Java tutorial
/* * org.openmicroscopy.shoola.agents.metadata.editor.EditorModel * *------------------------------------------------------------------------------ * Copyright (C) 2006-2014 University of Dundee. All rights reserved. * * * This program is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along * with this program; if not, write to the Free Software Foundation, Inc., * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. * *------------------------------------------------------------------------------ */ package org.openmicroscopy.shoola.agents.metadata.editor; //Java imports import java.awt.Color; import java.awt.image.BufferedImage; import java.io.File; import java.sql.Timestamp; import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.Comparator; import java.util.HashMap; import java.util.Iterator; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Set; import java.util.Map.Entry; import javax.swing.Icon; import javax.swing.JFrame; //Third-party libraries import org.apache.commons.collections.CollectionUtils; import org.apache.commons.lang.StringUtils; //Application-internal dependencies import omero.model.OriginalFile; import omero.model.PlaneInfo; import org.openmicroscopy.shoola.agents.metadata.AcquisitionDataLoader; import org.openmicroscopy.shoola.agents.metadata.AnalysisResultsFileLoader; import org.openmicroscopy.shoola.agents.metadata.FileAnnotationChecker; import org.openmicroscopy.shoola.agents.metadata.AttachmentsLoader; import org.openmicroscopy.shoola.agents.metadata.ChannelDataLoader; import org.openmicroscopy.shoola.agents.metadata.ChannelDataSaver; import org.openmicroscopy.shoola.agents.metadata.DiskSpaceLoader; import org.openmicroscopy.shoola.agents.metadata.EditorLoader; import org.openmicroscopy.shoola.agents.metadata.EnumerationLoader; import org.openmicroscopy.shoola.agents.metadata.FileLoader; import org.openmicroscopy.shoola.agents.metadata.FilesetLoader; import org.openmicroscopy.shoola.agents.metadata.IconManager; import org.openmicroscopy.shoola.agents.metadata.ImageSizeLoader; import org.openmicroscopy.shoola.agents.metadata.InstrumentDataLoader; import org.openmicroscopy.shoola.agents.metadata.MetadataViewerAgent; import org.openmicroscopy.shoola.agents.metadata.OriginalMetadataLoader; import org.openmicroscopy.shoola.agents.metadata.PasswordEditor; import org.openmicroscopy.shoola.agents.metadata.PlaneInfoLoader; import org.openmicroscopy.shoola.agents.metadata.ROILoader; import org.openmicroscopy.shoola.agents.metadata.RenderingControlLoader; import org.openmicroscopy.shoola.agents.metadata.ScriptLoader; import org.openmicroscopy.shoola.agents.metadata.ScriptsLoader; import org.openmicroscopy.shoola.agents.metadata.TagsLoader; import org.openmicroscopy.shoola.agents.metadata.UserPhotoLoader; import org.openmicroscopy.shoola.agents.metadata.UserPhotoUploader; import org.openmicroscopy.shoola.agents.metadata.browser.Browser; import org.openmicroscopy.shoola.agents.metadata.rnd.Renderer; import org.openmicroscopy.shoola.agents.metadata.rnd.RendererFactory; import org.openmicroscopy.shoola.agents.metadata.util.AnalysisResultsItem; import org.openmicroscopy.shoola.agents.metadata.util.DataToSave; import org.openmicroscopy.shoola.agents.metadata.view.MetadataViewer; import org.openmicroscopy.shoola.agents.util.EditorUtil; import org.openmicroscopy.shoola.agents.util.ViewerSorter; import org.openmicroscopy.shoola.agents.util.ui.PermissionMenu; import org.openmicroscopy.shoola.env.Environment; import org.openmicroscopy.shoola.env.LookupNames; import org.openmicroscopy.shoola.env.data.AdminService; import org.openmicroscopy.shoola.env.data.OmeroMetadataService; import org.openmicroscopy.shoola.env.data.model.AdminObject; import org.openmicroscopy.shoola.env.data.model.AnnotationLinkData; import org.openmicroscopy.shoola.env.data.model.DeletableObject; import org.openmicroscopy.shoola.env.data.model.DeleteActivityParam; import org.openmicroscopy.shoola.env.data.model.DownloadActivityParam; import org.openmicroscopy.shoola.env.data.model.DownloadArchivedActivityParam; import org.openmicroscopy.shoola.env.data.model.EnumerationObject; import org.openmicroscopy.shoola.env.data.model.SaveAsParam; import org.openmicroscopy.shoola.env.data.model.ScriptObject; import org.openmicroscopy.shoola.env.data.util.SecurityContext; import org.openmicroscopy.shoola.env.data.util.StructuredDataResults; import org.openmicroscopy.shoola.env.log.LogMessage; import org.openmicroscopy.shoola.env.rnd.RenderingControl; import org.openmicroscopy.shoola.env.ui.UserNotifier; import org.openmicroscopy.shoola.util.file.modulo.ModuloInfo; import org.openmicroscopy.shoola.util.file.modulo.ModuloParser; import org.openmicroscopy.shoola.util.ui.component.ObservableComponent; import pojos.AnnotationData; import pojos.BooleanAnnotationData; import pojos.ChannelAcquisitionData; import pojos.ChannelData; import pojos.DataObject; import pojos.DatasetData; import pojos.DoubleAnnotationData; import pojos.ExperimenterData; import pojos.FileAnnotationData; import pojos.FileData; import pojos.FilesetData; import pojos.GroupData; import pojos.ImageAcquisitionData; import pojos.ImageData; import pojos.InstrumentData; import pojos.LongAnnotationData; import pojos.MultiImageData; import pojos.PermissionData; import pojos.PixelsData; import pojos.PlateAcquisitionData; import pojos.PlateData; import pojos.ProjectData; import pojos.RatingAnnotationData; import pojos.ScreenData; import pojos.TagAnnotationData; import pojos.TermAnnotationData; import pojos.TextualAnnotationData; import pojos.WellData; import pojos.WellSampleData; import pojos.XMLAnnotationData; /** * The Model component in the <code>EditorViewer</code> MVC triad. * This class knows how to store and manipulate the results. * It provides a suitable data loader. * The {@link EditorComponent} intercepts the results of data loadings, * feeds them back to this class and fires state transitions as appropriate. * * * @author Jean-Marie Burel * <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a> * @author Donald MacDonald * <a href="mailto:donald@lifesci.dundee.ac.uk">donald@lifesci.dundee.ac.uk</a> * @version 3.0 * @since OME3.0 */ class EditorModel { /** Identifies <code>all</code> the objects.*/ static final int ALL = PermissionMenu.ALL; /** Identifies the objects added by current user.*/ static final int ME = PermissionMenu.ME; /** Identifies the objects added by others.*/ static final int OTHER = PermissionMenu.OTHER; /** The index of the default channel. */ static final int DEFAULT_CHANNEL = 0; /** The file namespaces to exclude.*/ private final static List<String> EXCLUDED_FILE_NS; static { EXCLUDED_FILE_NS = new ArrayList<String>(); EXCLUDED_FILE_NS.add(FileAnnotationData.COMPANION_FILE_NS); EXCLUDED_FILE_NS.add(FileAnnotationData.FLIM_NS); } /** The parent of this editor. */ private MetadataViewer parent; /** Reference to the component that embeds this model. */ private Editor component; /** The object this editor is for. */ private Object refObject; /** The parent of the object this editor is for. */ private Object parentRefObject; /** The parent of the object this editor is for. */ private Object gpRefObject; /** * Map containing the annotations made by users. * The keys are the user, the value the collection of * textual annotations. */ private Map<Long, List> textualAnnotationsByUsers; /** The annotations ordered by date. */ private List textualAnnotationsByDate; /** Collection of loaders. */ private List<EditorLoader> loaders; /** Collection of existing tags if any. */ private Collection existingTags; /** Collection of existing attachments if any. */ private Collection existingAttachments; /** The list of emission wavelengths for a given set of pixels. */ private Map emissionsWavelengths; /** Used to sort the various collections. */ private ViewerSorter sorter; /** Reference to the browser. */ private Browser browser; /** The image acquisition data. */ private ImageAcquisitionData imageAcquisitionData; /** The instrument data. */ private InstrumentData instrumentData; /** The enumerations related to channel metadata. */ private Map<String, List<EnumerationObject>> channelEnumerations; /** The enumerations related to image metadata. */ private Map<String, List<EnumerationObject>> imageEnumerations; /** The map hosting the channels acquisition data. */ private Map<Integer, ChannelAcquisitionData> channelAcquisitionDataMap; /** The map hosting the channels plane info. */ private Map<Integer, Collection> channelPlaneInfoMap; /** Reference to the renderer. */ private Renderer renderer; /** Collection of annotations to unlink and delete. */ private List<AnnotationData> toDelete; /** Collection of uploaded scripts. */ private Map<Long, ScriptObject> scripts; /** Scripts with a UI. */ private List<ScriptObject> scriptsWithUI; /** The file annotation with the original metadata. */ private FileAnnotationData originalMetadata; /** The collection of analysis results. */ private Map<AnalysisResultsItem, EditorLoader> resultsLoader; /** The photo of the current user.*/ private Map<Long, BufferedImage> usersPhoto; /** Flag indicating if the image is a big image or not.*/ private boolean largeImage; /** The file set associated to the image if an image is selected.*/ private Set<FilesetData> set; /** Checks if the image is a large image or not. */ private void fireLargeImageLoading() { ImageData img = null; if (refObject instanceof ImageData) { img = (ImageData) refObject; } else if (refObject instanceof WellSampleData) { img = ((WellSampleData) refObject).getImage(); } PixelsData data = img.getDefaultPixels(); if (data == null) { largeImage = false; return; } ImageSizeLoader loader = new ImageSizeLoader(component, parent.getSecurityContext(), data.getId()); loader.load(); } /** * Downloads the files. * * @param folder The folder to save the file into. * @param override Flag indicating to override the existing file if it * exists, <code>false</code> otherwise. */ private void downloadFiles(File folder, boolean override) { UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier(); FileAnnotationData fa = (FileAnnotationData) getRefObject(); OriginalFile f = (OriginalFile) fa.getContent(); IconManager icons = IconManager.getInstance(); DownloadActivityParam activity = new DownloadActivityParam(f, folder, icons.getIcon(IconManager.DOWNLOAD_22)); un.notifyActivity(getSecurityContext(), activity); Collection l = parent.getRelatedNodes(); if (l == null) return; Iterator i = l.iterator(); Object o; while (i.hasNext()) { o = i.next(); if (o instanceof FileAnnotationData) { fa = (FileAnnotationData) o; f = (OriginalFile) fa.getContent(); if (f.isLoaded()) { activity = new DownloadActivityParam(f, folder, icons.getIcon(IconManager.DOWNLOAD_22)); } else { long id = fa.getId(); Environment env = (Environment) MetadataViewerAgent.getRegistry().lookup(LookupNames.ENV); String path = env.getOmeroFilesHome(); path += File.separator + fa.getFileName(); activity = new DownloadActivityParam(id, DownloadActivityParam.FILE_ANNOTATION, new File(path), icons.getIcon(IconManager.DOWNLOAD_22)); } activity.setFileName(fa.getFileName()); un.notifyActivity(getSecurityContext(), activity); } } } /** * Downloads the archived images. * * @param file The file where to download the content. * @param override Flag indicating to override the existing file if it * exists, <code>false</code> otherwise. */ private void downloadImages(File file, boolean override) { List<ImageData> images = new ArrayList<ImageData>(); List<DataObject> l = getSelectedObjects(); if (!CollectionUtils.isEmpty(l)) { Iterator<DataObject> i = l.iterator(); DataObject o; List<Long> filesetIds = new ArrayList<Long>(); long id; ImageData image; while (i.hasNext()) { o = i.next(); if (isArchived(o)) { image = (ImageData) o; id = image.getFilesetId(); if (id < 0) images.add(image); else if (!filesetIds.contains(id)) { images.add(image); filesetIds.add(id); } } } } if (!CollectionUtils.isEmpty(images)) { Iterator<ImageData> i = images.iterator(); DownloadArchivedActivityParam p; UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier(); IconManager icons = IconManager.getInstance(); Icon icon = icons.getIcon(IconManager.DOWNLOAD_22); SecurityContext ctx = getSecurityContext(); while (i.hasNext()) { p = new DownloadArchivedActivityParam(file, i.next(), icon); p.setOverride(override); un.notifyActivity(ctx, p); } } } /** * Sorts the passed collection of annotations by date starting with the * most recent. * * @param annotations Collection of {@link AnnotationData} linked to * the currently edited <code>DataObject</code>. */ private void sortAnnotationByDate(List annotations) { if (annotations == null || annotations.size() == 0) return; Comparator c = new Comparator() { public int compare(Object o1, Object o2) { Timestamp t1 = ((AnnotationData) o1).getLastModified(), t2 = ((AnnotationData) o2).getLastModified(); long n1 = t1.getTime(); long n2 = t2.getTime(); int v = 0; if (n1 < n2) v = -1; else if (n1 > n2) v = 1; return -v; } }; Collections.sort(annotations, c); } /** * Sorts the passed nodes by row. * * @param nodes The nodes to sort. * @return See above. */ private List sortPlane(Collection nodes) { List<Object> l = new ArrayList<Object>(); if (nodes == null) return l; Iterator i = nodes.iterator(); while (i.hasNext()) { l.add(i.next()); } Comparator c = new Comparator() { public int compare(Object o1, Object o2) { PlaneInfo i1 = (PlaneInfo) o1, i2 = (PlaneInfo) o2; int t1 = i1.getTheT().getValue(); int t2 = i2.getTheT().getValue(); int v = 0; if (t1 < t2) v = -1; else if (t1 > t2) v = 1; return v; } }; Collections.sort(l, c); return l; } /** * Sorts the passed collection of enumerations. * * @param enumerations Collection of {@link EnumerationObject}. */ private void sortEnumerations(List<EnumerationObject> enumerations) { if (enumerations == null || enumerations.size() == 0) return; Comparator c = new Comparator() { public int compare(Object o1, Object o2) { String s1 = ((EnumerationObject) o1).getValue(), s2 = ((EnumerationObject) o2).getValue(); int v = 0; int result = (s1.toLowerCase()).compareTo(s2.toLowerCase()); if (result < 0) v = -1; else if (result > 0) v = 1; return v; } }; Collections.sort(enumerations, c); } /** * Starts an asynchronous call to load the photo of the currently * selected user. */ private void fireExperimenterPhotoLoading() { if (refObject instanceof ExperimenterData) { ExperimenterData exp = (ExperimenterData) refObject; if (usersPhoto == null || !usersPhoto.containsKey(exp.getId())) { UserPhotoLoader loader = new UserPhotoLoader(component, parent.getSecurityContext(), exp); loader.load(); } } } /** * Returns the group corresponding to the specified id or <code>null</code>. * * @param groupId The identifier of the group. * @return See above. */ private GroupData getGroup(long groupId) { Collection groups = MetadataViewerAgent.getAvailableUserGroups(); if (groups == null) return null; Iterator i = groups.iterator(); GroupData group; while (i.hasNext()) { group = (GroupData) i.next(); if (group.getId() == groupId) return group; } return null; } /** * Indicates to load all annotations available if the user can annotate * and is an administrator/group owner or to only load the user's * annotation. * * @return See above */ private boolean canRetrieveAll() { if (!canAnnotate()) return false; //check the group level GroupData group = getGroup(getRefObjectGroupID()); if (group == null) return false; switch (group.getPermissions().getPermissionsLevel()) { case GroupData.PERMISSIONS_GROUP_READ: if (MetadataViewerAgent.isAdministrator()) return true; Set leaders = group.getLeaders(); Iterator i = leaders.iterator(); long userID = getCurrentUser().getId(); ExperimenterData exp; while (i.hasNext()) { exp = (ExperimenterData) i.next(); if (exp.getId() == userID) return true; } return false; case GroupData.PERMISSIONS_PRIVATE: return false; } return true; } /** * Returns <code>true</code> if the object can be deleted, * <code>false</code> otherwise. * * @param data The data to handle. * @param result the object of reference. * @return See above. */ private boolean canDeleteLink(Object data, StructuredDataResults result) { if (!(data instanceof DataObject)) return false; DataObject d = (DataObject) data; if (result == null) return false; Collection<AnnotationLinkData> links = result.getAnnotationLinks(); if (links == null) return false; Iterator<AnnotationLinkData> i = links.iterator(); AnnotationLinkData link; while (i.hasNext()) { link = i.next(); if (d.getId() == link.getChild().getId()) return link.canDelete(); } return false; } /** * Creates a new instance. * * @param refObject The object this editor is for. * @param parent The parent of this browser. */ EditorModel(Object refObject, MetadataViewer parent) { if (refObject == null) throw new IllegalArgumentException("No object set."); this.parent = parent; this.refObject = refObject; loaders = new ArrayList<EditorLoader>(); sorter = new ViewerSorter(); } /** * Adds the annotation to the collection of annotation to be deleted. * * @param annotation The value to add. */ void deleteAnnotation(AnnotationData annotation) { if (annotation == null) return; if (toDelete == null) toDelete = new ArrayList<AnnotationData>(); toDelete.add(annotation); } /** * Returns the collection of annotation to delete. * * @return See above. */ List<AnnotationData> getAnnotationToDelete() { return toDelete; } /** * Returns <code>true</code> if multiple selection is on, * <code>false</code> otherwise. * * @return See above. */ boolean isMultiSelection() { return !parent.isSingleMode(); } /** * Returns the observable. * * @return See above. */ ObservableComponent getObservable() { return parent; } /** * Sets the browser. * * @param browser The value to set. */ void setBrowser(Browser browser) { this.browser = browser; } /** * Returns the browser. * * @return See above. */ Browser getBrowser() { return browser; } /** * Called by the <code>Editor</code> after creation to allow this * object to store a back reference to the embedding component. * * @param component The embedding component. */ void initialize(Editor component) { this.component = component; } /** * Returns <code>true</code> if the permissions can be shown, * <code>false</code> otherwise. * * @return See above. */ boolean isPermissionsShowable() { Object ref = getRefObject(); if (ref == null) return false; return ((ref instanceof ProjectData) || (ref instanceof DatasetData)); } /** * Returns the permission of the currently edited object. * Returns <code>null</code> if no permission associated. (This should never * happens). * * @return See above. */ PermissionData getRefObjectPermissions() { Object ref = getRefObject(); if (ref instanceof DataObject) return ((DataObject) ref).getPermissions(); return null; } /** * Returns the name of the object if any. * * @return See above. */ String getRefObjectName() { return getObjectName(getPrimarySelect()); } /** * Returns the name of the specified object. * * @param ref The object to handle. * @return See above. */ String getObjectName(Object ref) { String name = ""; if (ref instanceof ImageData) name = ((ImageData) ref).getName(); else if (ref instanceof DatasetData) name = ((DatasetData) ref).getName(); else if (ref instanceof ProjectData) name = ((ProjectData) ref).getName(); else if (ref instanceof TagAnnotationData || ref instanceof TermAnnotationData) name = ((AnnotationData) ref).getContentAsString(); else if (ref instanceof ScreenData) name = ((ScreenData) ref).getName(); else if (ref instanceof PlateData) name = ((PlateData) ref).getName(); else if (ref instanceof PlateAcquisitionData) name = ((PlateAcquisitionData) ref).getLabel(); else if (ref instanceof FileAnnotationData) name = ((FileAnnotationData) ref).getFileName(); else if (ref instanceof WellSampleData) { WellSampleData ws = (WellSampleData) ref; ImageData img = ws.getImage(); if (img != null && img.getId() >= 0) name = img.getName(); } else if (ref instanceof FileData) name = ((FileData) ref).getName(); else if (ref instanceof MultiImageData) name = ((MultiImageData) ref).getName(); if (name == null) return ""; return name.trim(); } /** * Returns the name associated to the specified object. * * @param ref The object to handle. * @return See above. */ String getObjectTypeAsString(Object ref) { if (ref instanceof ImageData) return "Image"; else if (ref instanceof DatasetData) return "Dataset"; else if (ref instanceof ProjectData) return "Project"; else if (ref instanceof ScreenData) return "Screen"; else if (ref instanceof PlateData) return "Plate"; else if (refObject instanceof PlateAcquisitionData) return "Plate Run"; else if (refObject instanceof FileAnnotationData) { FileAnnotationData fa = (FileAnnotationData) refObject; String ns = fa.getNameSpace(); if (FileAnnotationData.EDITOR_EXPERIMENT_NS.equals(ns)) return "Experiment"; else if (FileAnnotationData.EDITOR_PROTOCOL_NS.equals(ns)) return "Protocol"; return "File"; } else if (refObject instanceof WellSampleData) return "Field"; else if (refObject instanceof TagAnnotationData) { TagAnnotationData tag = (TagAnnotationData) refObject; if (TagAnnotationData.INSIGHT_TAGSET_NS.equals(tag.getNameSpace())) return "Tag Set"; else return "Tag"; } else if (refObject instanceof FileData) { FileData f = (FileData) refObject; if (f.isDirectory()) return "Folder"; return "File"; } else if (refObject instanceof TermAnnotationData) { return "Term"; } else if (refObject instanceof XMLAnnotationData) { return "XML file"; } else if (refObject instanceof LongAnnotationData || refObject instanceof DoubleAnnotationData) { return "Numerical value"; } return ""; } /** * Returns the description of the object if any. * * @return See above. */ String getRefObjectDescription() { String description = ""; Object ref = getPrimarySelect(); if (ref instanceof ImageData) description = ((ImageData) ref).getDescription(); else if (ref instanceof DatasetData) description = ((DatasetData) ref).getDescription(); else if (ref instanceof ProjectData) description = ((ProjectData) ref).getDescription(); else if (ref instanceof ScreenData) description = ((ScreenData) ref).getDescription(); else if (ref instanceof PlateData) description = ((PlateData) ref).getDescription(); else if (ref instanceof PlateAcquisitionData) description = ((PlateAcquisitionData) ref).getDescription(); else if (ref instanceof TagAnnotationData) { description = ((TagAnnotationData) ref).getTagDescription(); } else if (ref instanceof WellSampleData) { if (parentRefObject instanceof WellData) { WellData ws = (WellData) parentRefObject; description = ws.getWellType(); } ImageData img = ((WellSampleData) ref).getImage(); if (!StringUtils.isEmpty(img.getDescription())) description = img.getDescription(); } else if (ref instanceof FileData) description = null;//((FileData) ref).getDescription(); if (description == null) return ""; return description.trim(); } /** * Returns the id of the reference object if it is an instance of * <code>DataObject</code> or <code>-1</code> otherwise. * * @return See above. */ long getRefObjectID() { Object ref = getRefObject(); if (ref instanceof DataObject) return ((DataObject) ref).getId(); return -1; } /** * Returns the group's id of the reference object if it is an instance of * <code>DataObject</code> or <code>-1</code> otherwise. * * @return See above. */ long getRefObjectGroupID() { Object ref = getRefObject(); if (ref instanceof DataObject) return ((DataObject) ref).getGroupId(); return -1; } /** * Returns <code>true</code> if the user currently logged in is * the one currently edited, <code>false</code> otherwise. * * @return See above. */ boolean isSelf() { Object ref = getRefObject(); if (!(ref instanceof ExperimenterData)) return false; ExperimenterData exp = getCurrentUser(); return exp.getId() == getRefObjectID(); } /** * Returns the <code>DataObject</code> this editor is for. * * @return See above. */ Object getRefObject() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return refObject; return refObject; } /** * Returns the primary select object. * * @return See above. */ Object getPrimarySelect() { if (!isMultiSelection()) return getRefObject(); List list = parent.getRelatedNodes(); if (CollectionUtils.isEmpty(list)) return getRefObject(); return list.get(0); } /** * Returns <code>true</code> if the object can be edited, * <code>false</code> otherwise. * * @return See above. */ boolean canEdit() { return canEdit(refObject); } /** * Returns <code>true</code> if the object can be edited, * <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean canEdit(Object data) { if (!(data instanceof DataObject)) return false; DataObject d = (DataObject) data; return d.canEdit(); } /** * Returns <code>true</code> if the object can be linked, * <code>false</code> otherwise. * * @return See above. */ boolean canLink() { return canLink(refObject); } /** * Returns <code>true</code> if the object can be linked, e.g. * image added to dataset, <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean canLink(Object data) { switch (getDisplayMode()) { case LookupNames.GROUP_DISPLAY: if (data instanceof DataObject) return ((DataObject) data).canLink(); return false; case LookupNames.EXPERIMENTER_DISPLAY: default: return EditorUtil.isUserOwner(data, getUserID()); } } /** * Returns <code>true</code> if the object can be annotated, * <code>false</code> otherwise. * * @return See above. */ boolean canAnnotate() { return canAnnotate(refObject); } /** * Returns <code>true</code> if the object can be annotated, * <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean canAnnotate(Object data) { if (!(data instanceof DataObject)) return false; DataObject d = (DataObject) data; return d.canAnnotate(); } /** * Returns <code>true</code> if the object can be deleted, * <code>false</code> otherwise. * * @return See above. */ boolean canDelete() { return canDelete(refObject); } /** * Returns <code>true</code> if the object can be deleted, * <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean canDelete(Object data) { if (!