package org.docear.plugin.bibtex;
import java.io.File;
import java.net.MalformedURLException;
import java.net.URI;
import java.net.URL;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map.Entry;
import java.util.Set;
import net.sf.jabref.BibtexDatabase;
import net.sf.jabref.BibtexEntry;
import net.sf.jabref.GUIGlobals;
import net.sf.jabref.Globals;
import net.sf.jabref.export.DocearReferenceUpdateController;
import net.sf.jabref.labelPattern.LabelPatternUtil;
import org.docear.plugin.bibtex.jabref.JabRefAttributes;
import org.docear.plugin.bibtex.jabref.ResolveDuplicateEntryAbortedException;
import org.docear.plugin.core.DocearController;
import org.docear.plugin.core.features.DocearMapModelExtension;
import org.docear.plugin.core.features.MapModificationSession;
import org.docear.plugin.core.mindmap.AMindmapUpdater;
import org.docear.plugin.core.util.Tools;
import org.freeplane.core.util.LogUtils;
import org.freeplane.features.link.NodeLinks;
import org.freeplane.features.map.MapModel;
import org.freeplane.features.map.NodeModel;
import org.freeplane.plugin.workspace.WorkspaceUtils;
public class ReferenceUpdater extends AMindmapUpdater {
private final HashMap<BibtexEntry, Set<NodeModel>> referenceNodes;
private final HashMap<String, BibtexEntry> pdfReferences;
private final HashMap<String, BibtexEntry> urlReferences;
private JabRefAttributes jabRefAttributes;
private BibtexDatabase database;
private MapModificationSession session;
public ReferenceUpdater(String title) {
super(title);
referenceNodes = new HashMap<BibtexEntry, Set<NodeModel>>();
pdfReferences = new HashMap<String, BibtexEntry>();
urlReferences = new HashMap<String, BibtexEntry>();
}
public boolean updateMindmap(MapModel map) {
session = map.getExtension(DocearMapModelExtension.class).getMapModificationSession();
if(session == null) {
session = new MapModificationSession();
map.getExtension(DocearMapModelExtension.class).setMapModificationSession(session);
}
if (DocearController.getController().getSemaphoreController().isLocked("MindmapUpdate")) {
return false;
}
if(DocearReferenceUpdateController.isLocked()) {
return false;
}
try {
DocearReferenceUpdateController.lock();
DocearController.getController().getSemaphoreController().lock("MindmapUpdate");
jabRefAttributes = ReferencesController.getController().getJabRefAttributes();
database = ReferencesController.getController().getJabrefWrapper().getDatabase();
if (database == null) {
return false;
}
if (this.pdfReferences.size() == 0) {
buildPdfIndex();
}
if (this.urlReferences.size() == 0) {
buildUrlIndex();
}
return updateMap(map);
}
finally {
DocearController.getController().getSemaphoreController().unlock("MindmapUpdate");
DocearReferenceUpdateController.unlock();
}
}
private boolean updateMap(MapModel map) {
referenceNodes.clear();
buildIndex(map.getRootNode());
LogUtils.info("Updating references on map with "+nodeNum+" nodes ...");
long snap = System.currentTimeMillis();
try {
return updateReferenceNodes();
}
finally {
LogUtils.info("Updated references on map in "+(System.currentTimeMillis()-snap)/1000+"sec");
}
}
private void buildPdfIndex() {
if (session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST) == null) {
session.putSessionObject(MapModificationSession.FILE_IGNORE_LIST, new HashSet<String>());
}
for (BibtexEntry entry : database.getEntries()) {
String paths = entry.getField(GUIGlobals.FILE_FIELD);
if (paths == null || paths.trim().length() == 0) {
continue;
}
for (String path : jabRefAttributes.parsePathNames(entry, paths)) {
String name = new File(path).getName();
if(((Set<String>) session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST)).contains(name)) {
continue;
}
if (entry.getCiteKey() == null) {
LabelPatternUtil.makeLabel(Globals.prefs.getKeyPattern(), database, entry);
}
if (this.pdfReferences.get(name) == null) {
this.pdfReferences.put(name, entry);
}
else {
try {
BibtexEntry singleEntry = jabRefAttributes.resolveDuplicateLinks(new File(path));
this.pdfReferences.put(name, singleEntry);
}
catch (ResolveDuplicateEntryAbortedException e) {
this.pdfReferences.remove(name);
((Set<String>) session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST)).add(e.getFile().getName());
LogUtils.info("ignore pdf on mindmap update: " + e.getFile());
}
}
}
}
}
private void buildUrlIndex() {
if (session.getSessionObject(MapModificationSession.URL_IGNORE_LIST) == null) {
