() != objects.size()) {
docFlag = true;
} else {
while (i.hasNext()) {
data = (FileAnnotationData) i.next();
if (data != null) ids.add(data.getId());
}
i = attachments.iterator();
while (i.hasNext()) {
data = (FileAnnotationData) i.next();
if (data != null && !ids.contains(data.getId())) {
docFlag = true;
break;
}
}
}
}
buildGUI();
if (fire)
firePropertyChange(
EditorControl.SAVE_PROPERTY, Boolean.valueOf(false), Boolean.valueOf(true));
}
/**
* Sets the file annotation data.
*
* @param data The value to set.
*/
void setFileAnnotationData(FileAnnotationData data) {
fileAnnotation = data;
if (data == null) {
fileID = 0;
fileName = null;
nameSpace = null;
return;
}
this.fileID = data.getFileID();
this.fileName = data.getFileName();
nameSpace = data.getNameSpace();
}
/**
* Modifies the text of the component.
*
* @see ActivityComponent#notifyActivityEnd()
*/
protected void notifyActivityEnd() {
// Download the file.
if (result instanceof FileAnnotationData) {
FileAnnotationData data = (FileAnnotationData) result;
String name = "";
if (data.isLoaded()) name = data.getFileName();
else name = "Annotation_" + data.getId();
download("", result, new File(parameters.getFolder(), name));
}
type.setText(DESCRIPTION_CREATED + " " + parameters.getFolder().getName());
}
/**
* Returns the instrument transfer function linked to the edited object.
*
* @return See above
*/
FileAnnotationData getIRF() {
if (!(refObject instanceof ImageData)) return null;
if (data == null) return null;
Collection<FileAnnotationData> l = getStructuredData().getAttachments();
if (l == null || l.size() == 0) return null;
Iterator<FileAnnotationData> i = l.iterator();
FileAnnotationData fa;
while (i.hasNext()) {
fa = i.next();
if (fa.getFileName().contains("irf")) return fa;
}
return null;
}
/**
* Creates a new instance.
*
* @param viewer The viewer this data loader is for. Mustn't be <code>null</code>.
* @param data The annotation hosting the file to load.
* @param uiView The object to handle.
*/
public FileLoader(Editor viewer, FileAnnotationData data, Object uiView) {
super(viewer);
if (data == null) throw new IllegalArgumentException("No data set.");
this.data = data;
this.uiView = uiView;
file = new File(MetadataViewerAgent.getTmpDir() + File.separator + data.getFileName());
file.deleteOnExit();
}
/**
* Returns the list of attachments currently selected by the user.
*
* @return See above.
*/
List<FileAnnotationData> getCurrentAttachmentsSelection() {
List<FileAnnotationData> list = new ArrayList<FileAnnotationData>();
if (filesDocList.size() == 0) return list;
DocComponent doc;
Object object;
FileAnnotationData data;
Iterator<DocComponent> i = filesDocList.iterator();
while (i.hasNext()) {
doc = i.next();
object = doc.getData();
if (object instanceof FileAnnotationData) {
data = (FileAnnotationData) object;
if (data.getId() > 0) list.add(data);
}
}
return list;
}
/**
* Returns the collection of the attachments linked to the <code>DataObject</code>.
*
* @return See above.
*/
private List<FileAnnotationData> getTabularData() {
StructuredDataResults data = getStructuredData();
List<FileAnnotationData> l = new ArrayList<FileAnnotationData>();
if (data == null) return l;
Collection<FileAnnotationData> attachments = data.getAttachments();
if (attachments == null) return l;
Iterator<FileAnnotationData> i = attachments.iterator();
FileAnnotationData f;
String ns;
while (i.hasNext()) {
f = i.next();
ns = f.getNameSpace();
if (FileAnnotationData.BULK_ANNOTATIONS_NS.equals(ns)) {
l.add(f);
}
}
return l;
}
/**
* Starts the asynchronous loading of the file to edit. and sets the state to {@link
* Editor#LOADING}.
*/
void fireFileLoading() {
long size = 0;
if (fileAnnotation != null) size = fileAnnotation.getFileSize();
// fileID can be annotationID if fileName is null
// E.g. if EditorModel(long annotationID) was the constructor.
currentLoader = new FileLoader(component, ctx, fileName, fileID, size);
currentLoader.load();
state = Editor.LOADING;
}
/**
* Removes the passed file from the display.
