2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import jalview.bin.Cache;
22 import jalview.datamodel.DBRefEntry;
23 import jalview.datamodel.SequenceGroup;
24 import jalview.datamodel.SequenceI;
25 import jalview.gui.AlignFrame;
26 import jalview.gui.Desktop;
27 import jalview.gui.JvSwingUtils;
28 import jalview.util.GroupUrlLink;
29 import jalview.util.GroupUrlLink.UrlStringTooLongException;
31 import java.awt.Component;
32 import java.awt.Cursor;
33 import java.awt.event.ActionEvent;
34 import java.io.UnsupportedEncodingException;
36 import java.net.URLEncoder;
37 import java.util.Hashtable;
39 import java.util.Vector;
40 import java.util.regex.Pattern;
42 import javax.swing.JMenu;
43 import javax.swing.JMenuItem;
44 import javax.swing.JOptionPane;
45 import javax.swing.event.MenuEvent;
46 import javax.swing.event.MenuListener;
47 import javax.xml.parsers.SAXParser;
48 import javax.xml.parsers.SAXParserFactory;
50 import org.xml.sax.Attributes;
51 import org.xml.sax.SAXException;
52 import org.xml.sax.helpers.DefaultHandler;
54 import com.lowagie.text.html.HtmlEncoder;
57 * Lightweight runnable to discover dynamic 'one way' group URL services
59 * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
64 public class EnfinEnvision2OneWay extends DefaultHandler implements
65 Runnable, WSMenuEntryProviderI
67 private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
69 public static EnfinEnvision2OneWay getInstance()
71 if (groupURLLinksGatherer == null)
73 groupURLLinksGatherer = new EnfinEnvision2OneWay();
75 return groupURLLinksGatherer;
78 private void waitForCompletion()
80 if (groupURLLinksGatherer.isRunning())
82 // wait around and show a visual delay indicator
83 Cursor oldCursor = Desktop.instance.getCursor();
84 Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
85 while (groupURLLinksGatherer.isRunning())
90 } catch (InterruptedException e)
95 Desktop.instance.setCursor(oldCursor);
99 public Vector getEnvisionServiceGroupURLS()
102 return groupURLLinks;
108 private static String BACKGROUND = "BACKGROUNDPARAM";
111 * contains null strings or one of the above constants - indicate if this URL
114 private Vector additionalPar = new Vector();
117 * the enfin service URL
119 private String enfinService = null;
121 private String description = null;
123 private String wfname;
128 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
129 * java.lang.String, java.lang.String)
131 public void endElement(String uri, String localName, String qName)
135 // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
136 if (qName.equalsIgnoreCase("workflow") && description != null
137 && description.length() > 0)
139 // 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|,");
140 // 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|,");
141 System.err.println("Adding entry for " + wfname + " " + description);
142 if (wfname.toLowerCase().indexOf("funcnet") == -1)
144 description = Pattern.compile("\\s+", Pattern.MULTILINE)
145 .matcher(description).replaceAll(" ");
146 groupURLdescr.addElement(description);
147 groupURLdescr.addElement(description);
148 String urlstub = wfname;
149 if (wfname.indexOf(" ") > -1)
151 // make the name safe!
154 urlstub = URLEncoder.encode(wfname, "utf-8");
155 } catch (UnsupportedEncodingException e)
157 // TODO Auto-generated catch block
164 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
166 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
170 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
172 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
180 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
182 public void characters(char[] ch, int start, int length)
185 if (description != null)
187 for (int i = start; i < start + length; i++)
189 description += ch[i];
197 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
198 * java.lang.String, java.lang.String, org.xml.sax.Attributes)
200 public void startElement(String uri, String localName, String qName,
201 Attributes attributes) throws SAXException
203 if (qName.equalsIgnoreCase("workflow"))
206 wfname = attributes.getValue("name");
208 if (qName.equalsIgnoreCase("description"))
213 // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
214 // super.startElement(uri,localName,qname,attributes);
217 private boolean started = false;
219 private boolean running = false;
221 private Vector groupURLLinks = null;
223 private Vector groupURLdescr = null;
225 private static String[] allowedDb = new String[]
226 { "UNIPROT", "EMBL", "PDB" };
228 public EnfinEnvision2OneWay()
230 groupURLLinks = new Vector();
231 groupURLdescr = new Vector();
233 enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
234 "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
235 new Thread(this).start();
244 SAXParserFactory spf = SAXParserFactory.newInstance();
245 SAXParser sp = spf.newSAXParser();
246 sp.parse(new URL(enfinService).openStream(), this);
247 } catch (Exception e)
249 Cache.log.warn("Exception when discovering One Way services: ", e);
252 Cache.log.warn("Error when discovering One Way services: ", e);
255 Cache.log.debug("Finished running.");
259 * have we finished running yet ?
