/**
* 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);
}
}
}
/**
* Handles the exception thrown if any while creating the images for the split view.
*
* @param e The exception to handle.
*/
private void handleGridImageCreationException(Exception e) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo("Split View", "Unable to create the images for the view");
LogMessage msg = new LogMessage();
msg.print("Grid Images creation");
msg.print(e);
ImViewerAgent.getRegistry().getLogger().error(this, msg);
gridImages.clear();
gridImagesAsTextures.clear();
}
/** Brings up the folder chooser. */
private void export() {
DowngradeChooser chooser =
new DowngradeChooser(
new RefWindow(),
FileChooser.SAVE,
"Export",
"Select where to export the image as OME-TIFF.",
exportFilters);
try {
String path =
MetadataViewerAgent.getRegistry()
.getTaskBar()
.getLibFileRelative(TransformsParser.SPECIFICATION + ".jar");
chooser.parseData(path);
} catch (Exception e) {
LogMessage msg = new LogMessage();
msg.print(e);
MetadataViewerAgent.getRegistry().getLogger().debug(this, msg);
}
String s = UIUtilities.removeFileExtension(view.getRefObjectName());
if (s != null && s.trim().length() > 0) chooser.setSelectedFile(s);
chooser.setApproveButtonText("Export");
IconManager icons = IconManager.getInstance();
chooser.setTitleIcon(icons.getIcon(IconManager.EXPORT_AS_OMETIFF_48));
chooser.addPropertyChangeListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
String name = evt.getPropertyName();
if (FileChooser.APPROVE_SELECTION_PROPERTY.equals(name)) {
File[] files = (File[]) evt.getNewValue();
File folder = files[0];
if (folder == null) folder = UIUtilities.getDefaultFolder();
Object src = evt.getSource();
Target target = null;
if (src instanceof DowngradeChooser) {
((FileChooser) src).setVisible(false);
((FileChooser) src).dispose();
target = ((DowngradeChooser) src).getSelectedSchema();
}
model.exportImageAsOMETIFF(folder, target);
} else if (DowngradeChooser.HELP_DOWNGRADE_PROPERTY.equals(name)) {
Registry reg = MetadataViewerAgent.getRegistry();
String url = (String) reg.lookup("HelpDowngrade");
reg.getTaskBar().openURL(url);
}
}
});
chooser.centerDialog();
}
/**
* Sets the file to edit. If the file cannot be read by {@link TreeModelFactory#getTree()} then
* the state of this model is re-set to {@link Editor#NEW}.
*
* @param file The file to edit.
* @return See above.
*/
boolean setFileToEdit(File file) {
if (file == null) {
fileToEdit = null;
state = Editor.NEW;
fileName = EditorFactory.BLANK_MODEL;
return false;
}
TreeModel treeModel = null;
// try opening file as recognised OMERO.editor file (pro.xml or cpe.xml)
try {
treeModel = TreeModelFactory.getTree(file);
fileToEdit = file;
} catch (ParsingException e) {
// may get a parsing exception simply because the file was not
// recognised as Editor File..
Registry reg = EditorAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
// ... try opening as ANY xml file
try {
treeModel = TreeModelFactory.getTreeXml(file);
// if this worked, we have an XML file converted to cpe.xml
// .. tell user..
un.notifyInfo(
"File not recognised",
"File was converted from an unrecognised format into\n"
+ "OMERO.editor's cpe.xml format.\nOverwriting the "
+ "original file will erase the original XML format.");
// must avoid overwriting the original file...
// 'Save' won't work.
if (fileID > 0) { // try to read a file downloaded
file.delete();
}
fileToEdit = null;
setFileAnnotationData(null);
} catch (ParsingException ex) {
LogMessage message = new LogMessage();
message.print(ex);
reg.getLogger().error(this, message);
// ...and notify the user. Use the exception message.