(data instanceof DataObject)) return false; DataObject d = (DataObject) data; return d.canDelete(); } /** * Returns <code>true</code> if the object can be deleted, * <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean canDeleteLink(Object data) { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return false; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); while (i.hasNext()) { e = i.next(); if (canDeleteLink(data, e.getValue())) return true; } return false; } /** * Returns <code>true</code> if the object is a modulo annotation, * <code>false</code> otherwise. * * @param data The data to handle. * @return See above. */ boolean isModulo(Object data) { if (!(data instanceof XMLAnnotationData)) return false; //parse the annotation. XMLAnnotationData d = (XMLAnnotationData) data; ModuloParser parser = new ModuloParser(d.getText()); try { parser.parse(); return !CollectionUtils.isEmpty(parser.getModulos()); } catch (Exception e) { LogMessage msg = new LogMessage(); msg.append("Error while reading modulo annotation."); msg.print(e); MetadataViewerAgent.getRegistry().getLogger().error(this, msg); } return false; } /** * Returns <code>true</code> if the selected objects belong to several * groups, <code>false</code> otherwise. * * @return See above. */ boolean isAcrossGroups() { List<DataObject> l = getSelectedObjects(); if (l == null || l.size() == 0) return false; List<Long> ids = new ArrayList<Long>(); Iterator<DataObject> i = l.iterator(); DataObject data; while (i.hasNext()) { data = i.next(); if (!ids.contains(data.getGroupId())) ids.add(data.getGroupId()); } return ids.size() > 1; } /** * Returns <code>true</code> if the annotation can be added, should * only be invoked for tagging or adding attachments, <code>false</code> * otherwise. * * @return See above. */ boolean canAddAnnotationLink() { if (!canAnnotate()) return false; if (!isMultiSelection()) return true; //multi selection. List l = parent.getRelatedNodes(); if (l == null) return false; Iterator i = l.iterator(); DataObject data; List<Long> ids = new ArrayList<Long>(); while (i.hasNext()) { data = (DataObject) i.next(); if (!(data instanceof GroupData || data instanceof ExperimenterData)) { if (!ids.contains(data.getGroupId())) ids.add(data.getGroupId()); } } return ids.size() <= 1; } /** * Returns <code>true</code> if the annotation can be deleted, should * only be invoked for tagging or adding attachments, <code>false</code> * otherwise. * * @return See above. */ boolean canDeleteAnnotationLink() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return false; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); StructuredDataResults data; Collection<AnnotationLinkData> links; Iterator<AnnotationLinkData> j; while (i.hasNext()) { e = i.next(); data = e.getValue(); links = data.getAnnotationLinks(); if (links != null) { j = links.iterator(); while (j.hasNext()) if (j.next().canDelete()) return true; } } return false; } /** * Returns <code>true</code> if the currently logged in user is the * owner of the object, <code>false</code> otherwise. * * @param object The object to handle. * @return See above. */ boolean isUserOwner(Object object) { long id = getUserID(); if (object == null) return false; if (object instanceof ExperimenterData) return (((ExperimenterData) object).getId() == id); if (!(object instanceof DataObject)) return false; if (object instanceof FileData || object instanceof ImageData) { DataObject f = (DataObject) object; if (f.getId() < 0) return id == getUserID(); } return EditorUtil.isUserOwner(object, id); } /** * Returns <code>true</code> if the current user is the owner of the link * between the passed annotation and the currently selected object. * * @param annotation The annotation to handle. * @return See above. */ boolean isLinkOwner(Object annotation) { Map<DataObject, StructuredDataResults> data = getAllStructuredData(); if (data == null) return false; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> j = data.entrySet().iterator(); Iterator<AnnotationLinkData> i; Collection<AnnotationLinkData> links; AnnotationLinkData link; DataObject ann = (DataObject) annotation; long id = getUserID(); while (j.hasNext()) { e = j.next(); links = e.getValue().getAnnotationLinks(); if (links != null) { i = links.iterator(); while (i.hasNext()) { link = i.next(); if (link.getChild().getId() == ann.getId() && link.getOwner().getId() == id) { return true; } } } } return false; } /** * Returns <code>true</code> if the annotation has been added by others, * <code>false</code> otherwise. * * @param data The annotation to handle. * @return See above. */ boolean isAnnotatedByOther(DataObject data) { if (data == null) return false; List<ExperimenterData> annotators = getAnnotators(data); if (annotators == null || annotators.size() == 0) return false; if (annotators.size() == 1) { ExperimenterData exp = annotators.get(0); long id = getUserID(); return exp.getId() != id; } return true; } /** * Returns the collection of experimenters who use the annotation. * * @param annotation The annotation to handle. * @return See above. */ List<ExperimenterData> getAnnotators(Object annotation) { return getAnnotators(null, annotation); } /** * Returns the collection of experimenters who use the annotation. * * @param ref The object of reference. * @param annotation The annotation to handle. * @return See above. */ List<ExperimenterData> getAnnotators(DataObject ref, Object annotation) { List<ExperimenterData> list = new ArrayList<ExperimenterData>(); Map<DataObject, StructuredDataResults> data = getAllStructuredData(); if (data == null) return list; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> j = data.entrySet().iterator(); Iterator<AnnotationLinkData> i; Collection<AnnotationLinkData> links; AnnotationLinkData link; DataObject ann = (DataObject) annotation; List<Long> ids = new ArrayList<Long>(); while (j.hasNext()) { e = j.next(); if (ref == null) { links = e.getValue().getAnnotationLinks(); if (links != null) { i = links.iterator(); while (i.hasNext()) { link = i.next(); if (link.getChild().getId() == ann.getId()) { if (!ids.contains(link.getOwner().getId())) { list.add(link.getOwner()); ids.add(link.getOwner().getId()); } } } } } else { if (ref.getId() == e.getKey().getId()) { links = e.getValue().getAnnotationLinks(); if (links != null) { i = links.iterator(); while (i.hasNext()) { link = i.next(); if (link.getChild().getId() == ann.getId()) { if (!ids.contains(link.getOwner().getId())) { list.add(link.getOwner()); ids.add(link.getOwner().getId()); } } } } break; } } } return list; } /** * Returns the links corresponding to the level and the annotation. * * @param level The level to handle. * @param ho The annotation. * @return */ List<Object> getLinks(int level, AnnotationData ho) { Map<DataObject, StructuredDataResults> data = getAllStructuredData(); if (data == null) return null; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> j = data.entrySet().iterator(); Iterator<AnnotationLinkData> i; AnnotationLinkData d; List<Object> results = new ArrayList<Object>(); long userID = getCurrentUser().getId(); Collection<AnnotationLinkData> links; while (j.hasNext()) { e = j.next(); links = e.getValue().getAnnotationLinks(); if (links != null) { i = links.iterator(); switch (level) { case ALL: while (i.hasNext()) { d = i.next(); if (ho.getId() == d.getChild().getId()) { results.add(d.getLink()); } } break; case ME: while (i.hasNext()) { d = i.next(); if (ho.getId() == d.getChild().getId() && userID == d.getOwner().getId()) { results.add(d.getLink()); } } break; case OTHER: while (i.hasNext()) { d = i.next(); if (ho.getId() == d.getChild().getId() && userID != d.getOwner().getId()) { results.add(d.getLink()); } } } } } return results; } /** * Returns the FileAnnotations corresponding to the given level. * * @param level The level to handle. * @return See above. */ List<FileAnnotationData> getFileAnnotatationsByLevel(int level) { List<FileAnnotationData> result = new ArrayList<FileAnnotationData>(); Collection<FileAnnotationData> all = getAllAttachments(); for (FileAnnotationData f : all) { switch (level) { case ALL: result.add(f); break; case ME: if (MetadataViewerAgent.getUserDetails().getId() == f.getOwner().getId()) { result.add(f); } break; case OTHER: if (MetadataViewerAgent.getUserDetails().getId() != f.getOwner().getId()) { result.add(f); } } } return result; } /** * Returns <code>true</code> if the annotation is already used by the * current user, <code>false</code> otherwise. * * @param annotation The annotation to handle. * @return See above. */ boolean isAnnotationUsedByUser(Object annotation) { Map<DataObject, StructuredDataResults> data = getAllStructuredData(); if (data == null) return false; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> j = data.entrySet().iterator(); Collection<AnnotationLinkData> links; Iterator<AnnotationLinkData> i; AnnotationLinkData link; long id = MetadataViewerAgent.getUserDetails().getId(); DataObject ann = (DataObject) annotation; while (j.hasNext()) { e = j.next(); links = e.getValue().getAnnotationLinks(); i = links.iterator(); while (i.hasNext()) { link = i.next(); if (link.getChild().getId() == ann.getId() && link.getOwner().getId() == id) return true; } } return false; } /** * Returns <code>true</code> if the user currently logged in, is a leader * of the selected group, <code>false</code> otherwise. * * @return */ boolean isAdministrator() { return MetadataViewerAgent.isAdministrator(); } /** * Returns <code>true</code> if the user currently logged in, is a leader * of the selected group, <code>false</code> otherwise. * * @return */ boolean isGroupLeader() { ExperimenterData exp = MetadataViewerAgent.getUserDetails(); Collection groups = MetadataViewerAgent.getAvailableUserGroups(); if (groups == null) return false; long groupID = exp.getDefaultGroup().getId(); Iterator i = groups.iterator(); GroupData g; Set leaders = null; while (i.hasNext()) { g = (GroupData) i.next(); if (g.getId() == groupID) { leaders = g.getLeaders(); break; } } if (leaders == null) return false; i = leaders.iterator(); ExperimenterData data; while (i.hasNext()) { data = (ExperimenterData) i.next(); if (data.getId() == exp.getId()) return true; } return false; } /** * Returns the first name and the last name of the owner. * * @param object The object to handle. * @return See above. */ String formatOwner(DataObject object) { if (object == null) return ""; if (object instanceof ExperimenterData) { return EditorUtil.formatExperimenter((ExperimenterData) object); } return formatOwner(object.getOwner()); } /** * Returns the date. * * @param object The object to handle. * @return See above. */ String formatDate(DataObject object) { return EditorUtil.formatDate(object); } /** * Returns the number of URLs linked to the <code>DataObject</code>. * * @return See above. */ int getTermsCount() { Collection<TermAnnotationData> terms = getTerms(); if (terms == null) return 0; return terms.size(); } /** * Returns the collection of the URLs linked to the <code>DataObject</code>. * * @return See above. */ Collection<TermAnnotationData> getTerms() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return null; return data.getTerms(); } /** * Returns the number of tags linked to the <code>DataObject</code>. * * @return See above. */ int getTagsCount() { Collection tags = getTags(); if (tags == null) return 0; return tags.size(); } /** * Returns the collection of the tags linked to the <code>DataObject</code>. * * @return See above. */ Collection<TagAnnotationData> getTags() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return new ArrayList<TagAnnotationData>(); Collection<TagAnnotationData> tags = data.getTags(); if (tags == null || tags.size() == 0) return new ArrayList<TagAnnotationData>(); return (Collection<TagAnnotationData>) sorter.sort(tags); } /** * Returns the collection of the tags linked to the * <code>DataObject</code>s. * * @return See above. */ Collection<TagAnnotationData> getAllTags() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<TagAnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<TagAnnotationData> tags; List<TagAnnotationData> results = new ArrayList<TagAnnotationData>(); List<Long> ids = new ArrayList<Long>(); Iterator<TagAnnotationData> j; TagAnnotationData tag; while (i.hasNext()) { e = i.next(); tags = e.getValue().getTags(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); if (!ids.contains(tag.getId())) { results.add(tag); ids.add(tag.getId()); } } } } return (Collection<TagAnnotationData>) sorter.sort(results); } /** * Returns the collection of the tags that are linked to all the selected * objects. * * @return See above. */ Collection<TagAnnotationData> getCommonTags() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<TagAnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<TagAnnotationData> tags; Map<Long, Integer> ids = new HashMap<Long, Integer>(); Iterator<TagAnnotationData> j; TagAnnotationData tag; Integer value; while (i.hasNext()) { e = i.next(); tags = e.getValue().getTags(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); value = ids.get(tag.getId()); if (value != null) { value++; } else value = 1; ids.put(tag.getId(), value); } } } //Extract the common tags. //The number of selected objects. List<TagAnnotationData> results = new ArrayList<TagAnnotationData>(); List<Long> count = new ArrayList<Long>(); int max = r.size(); i = r.entrySet().iterator(); while (i.hasNext()) { e = i.next(); tags = e.getValue().getTags(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); value = ids.get(tag.getId()); if (value != null && value == max && !count.contains(tag.getId())) { results.add(tag); count.add(tag.getId()); } } } } return (Collection<TagAnnotationData>) sorter.sort(results); } /** * Returns the objects tagged by the specified object. * * @param refTag The tag of reference. * @return See above. */ Map<DataObject, Boolean> getTaggedObjects(AnnotationData refTag) { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); Map<DataObject, Boolean> m = new HashMap<DataObject, Boolean>(); if (r == null) return m; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<TagAnnotationData> tags; Iterator<TagAnnotationData> j; TagAnnotationData tag; DataObject o; StructuredDataResults result; while (i.hasNext()) { e = i.next(); result = e.getValue(); tags = result.getTags(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); if (tag.getId() == refTag.getId()) { o = (DataObject) result.getRelatedObject(); m.put(o, canDeleteLink(tag, result)); break; } } } } return m; } /** * Returns the objects linked by the specified object. * * @param refFile The file of reference. * @return See above. */ Map<DataObject, Boolean> getObjectsWith(AnnotationData refFile) { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); Map<DataObject, Boolean> m = new HashMap<DataObject, Boolean>(); if (r == null) return m; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); if (refFile instanceof TermAnnotationData) { Collection<TermAnnotationData> files; Iterator<TermAnnotationData> j; TermAnnotationData file; DataObject o; StructuredDataResults result; while (i.hasNext()) { e = i.next(); result = e.getValue(); files = result.getTerms(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); if (file.getId() == refFile.getId()) { o = (DataObject) result.getRelatedObject(); m.put(o, canDeleteLink(file, result)); break; } } } } } else if (refFile instanceof FileAnnotationData) { Collection<FileAnnotationData> files; Iterator<FileAnnotationData> j; FileAnnotationData file; DataObject o; StructuredDataResults result; while (i.hasNext()) { e = i.next(); result = e.getValue(); files = result.getAttachments(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); if (file.getId() == refFile.getId()) { o = (DataObject) result.getRelatedObject(); m.put(o, canDeleteLink(file, result)); break; } } } } } else if (refFile instanceof XMLAnnotationData) { Collection<XMLAnnotationData> files; Iterator<XMLAnnotationData> j; XMLAnnotationData file; DataObject o; StructuredDataResults result; while (i.hasNext()) { e = i.next(); result = e.getValue(); files = result.getXMLAnnotations(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); if (file.getId() == refFile.getId()) { o = (DataObject) result.getRelatedObject(); m.put(o, canDeleteLink(file, result)); break; } } } } } return m; } /** * Returns the collection of the files linked to the * <code>DataObject</code> at import. * * @return See above. */ Collection<FileAnnotationData> getCompanionFiles() { StructuredDataResults data = parent.getStructuredData(); List<FileAnnotationData> list = new ArrayList<FileAnnotationData>(); if (data == null) return list; Collection<FileAnnotationData> attachments = data.getAttachments(); if (attachments == null) return list; Iterator<FileAnnotationData> i = attachments.iterator(); FileAnnotationData f; String ns; while (i.hasNext()) { f = i.next(); ns = f.getNameSpace(); if (FileAnnotationData.COMPANION_FILE_NS.equals(ns) && f != originalMetadata) { list.add(f); } } if (refObject instanceof WellSampleData) { data = parent.getParentStructuredData(); if (data != null) { attachments = data.getAttachments(); if (attachments != null) { while (i.hasNext()) { f = i.next(); ns = f.getNameSpace(); if (FileAnnotationData.COMPANION_FILE_NS.equals(ns) && f != originalMetadata) { list.add(f); } } } } } return (Collection<FileAnnotationData>) sorter.sort(list); } /** * Returns the collection of the attachments linked to the * <code>DataObject</code>. * * @return See above. */ Collection<FileAnnotationData> getAttachments() { StructuredDataResults data = parent.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.COMPANION_FILE_NS.equals(ns)) { //tmp String name = f.getFileName(); if (name.contains(FileAnnotationData.ORIGINAL_METADATA_NAME)) originalMetadata = f; } else if (!isNameSpaceExcluded(ns)) { l.add(f); } } if (getRefObject() instanceof WellSampleData) { data = parent.getParentStructuredData(); if (data != null) { attachments = data.getAttachments(); if (attachments != null) { i = attachments.iterator(); while (i.hasNext()) { f = i.next(); ns = f.getNameSpace(); if (FileAnnotationData.COMPANION_FILE_NS.equals(ns)) { String name = f.getFileName(); if (name.contains(FileAnnotationData.ORIGINAL_METADATA_NAME)) originalMetadata = f; } } } } } return (Collection<FileAnnotationData>) sorter.sort(l); } /** * Returns the collection of the attachments linked to the * <code>DataObject</code>. * * @return See above. */ Collection<FileAnnotationData> getAllAttachments() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<FileAnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<FileAnnotationData> files; List<FileAnnotationData> results = new ArrayList<FileAnnotationData>(); List<Long> ids = new ArrayList<Long>(); Iterator<FileAnnotationData> j; FileAnnotationData file; String ns; while (i.hasNext()) { e = i.next(); files = e.getValue().getAttachments(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); ns = file.getNameSpace(); if (!isNameSpaceExcluded(ns)) { if (!ids.contains(file.getId())) { results.add(file); ids.add(file.getId()); } } } } } return (Collection<FileAnnotationData>) sorter.sort(results); } /** * Returns the collection of the files that are linked to all the selected * objects. * * @return See above. */ Collection<FileAnnotationData> getCommonAttachments() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<FileAnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<FileAnnotationData> tags; Map<Long, Integer> ids = new HashMap<Long, Integer>(); Iterator<FileAnnotationData> j; FileAnnotationData tag; Integer value; String ns; while (i.hasNext()) { e = i.next(); tags = e.getValue().getAttachments(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); ns = tag.getNameSpace(); if (!isNameSpaceExcluded(ns)) { value = ids.get(tag.getId()); if (value != null) { value++; } else value = 1; ids.put(tag.getId(), value); } } } } //Extract the common tags. //The number of selected objects. List<FileAnnotationData> results = new ArrayList<FileAnnotationData>(); List<Long> count = new ArrayList<Long>(); int max = r.size(); i = r.entrySet().iterator(); while (i.hasNext()) { e = i.next(); tags = e.getValue().getAttachments(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); value = ids.get(tag.getId()); if (value != null && value == max && !count.contains(tag.getId())) { results.add(tag); count.add(tag.getId()); } } } } return (Collection<FileAnnotationData>) sorter.sort(results); } /** * Returns the collection of others annotations like Term, XML * * @return See above. */ Collection<AnnotationData> getOtherAnnotations() { StructuredDataResults data = parent.getStructuredData(); List<AnnotationData> l = new ArrayList<AnnotationData>(); if (data == null) return l; Collection<XMLAnnotationData> xml = data.getXMLAnnotations(); if (xml != null && !xml.isEmpty()) l.addAll(xml); Collection<AnnotationData> others = data.getOtherAnnotations(); if (others != null && !others.isEmpty()) l.addAll(others); return l; } /** * Returns the collection of the other annotations linked to the * <code>DataObject</code>. * * @return See above. */ Collection<AnnotationData> getAllOtherAnnotations() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<AnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<XMLAnnotationData> files; Collection<AnnotationData> others; List<AnnotationData> results = new ArrayList<AnnotationData>(); List<Long> ids = new ArrayList<Long>(); Iterator<XMLAnnotationData> j; Iterator<AnnotationData> k; XMLAnnotationData file; AnnotationData other; while (i.hasNext()) { e = i.next(); files = e.getValue().getXMLAnnotations(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); if (!ids.contains(file.getId())) { results.add(file); ids.add(file.getId()); } } } others = e.getValue().getOtherAnnotations(); if (others != null) { k = others.iterator(); while (k.hasNext()) { other = k.next(); if (!ids.contains(other.getId())) { results.add(other); ids.add(other.getId()); } } } } return (Collection<AnnotationData>) sorter.sort(results); } /** * Returns the modulo information if any associated to a given image. * * @return See above. */ Map<Integer, ModuloInfo> getModulo() { Collection<XMLAnnotationData> annotations = getXMLAnnotations(); Map<Integer, ModuloInfo> modulo = new HashMap<Integer, ModuloInfo>(); if (CollectionUtils.isEmpty(annotations)) return modulo; ModuloParser parser; Iterator<XMLAnnotationData> i = annotations.iterator(); XMLAnnotationData data; List<ModuloInfo> infos; Iterator<ModuloInfo> j; ModuloInfo info; while (i.hasNext()) { data = i.next(); parser = new ModuloParser(data.getText()); try { parser.parse(); infos = parser.getModulos(); j = infos.iterator(); while (j.hasNext()) { info = j.next(); modulo.put(info.getModuloIndex(), info); } } catch (Exception e) { LogMessage msg = new LogMessage(); msg.append("Error while reading modulo annotation."); msg.print(e); MetadataViewerAgent.getRegistry().getLogger().error(this, msg); } } return modulo; } /** * Returns the collection of XML annotations linked to the * <code>DataObject</code>. * * @return See above. */ Collection<XMLAnnotationData> getXMLAnnotations() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<XMLAnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<XMLAnnotationData> files; List<AnnotationData> results = new ArrayList<AnnotationData>(); List<Long> ids = new ArrayList<Long>(); Iterator<XMLAnnotationData> j; XMLAnnotationData file; while (i.hasNext()) { e = i.next(); files = e.getValue().getXMLAnnotations(); if (files != null) { j = files.iterator(); while (j.hasNext()) { file = j.next(); if (!ids.contains(file.getId())) { results.add(file); ids.add(file.getId()); } } } } return (Collection<XMLAnnotationData>) sorter.sort(results); } /** * Returns the collection of the other annotations that are linked to all * the selected objects. * * @return See above. */ Collection<AnnotationData> getCommonOtherAnnotations() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return new ArrayList<AnnotationData>(); Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = r.entrySet().iterator(); Collection<XMLAnnotationData> tags; Collection<AnnotationData> others; Map<Long, Integer> ids = new HashMap<Long, Integer>(); Iterator<XMLAnnotationData> j; XMLAnnotationData tag; Iterator<AnnotationData> k; AnnotationData other; Integer value; String ns; while (i.hasNext()) { e = i.next(); tags = e.getValue().getXMLAnnotations(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); value = ids.get(tag.getId()); if (value != null) { value++; } else value = 1; ids.put(tag.getId(), value); } } others = e.getValue().getOtherAnnotations(); if (others != null) { k = others.iterator(); while (k.hasNext()) { other = k.next(); value = ids.get(other.getId()); if (value != null) { value++; } else value = 1; ids.put(other.getId(), value); } } } //The number of selected objects. List<AnnotationData> results = new ArrayList<AnnotationData>(); List<Long> count = new ArrayList<Long>(); int max = r.size(); i = r.entrySet().iterator(); while (i.hasNext()) { e = i.next(); tags = e.getValue().getXMLAnnotations(); if (tags != null) { j = tags.iterator(); while (j.hasNext()) { tag = j.next(); value = ids.get(tag.getId()); if (value != null && value == max && !count.contains(tag.getId())) { results.add(tag); count.add(tag.getId()); } } } others = e.getValue().getOtherAnnotations(); if (others != null) { k = others.iterator(); while (k.hasNext()) { other = k.next(); value = ids.get(other.getId()); if (value != null && value == max && !count.contains(other.getId())) { results.add(other); count.add(other.getId()); } } } } return (Collection<AnnotationData>) sorter.sort(results); } /** * Returns the objects displaying analysis results. * * @return See