session.putSessionObject(MapModificationSession.URL_IGNORE_LIST, new HashSet<String>());
}
for (BibtexEntry entry : database.getEntries()) {
String url = entry.getField("url");
if (url == null || url.trim().length() == 0 || ((Set<String>) session.getSessionObject(MapModificationSession.URL_IGNORE_LIST)).contains(url)) {
continue;
}
if (entry.getCiteKey() == null) {
LabelPatternUtil.makeLabel(Globals.prefs.getKeyPattern(), database, entry);
}
if (this.urlReferences.get(url) == null) {
this.urlReferences.put(url, entry);
}
else {
try {
BibtexEntry singleEntry = jabRefAttributes.resolveDuplicateLinks(new URL(url));
this.urlReferences.put(url, singleEntry);
}
catch (MalformedURLException e) {
LogUtils.warn(e);
}
catch (ResolveDuplicateEntryAbortedException e) {
this.urlReferences.remove(url);
((Set<String>) session.getSessionObject(MapModificationSession.URL_IGNORE_LIST)).add(e.getUrl().toExternalForm());
LogUtils.info("ignore url on mindmap update: " + e.getUrl());
}
}
}
}
private boolean isIgnored(Reference reference, NodeModel node) {
if (reference.getUris().size() > 0) {
File file = WorkspaceUtils.resolveURI(reference.getUris().iterator().next(), node.getMap());
if (file != null) {
if (((Set<String>) session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST)).contains(file.getName())) {
return true;
}
}
}
URL u = reference.getUrl();
if (u != null) {
if (((Set<String>) session.getSessionObject(MapModificationSession.URL_IGNORE_LIST)).contains(u.toExternalForm())) {
return true;
}
}
URI uri = Tools.getAbsoluteUri(node);
if (uri != null) {
File file = WorkspaceUtils.resolveURI(uri, node.getMap());
if (file != null) {
if (!reference.containsLink(uri)) {
return true;
}
if (file != null) {
if (((Set<String>) session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST)).contains(file.getName())) {
return true;
}
}
}
else {
u = null;
try {
u = uri.toURL();
}
catch (MalformedURLException e) {
LogUtils.warn(e.getMessage());
}
if (u != null) {
if (((Set<String>) session.getSessionObject(MapModificationSession.URL_IGNORE_LIST)).contains(u.toExternalForm())) {
return true;
}
}
}
}
return false;
}
private boolean updateReferenceNodes() {
boolean changes = false;
for (Entry<BibtexEntry, Set<NodeModel>> entry : referenceNodes.entrySet()) {
// BibtexEntry bibtexEntry = database.getEntryByKey(entry.getKey());
// if (bibtexEntry != null) {
BibtexEntry bibtexEntry = entry.getKey();
Reference reference = new Reference(bibtexEntry);
for (NodeModel node : entry.getValue()) {
if (isIgnored(reference, node)) {
continue;
}
String key = jabRefAttributes.getBibtexKey(node);
try {
if (key == null) {
changes = true;
ReferencesController.getController().getJabRefAttributes().setReferenceToNode(reference, node);
}
else {
changes = changes | ReferencesController.getController().getJabRefAttributes().setReferenceToNode(bibtexEntry, node);
}
}
catch (ResolveDuplicateEntryAbortedException e) {
if (e.getFile() != null) {
((Set<String>) session.getSessionObject(MapModificationSession.FILE_IGNORE_LIST)).add(e.getFile().getName());
}
else {
((Set<String>) session.getSessionObject(MapModificationSession.URL_IGNORE_LIST)).add(e.getUrl().toExternalForm());
}
}
if(Thread.currentThread().isInterrupted()) {
return changes;
}
}
}
return changes;
}
int nodeNum = 0;
private void buildIndex(NodeModel parent) {
nodeNum++;
addNodeToReferenceIndex(parent);
for (NodeModel child : parent.getChildren()) {
buildIndex(child);
}
}
private void addNodeToReferenceIndex(NodeModel node) {
try {
String key = jabRefAttributes.getBibtexKey(node);
URI uri = NodeLinks.getLink(node);
if (uri != null) {
File file;
file = WorkspaceUtils.resolveURI(uri, node.getMap());
if (file != null) {
String fileName = file.getName();
BibtexEntry entry = this.pdfReferences.get(fileName);
if (entry != null) {
addReferenceToIndex(node, entry);
}
return;
}
BibtexEntry entry = this.urlReferences.get(uri.toURL().toExternalForm());
if (entry != null) {
addReferenceToIndex(node, entry);
return;
}
}
if (key != null) {
BibtexEntry bibtexEntry = database.getEntryByKey(key);
addReferenceToIndex(node, bibtexEntry);
return;
}
}
catch (Exception e) {
LogUtils.warn("referenceupdater uri: " + NodeLinks.getLink(node));
LogUtils.warn(e);
}
}
private void addReferenceToIndex(NodeModel node, BibtexEntry entry) {
Set<NodeModel> nodes = referenceNodes.get(entry);
if (nodes == null) {
nodes = new HashSet<NodeModel>();
referenceNodes.put(entry, nodes);
}
nodes.add(node);
}
}