2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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
62 public class EnfinEnvision2OneWay extends DefaultHandler implements
63 Runnable, WSMenuEntryProviderI
65 private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
67 public static EnfinEnvision2OneWay getInstance()
69 if (groupURLLinksGatherer == null)
71 groupURLLinksGatherer = new EnfinEnvision2OneWay();
73 return groupURLLinksGatherer;
76 private void waitForCompletion()
78 if (groupURLLinksGatherer.isRunning())
80 // wait around and show a visual delay indicator
81 Cursor oldCursor = Desktop.instance.getCursor();
82 Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
83 while (groupURLLinksGatherer.isRunning())
88 } catch (InterruptedException e)
93 Desktop.instance.setCursor(oldCursor);
97 public Vector getEnvisionServiceGroupURLS()
100 return groupURLLinks;
106 private static String BACKGROUND = "BACKGROUNDPARAM";
109 * contains null strings or one of the above constants - indicate if this URL
112 private Vector additionalPar = new Vector();
115 * the enfin service URL
117 private String enfinService = null;
119 private String description = null;
121 private String wfname;
126 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
127 * java.lang.String, java.lang.String)
129 public void endElement(String uri, String localName, String qName)
133 // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
134 if (qName.equalsIgnoreCase("workflow") && description != null
135 && description.length() > 0)
137 // 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|,");
138 // 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|,");
139 System.err.println("Adding entry for " + wfname + " " + description);
140 if (wfname.toLowerCase().indexOf("funcnet") == -1)
142 description = Pattern.compile("\\s+", Pattern.MULTILINE)
143 .matcher(description).replaceAll(" ");
144 groupURLdescr.addElement(description);
145 groupURLdescr.addElement(description);
146 String urlstub = wfname;
147 if (wfname.indexOf(" ") > -1)
149 // make the name safe!
152 urlstub = URLEncoder.encode(wfname, "utf-8");
153 } catch (UnsupportedEncodingException e)
155 // TODO Auto-generated catch block
162 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
164 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
168 + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
170 + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
178 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
180 public void characters(char[] ch, int start, int length)
183 if (description != null)
185 for (int i = start; i < start + length; i++)
187 description += ch[i];
195 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
196 * java.lang.String, java.lang.String, org.xml.sax.Attributes)
198 public void startElement(String uri, String localName, String qName,
199 Attributes attributes) throws SAXException
201 if (qName.equalsIgnoreCase("workflow"))
204 wfname = attributes.getValue("name");
206 if (qName.equalsIgnoreCase("description"))
211 // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
212 // super.startElement(uri,localName,qname,attributes);
215 private boolean started = false;
217 private boolean running = false;
219 private Vector groupURLLinks = null;
221 private Vector groupURLdescr = null;
223 private static String[] allowedDb = new String[]
224 { "UNIPROT", "EMBL", "PDB" };
226 public EnfinEnvision2OneWay()
228 groupURLLinks = new Vector();
229 groupURLdescr = new Vector();
231 enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
232 "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
233 new Thread(this).start();
242 SAXParserFactory spf = SAXParserFactory.newInstance();
243 SAXParser sp = spf.newSAXParser();
244 sp.parse(new URL(enfinService).openStream(), this);
245 } catch (Exception e)
247 Cache.log.warn("Exception when discovering One Way services: ", e);
250 Cache.log.warn("Error when discovering One Way services: ", e);
253 Cache.log.debug("Finished running.");
257 * have we finished running yet ?
259 * @return false if we have been run.
261 public boolean isRunning()
264 // TODO Auto-generated method stub
265 return !started || running;
268 public static void main(String[] args)
271 EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
272 while (ow.isRunning())
277 } catch (Exception e)
283 for (int i = 0; i < ow.groupURLLinks.size(); i++)
285 System.err.println("Description" + ow.groupURLdescr.elementAt(i)
286 + "Service URL: " + ow.groupURLLinks.elementAt(i));
290 // / Copied from jalview.gui.PopupMenu
292 * add a late bound URL service item to the given menu
296 * - menu label string
297 * @param urlgenerator
298 * GroupURLLink used to generate URL
300 * Object array returned from the makeUrlStubs function.