String errMsg = ex.getMessage();
un.notifyInfo("File Failed to Open", errMsg);
}
}
if (treeModel == null) {
fileToEdit = null;
state = Editor.NEW;
fileName = EditorFactory.BLANK_MODEL;
return false;
}
fileName = file.getName();
browser.setTreeModel(treeModel);
state = Editor.READY;
return true;
}
/**
* Reacts to property change.
*
* @see PropertyChangeListener#propertyChange(PropertyChangeEvent)
*/
public void propertyChange(PropertyChangeEvent evt) {
String name = evt.getPropertyName();
if (SAVE_PROPERTY.equals(name)
|| DataComponent.DATA_MODIFIED_PROPERTY.equals(name)
|| PreviewPanel.PREVIEW_EDITED_PROPERTY.equals(name)) {
view.setDataToSave(view.hasDataToSave());
} else if (MetadataViewer.SAVE_DATA_PROPERTY.equals(name)) {
Boolean b = (Boolean) evt.getNewValue();
view.saveData(b.booleanValue());
} else if (MetadataViewer.CLEAR_SAVE_DATA_PROPERTY.equals(name)
|| MetadataViewer.ON_DATA_SAVE_PROPERTY.equals(name)
|| MetadataViewer.ADMIN_UPDATED_PROPERTY.equals(name)) {
view.clearData();
} else if (UIUtilities.COLLAPSED_PROPERTY_JXTASKPANE.equals(name)) {
view.handleTaskPaneCollapsed((JXTaskPane) evt.getSource());
} else if (FileChooser.APPROVE_SELECTION_PROPERTY.equals(name)) {
File[] files = (File[]) evt.getNewValue();
view.attachFiles(files);
} else if (AnnotationUI.REMOVE_ANNOTATION_PROPERTY.equals(name)) {
Object object = evt.getNewValue();
if (object instanceof DocComponent) {
DocComponent doc = (DocComponent) object;
Object data = doc.getData();
if (data instanceof File) view.removeAttachedFile(data);
else if (data instanceof FileAnnotationData) view.removeAttachedFile(data);
else if (data instanceof TagAnnotationData) view.removeObject((DataObject) data);
}
} else if (AnnotationUI.DELETE_ANNOTATION_PROPERTY.equals(name)) {
Object object = evt.getNewValue();
if (object instanceof DocComponent) {
DocComponent doc = (DocComponent) object;
Object data = doc.getData();
if (data instanceof FileAnnotationData) {
view.deleteAnnotation((FileAnnotationData) data);
view.removeAttachedFile(data);
}
} else if (object instanceof TextualAnnotationComponent) {
TextualAnnotationComponent doc = (TextualAnnotationComponent) object;
TextualAnnotationData data = doc.getData();
// view.deleteAnnotation((TextualAnnotationData) data);
view.removeObject(data);
}
} else if (AnnotationUI.EDIT_TAG_PROPERTY.equals(name)) {
Object object = evt.getNewValue();
if (object instanceof DocComponent) {
// Save the tag w/o update.
