Java tutorial
/* * org.openmicroscopy.shoola.env.data.views.calls.DMRefreshLoader * *------------------------------------------------------------------------------ * 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.env.data.views.calls; //Java imports import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.Map.Entry; //Third-party libraries import org.apache.commons.collections.CollectionUtils; //Application-internal dependencies import org.openmicroscopy.shoola.env.LookupNames; import org.openmicroscopy.shoola.env.config.AgentInfo; import org.openmicroscopy.shoola.env.config.Registry; import org.openmicroscopy.shoola.env.data.AdminService; import org.openmicroscopy.shoola.env.data.OmeroDataService; import org.openmicroscopy.shoola.env.data.OmeroMetadataService; import org.openmicroscopy.shoola.env.data.model.TimeRefObject; import org.openmicroscopy.shoola.env.data.util.SecurityContext; import org.openmicroscopy.shoola.env.data.views.BatchCall; import org.openmicroscopy.shoola.env.data.views.BatchCallTree; import pojos.DataObject; import pojos.DatasetData; import pojos.ExperimenterData; import pojos.FileAnnotationData; import pojos.GroupData; import pojos.ImageData; import pojos.ProjectData; import pojos.ScreenData; import pojos.TagAnnotationData; /** * Command to refresh a data trees. * * @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 OME2.2 */ public class DMRefreshLoader extends BatchCallTree { /** The results of the call. */ private Object results; /** Loads the specified tree. */ private BatchCall loadCall; /** * Retrieve the data. * * @param rootNodeType The root node. * @param nodes The nodes to handle. * @param mapResult Map hosting the results. * @throws Exception Thrown if an error occurred. */ private void retrieveData(Class rootNodeType, Map<SecurityContext, List> nodes, Map<SecurityContext, Object> mapResult) throws Exception { OmeroDataService os = context.getDataService(); Iterator<Entry<SecurityContext, List>> users = nodes.entrySet().iterator(); long userID; List containers; Object result; Set set, children, newChildren, r; List<Long> ids; Iterator i, j, c, k; Long id; Class klass; Map topNodes; DataObject child, parent; Set s; Entry<SecurityContext, List> entry; SecurityContext ctx; TimeRefObject ref; Object object; while (users.hasNext()) { entry = users.next(); ctx = entry.getKey(); userID = ctx.getExperimenter(); containers = entry.getValue(); if (CollectionUtils.isEmpty(containers)) { result = os.loadContainerHierarchy(ctx, rootNodeType, null, false, ctx.getExperimenter()); if (mapResult.containsKey(ctx)) { s = (Set) mapResult.get(userID); s.addAll((Set) result); } else { mapResult.put(ctx, result); } } else { //First need to extract any TimeRefObject topNodes = new HashMap(); i = containers.iterator(); ids = new ArrayList<Long>(); while (i.hasNext()) { object = i.next(); if (object instanceof TimeRefObject) { ref = (TimeRefObject) object; if (ref.getFileType() == TimeRefObject.FILE_IMAGE_TYPE) ref.setResults(os.getExperimenterImages(ctx, userID, true)); topNodes.put(ref, ref); } else { ids.add(Long.valueOf(((DataObject) object).getId())); } } //load the rest. set = os.loadContainerHierarchy(ctx, rootNodeType, null, false, userID); j = set.iterator(); children = null; klass = null; while (j.hasNext()) { newChildren = new HashSet(); parent = (DataObject) j.next(); if (parent instanceof ProjectData) { children = ((ProjectData) parent).getDatasets(); klass = DatasetData.class; } else if (parent instanceof ScreenData) { children = null;//((ScreenData) parent).getPlates(); klass = ScreenData.class; } else if (parent instanceof DatasetData) { children = new HashSet(1); children.add(parent); klass = DatasetData.class; } topNodes.put(parent, newChildren); if (children != null) { c = children.iterator(); while (c.hasNext()) { child = (DataObject) c.next(); id = Long.valueOf(child.getId()); if (ids.contains(id)) { r = os.loadContainerHierarchy(ctx, klass, Arrays.asList(id), true, userID); k = r.iterator(); while (k.hasNext()) { newChildren.add(k.next()); } } else newChildren.add(child); } } } result = topNodes; if (mapResult.containsKey(ctx)) { Map map = (Map) mapResult.get(userID); map.putAll((Map) result); } else mapResult.put(ctx, result); } } } /** * Creates a {@link BatchCall} to retrieve a Container tree, either * <code>Project</code> or <code>Screen</code>. * * @param rootNodeType The type of the root node. Can either: * {@link ProjectData}. * @param nodes The nodes to handle. * @return The {@link BatchCall}. */ private BatchCall makeBatchCall(final Class rootNodeType, final Map<SecurityContext, List> nodes) { return new BatchCall("Loading container tree: ") { public void doCall() throws Exception { Map<SecurityContext, Object> r = new HashMap<SecurityContext, Object>(nodes.size()); results = r; retrieveData(rootNodeType, nodes, r); } }; } /** * Creates a {@link BatchCall} to retrieve the images. * * @param nodes The map whose keys are the security context and the values * are the corresponding collections of data objects to reload. * @return The {@link BatchCall}. */ private BatchCall makeImagesBatchCall(final Map<SecurityContext, List> nodes) { return new BatchCall("Loading images: ") { public void doCall() throws Exception { OmeroDataService os = context.getDataService(); Iterator i = nodes.entrySet().iterator(); long userID; List containers; Iterator j; TimeRefObject ref; Entry entry; SecurityContext ctx; while (i.hasNext()) { entry = (Entry) i.next(); ctx = (SecurityContext) entry.getKey(); userID = ctx.getExperimenter(); containers = (List) entry.getValue(); j = containers.iterator(); while (j.hasNext()) { ref = (TimeRefObject) j.next(); ref.setResults(os.getImagesPeriod(ctx, ref.getStartTime(), ref.getEndTime(), userID, true)); } } results = nodes; } }; } /** * Returns all the groups the user is a member of. * * @return See above. */ private Collection getAllGroups() { return (Collection) context.lookup(LookupNames.USER_GROUP_DETAILS); } /** * Returns the collection of groups the current user is the leader of. * * @return See above. */ public Set getGroupsLeaderOf() { Set values = new HashSet(); Collection groups = getAllGroups(); Iterator i = groups.iterator(); GroupData g; Set leaders; ExperimenterData exp = (ExperimenterData) context.lookup(LookupNames.CURRENT_USER_DETAILS); long id = exp.getId(); Iterator j; while (i.hasNext()) { g = (GroupData) i.next(); leaders = g.getLeaders(); if (leaders != null && leaders.size() > 0) { j = leaders.iterator(); while (j.hasNext()) { exp = (ExperimenterData) j.next(); if (exp.getId() == id) { values.add(g); break; } } } } return values; } /** * Creates a {@link BatchCall} to retrieve the groups. * * @param nodes The map whose keys are the security context and the values * are the corresponding collections of data objects to reload. * @return The {@link BatchCall}. */ private BatchCall makeGroupsBatchCall(final Map<SecurityContext, List> nodes) { return new BatchCall("Loading groups: ") { public void doCall() throws Exception { AdminService svc = context.getAdminService(); //Check if the user is an administrator Boolean admin = (Boolean) context.lookup(LookupNames.USER_ADMINISTRATOR); if (admin != null && admin.booleanValue()) { Iterator<Entry<SecurityContext, List>> i = nodes.entrySet().iterator(); Entry<SecurityContext, List> e; SecurityContext ctx; while (i.hasNext()) { e = i.next(); ctx = e.getKey(); List<GroupData> groups = svc.loadGroups(ctx, -1); List<GroupData> r = new ArrayList<GroupData>(); List<Long> toRemove = new ArrayList<Long>(); List<GroupData> l; List list; list = e.getValue(); Iterator j = list.iterator(); while (j.hasNext()) { long groupID = (Long) j.next(); l = svc.loadGroups(ctx, groupID); toRemove.add(groupID); if (l.size() == 1) r.add(l.get(0)); } Iterator<GroupData> k = groups.iterator(); GroupData g; while (k.hasNext()) { g = (GroupData) k.next(); if (!toRemove.contains(g.getId())) r.add(g); } results = r; } } else { //Not admin groups owner. Collection allgroups = getAllGroups(); Collection groups = getGroupsLeaderOf(); Iterator