261 * @return false if we have been run.
263 public boolean isRunning()
266 // TODO Auto-generated method stub
267 return !started || running;
270 public static void main(String[] args)
273 EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
274 while (ow.isRunning())
279 } catch (Exception e)
285 for (int i = 0; i < ow.groupURLLinks.size(); i++)
287 System.err.println("Description" + ow.groupURLdescr.elementAt(i)
288 + "Service URL: " + ow.groupURLLinks.elementAt(i));
292 // / Copied from jalview.gui.PopupMenu
294 * add a late bound URL service item to the given menu
298 * - menu label string
299 * @param urlgenerator
300 * GroupURLLink used to generate URL
302 * Object array returned from the makeUrlStubs function.
304 private void addshowLink(JMenu linkMenu, String label, String descr,
305 String dbname, final GroupUrlLink urlgenerator,
306 final Object[] urlstub)
308 Component[] jmi = linkMenu.getMenuComponents();
309 for (int i = 0; i < jmi.length; i++)
311 if (jmi[i] instanceof JMenuItem
312 && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
314 // don't add this - its a repeat of an existing URL.
320 descr = HtmlEncoder.encode(descr);
321 } catch (Exception e)
326 boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
327 int i = urlgenerator.getNumberInvolved(urlstub);
328 JMenuItem item = new JMenuItem(label);
330 if (dbname == null || dbname.trim().length() == 0)
334 item.setToolTipText("<html>"
335 + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
336 + (seqsorids ? "sequence" : "sequence id")
339 + " to<br/>" + descr) + "</html>");
340 item.addActionListener(new java.awt.event.ActionListener()
342 public void actionPerformed(ActionEvent e)
344 new Thread(new Runnable()
351 showLink(urlgenerator.constructFrom(urlstub));
352 } catch (UrlStringTooLongException ex)
354 Cache.log.warn("Not showing link: URL is too long!", ex);
366 * open the given link in a new browser window
370 public void showLink(String url)
374 jalview.util.BrowserLauncher.openURL(url);
375 } catch (Exception ex)
378 .showInternalMessageDialog(
380 "Unixers: Couldn't find default web browser."
381 + "\nAdd the full path to your browser in Preferences.",
382 "Web browser not found", JOptionPane.WARNING_MESSAGE);
384 ex.printStackTrace();
389 * called by a web service menu instance when it is opened.
391 * @param enfinServiceMenu
394 private void buildGroupLinkMenu(JMenu enfinServiceMenu,
395 AlignFrame alignFrame)
397 if (running || !started)
401 SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
402 SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
405 // consider visible regions here/
407 enfinServiceMenu.removeAll();
408 JMenu entries = buildGroupURLMenu(seqs, sg);
411 for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
413 // transfer - menu component is removed from entries automatically
414 enfinServiceMenu.add(entries.getMenuComponent(0));
416 // entries.removeAll();
417 enfinServiceMenu.setEnabled(true);
421 enfinServiceMenu.setEnabled(false);
426 * construct a dynamic enfin services menu given a sequence selection
433 private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
435 if (groupURLdescr == null || groupURLLinks == null)
437 // TODO: usability: thread off the generation of group url content so root
439 // sequence only URLs
440 // ID/regex match URLs
441 JMenu groupLinksMenu = new JMenu("Group Link");
442 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
443 Hashtable commonDbrefs = new Hashtable();
444 for (int sq = 0; sq < seqs.length; sq++)
450 start = seqs[sq].findPosition(sg.getStartRes());
451 end = seqs[sq].findPosition(sg.getEndRes());
455 // get total width of alignment.
456 start = seqs[sq].getStart();
457 end = seqs[sq].findPosition(seqs[sq].getLength());
459 // we skip sequences which do not have any non-gaps in the region of
465 // just collect ids from dataset sequence
466 // TODO: check if IDs collected from selecton group intersects with the
467 // current selection, too
468 SequenceI sqi = seqs[sq];
469 while (sqi.getDatasetSequence() != null)
471 sqi = sqi.getDatasetSequence();
473 DBRefEntry[] dbr = sqi.getDBRef();
474 if (dbr != null && dbr.length > 0)
476 for (int d = 0; d < dbr.length; d++)
478 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
479 Object[] sarray = (Object[]) commonDbrefs.get(src);
482 sarray = new Object[2];
483 sarray[0] = new int[]
485 sarray[1] = new String[seqs.length];
487 commonDbrefs.put(src, sarray);
490 if (((String[]) sarray[1])[sq] == null)
493 || (dbr[d].getMap().locateMappedRange(start, end) != null))
495 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
496 ((int[]) sarray[0])[0]++;
502 // now create group links for all distinct ID/sequence sets.