DataObject d = (DataObject) ((DocComponent) object).getData();
// Save the tag
OmeroMetadataService svc = MetadataViewerAgent.getRegistry().getMetadataService();
long id = MetadataViewerAgent.getUserDetails().getId();
try {
svc.saveData(model.getSecurityContext(), Arrays.asList(d), null, null, id);
} catch (Exception e) {
Logger l = MetadataViewerAgent.getRegistry().getLogger();
LogMessage msg = new LogMessage();
msg.print("Saving object");
msg.print(e);
l.error(this, msg);
}
}
} else if (OMEWikiComponent.WIKI_DATA_OBJECT_PROPERTY.equals(name)) {
WikiDataObject object = (WikiDataObject) evt.getNewValue();
long id;
switch (object.getIndex()) {
case WikiDataObject.IMAGE:
id = object.getId();
if (id < 0) viewImage(object.getName());
else viewImage(id);
break;
case WikiDataObject.PROTOCOL:
viewProtocol(object.getId());
break;
}
} else if (SelectionWizard.SELECTED_ITEMS_PROPERTY.equals(name)) {
Map m = (Map) evt.getNewValue();
if (m == null || m.size() != 1) return;
Set set = m.entrySet();
Entry entry;
Iterator i = set.iterator();
Class type;
while (i.hasNext()) {
entry = (Entry) i.next();
type = (Class) entry.getKey();
view.handleObjectsSelection(type, (Collection) entry.getValue());
}
} else if (PreviewPanel.OPEN_FILE_PROPERTY.equals(name)) {
Long id = (Long) evt.getNewValue();
if (id != null) viewProtocol(id.longValue());
} else if (MetadataViewer.SETTINGS_APPLIED_PROPERTY.equals(name)) {
model.loadRenderingControl(RenderingControlLoader.RELOAD);
view.onSettingsApplied(true);
} else if (MetadataViewer.ACTIVITY_OPTIONS_PROPERTY.equals(name)) {
List l = (List) evt.getNewValue();
view.activityOptions((Component) l.get(0), (Point) l.get(1), (Integer) l.get(2));
} else if (FigureDialog.CREATE_FIGURE_PROPERTY.equals(name)) {
view.createFigure(evt.getNewValue());
} else if (FigureDialog.CLOSE_FIGURE_PROPERTY.equals(name)) {
figureDialog = null;
} else if (MetadataViewer.CLOSE_RENDERER_PROPERTY.equals(name)) {
view.discardRenderer(evt.getNewValue());
} else if (MetadataViewer.RELATED_NODES_PROPERTY.equals(name)) {
view.onRelatedNodesSet();
} else if (ScriptingDialog.RUN_SELECTED_SCRIPT_PROPERTY.equals(name)) {
// view.manageScript((ScriptObject) evt.getNewValue(),
// MetadataViewer.RUN);
} else if (ScriptingDialog.DOWNLOAD_SELECTED_SCRIPT_PROPERTY.equals(name)) {
Object value = evt.getNewValue();
if (value instanceof ScriptObject)
view.manageScript((ScriptObject) value, MetadataViewer.DOWNLOAD);
else if (value instanceof String) {
ScriptObject script = view.getScriptFromName((String) value);
if (script != null) view.manageScript(script, MetadataViewer.DOWNLOAD);
}
} else if (ScriptingDialog.VIEW_SELECTED_SCRIPT_PROPERTY.equals(name)) {
Object value = evt.getNewValue();
if (value instanceof ScriptObject)
view.manageScript((ScriptObject) value, MetadataViewer.VIEW);
else if (value instanceof String) {
ScriptObject script = view.getScriptFromName((String) value);
if (script != null) view.manageScript(script, MetadataViewer.VIEW);
}
} else if (AnalysisResultsItem.ANALYSIS_RESULTS_DELETE.equals(name)) {
AnalysisResultsItem item = (AnalysisResultsItem) evt.getNewValue();
List<FileAnnotationData> list = item.getAttachments();
view.fireAnnotationsDeletion(list);
} else if (AnalysisResultsItem.ANALYSIS_RESULTS_VIEW.equals(name)) {
AnalysisResultsItem item = (AnalysisResultsItem) evt.getNewValue();
if (view.getRndIndex() == MetadataViewer.RND_GENERAL) {
model.displayAnalysisResults(item);
/*
ViewImage event = new ViewImage(item.getData(), null);
event.setAnalysis(item);
EventBus bus = MetadataViewerAgent.getRegistry().getEventBus();
bus.post(event);
*/
} else {
model.displayAnalysisResults(item);
}
} else if (AnalysisResultsItem.ANALYSIS_RESULTS_CANCEL.equals(name)) {
AnalysisResultsItem item = (AnalysisResultsItem) evt.getNewValue();
view.cancelAnalysisResultsLoading(item);
}
}