i = groups.iterator(); GroupData group; SecurityContext ctx; List<GroupData> l = new ArrayList<GroupData>(); while (i.hasNext()) { group = (GroupData) i.next(); ctx = new SecurityContext(group.getId()); l.addAll(svc.loadGroups(ctx, group.getId())); allgroups.remove(group); } Collection all = new ArrayList(); all.addAll(l); all.addAll(allgroups); context.bind(LookupNames.USER_GROUP_DETAILS, all); List agents = (List) context.lookup(LookupNames.AGENTS); Iterator kk = agents.iterator(); AgentInfo agentInfo; Registry reg; while (kk.hasNext()) { agentInfo = (AgentInfo) kk.next(); if (agentInfo.isActive()) { reg = agentInfo.getRegistry(); reg.bind(LookupNames.USER_GROUP_DETAILS, all); } } results = l; } } }; } /** * Creates a {@link BatchCall} to retrieve the files. * * @param nodes The map whose keys are the security context and the values * are the corresponding collections of data objects to reload. * @return The {@link BatchCall}. */ private BatchCall makeFilesBatchCall(final Map<SecurityContext, List> nodes) { return new BatchCall("Loading files: ") { public void doCall() throws Exception { OmeroMetadataService os = context.getMetadataService(); //Iterator users = nodes.keySet().iterator(); long userID; List containers; Iterator j; TimeRefObject ref; Entry entry; SecurityContext ctx; Iterator i = nodes.entrySet().iterator(); while (i.hasNext()) { entry = (Entry) i.next(); ctx = (SecurityContext) entry.getKey(); userID = ctx.getExperimenter(); containers = (List) entry.getValue(); j = containers.iterator(); while (j.hasNext()) { ref = (TimeRefObject) j.next(); ref.setResults(os.loadFiles(ctx, ref.getFileType(), userID)); } } results = nodes; } }; } /** * Creates a {@link BatchCall} to retrieve the files. * * @param nodes The map whose keys are the security context and the values * are the corresponding collections of data objects to reload. * @return The {@link BatchCall}. */ private BatchCall makeTagsBatchCall(final Map<SecurityContext, List> nodes) { return new BatchCall("Loading files: ") { public void doCall() throws Exception { OmeroMetadataService os = context.getMetadataService(); OmeroDataService ds = context.getDataService(); Map<SecurityContext, Object> r = new HashMap<SecurityContext, Object>(nodes.size()); long userID; Entry<SecurityContext, List> entry; Iterator<Entry<SecurityContext, List>> j = nodes.entrySet().iterator(); List<?> l; Collection tags; Iterator k; Iterator<TagAnnotationData> i; TagAnnotationData tag, child; Map<Long, Collection<?>> values; SecurityContext ctx; Map<DataObject, Set<?>> mapForDataObject; while (j.hasNext()) { entry = j.next(); ctx = entry.getKey(); userID = ctx.getExperimenter(); l = entry.getValue(); tags = os.loadTags(ctx, -1L, true, userID, ctx.getGroupID()); List<Object> tagResults = new ArrayList<Object>(); mapForDataObject = new HashMap<DataObject, Set<?>>(); if (CollectionUtils.isEmpty(l)) { r.put(ctx, tags); } else { values = new HashMap<Long, Collection<?>>(); k = l.iterator(); Object ob; TimeRefObject ref; DataObject ho; List<TagAnnotationData> refTags = new ArrayList<TagAnnotationData>(); while (k.hasNext()) { ob = k.next(); if (ob instanceof TagAnnotationData) { tag = (TagAnnotationData) ob; values.put(tag.getId(), os.loadTags(ctx, tag.getId(), false, userID, ctx.getGroupID())); } else if (ob instanceof TimeRefObject) { ref = (TimeRefObject) ob; ref.setResults(os.loadFiles(ctx, ref.getFileType(), userID)); refTags.addAll(ref.getResults()); tagResults.add(ref); } else if (ob instanceof DataObject) { //retrieve the data for the data object ho = (DataObject) ob; mapForDataObject.put(ho, ds.loadContainerHierarchy(ctx, ob.getClass(), Arrays.asList(ho.getId()), true, userID)); } } handleTags(tags, tagResults, values, mapForDataObject); if (refTags.size() > 0) { handleTags(refTags, null, values, mapForDataObject); } r.put(ctx, tagResults); } } results = r; } }; } /** * Maps the tags to the correct objects. * * @param tags The tags to handle. * @param tagResults The tags loading for smart folder. * @param values The value for the loaded objects. * @param mapForDataObject The loaded values. */ private void handleTags(Collection<TagAnnotationData> tags, List<Object> tagResults, Map<Long, Collection<?