6 import jalview.bin.Cache;
7 import jalview.datamodel.DBRefEntry;
8 import jalview.datamodel.SequenceGroup;
9 import jalview.datamodel.SequenceI;
10 import jalview.gui.AlignFrame;
11 import jalview.gui.Desktop;
12 import jalview.util.GroupUrlLink;
14 import java.awt.Component;
15 import java.awt.Cursor;
16 import java.awt.event.ActionEvent;
17 import java.awt.event.ActionListener;
18 import java.awt.event.ItemEvent;
19 import java.awt.event.ItemListener;
20 import java.io.BufferedReader;
21 import java.io.InputStreamReader;
23 import java.util.Hashtable;
24 import java.util.Vector;
26 import javax.swing.JMenu;
27 import javax.swing.JMenuItem;
28 import javax.swing.JOptionPane;
29 import javax.swing.event.MenuEvent;
30 import javax.swing.event.MenuListener;
31 import javax.xml.parsers.SAXParser;
32 import javax.xml.parsers.SAXParserFactory;
34 import org.xml.sax.Attributes;
35 import org.xml.sax.SAXException;
36 import org.xml.sax.helpers.DefaultHandler;
39 * Lightweight runnable to discover dynamic 'one way' group URL services
43 public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSMenuEntryProviderI
45 private static EnfinEnvision2OneWay groupURLLinksGatherer=null;
46 public static EnfinEnvision2OneWay getInstance() {
47 if (groupURLLinksGatherer==null) {
48 groupURLLinksGatherer = new EnfinEnvision2OneWay();
50 return groupURLLinksGatherer;
52 private void waitForCompletion() {
53 if (groupURLLinksGatherer.isRunning())
55 // wait around and show a visual delay indicator
56 Cursor oldCursor = Desktop.instance.getCursor();
57 Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
58 while (groupURLLinksGatherer.isRunning())
62 } catch (InterruptedException e ){};
64 Desktop.instance.setCursor(oldCursor);
67 public Vector getEnvisionServiceGroupURLS() {
74 private static String BACKGROUND="BACKGROUNDPARAM";
76 * contains null strings or one of the above constants - indicate if this URL is a special case.
78 private Vector additionalPar = new Vector();
80 * the enfin service URL
82 private String enfinService=null;
83 private String description=null;
84 private String wfname;
86 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
88 public void endElement(String uri, String localName, String qName)
92 // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
93 if (qName.equalsIgnoreCase("workflow") && description!=null && description.length()>0)
95 //groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
96 //groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
97 System.err.println("Adding entry for "+wfname+" "+description);
98 if (wfname.toLowerCase().indexOf("funcnet")==-1)
100 groupURLdescr.addElement(description);
101 groupURLdescr.addElement(description);
102 groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
103 groupURLLinks.addElement(wfname+"|"+"http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="+wfname+"&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
109 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
111 public void characters(char[] ch, int start, int length)
114 if (description!=null) {
115 for (int i=start; i<start+length; i++) {
122 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
124 public void startElement(String uri, String localName, String qName,
125 Attributes attributes) throws SAXException
127 if (qName.equalsIgnoreCase("workflow"))
130 wfname = attributes.getValue("name");
132 if (qName.equalsIgnoreCase("description"))
138 //System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
139 // super.startElement(uri,localName,qname,attributes);
142 private boolean started=false;
143 private boolean running=false;
144 private Vector groupURLLinks = null;
145 private Vector groupURLdescr = null;
146 private static String[] allowedDb=new String[] {"UNIPROT","EMBL","PDB"} ;
148 public EnfinEnvision2OneWay() {
149 groupURLLinks = new Vector();
150 groupURLdescr = new Vector();
152 enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE", "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
153 new Thread(this).start();
161 SAXParserFactory spf = SAXParserFactory.newInstance();
162 SAXParser sp = spf.newSAXParser();
163 sp.parse(new URL(enfinService).openStream(), this);
164 } catch (Exception e)
166 Cache.log.warn("Exception when discovering One Way services: ",e);
170 Cache.log.warn("Error when discovering One Way services: ",e);
173 Cache.log.debug("Finished running.");
177 * have we finished running yet ?
178 * @return false if we have been run.
180 public boolean isRunning()
183 // TODO Auto-generated method stub
184 return !started || running;
186 public static void main(String[] args){
188 EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
189 while (ow.isRunning())
193 } catch (Exception e){};
196 for (int i=0;i<ow.groupURLLinks.size();i++) {
197 System.err.println("Description"+ow.groupURLdescr.elementAt(i)+"Service URL: "+ow.groupURLLinks.elementAt(i));
200 /// Copied from jalview.gui.PopupMenu
202 * add a late bound URL service item to the given menu
207 * @param urlgenerator GroupURLLink used to generate URL
208 * @param urlstub Object array returned from the makeUrlStubs function.
210 private void addshowLink(JMenu linkMenu, String label, String descr, final GroupUrlLink urlgenerator, final Object[] urlstub)
212 Component[] jmi=linkMenu.getMenuComponents();
213 for (int i=0; i<jmi.length; i++)
215 if (jmi[i] instanceof JMenuItem && ((JMenuItem)jmi[i]).getText().equalsIgnoreCase(label))
217 // don't add this - its a repeat of an existing URL.
221 JMenuItem item = new JMenuItem(label);
222 item.setToolTipText("Submit ("+urlgenerator.getNumberInvolved(urlstub)+" seqs) to workflow: "+descr);
223 item.addActionListener(new java.awt.event.ActionListener()
225 public void actionPerformed(ActionEvent e)
227 new Thread(new Runnable()
232 showLink(urlgenerator.constructFrom(urlstub));
243 * open the given link in a new browser window
246 public void showLink(String url)
250 jalview.util.BrowserLauncher.openURL(url);
251 } catch (Exception ex)
254 .showInternalMessageDialog(
256 "Unixers: Couldn't find default web browser."