above. */ List<AnalysisResultsItem> getAnalysisResults() { Map<DataObject, StructuredDataResults> r = parent.getAllStructuredData(); if (r == null) return null; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> j = r.entrySet().iterator(); StructuredDataResults data; Collection<FileAnnotationData> attachments; Iterator<FileAnnotationData> i; FileAnnotationData f; String ns; AnalysisResultsItem item; Map<Long, FileAnnotationData> ids = new HashMap<Long, FileAnnotationData>(); while (j.hasNext()) { e = j.next(); data = e.getValue(); if (data != null) { attachments = data.getAttachments(); if (attachments != null) { i = attachments.iterator(); while (i.hasNext()) { f = i.next(); ns = f.getNameSpace(); if (FileAnnotationData.FLIM_NS.equals(ns)) { ids.put(f.getId(), f); } } } } } if (ids.size() == 0) return null; List<Long> orderedIds = (List<Long>) sorter.sort(ids.keySet()); int index = 0; //this should be modified. Iterator<Long> k = orderedIds.iterator(); Long id; List<AnalysisResultsItem> results = new ArrayList<AnalysisResultsItem>(); item = null; int n = 6; int number = 1; while (k.hasNext()) { id = k.next(); if (index == 0) { item = new AnalysisResultsItem((DataObject) getRefObject(), FileAnnotationData.FLIM_NS, number); results.add(item); number++; } else if (index == n) { index = -1; } item.addAttachment(ids.get(id)); index++; } return results; } /** * Returns the companion file generated while importing the file * and containing the metadata found in the file, or <code>null</code> * if no file was generated. * * @return See above */ FileAnnotationData getOriginalMetadata() { return originalMetadata; } /** * Returns the number of people who viewed the image. * * @return See above. */ int getViewedByCount() { Collection viewedBy = getViewedBy(); if (viewedBy == null) return 0; return viewedBy.size(); } /** * Returns the collection of people who viewed the image. * * @return See above. */ Collection getViewedBy() { /* StructuredDataResults data = parent.getStructuredData(); if (data == null) return null; Collection l = data.getViewedBy(); if (l == null) return null; Iterator i = l.iterator(); ViewedByDef def; long userID = MetadataViewerAgent.getUserDetails().getId(); List<ViewedByDef> results = new ArrayList<ViewedByDef>(); Map<String, ViewedByDef> m = new HashMap<String, ViewedByDef>(); String value; List<String> names = new ArrayList<String>(); ExperimenterData exp; while (i.hasNext()) { def = (ViewedByDef) i.next(); exp = def.getExperimenter(); if (exp.getId() != userID) { value = formatOwner(exp); names.add(value); m.put(value, def); def.setFormattedExperimenter(value); } } l = sorter.sort(names); i = l.iterator(); while (i.hasNext()) { value = (String) i.next(); results.add(m.get(value)); } return results; */ return null; } /** * Returns the number of ratings for that object. * * @param filter One of the filtering components defined by this class. * @return See above. */ int getRatingCount(int filter) { Map<DataObject, StructuredDataResults> data = parent.getAllStructuredData(); if (data == null) return 0; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = data.entrySet().iterator(); Collection<RatingAnnotationData> ratings; StructuredDataResults results; Iterator<RatingAnnotationData> j; int n = 0; long userID = getUserID(); while (i.hasNext()) { e = i.next(); results = e.getValue(); ratings = results.getRatings(); if (ratings != null) { switch (filter) { case ALL: n += ratings.size(); break; case ME: j = ratings.iterator(); while (j.hasNext()) { if (j.next().getOwner().getId() == userID) n++; } case OTHER: default: j = ratings.iterator(); while (j.hasNext()) { if (j.next().getOwner().getId() != userID) n++; } } } } return n; } /** * Returns the rating annotation related to the logged in user, * or <code>null</code> if no annotation. * * @return See above. */ RatingAnnotationData getUserRatingAnnotation() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return null; Collection<RatingAnnotationData> ratings = data.getRatings(); if (ratings == null || ratings.size() == 0) return null; Iterator<RatingAnnotationData> i = ratings.iterator(); RatingAnnotationData rate; long id = getUserID(); while (i.hasNext()) { rate = i.next(); if (rate.getOwner().getId() == id) return rate; } return null; } /** * Returns the rating annotation related to the logged in user, * or <code>null</code> if no annotation. * * @return See above. */ Map<DataObject, RatingAnnotationData> getAllUserRatingAnnotation() { Map<DataObject, StructuredDataResults> data = parent.getAllStructuredData(); if (data == null) return null; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = data.entrySet().iterator(); Collection<RatingAnnotationData> ratings; StructuredDataResults results; Iterator<RatingAnnotationData> j; RatingAnnotationData rating; Map<DataObject, RatingAnnotationData> map = new HashMap<DataObject, RatingAnnotationData>(); long id = getUserID(); while (i.hasNext()) { e = i.next(); results = e.getValue(); if (results != null) { ratings = results.getRatings(); if (ratings != null) { j = ratings.iterator(); while (j.hasNext()) { rating = j.next(); if (rating.getOwner().getId() == id) { map.put(e.getKey(), rating); } } } } } return map; } /** * Returns the published annotation. * * @return See above. */ BooleanAnnotationData getPublishedAnnotation() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return null; return null; } /** * Returns the rating done by the current user. * * @return See above */ int getUserRating() { RatingAnnotationData data = getUserRatingAnnotation(); if (data == null) return 0; return data.getRating(); } /** * Returns the rating done by the current user. * * @return See above */ int getAllUserRating() { Map<DataObject, RatingAnnotationData> map = getAllUserRatingAnnotation(); if (map == null) return 0; Collection<RatingAnnotationData> ratings = map.values(); Iterator<RatingAnnotationData> i = ratings.iterator(); int n = 0; while (i.hasNext()) { n += i.next().getRating(); } return n; } /** * Returns the average rating value. * * @param filter One of the filtering components defined by this class. * @return See above. */ int getRatingAverage(int filter) { Map<DataObject, StructuredDataResults> data = parent.getAllStructuredData(); if (data == null) return 0; Entry<DataObject, StructuredDataResults> e; Iterator<Entry<DataObject, StructuredDataResults>> i = data.entrySet().iterator(); Collection<RatingAnnotationData> ratings; StructuredDataResults results; Iterator<RatingAnnotationData> j; RatingAnnotationData rating; int n = 0; int value = 0; long userID = getUserID(); while (i.hasNext()) { e = i.next(); results = e.getValue(); ratings = results.getRatings(); if (ratings != null) { j = ratings.iterator(); switch (filter) { case ALL: while (j.hasNext()) { rating = j.next(); value += rating.getRating(); n++; } break; case ME: while (j.hasNext()) { rating = j.next(); if (rating.getOwner().getId() == userID) { value += rating.getRating(); n++; } } case OTHER: default: j = ratings.iterator(); while (j.hasNext()) { rating = j.next(); if (rating.getOwner().getId() != userID) { value += rating.getRating(); n++; } } } } } if (n == 0) return 0; return value / n; } /** * Returns the number of textual annotations for that object. * * @return See above. */ int getTextualAnnotationCount() { Collection<TextualAnnotationData> annotations = getTextualAnnotations(); if (annotations == null) return 0; return annotations.size(); } /** * Returns the collection of textual annotations. * * @return See above. */ Collection<TextualAnnotationData> getTextualAnnotations() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return null; return data.getTextualAnnotations(); } /** * Returns the annotations ordered by date. * * @return See above. */ List getTextualAnnotationsByDate() { if (textualAnnotationsByDate != null) return textualAnnotationsByDate; textualAnnotationsByDate = (List) getTextualAnnotations(); sortAnnotationByDate(textualAnnotationsByDate); return textualAnnotationsByDate; } /** * Returns the annotation made by the currently selected user. * * @return See above. */ TextualAnnotationData getLastUserAnnotation() { Map<Long, List> m = getTextualAnnotationByOwner(); long userID = MetadataViewerAgent.getUserDetails().getId(); List l = m.get(userID); if (l == null || l.size() == 0) return null; return (TextualAnnotationData) l.get(0); } /** * Returns the annotations organized by users. * * @return See above. */ Map<Long, List> getTextualAnnotationByOwner() { if (textualAnnotationsByUsers != null && textualAnnotationsByUsers.size() > 0) return textualAnnotationsByUsers; textualAnnotationsByUsers = new HashMap<Long, List>(); Collection<TextualAnnotationData> original = getTextualAnnotations(); if (original == null) return textualAnnotationsByUsers; Iterator i = original.iterator(); AnnotationData annotation; Long ownerID; List<AnnotationData> userAnnos; while (i.hasNext()) { annotation = (AnnotationData) i.next(); ownerID = Long.valueOf(annotation.getOwner().getId()); userAnnos = textualAnnotationsByUsers.get(ownerID); if (userAnnos == null) { userAnnos = new ArrayList<AnnotationData>(); textualAnnotationsByUsers.put(ownerID, userAnnos); } userAnnos.add(annotation); } i = textualAnnotationsByUsers.keySet().iterator(); while (i.hasNext()) { ownerID = (Long) i.next(); sortAnnotationByDate(textualAnnotationsByUsers.get(ownerID)); } //sort users by name. /* REMOVE Comments when user is not root Map groups = (Map) MetadataViewerAgent.getRegistry().lookup( LookupNames.USER_GROUP_DETAILS); GroupData g; i = groups.keySet().iterator(); ViewerSorter sorter = new ViewerSorter(); List orderedUsers = new ArrayList(); while (i.hasNext()) { g = (GroupData) i.next(); orderedUsers.addAll(sorter.sort((Set) groups.get(g))); } Map<Long, List> orderedAnnotationsByUser = new HashMap<Long, List>(); i = orderedUsers.iterator(); ExperimenterData exp; List ann; while (i.hasNext()) { exp = (ExperimenterData) i.next(); ann = textualAnnotationsByUsers.get(exp.getId()); if (ann != null) orderedAnnotationsByUser.put(exp.getId(), ann); } textualAnnotationsByUsers = orderedAnnotationsByUser; */ return textualAnnotationsByUsers; } /** * Returns <code>true</code> if it is the same object, * <code>false</code> otherwise. * * @param object The object to handle. * @return See above. */ boolean isSameObject(Object object) { return parent.isSameObject(object); } /** * Sets the object of reference. * * @param refObject The value to set. */ void setRootObject(Object refObject) { boolean b = isSameObject(this.refObject); set = null; largeImage = false; this.refObject = refObject; if (existingTags != null) existingTags.clear(); existingTags = null; if (textualAnnotationsByUsers != null) textualAnnotationsByUsers.clear(); textualAnnotationsByUsers = null; if (textualAnnotationsByDate != null) textualAnnotationsByDate.clear(); textualAnnotationsByDate = null; if (existingAttachments != null) existingAttachments.clear(); existingAttachments = null; if (resultsLoader != null) resultsLoader.clear(); resultsLoader = null; if (!b) { parentRefObject = null; gpRefObject = null; if (emissionsWavelengths != null) emissionsWavelengths.clear(); emissionsWavelengths = null; if (channelAcquisitionDataMap != null) channelAcquisitionDataMap.clear(); if (channelPlaneInfoMap != null) channelPlaneInfoMap.clear(); imageAcquisitionData = null; instrumentData = null; originalMetadata = null; if (refObject instanceof ImageData || refObject instanceof WellSampleData) { fireChannelEnumerationsLoading(); fireImageEnumerationsLoading(); fireLargeImageLoading(); } else if (refObject instanceof ExperimenterData) { fireExperimenterPhotoLoading(); } if (renderer != null) { renderer.discard(); renderer = null; } } } /** * Sets the parent of the object of reference. * * @param parentRefObject The value to set. * @param gpRefObject The value to set. */ void setParentRootObject(Object parentRefObject, Object gpRefObject) { this.parentRefObject = parentRefObject; this.gpRefObject = gpRefObject; } /** * Returns the parent of the object of reference. * * @return See above. */ Object getParentRootObject() { return parentRefObject; } /** * Returns the parent of the object of reference. * * @return See above. */ Object getGrandParentRootObject() { return gpRefObject; } /** * Returns the owner of the reference object or <code>null</code> * if the object is not a <code>DataObject</code>. * * @return See above. */ ExperimenterData getRefObjectOwner() { Object ref = getRefObject(); if (ref instanceof DataObject) return getOwner((DataObject) ref); return null; } /** Fires an asynchronous retrieval of existing tags. */ void loadExistingTags() { EditorLoader l; boolean exist = false; Iterator i = loaders.iterator(); while (i.hasNext()) { l = (EditorLoader) i.next(); if (l instanceof TagsLoader) { exist = true; break; } } if (exist) return; TagsLoader loader = new TagsLoader(component, parent.getSecurityContext(), canRetrieveAll()); loader.load(); loaders.add(loader); } /** * Fires