302 private void addshowLink(JMenu linkMenu, String label, String descr,
303 String dbname, final GroupUrlLink urlgenerator,
304 final Object[] urlstub)
306 Component[] jmi = linkMenu.getMenuComponents();
307 for (int i = 0; i < jmi.length; i++)
309 if (jmi[i] instanceof JMenuItem
310 && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
312 // don't add this - its a repeat of an existing URL.
318 descr = HtmlEncoder.encode(descr);
319 } catch (Exception e)
324 boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
325 int i = urlgenerator.getNumberInvolved(urlstub);
326 JMenuItem item = new JMenuItem(label);
328 if (dbname == null || dbname.trim().length() == 0)
332 item.setToolTipText("<html>"
333 + JvSwingUtils.wrapTooltip("Submit " + i + " " + dbname + " "
334 + (seqsorids ? "sequence" : "sequence id")
337 + " to<br/>" + descr) + "</html>");
338 item.addActionListener(new java.awt.event.ActionListener()
340 public void actionPerformed(ActionEvent e)
342 new Thread(new Runnable()
349 showLink(urlgenerator.constructFrom(urlstub));
350 } catch (UrlStringTooLongException ex)
352 Cache.log.warn("Not showing link: URL is too long!", ex);
364 * open the given link in a new browser window
368 public void showLink(String url)
372 jalview.util.BrowserLauncher.openURL(url);
373 } catch (Exception ex)
376 .showInternalMessageDialog(
378 "Unixers: Couldn't find default web browser."
379 + "\nAdd the full path to your browser in Preferences.",
380 "Web browser not found", JOptionPane.WARNING_MESSAGE);
382 ex.printStackTrace();
387 * called by a web service menu instance when it is opened.
389 * @param enfinServiceMenu
392 private void buildGroupLinkMenu(JMenu enfinServiceMenu,
393 AlignFrame alignFrame)
395 if (running || !started)
399 SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
400 SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
403 // consider visible regions here/
405 enfinServiceMenu.removeAll();
406 JMenu entries = buildGroupURLMenu(seqs, sg);
409 for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
411 // transfer - menu component is removed from entries automatically
412 enfinServiceMenu.add(entries.getMenuComponent(0));
414 // entries.removeAll();
415 enfinServiceMenu.setEnabled(true);
419 enfinServiceMenu.setEnabled(false);
424 * construct a dynamic enfin services menu given a sequence selection
431 private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
433 if (groupURLdescr == null || groupURLLinks == null)
435 // TODO: usability: thread off the generation of group url content so root
437 // sequence only URLs
438 // ID/regex match URLs
439 JMenu groupLinksMenu = new JMenu("Group Link");
440 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
441 Hashtable commonDbrefs = new Hashtable();
442 for (int sq = 0; sq < seqs.length; sq++)
448 start = seqs[sq].findPosition(sg.getStartRes());
449 end = seqs[sq].findPosition(sg.getEndRes());
453 // get total width of alignment.
454 start = seqs[sq].getStart();
455 end = seqs[sq].findPosition(seqs[sq].getLength());
457 // we skip sequences which do not have any non-gaps in the region of
463 // just collect ids from dataset sequence
464 // TODO: check if IDs collected from selecton group intersects with the
465 // current selection, too
466 SequenceI sqi = seqs[sq];
467 while (sqi.getDatasetSequence() != null)
469 sqi = sqi.getDatasetSequence();
471 DBRefEntry[] dbr = sqi.getDBRef();
472 if (dbr != null && dbr.length > 0)
474 for (int d = 0; d < dbr.length; d++)
476 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
477 Object[] sarray = (Object[]) commonDbrefs.get(src);
480 sarray = new Object[2];
481 sarray[0] = new int[]
483 sarray[1] = new String[seqs.length];
485 commonDbrefs.put(src, sarray);
488 if (((String[]) sarray[1])[sq] == null)
491 || (dbr[d].getMap().locateMappedRange(start, end) != null))
493 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
494 ((int[]) sarray[0])[0]++;
500 // now create group links for all distinct ID/sequence sets.