>> values, Map<DataObject, Set<?>> mapForDataObject) { Iterator<TagAnnotationData> k = tags.iterator(); TagAnnotationData tag, child; String ns; Set<TagAnnotationData> set; Iterator<TagAnnotationData> i; while (k.hasNext()) { tag = (TagAnnotationData) k.next(); if (tagResults != null) tagResults.add(tag); ns = tag.getNameSpace(); if (TagAnnotationData.INSIGHT_TAGSET_NS.equals(ns)) { set = tag.getTags(); i = set.iterator(); while (i.hasNext()) { child = i.next(); if (values.containsKey(child.getId())) { populateTag(child, values, mapForDataObject); } } } else { if (values.containsKey(tag.getId())) { populateTag(tag, values, mapForDataObject); } } } } /** * Populates the specified tag with the passed value. * * @param tag The tag to populate * @param values Track the object. * @param mapForDataObject The values to set. */ private void populateTag(TagAnnotationData tag, Map<Long, Collection<?>> values, Map<DataObject, Set<?>> mapForDataObject) { if (mapForDataObject.isEmpty()) { tag.setDataObjects((Set<DataObject>) values.get(tag.getId())); } else { Set<DataObject> objects = (Set<DataObject>) values.get(tag.getId()); Set<DataObject> newList = new HashSet<DataObject>(objects.size()); Iterator<DataObject> kk = objects.iterator(); while (kk.hasNext()) { newList.add(getLoadedObject(mapForDataObject, kk.next())); } tag.setDataObjects(newList); } } /** * Checks the object has been reloaded. * * @param map The list of reloaded object. * @param ho The data object of reference. */ private DataObject getLoadedObject(Map<DataObject, Set<?>> map, DataObject ho) { Set<DataObject> sets = map.keySet(); Iterator<DataObject> i = sets.iterator(); DataObject object; Set<?> s; while (i.hasNext()) { object = i.next(); if (object.getClass().equals(ho.getClass()) && object.getId() == ho.getId()) { s = map.get(object); return (DataObject) s.iterator().next(); } else if (ho instanceof ProjectData) { //need to check the dataset ProjectData p = (ProjectData) ho; Set<DatasetData> datasets = p.getDatasets(); Iterator<DatasetData> j = datasets.iterator(); Set<DatasetData> loaded = new HashSet<DatasetData>(); boolean modified = false; while (j.hasNext()) { DataObject data = j.next(); if (object.getClass().equals(data.getClass()) && object.getId() == data.getId()) { s = map.get(object); loaded.add((DatasetData) s.iterator().next()); modified = true; } else loaded.add((DatasetData) data); } if (modified) { p.setDatasets(loaded); return p; } } } return ho; } /** * Adds the {@link #loadCall} to the computation tree. * @see BatchCallTree#buildTree() */ protected void buildTree() { add(loadCall); } /** * Returns the root node of the requested tree. * @see BatchCallTree#getResult() */ protected Object getResult() { return results; } /** * Creates a new instance. * If bad arguments are passed, we throw a runtime * exception so to fail early and in the caller's thread. * * @param rootNodeType The type of the root node. * @param nodes The map whose keys are the security context * and the values are the corresponding collections of * data objects to reload. */ public DMRefreshLoader(Class rootNodeType, Map<SecurityContext, List> nodes) { if (rootNodeType == null) throw new IllegalArgumentException("No root node type."); if (nodes == null || nodes.size() == 0) throw new IllegalArgumentException("No container with images."); if (ImageData.class.equals(rootNodeType)) loadCall = makeImagesBatchCall(nodes); else if (ProjectData.class.equals(rootNodeType) || ScreenData.class.equals(rootNodeType)) loadCall = makeBatchCall(rootNodeType, nodes); else if (FileAnnotationData.class.equals(rootNodeType)) { loadCall = makeFilesBatchCall(nodes); } else if (TagAnnotationData.class.equals(rootNodeType)) { loadCall = makeTagsBatchCall(nodes); } else if (GroupData.class.equals(rootNodeType)) { loadCall = makeGroupsBatchCall(nodes); } } }