257 + "\nAdd the full path to your browser in Preferences.",
258 "Web browser not found", JOptionPane.WARNING_MESSAGE);
260 ex.printStackTrace();
264 * called by a web service menu instance when it is opened.
265 * @param enfinServiceMenu
268 private void buildGroupLinkMenu(JMenu enfinServiceMenu,
269 AlignFrame alignFrame)
271 SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
272 SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
274 // consider visible regions here/
276 enfinServiceMenu.removeAll();
277 JMenu entries = buildGroupURLMenu(seqs,sg);
280 for (int i=0,iSize=entries.getMenuComponentCount();i<iSize;i++)
282 // transfer - menu component is removed from entries automatically
283 enfinServiceMenu.add(entries.getMenuComponent(0));
285 // entries.removeAll();
286 enfinServiceMenu.setEnabled(true);
288 enfinServiceMenu.setEnabled(false);
293 * construct a dynamic enfin services menu given a sequence selection
299 private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
302 // TODO: usability: thread off the generation of group url content so root menu appears asap
303 // sequence only URLs
304 // ID/regex match URLs
305 JMenu groupLinksMenu = new JMenu("Group Link");
306 JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
307 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
308 Hashtable commonDbrefs = new Hashtable();
309 for (int sq = 0; sq<seqs.length;sq++) {
313 start = seqs[sq].findPosition(sg.getStartRes());
314 end=seqs[sq].findPosition(sg.getEndRes());
316 // get total width of alignment.
317 start = seqs[sq].getStart();
318 end = seqs[sq].findPosition(seqs[sq].getLength());
320 // we skip sequences which do not have any non-gaps in the region of interest
325 // just collect ids from dataset sequence
326 // TODO: check if IDs collected from selecton group intersects with the current selection, too
327 SequenceI sqi = seqs[sq];
328 while (sqi.getDatasetSequence()!=null) {
329 sqi = sqi.getDatasetSequence(); }
330 DBRefEntry[] dbr = sqi.getDBRef();
331 if (dbr!=null && dbr.length>0)
333 for (int d=0;d<dbr.length;d++)
335 String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
336 Object[] sarray = (Object[]) commonDbrefs.get(src);
339 sarray = new Object[2];
340 sarray[0] = new int[] { 0 };
341 sarray[1] = new String[seqs.length];
343 commonDbrefs.put(src,sarray);
346 if (((String[])sarray[1])[sq]==null) {
347 if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
348 ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
349 ((int[])sarray[0])[0]++;
355 // now create group links for all distinct ID/sequence sets.
356 boolean addMenu = false; // indicates if there are any group links to give to user
357 for (int i = 0; i < groupURLLinks.size(); i++) {
358 String link = groupURLLinks.elementAt(i).toString();
359 String descr = groupURLdescr.elementAt(i).toString();
360 // boolean specialCase = additionalPar.elementAt(i).toString().equals(BACKGROUND);
361 GroupUrlLink urlLink = null;
364 urlLink = new GroupUrlLink(link);
365 } catch (Exception foo)
367 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
372 if (!urlLink.isValid())
374 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
377 final String label = urlLink.getLabel();
378 boolean usingNames = false;
379 // Now see which parts of the group apply for this URL
381 String[] seqstr,ids; // input to makeUrl
382 for (int t=0;t<allowedDb.length; t++) {
383 ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
384 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
387 int numinput = ((int[])idset[0])[0];
388 String[] allids = ((String[])idset[1]);
389 seqstr = new String[numinput];
390 ids = new String[numinput];
391 for (int sq=0,idcount=0;sq<seqs.length;sq++)
393 if (allids[sq]!=null) {
394 ids[idcount] = allids[sq];
395 seqstr[idcount++] = idandseqs[1][sq];
398 addMenu = addMenu | createAndAddLinks(linkMenus,false,urlLink,label,ltarget,descr, ids,seqstr);
401 // also do names only.
402 seqstr = idandseqs[1];
404 addMenu = addMenu | createAndAddLinks(linkMenus,true,urlLink,label,"Names",descr, ids,seqstr);
408 groupLinksMenu = new JMenu("Group Links");
409 for (int m=0;m<linkMenus.length; m++)
411 if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
413 groupLinksMenu.add(linkMenus[m]);
417 return groupLinksMenu;
422 private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
423 GroupUrlLink urlLink, String label, String ltarget, String descr, String[] ids,
426 Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
429 int type = urlLink.getGroupURLType() & 3;
430 //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
431 // first two bits ofurlLink type bitfield are sequenceids and sequences
432 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
433 addshowLink(linkMenus[type], label + " "+(usingNames ? (((type & 1)==1) ? "(Names)" : "") : ("("+ltarget+")")), descr, urlLink, urlset);
438 /// end of stuff copied from popupmenu
439 public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
441 final JMenu enfinServiceMenu = new JMenu("Envision 2");
442 wsmenu.add(enfinServiceMenu);
443 enfinServiceMenu.setEnabled(false);
444 wsmenu.addMenuListener(new MenuListener()
446 // this listener remembers when the menu was first selected, and
447 // doesn't rebuild the session list until it has been cleared and
449 boolean refresh = true;
451 public void menuCanceled(MenuEvent e)
456 public void menuDeselected(MenuEvent e)
461 public void menuSelected(MenuEvent e)
466 buildGroupLinkMenu(enfinServiceMenu,alignFrame);
467 } catch (OutOfMemoryError ex)
469 Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
470 enfinServiceMenu.setEnabled(false);