an asynchronous retrieval of existing attachments * for the currently logged in user. */ void loadExistingAttachments() { EditorLoader l; boolean exist = false; Iterator i = loaders.iterator(); while (i.hasNext()) { l = (EditorLoader) i.next(); if (l instanceof AttachmentsLoader) { exist = true; break; } } if (exist) return; AttachmentsLoader loader = new AttachmentsLoader(component, parent.getSecurityContext(), canRetrieveAll()); loader.load(); loaders.add(loader); } /** Cancels any ongoing tags retrieval. */ void cancelExistingTagsLoading() { Iterator i = loaders.iterator(); EditorLoader loader; List<EditorLoader> toKeep = new ArrayList<EditorLoader>(); while (i.hasNext()) { loader = (EditorLoader) i.next(); if (loader instanceof TagsLoader) loader.cancel(); else toKeep.add(loader); } loaders.clear(); loaders.addAll(toKeep); } /** Fires an asynchronous retrieval of the channel data. */ void loadChannelData() { Object refObject = getRefObject(); ImageData data = null; if (refObject instanceof ImageData) data = (ImageData) refObject; else if (refObject instanceof WellSampleData) { WellSampleData wsd = (WellSampleData) refObject; data = wsd.getImage(); if (data != null && data.getId() < 0) data = null; } if (data == null) return; try { PixelsData pixs = data.getDefaultPixels(); ChannelDataLoader loader = new ChannelDataLoader(component, parent.getSecurityContext(), pixs.getId(), parent.getUserID()); loader.load(); loaders.add(loader); } catch (Exception e) { } } /** Cancels any ongoing tags retrieval. */ void cancelChannelDataLoading() { Iterator i = loaders.iterator(); EditorLoader loader; List<EditorLoader> toKeep = new ArrayList<EditorLoader>(); while (i.hasNext()) { loader = (EditorLoader) i.next(); if (loader instanceof ChannelDataLoader) loader.cancel(); else toKeep.add(loader); } loaders.clear(); loaders.addAll(toKeep); } /** * Sets the collection of existing tags. * * @param tags The value to set. */ void setExistingTags(Collection tags) { if (tags != null) existingTags = sorter.sort(tags); Iterator i = loaders.iterator(); EditorLoader loader; EditorLoader toRemove = null; while (i.hasNext()) { loader = (EditorLoader) i.next(); if (loader instanceof TagsLoader) { toRemove = loader; break; } } if (toRemove != null) loaders.remove(toRemove); } /** * Returns the collection of existing tags. * * @return See above. */ Collection getExistingTags() { return existingTags; } /** * Sets the collection of existing attachments. * * @param attachments The value to set. */ void setExistingAttachments(Collection attachments) { if (attachments != null) existingAttachments = sorter.sort(attachments); Iterator i = loaders.iterator(); EditorLoader loader; EditorLoader toRemove = null; while (i.hasNext()) { loader = (EditorLoader) i.next(); if (loader instanceof AttachmentsLoader) { toRemove = loader; break; } } if (toRemove != null) loaders.remove(toRemove); } /** * Returns the collection of existing attachments. * * @return See above. */ Collection getExistingAttachments() { return existingAttachments; } /** * Sets the channel data. * * @param data The value to set. */ void setChannelData(Map data) { List l = sorter.sort(data.keySet()); emissionsWavelengths = new LinkedHashMap(); Iterator i = l.iterator(); Object channel; while (i.hasNext()) { channel = i.next(); emissionsWavelengths.put(channel, data.get(channel)); } } /** * Returns the channels data related to the image. * * @return See above. */ Map getChannelData() { if (getRndIndex() == MetadataViewer.RND_SPECIFIC) { if (renderer != null) { List<ChannelData> l = renderer.getChannelData(); Map m = new LinkedHashMap(); Iterator<ChannelData> i = l.iterator(); ChannelData data; while (i.hasNext()) { data = i.next(); m.put(data, renderer.getChannelColor(data.getIndex())); } return m; } } return emissionsWavelengths; } /** * Starts an asynchronous call to save the annotations. * * @param object The annotation/link to add or remove. * @param metadata The metadata to save. * @param asynch Pass <code>true</code> to save data asynchronously, * <code>false</code> otherwise. */ void fireAnnotationSaving(DataToSave object, List<Object> metadata, boolean asynch) { Object ref = getRefObject(); if (ref instanceof DataObject) { DataObject data = (DataObject) ref; if (data instanceof WellSampleData) { data = ((WellSampleData) ref).getImage(); } List<AnnotationData> list = null; if (CollectionUtils.isNotEmpty(toDelete)) { list = new ArrayList<AnnotationData>(); Iterator<AnnotationData> i = toDelete.iterator(); while (i.hasNext()) list.add(i.next()); toDelete.clear(); } parent.saveData(object, list, metadata, data, asynch); } } /** * Updates the specified channels. If <code>applyToAll</code> is * <code>true</code>, the channels of all the images in the dataset or * the plate will be updated, * * @param channels The channels to update. * @param applyToAll Pass <code>true</code> to update the channels of all * the images in the dataset or the plate. * Pass <code>false</code> to only update the image. */ void fireChannelSaving(List<ChannelData> channels, boolean applyToAll) { DataObject object = null; if (applyToAll) { if (parentRefObject instanceof DatasetData) object = (DataObject) parentRefObject; else if (gpRefObject instanceof PlateData) object = (DataObject) gpRefObject; else return; } else object = (DataObject) refObject; ChannelDataSaver loader = new ChannelDataSaver(component, getSecurityContext(), channels, object); loader.load(); } /** * Starts an asynchronous call to delete the annotations. * * @param annotations The annotations to delete. */ void fireAnnotationsDeletion(List<AnnotationData> annotations) { Object ref = getRefObject(); if (ref instanceof DataObject) { DataObject data = (DataObject) ref; if (data instanceof WellSampleData) { data = ((WellSampleData) ref).getImage(); } parent.saveData(null, annotations, new ArrayList<Object>(), data, true); } } /** * Starts an asynchronous call to check the removal of the given FileAnnotations. * * @param data The annotations to check */ void fireFileAnnotationRemoveCheck(List<FileAnnotationData> annotations) { FileAnnotationChecker check = new FileAnnotationChecker(component, getSecurityContext(), annotations); check.load(); } /** * Starts an asynchronous call to update the experimenter or the group. * * @param data The experimenter or the group to save. * @param asynch Pass <code>true</code> to save data asynchronously, * <code>false</code> otherwise. */ void fireAdminSaving(Object data, boolean asynch) { if (data instanceof ExperimenterData || data instanceof AdminObject || data instanceof GroupData) parent.updateAdminObject(data, asynch); } /** * Returns <code>true</code> if the imported set of pixels has been * archived, <code>false</code> otherwise. * * @return See above. */ boolean isArchived() { return isArchived(getImage()); } /** * Returns <code>true</code> if the imported set of pixels has been * archived, <code>false</code> otherwise. * * @param ho The object to handle. * @return See above. */ boolean isArchived(DataObject ho) { ImageData img = null; if (ho instanceof ImageData) img = (ImageData) ho; if (img == null) return false; return img.isArchived(); } /** * Starts an asynchronous loading. * * @param file The file where to download the content. * If it is a multi-images file a zip will be created. * @param override Flag indicating to override the existing file if it * exists, <code>false</code> otherwise. */ void download(File file, boolean override) { if (refObject instanceof ImageData) { downloadImages(file, override); } else if (refObject instanceof FileAnnotationData) { downloadFiles(file, override); } } /** * Starts an asynchronous call to retrieve disk space information. * * @param type Either <code>ExperimenterData</code> or * <code>GroupData</code>. * @param id The identifier of the user or group. */ void loadDiskSpace(Class type, long id) { DiskSpaceLoader loader = new DiskSpaceLoader(component, parent.getSecurityContext(), type, id); loader.load(); loaders.add(loader); } /** Cancels the disk space loading. */ void cancelDiskSpaceLoading() { Iterator i = loaders.iterator(); EditorLoader loader; List<EditorLoader> toKeep = new ArrayList<EditorLoader>(); while (i.hasNext()) { loader = (EditorLoader) i.next(); if (loader instanceof DiskSpaceLoader) { loader.cancel(); } else toKeep.add(loader); } loaders.clear(); loaders.addAll(toKeep); } /** * Fires an asynchronous call to modify the password. * * @param old The old password. * @param confirm The new password. */ void changePassword(String old, String confirm) { EditorLoader loader = new PasswordEditor(component, parent.getSecurityContext(), old, confirm); loader.load(); loaders.add(loader); } /** * Returns <code>true</code> if the object of reference is tag of another * tag, <code>false</code> if it is tag linked to images, without any links * or if it is not a tag. * * @return See above. */ boolean hasTagsAsChildren() { Object ref = getRefObject(); if (!(ref instanceof TagAnnotationData)) return false; TagAnnotationData tag = (TagAnnotationData) ref; Set tags = tag.getTags(); if (tags != null && tags.size() > 0) return true; return false; } /** * Returns the owner of the passed annotation. * * @param data The annotation to handle. * @return See above. */ ExperimenterData getOwner(DataObject data) { if (data == null) return null; long id = data.getOwner().getId(); return MetadataViewerAgent.getExperimenter(id); } /** * Fires an asynchronous retrieval of containers hosting the currently * edited object. */ void loadParents() { parent.loadParents(); } /** Cancels any ongoing parents retrieval. */ void cancelParentsLoading() { } /** * Returns <code>true</code> if the image has been viewed by other users, * <code>false</code> otherwise. * * @return See above. */ boolean hasBeenViewedBy() { if (!(getRefObject() instanceof ImageData)) return false; return getViewedByCount() != 0; } /** Loads the image metadata enumerations. */ void fireImageEnumerationsLoading() { EnumerationLoader loader = new EnumerationLoader(component, parent.getSecurityContext(), EnumerationLoader.IMAGE); loader.load(); } /** Loads the channel metadata enumerations. */ void fireChannelEnumerationsLoading() { EnumerationLoader loader = new EnumerationLoader(component, parent.getSecurityContext(), EnumerationLoader.CHANNEL); loader.load(); } /** Loads the image acquisition data. */ void fireImagAcquisitionDataLoading() { Object ref = getRefObject(); ImageData data = null; if (ref instanceof WellSampleData) { data = ((WellSampleData) ref).getImage(); } else if (ref instanceof ImageData) { data = (ImageData) ref; } if (data == null) return; AcquisitionDataLoader loader = new AcquisitionDataLoader(component, parent.getSecurityContext(), data); loader.load(); } /** * Loads the image acquisition data. * * @param channel The channel to handle. */ void fireChannelAcquisitionDataLoading(ChannelData channel) { AcquisitionDataLoader loader = new AcquisitionDataLoader(component, parent.getSecurityContext(), channel); loader.load(); } /** * Starts an asynchronous call to load the instrument linked to the image. * * @param instrumentID The id of the instrument. */ void fireInstrumentDataLoading(long instrumentID) { InstrumentDataLoader loader = new InstrumentDataLoader(component, parent.getSecurityContext(), instrumentID); loader.load(); } /** * Sets the image acquisition data. * * @param data The value to set. */ void setImageAcquisitionData(ImageAcquisitionData data) { imageAcquisitionData = data; } /** * Returns the image acquisition data. * * @return See above. */ ImageAcquisitionData getImageAcquisitionData() { return imageAcquisitionData; } /** * Sets the acquisition data for the specified channel. * * @param index The index of the channel. * @param data The value to set. */ void setChannelAcquisitionData(int index, ChannelAcquisitionData data) { if (channelAcquisitionDataMap == null) channelAcquisitionDataMap = new HashMap<Integer, ChannelAcquisitionData>(); channelAcquisitionDataMap.put(index, data); } /** * Returns the channel acquisition data. * * @param index The index of the channels. * @return See above. */ ChannelAcquisitionData getChannelAcquisitionData(int index) { if (channelAcquisitionDataMap == null) return null; return channelAcquisitionDataMap.get(index); } /** * Sets the collection of plane info for the specified channel. * * @param index The index of the channel. * @param data The value to set. */ void setPlaneInfo(int index, Collection data) { if (channelPlaneInfoMap == null) channelPlaneInfoMap = new HashMap<Integer, Collection>(); channelPlaneInfoMap.put(index, sortPlane(data)); } /** * Returns the channel acquisition data. * * @param index The index of the channel. * @return See above. */ Collection getChannelPlaneInfo(int index) { if (channelPlaneInfoMap == null) return null; return channelPlaneInfoMap.get(index); } /** * Returns the collection of objects corresponding to the passed