501 Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
503 * last number of sequences where URL generation failed
505 int[] nsqtype = new int[]
506 { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
507 for (int i = 0; i < groupURLLinks.size(); i++)
509 String link = (String) groupURLLinks.elementAt(i);
510 String descr = (String) groupURLdescr.elementAt(i);
512 // boolean specialCase =
513 // additionalPar.elementAt(i).toString().equals(BACKGROUND);
514 GroupUrlLink urlLink = null;
517 urlLink = new GroupUrlLink(link);
518 } catch (Exception foo)
520 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
525 if (!urlLink.isValid())
527 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
530 final String label = urlLink.getLabel();
531 // create/recover the sub menus that might be populated for this link.
532 JMenu[] wflinkMenus = gurlMenus.get(label);
533 if (wflinkMenus == null)
535 // three types of url that might be
537 wflinkMenus = new JMenu[]
538 { null, new JMenu("IDS"), new JMenu("Sequences"),
539 new JMenu("IDS and Sequences") };
540 gurlMenus.put(label, wflinkMenus);
543 boolean usingNames = false;
544 // Now see which parts of the group apply for this URL
546 String[] seqstr, ids; // input to makeUrl
547 for (int t = 0; t < allowedDb.length; t++)
549 ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
550 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
553 int numinput = ((int[]) idset[0])[0];
554 String[] allids = ((String[]) idset[1]);
555 seqstr = new String[numinput];
556 ids = new String[numinput];
557 if (nsqtype[urlLink.getGroupURLType()] > 0
558 && numinput >= nsqtype[urlLink.getGroupURLType()])
562 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
564 if (allids[sq] != null)
566 ids[idcount] = allids[sq];
567 seqstr[idcount++] = idandseqs[1][sq];
572 createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
574 } catch (UrlStringTooLongException ex)
576 nsqtype[urlLink.getGroupURLType()] = numinput;
580 // also do names only.
581 seqstr = idandseqs[1];
583 if (nsqtype[urlLink.getGroupURLType()] > 0
584 && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
591 createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
593 } catch (UrlStringTooLongException ex)
595 nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
598 boolean anyadded = false; // indicates if there are any group links to give
600 for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
602 JMenu grouplinkset = new JMenu(menues.getKey());
603 JMenu[] wflinkMenus = menues.getValue();
604 for (int m = 0; m < wflinkMenus.length; m++)
606 if (wflinkMenus[m] != null
607 && wflinkMenus[m].getMenuComponentCount() > 0)
610 grouplinkset.add(wflinkMenus[m]);
613 groupLinksMenu.add(grouplinkset);
617 return groupLinksMenu;
622 private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
623 GroupUrlLink urlLink, String label, String ltarget, String descr,
624 String[] ids, String[] seqstr) throws UrlStringTooLongException
626 Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
627 + System.currentTimeMillis(), false);
631 int type = urlLink.getGroupURLType() & 3;
632 // System.out.println(urlLink.getGroupURLType()
633 // +" "+((String[])urlset[3])[0]);
634 // first two bits ofurlLink type bitfield are sequenceids and sequences
635 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
640 + (ltarget == null ? (((type & 1) == 1 ? "ID"
641 : "Sequence") + (urlLink
642 .getNumberInvolved(urlset) > 1 ? "s" : ""))
643 : (usingNames ? (((type & 1) == 1) ? "(Names)"
645 : ("(" + ltarget + ")"))), descr,
646 usingNames ? null : label, urlLink, urlset);
652 // / end of stuff copied from popupmenu
653 public void attachWSMenuEntry(final JMenu wsmenu,
654 final AlignFrame alignFrame)
656 final JMenu enfinServiceMenu = new JMenu("Envision 2");
657 wsmenu.add(enfinServiceMenu);
658 enfinServiceMenu.setEnabled(false);
659 wsmenu.addMenuListener(new MenuListener()
661 // this listener remembers when the menu was first selected, and
662 // doesn't rebuild the session list until it has been cleared and
664 boolean refresh = true;
666 public void menuCanceled(MenuEvent e)
671 public void menuDeselected(MenuEvent e)
676 public void menuSelected(MenuEvent e)
678 if (refresh && !isRunning())
680 new Thread(new Runnable()
686 buildGroupLinkMenu(enfinServiceMenu, alignFrame);
687 } catch (OutOfMemoryError ex)
690 .error("Out of memory when calculating the Envision2 links.",
692 enfinServiceMenu.setEnabled(false);