*
* @param file The file to remove.
*/
void removeAttachedFile(Object file) {
if (file == null) return;
FileAnnotationData fData = (FileAnnotationData) file;
List<FileAnnotationData> attachments = getCurrentAttachmentsSelection();
Iterator<FileAnnotationData> i = attachments.iterator();
FileAnnotationData data;
List<FileAnnotationData> toKeep = new ArrayList<FileAnnotationData>();
while (i.hasNext()) {
data = i.next();
if (data.getId() != fData.getId()) toKeep.add(data);
}
if (filesDocList.size() > 0) {
Iterator<DocComponent> j = filesDocList.iterator();
DocComponent doc;
Object fa;
while (j.hasNext()) {
doc = j.next();
fa = doc.getData();
if (fa instanceof FileAnnotationData) {
data = (FileAnnotationData) fa;
if (data.getId() <= 0 && !data.equals(file)) {
toKeep.add(data);
}
}
}
}
handleObjectsSelection(FileAnnotationData.class, toKeep, true);
}
/**
* Downloads the file.
*
* @see EditorLoader#cancel()
*/
public void load() {
if (data != null) {
OriginalFile f = ((FileAnnotation) data.asAnnotation()).getFile();
if (f.isLoaded()) {
handle = mhView.loadFile(file, f.getId().getValue(), f.getSize().getValue(), this);
}
} else {
Entry entry;
Iterator i = files.entrySet().iterator();
FileAnnotationData fa;
filesMap = new HashMap<FileAnnotationData, File>(files.size());
File f;
// int index = 0;
String dir = MetadataViewerAgent.getTmpDir();
while (i.hasNext()) {
entry = (Entry) i.next();
fa = (FileAnnotationData) entry.getKey();
f = new File(dir + File.separator + fa.getFileID() + "_" + fa.getFileName());
f.deleteOnExit();
filesMap.put(fa, f);
}
handle = mhView.loadFiles(filesMap, this);
}
}
/**
* Gets a reference to the Original File if this file has been saved to the server. Otherwise
* returns 0.
*
* @return See above
*/
long getAnnotationId() {
if (fileAnnotation == null) return annotationID;
return fileAnnotation.getId();
}
/**
* Returns the collection of annotation to remove.
*
* @see AnnotationUI#getAnnotationToRemove()
*/
protected List<Object> getAnnotationToRemove() {
List<Object> l = new ArrayList<Object>();
if (selectedValue != initialValue && selectedValue == 0) {
RatingAnnotationData rating = model.getUserRatingAnnotation();
if (rating != null) l.add(rating);
}
List<Long> idsToKeep;
DocComponent doc;
long id;
Object object;
Iterator<DocComponent> i;
Collection original;
Iterator j;
if (tagFlag && !model.isMultiSelection()) {
idsToKeep = new ArrayList<Long>();
TagAnnotationData tag;
i = tagsDocList.iterator();
while (i.hasNext()) {
doc = i.next();
object = doc.getData();
if (object instanceof TagAnnotationData) {
tag = (TagAnnotationData) object;
id = tag.getId();
if (id > 0) idsToKeep.add(id);
}
}
original = model.getTags();
j = original.iterator();
while (j.hasNext()) {
tag = (TagAnnotationData) j.next();
id = tag.getId();
if (!idsToKeep.contains(id)) // && model.isAnnotationToDelete(tag))
l.add(tag);
}
}
if (docFlag) {
idsToKeep = new ArrayList<Long>();
i = filesDocList.iterator();
FileAnnotationData fa;
while (i.hasNext()) {
doc = i.next();
object = doc.getData();
if (object instanceof FileAnnotationData) {
fa = (FileAnnotationData) object;
id = fa.getId();
if (id > 0) idsToKeep.add(id);
}
}
original = model.getAttachments();
j = original.iterator();
while (j.hasNext()) {
fa = (FileAnnotationData) j.next();
id = fa.getId();
if (!idsToKeep.contains(id)) // && model.isAnnotationToDelete(fa))
l.add(fa);
}
}
if (model.hasBeenPublished()) {
if (!publishedBox.isSelected()) {
BooleanAnnotationData b = model.getPublishedAnnotation();
if (b.getValue().booleanValue()) l.add(b);
}
}
return l;
}