503 Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
505 * last number of sequences where URL generation failed
507 int[] nsqtype = new int[]
508 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
509 for (int i = 0; i < groupURLLinks.size(); i++)
511 String link = (String) groupURLLinks.elementAt(i);
512 String descr = (String) groupURLdescr.elementAt(i);
514 // boolean specialCase =
515 // additionalPar.elementAt(i).toString().equals(BACKGROUND);
516 GroupUrlLink urlLink = null;
519 urlLink = new GroupUrlLink(link);
520 } catch (Exception foo)
522 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
527 if (!urlLink.isValid())
529 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
532 final String label = urlLink.getLabel();
533 // create/recover the sub menus that might be populated for this link.
534 JMenu[] wflinkMenus = gurlMenus.get(label);
535 if (wflinkMenus == null)
537 // three types of url that might be
539 wflinkMenus = new JMenu[]
540 { null, new JMenu("IDS"), new JMenu("Sequences"),
541 new JMenu("IDS and Sequences") };
542 gurlMenus.put(label, wflinkMenus);
545 boolean usingNames = false;
546 // Now see which parts of the group apply for this URL
548 String[] seqstr, ids; // input to makeUrl
549 for (int t = 0; t < allowedDb.length; t++)
551 ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
552 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
555 int numinput = ((int[]) idset[0])[0];
556 String[] allids = ((String[]) idset[1]);
557 seqstr = new String[numinput];
558 ids = new String[numinput];
559 if (nsqtype[urlLink.getGroupURLType()] > 0
560 && numinput >= nsqtype[urlLink.getGroupURLType()])
564 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
566 if (allids[sq] != null)
568 ids[idcount] = allids[sq];
569 seqstr[idcount++] = idandseqs[1][sq];
574 createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
576 } catch (UrlStringTooLongException ex)
578 nsqtype[urlLink.getGroupURLType()] = numinput;
582 // also do names only.
583 seqstr = idandseqs[1];
585 if (nsqtype[urlLink.getGroupURLType()] > 0
586 && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
593 createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
595 } catch (UrlStringTooLongException ex)
597 nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
600 boolean anyadded = false; // indicates if there are any group links to give
602 for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
604 JMenu grouplinkset = new JMenu(menues.getKey());
605 JMenu[] wflinkMenus = menues.getValue();
606 for (int m = 0; m < wflinkMenus.length; m++)
608 if (wflinkMenus[m] != null
609 && wflinkMenus[m].getMenuComponentCount() > 0)
612 grouplinkset.add(wflinkMenus[m]);
615 groupLinksMenu.add(grouplinkset);
619 return groupLinksMenu;
624 private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
625 GroupUrlLink urlLink, String label, String ltarget, String descr,
626 String[] ids, String[] seqstr) throws UrlStringTooLongException
628 Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
629 + System.currentTimeMillis(), false);
633 int type = urlLink.getGroupURLType() & 3;
634 // System.out.println(urlLink.getGroupURLType()
635 // +" "+((String[])urlset[3])[0]);
636 // first two bits ofurlLink type bitfield are sequenceids and sequences
637 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
642 + (ltarget == null ? (((type & 1) == 1 ? "ID"
643 : "Sequence") + (urlLink
644 .getNumberInvolved(urlset) > 1 ? "s" : ""))
645 : (usingNames ? (((type & 1) == 1) ? "(Names)"
647 : ("(" + ltarget + ")"))), descr,
648 usingNames ? null : label, urlLink, urlset);
654 // / end of stuff copied from popupmenu
655 public void attachWSMenuEntry(final JMenu wsmenu,
656 final AlignFrame alignFrame)
658 final JMenu enfinServiceMenu = new JMenu("Envision 2");
659 wsmenu.add(enfinServiceMenu);
660 enfinServiceMenu.setEnabled(false);
661 wsmenu.addMenuListener(new MenuListener()
663 // this listener remembers when the menu was first selected, and
664 // doesn't rebuild the session list until it has been cleared and
666 boolean refresh = true;
668 public void menuCanceled(MenuEvent e)
673 public void menuDeselected(MenuEvent e)
678 public void menuSelected(MenuEvent e)
680 if (refresh && !isRunning())
682 new Thread(new Runnable()
688 buildGroupLinkMenu(enfinServiceMenu, alignFrame);
689 } catch (OutOfMemoryError ex)
692 .error("Out of memory when calculating the Envision2 links.",
694 enfinServiceMenu.setEnabled(false);