name. * * @param name The name of the enumeration. * @return See above. */ List<EnumerationObject> getImageEnumerations(String name) { if (imageEnumerations != null) return (List<EnumerationObject>) imageEnumerations.get(name); return new ArrayList<EnumerationObject>(); } /** * Returns the collection of objects corresponding to the passed name. * * @param name The name of the enumeration. * @return See above. */ List<EnumerationObject> getChannelEnumerations(String name) { if (channelEnumerations != null) return (List<EnumerationObject>) channelEnumerations.get(name); return new ArrayList<EnumerationObject>(); } /** * Returns the enumeration object corresponding to the passed enumeration * name and value for the image metadata. * * @param name The type of enumeration. * @param value The value to select. * @return See above. */ Object getImageEnumerationSelected(String name, String value) { List<EnumerationObject> l = getImageEnumerations(name); if (l.size() == 0) return null; EnumerationObject o; Iterator i = l.iterator(); String v; while (i.hasNext()) { o = (EnumerationObject) i.next(); v = o.getValue(); v = v.trim(); if (v.equals(value)) return o; } return null; } /** * Returns the enumeration object corresponding to the passed enumeration * name and value for the channel metadata. * * @param name The type of enumeration. * @param value The value to select. * @return See above. */ Object getChannelEnumerationSelected(String name, String value) { if (value == null) return null; List<EnumerationObject> l = getChannelEnumerations(name); if (l.size() == 0) return null; EnumerationObject o; Iterator i = l.iterator(); value = value.trim(); String v; while (i.hasNext()) { o = (EnumerationObject) i.next(); v = o.getValue(); v = v.trim(); if (v.equals(value)) return o; } return null; } /** * Sets the enumerations related to channel metadata. * * @param enumerations The value to set. */ void setChannelEnumerations(Map enumerations) { channelEnumerations = new HashMap<String, List<EnumerationObject>>(); Set set = enumerations.entrySet(); Entry entry; Iterator i = set.iterator(); String key; List<EnumerationObject> values; while (i.hasNext()) { entry = (Entry) i.next(); key = (String) entry.getKey(); values = (List<EnumerationObject>) entry.getValue(); sortEnumerations(values); channelEnumerations.put(key, values); } } /** * Sets the enumerations related to image metadata. * * @param enumerations The value to set. */ void setImageEnumerations(Map enumerations) { imageEnumerations = new HashMap<String, List<EnumerationObject>>(); Set set = enumerations.entrySet(); Entry entry; Iterator i = set.iterator(); String key; List<EnumerationObject> values; while (i.hasNext()) { entry = (Entry) i.next(); key = (String) entry.getKey(); values = (List<EnumerationObject>) entry.getValue(); sortEnumerations(values); imageEnumerations.put(key, values); } } /** * Returns the description of the passed annotation. * * @param annotation The annotation to handle. * @return See above. */ String getAnnotationDescription(AnnotationData annotation) { if (annotation == null) return ""; if (annotation instanceof TagAnnotationData) return ((TagAnnotationData) annotation).getTagDescription(); else if (annotation instanceof TermAnnotationData) return ((TermAnnotationData) annotation).getTermDescription(); else if (annotation instanceof XMLAnnotationData) return ((XMLAnnotationData) annotation).getDescription(); return ""; } /** * Returns <code>true</code> if the display is for a single * object, <code>false</code> otherwise. * * @return See above. */ boolean isSingleMode() { return parent.isSingleMode(); } /** * Returns the object path i.e. if a dataset is selected, * the name of the project_name of the dataset. * * @return See above. */ String getObjectPath() { return parent.getObjectPath(); } /** * Starts asynchronous load of the plane info. * * @param channel The selected channel. * @param z The selected z-section. */ void firePlaneInfoLoading(int channel, int z) { Object ref = getRefObject(); if (ref instanceof WellSampleData) { WellSampleData wsd = (WellSampleData) ref; ref = wsd.getImage(); } if (!(ref instanceof ImageData)) return; ImageData img = (ImageData) ref; PlaneInfoLoader loader = new PlaneInfoLoader(component, parent.getSecurityContext(), img.getDefaultPixels().getId(), channel, z); loader.load(); } /** * Brings up the dialog to create a movie. * * @param scaleBar The value of the scale bar. * If not greater than <code>0</code>, the value is not * taken into account. * @param overlayColor The color of the scale bar and text. */ void makeMovie(int scaleBar, Color overlayColor) { parent.makeMovie(scaleBar, overlayColor); } /** * Analyzes the data. * * @param index The index identifying the analysis to perform. */ void analyse(int index) { parent.analyse(index); } /** * Returns <code>true</code> if the renderer has been loaded, * <code>false</code> otherwise. * * @return See above. */ boolean isRendererLoaded() { return renderer != null; } /** * Starts an asynchronous call to load the rendering control. * Returns <code>false</code> if already loaded, <code>true</code> * otherwise. * * @param pixelsID The id of the pixels set. * @param index One of the constants defined by the RenderingControlLoader * class * @return */ boolean fireRenderingControlLoading(long pixelsID, int index) { if (isRendererLoaded() && index == RenderingControlLoader.LOAD) return false; RenderingControlLoader loader = new RenderingControlLoader(component, parent.getSecurityContext(), pixelsID, index); loader.load(); return true; } /** * Sets the rendering control. * * @param rndControl The value to set. */ void setRenderingControl(RenderingControl rndControl) { if (renderer != null) { renderer.onSettingsApplied(rndControl); } else { renderer = RendererFactory.createRenderer(getSecurityContext(), rndControl, getImage(), getRndIndex(), getXMLAnnotations()); } } /** * Returns the renderer. * * @return See above. */ Renderer getRenderer() { return renderer; } /** * Returns the rendering constants. * * @return See above. */ int getRndIndex() { return parent.getRndIndex(); } /** * Returns <code>true </code> if the object e.g. image has been published, * <code>false</code> otherwise. * * @return See above. */ boolean hasBeenPublished() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return false; return getPublishedAnnotation() != null; } /** * Loads the original metadata file for the image currently selected. * * @param uiView The view to notify. */ void loadOriginalMetadata(Object uiView) { ImageData img = getImage(); OriginalMetadataLoader loader = new OriginalMetadataLoader(component, parent.getSecurityContext(), img.getId(), uiView); loader.load(); } /** * Loads the specified files. * * @param files The file to load. */ void loadFiles(Map<FileAnnotationData, Object> files) { if (!MetadataViewerAgent.isBinaryAvailable()) return; FileLoader loader = new FileLoader(component, parent.getSecurityContext(), files); loader.load(); } /** * Notifies that the rendering control has been loaded. * * @param reload Pass <code>true</code> if the rendering control has been * reloaded following an exception, <code>false</code> if * it is an initial load. */ void onRndLoaded(boolean reload) { if (renderer == null) return; parent.onRndLoaded(reload); } /** * Sets the instrument used to capture the image. * * @param data The value to set. */ void setInstrumentData(InstrumentData data) { instrumentData = data; } /** * Returns the instrument data. * * @return See above. */ InstrumentData getInstrumentData() { return instrumentData; } /** * Sorts the passed collection of data objects by ID. * * @param values Collection of <code>DataObject</code>s to sort. */ void sortDataObjectByID(List values) { if (values == null || values.size() == 0) return; Comparator c = new Comparator() { public int compare(Object o1, Object o2) { long n1 = ((DataObject) o1).getId(), n2 = ((DataObject) o2).getId(); int v = 0; if (n1 < n2) v = -1; else if (n1 > n2) v = 1; return -v; } }; Collections.sort(values, c); } /** Updates the permissions. */ void upgradePermissions() { } /** * Invokes when the color of the channel has been modified using the * renderer. * * @param index The index of the channel. * @return See above. */ Color getChannelColor(int index) { if (renderer == null) return null; return renderer.getChannelColor(index); } /** * Returns <code>true</code> if it is an image with a lot of channels. * <code>false</code> otherwise. * * @return See above. */ boolean isNumerousChannel() { if (!(refObject instanceof ImageData || refObject instanceof WellSampleData)) return false; if (renderer != null) return renderer.getPixelsDimensionsC() >= Renderer.MAX_CHANNELS; ImageData img = null; if (refObject instanceof WellSampleData) img = ((WellSampleData) refObject).getImage(); if (refObject instanceof ImageData) img = (ImageData) refObject; PixelsData pixels = null; try { pixels = img.getDefaultPixels(); } catch (Exception e) { //ignore } if (pixels == null) return false; return pixels.getSizeC() >= Renderer.MAX_CHANNELS; } /** * Returns <code>true</code> if the preview is available, * <code>false</code> otherwise. * * @return See above. */ boolean isPreviewAvailable() { if (!(refObject instanceof ImageData || refObject instanceof WellSampleData)) return false; if (!MetadataViewerAgent.isBinaryAvailable()) return false; ImageData img = null; if (refObject instanceof WellSampleData) img = ((WellSampleData) refObject).getImage(); if (refObject instanceof ImageData) img = (ImageData) refObject; if (img.getId() < 0) return false; PixelsData pixels = null; try { pixels = img.getDefaultPixels(); } catch (Exception e) { //ignore } if (pixels == null) return false; int size = 1500; if (pixels.getSizeX() <= size && pixels.getSizeY() <= size) return true; return false; } /** * Creates a figure. * * @param value The value containing the parameters for the figure. */ void createFigure(Object value) { //reset the rendering settings. parent.createFigure(value); } /** * Runs the passed script. * * @param script The script to run. * @param index Indicated to run, download or view. */ void manageScript(ScriptObject script, int index) { parent.manageScript(script, index); } /** * Returns the pixels data objects. * * @return See above. */ PixelsData getPixels() { ImageData img = getImage(); if (img == null) return null; return img.getDefaultPixels(); } /** * Returns the image or <code>null</code> if the primary select * node is an image or a well. * * @return See above. */ ImageData getImage() { Object object = getPrimarySelect(); ImageData img = null; if (object instanceof WellSampleData) img = ((WellSampleData) object).getImage(); if (object instanceof ImageData) img = (ImageData) object; return img; } /** * Loads the ROI for the selected image. * * @param index The index of the figure to create. */ void fireROILoading(int index) { ImageData img = getImage(); if (img == null) return; long userID = MetadataViewerAgent.getUserDetails().getId(); ROILoader loader = new ROILoader(component, parent.getSecurityContext(), img.getId(), userID, index); loader.load(); } /** Discards the renderer. */ void discardRenderer() { if (renderer != null) renderer.discard(); renderer = null; } /** Refreshes the view. */ void refresh() { parent.refresh(); } /** * Sets the collection of scripts. * * @param scripts The value to set. */ void setScripts(List scripts) { if (scripts == null) { this.scripts = null; return; } //sort the scripts. Map<Long, ScriptObject> map = new LinkedHashMap<Long, ScriptObject>(); List l = sorter.sort(scripts); Iterator i = l.iterator(); ScriptObject s; while (i.hasNext()) { s = (ScriptObject) i.next(); map.put(s.getScriptID(), s); } this.scripts = map; } /** * Returns the collection of scripts. * * @return See above. */ Collection<ScriptObject> getScripts() { if (scripts == null) return null; return scripts.values(); } /** * Loads the specified script. * * @param scriptID The identifier of the script to load. */ void loadScript(long scriptID) { ScriptLoader loader = new ScriptLoader(component, parent.getSecurityContext(), scriptID); loader.load(); loaders.add(loader); } /** * Sets the specified script. * * @param script The loaded script. */ void setScript(ScriptObject script) { if (scripts == null || scripts.size() == 0) return; ScriptObject sc = scripts.get(script.getScriptID()); if (sc != null) sc.setJobParams(script.getParameters()); } /** * Returns the script corresponding to the passed identifier. * * @param scriptID The identifier of the script. * @return See above. */ ScriptObject getScript(long scriptID) { return scripts.get(scriptID); } /** Loads the scripts. */ void loadScripts() { ScriptsLoader loader = new ScriptsLoader(component, parent.getSecurityContext(), false); loader.load(); loaders.add(loader); } /** * Returns the id of the possible owner. This should only be used to * handle <code>FileData</code> objects. * * @return See above. */ long getUserID() { return parent.getUserID(); } /** * Returns the user currently logged in. * * @return See above. */ ExperimenterData getCurrentUser() { return MetadataViewerAgent.getUserDetails(); } /** * Returns the experimenter corresponding to the specified identifier. * or <code>null</code>. * * @param expID The identifier of the experimenter. * @return see above. */ ExperimenterData getExperimenter(long expID) { List l = (List) MetadataViewerAgent.getRegistry().lookup(LookupNames.USERS_DETAILS); if (l == null) return null; Iterator i = l.iterator(); ExperimenterData exp; while (i.hasNext()) { exp = (ExperimenterData) i.next(); if (exp.getId() == expID) return exp; } return null; } /** * Returns the name of the owner or <code>null</code> if the current owner * is the user currently logged in. * @return */ String getOwnerName() { Object o = getRefObject(); if (o == null) return null; if (o instanceof ExperimenterData || o instanceof GroupData) return null; if (o instanceof DataObject) { ExperimenterData user = getCurrentUser(); DataObject data = (DataObject) o; long id = user.getId(); if (data.getId() < 0) return null; if (!((DataObject) o).isLoaded()) return null; try { ExperimenterData owner = data.getOwner(); if (owner.getId() == id) return EditorUtil.formatExperimenter(user); if (owner.isLoaded()) return EditorUtil.formatExperimenter(owner); owner = getExperimenter(owner.getId()); if (owner != null) return EditorUtil.formatExperimenter(owner); } catch (Exception e) { } } return null; } /** * Resets the password of the user currently edited. * * @param newPass The value to set. */ void resetPassword(String newPass) { if (refObject instanceof ExperimenterData && MetadataViewerAgent.isAdministrator()) { parent.resetPassword(newPass); } } /** Uploads the user's photo. * * @param photo The photo to upload. * @param format The format of the photo. */ void uploadPicture(File photo, String format) { if (refObject instanceof ExperimenterData) { //ExperimenterData exp = (ExperimenterData) refObject; ExperimenterData exp = MetadataViewerAgent.getUserDetails(); UserPhotoUploader loader = new UserPhotoUploader(component, parent.getSecurityContext(), exp, photo, format); loader.load(); } } /** Deletes the user's photos.*/ void deletePicture() { if (refObject instanceof ExperimenterData) { try { ExperimenterData exp = MetadataViewerAgent.getUserDetails(); if (usersPhoto != null) usersPhoto.remove(exp.getId()); OmeroMetadataService svc = MetadataViewerAgent.getRegistry().getMetadataService(); Collection photos = svc.loadAnnotations(parent.getSecurityContext(), FileAnnotationData.class, FileAnnotationData.EXPERIMENTER_PHOTO_NS, exp.getId()); if (photos == null || photos.size() == 0) return; List<DeletableObject> l = new ArrayList<DeletableObject>(); Iterator<AnnotationData> j = photos.iterator(); while (j.hasNext()) l.add(new DeletableObject(j.next())); IconManager icons = IconManager.getInstance(); DeleteActivityParam p = new DeleteActivityParam(icons.getIcon(IconManager.APPLY_22), l); p.setUIRegister(false); p.setFailureIcon(icons.getIcon(IconManager.DELETE_22)); UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier(); un.notifyActivity(getSecurityContext(), p); } catch (Exception e) { // TODO: handle exception } } } /** Notifies the parent to upload the script. */ void uploadScript() { parent.uploadScript(); } /** * Returns the collection of scripts with a UI, mainly the figure scripts. * * @return See above. */ private List<ScriptObject> getScriptsWithUI() { /* if (scriptsWithUI != null) return scriptsWithUI; try { OmeroImageService svc = MetadataViewerAgent.getRegistry().getImageService(); scriptsWithUI = svc.loadAvailableScriptsWithUI(); return scriptsWithUI; } catch (Exception e) { LogMessage msg = new LogMessage(); msg.print("Scripts with UI"); msg.print(e); MetadataViewerAgent.getRegistry().getLogger().error(this, msg); } */ return new ArrayList<ScriptObject>(); } /** * Returns the script corresponding to the specified name. * * @return See above. */ ScriptObject getScriptFromName(String name) { List<ScriptObject> scripts = getScriptsWithUI(); Iterator<ScriptObject> i = scripts.iterator(); ScriptObject script; while (i.hasNext()) { script = i.next(); if (name.contains(script.getName())) return script; } return null; } /** * Loads the attachments. * * @param analysis The object hosting the results. */ void loadAnalysisResults(AnalysisResultsItem analysis) { if (resultsLoader == null) resultsLoader = new HashMap<AnalysisResultsItem, EditorLoader>(); AnalysisResultsFileLoader loader = new AnalysisResultsFileLoader(component, parent.getSecurityContext(), analysis); resultsLoader.put(analysis, loader); loader.load(); } /** * Cancels on-going loading of results. * * @param item The object hosting the results. */ void cancelAnalysisResultsLoading(AnalysisResultsItem item) { if (resultsLoader == null) return; EditorLoader loader = resultsLoader.get(item); if (loader != null) loader.cancel(); } /** * Cancels on-going loading of results. * * @param item The object hosting the results. */ void removeAnalysisResultsLoading(AnalysisResultsItem item) { if (resultsLoader == null) return; resultsLoader.remove(item); } /** * Returns <code>true</code> if the passed annotation has to be * deleted, <code>false</code> otherwise. * * @param annotation The annotation to handle. * @return See above. */ boolean isAnnotationToDelete(AnnotationData annotation) { if (toDelete == null || toDelete.size() == 0) return false; Iterator<AnnotationData> i = toDelete.iterator(); AnnotationData data; while (i.hasNext()) { data = i.next(); if (data.getId() == annotation.getId()) return true; } return false; } /** * Returns the collection of the attachments linked to the * <code>DataObject</code>. * * @return See above. */ List<FileAnnotationData> getTabularData() { StructuredDataResults data = parent.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; } /** * Returns the object to save as. * * @param ho The data object. * @return See above. */ private DataObject saveAsObject(Object ho) { if (ho instanceof ImageData || ho instanceof DatasetData) { return (DataObject) ho; } if (ho instanceof WellSampleData) { return ((WellSampleData) ho).getImage(); } return null; } /** * Saves locally the images as <code>JPEG</code>, <code>PNG</code> * or <code>TIFF</code>. * * @param folder The folder where to save the images. * @param format The format to use. */ void saveAs(File folder, int format) { Collection l = parent.getRelatedNodes(); List<DataObject> objects = new ArrayList<DataObject>(); Object o; DataObject data; if (l != null) { Iterator i = l.iterator(); while (i.hasNext()) { data = saveAsObject(i.next()); if (data != null) objects.add(data); } } data = saveAsObject(getRefObject()); if (data != null) objects.add(data); if (objects.size() > 0) { IconManager icons = IconManager.getInstance(); SaveAsParam p = new SaveAsParam(folder, objects); p.setIndex(format); p.setIcon(icons.getIcon(IconManager.SAVE_AS_22)); UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier(); un.notifyActivity(getSecurityContext(), p); } } /** * Returns the collection of selected objects. * * @return See above. */ List<DataObject> getSelectedObjects() { List<DataObject> objects = new ArrayList<DataObject>(); Collection l = parent.getRelatedNodes(); if (CollectionUtils.isEmpty(l)) { if (getRefObject() instanceof DataObject) objects.add((DataObject) getRefObject()); return objects; } Iterator i = l.iterator(); Object o; while (i.hasNext()) { o = i.next(); if (o instanceof DataObject) objects.add((DataObject) o); } return objects; } /** * Returns <code>true</code> if the image is a large image, * <code>false</code> otherwise. * * @return See above. */ boolean isLargeImage() { return largeImage; } /** * Indicates if the image is a big image or not. * * @param value The value to set. */ void setLargeImage(Boolean value) { if (value == null) largeImage = false; largeImage = value.booleanValue(); } /** * Returns the parent UI. * * @return See above. */ JFrame getRefFrame() { return parent.getParentUI(); } /** * Sets the photo associated to the current user. * * @param photo The photo to set. * @param expId The identifier of the experimenter. */ void setUserPhoto(BufferedImage photo, long expId) { if (usersPhoto == null) usersPhoto = new HashMap<Long, BufferedImage>(); usersPhoto.put(expId, photo); } /** * Returns the photo associated to the current user. * * @param expId The identifier of the experimenter. * @return See above. */ BufferedImage getUserPhoto(long expId) { if (usersPhoto == null) return null; return usersPhoto.get(expId); } /** * Returns the security context. * * @return See above. */ SecurityContext getSecurityContext() { return parent.getSecurityContext(); } /** * Returns <code>true</code> if the name of the group already exists, * <code>false</code> otherwise. * * @param data The group to handle. * @param name The name to check. * @return */ boolean doesGroupExist(GroupData data, String name) { if (data == null) return false; AdminService svc = MetadataViewerAgent.getRegistry().getAdminService(); try { GroupData g = svc.lookupGroup(getSecurityContext(), name); if (g != null && data.getId() != g.getId()) { return true; } } catch (Exception e) { } return false; } /** * Returns the annotations associated to the selected objects. * * @return See above. */ Map<DataObject, StructuredDataResults> getAllStructuredData() { return parent.getAllStructuredData(); } /** * Returns <code>true</code> if the specified namespace is excluded. * <code>false</code> otherwise. * * @param ns The namespace to handle. * @return See above. */ boolean isNameSpaceExcluded(String ns) { if (ns == null) return false; return EXCLUDED_FILE_NS.contains(ns); } /** * Update the channels. * * @param channels The value to set. */ void updateChannels(List<ChannelData> channels) { List l = sorter.sort(channels); emissionsWavelengths = new LinkedHashMap(); Iterator i = l.iterator(); Object channel; while (i.hasNext()) { channel = i.next(); emissionsWavelengths.put(channel, emissionsWavelengths.get(channel)); } } /** * Returns the file set associated to the image if any. * * @return See above. */ Set<FilesetData> getFileset() { return set; } /** * Sets the file set associated to the image if any. * * @param set The value to set. */ void setFileset(Set<FilesetData> set) { this.set = set; } /** Loads the file set if the specified object is an image.*/ void fireFilesetLoading() { ImageData img = getImage(); if (img == null) return; FilesetLoader loader = new FilesetLoader(component, getSecurityContext(), img.getId()); loader.load(); } /*** Returns the display mode. One of the constants defined by * {@link LookupNames}. * * @return See above. */ int getDisplayMode() { Integer value = (Integer) MetadataViewerAgent.getRegistry().lookup(LookupNames.DATA_DISPLAY); if (value == null) return LookupNames.EXPERIMENTER_DISPLAY; switch (value.intValue()) { case LookupNames.EXPERIMENTER_DISPLAY: case LookupNames.GROUP_DISPLAY: return value.intValue(); } return LookupNames.EXPERIMENTER_DISPLAY; } /** * Returns <code>true</code> if the annotations are loaded, * <code>false</code> otherwise. * * @return See above. */ boolean isAnnotationLoaded() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return false; return data.isLoaded(); } /** * Returns <code>true</code> if the image has an original metadata file * linked to it, <code>false</code> otherwise. * * @return See above. */ boolean hasOriginalMetadata() { //FileAnnotationData fa = getOriginalMetadata(); //return fa != null; return true; } /** * Returns the groups the user is member of. * * @return See above. */ Collection<GroupData> getAvailableGroups() { return MetadataViewerAgent.getAvailableUserGroups(); } /** * Returns <code>true</code> if the user is a system user e.g. root * <code>false</code> otherwise. * * @param id The identifier of the user. * @return See above. */ boolean isSystemUser(long id) { return MetadataViewerAgent.getRegistry().getAdminService().isSystemUser(id); } /** * Returns <code>true</code> if the group is a system group e.g. System * <code>false</code> otherwise. * * @param id The identifier of the group. * @return See above. */ boolean isSystemGroup(long id) { return MetadataViewerAgent.getRegistry().getAdminService().isSecuritySystemGroup(id); } /** * Returns <code>true</code> if the group is a system group e.g. System * <code>false</code> otherwise. * * @param id The identifier of the group. * @param key The type of group to check. * @return See above. */ boolean isSystemGroup(long id, String key) { return MetadataViewerAgent.getRegistry().getAdminService().isSecuritySystemGroup(id, key); } /** * Returns <code>true</code> if the file is an inplace import <code>false</code> otherwise. * @return See above. */ boolean isInplaceImport() { StructuredDataResults data = parent.getStructuredData(); if (data == null) return false; return CollectionUtils.isNotEmpty(data.getTransferLinks()); } }