+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview 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 3
- * of the License, or (at your option) any later version.
- *
- * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws;
-
-import java.awt.Component;
-import java.awt.Cursor;
-import java.awt.event.ActionEvent;
-import java.io.UnsupportedEncodingException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Hashtable;
-import java.util.Map;
-import java.util.Vector;
-import java.util.regex.Pattern;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
-import javax.xml.parsers.SAXParser;
-import javax.xml.parsers.SAXParserFactory;
-
-import org.xml.sax.Attributes;
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.DefaultHandler;
-
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvSwingUtils;
-import jalview.util.GroupUrlLink;
-import jalview.util.GroupUrlLink.UrlStringTooLongException;
-import jalview.util.MessageManager;
-
-/**
- * Lightweight runnable to discover dynamic 'one way' group URL services
- *
- * as of Jalview 2.8.1 this class is mothballed and will be dropped in v3.
- *
- * @author JimP
- * @deprecated
- *
- */
-@Deprecated
-public class EnfinEnvision2OneWay extends DefaultHandler implements
- Runnable, WSMenuEntryProviderI
-{
- private static EnfinEnvision2OneWay groupURLLinksGatherer = null;
-
- public static EnfinEnvision2OneWay getInstance()
- {
- if (groupURLLinksGatherer == null)
- {
- groupURLLinksGatherer = new EnfinEnvision2OneWay();
- }
- return groupURLLinksGatherer;
- }
-
- private void waitForCompletion()
- {
- if (groupURLLinksGatherer.isRunning())
- {
- // wait around and show a visual delay indicator
- Cursor oldCursor = Desktop.instance.getCursor();
- Desktop.instance.setCursor(new Cursor(Cursor.WAIT_CURSOR));
- while (groupURLLinksGatherer.isRunning())
- {
- try
- {
- Thread.sleep(100);
- } catch (InterruptedException e)
- {
- }
- ;
- }
- Desktop.instance.setCursor(oldCursor);
- }
- }
-
- public Vector getEnvisionServiceGroupURLS()
- {
- waitForCompletion();
- return groupURLLinks;
- }
-
- /**
- * indicate if
- */
- private static String BACKGROUND = "BACKGROUNDPARAM";
-
- /**
- * contains null strings or one of the above constants - indicate if this URL
- * is a special case.
- */
- private Vector additionalPar = new Vector();
-
- /**
- * the enfin service URL
- */
- private String enfinService = null;
-
- private String description = null;
-
- private String wfname;
-
- /*
- * (non-Javadoc)
- *
- * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String,
- * java.lang.String, java.lang.String)
- */
- public void endElement(String uri, String localName, String qName)
- throws SAXException
- {
-
- // System.err.println("End element: : '"+uri+" "+localName+" "+qName);
- if (qName.equalsIgnoreCase("workflow") && description != null
- && description.length() > 0)
- {
- // 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|,");
- // 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|,");
- System.err.println("Adding entry for " + wfname + " " + description);
- if (wfname.toLowerCase().indexOf("funcnet") == -1)
- {
- description = Pattern.compile("\\s+", Pattern.MULTILINE)
- .matcher(description).replaceAll(" ");
- groupURLdescr.addElement(description);
- groupURLdescr.addElement(description);
- String urlstub = wfname;
- if (wfname.indexOf(" ") > -1)
- {
- // make the name safe!
- try
- {
- urlstub = URLEncoder.encode(wfname, "utf-8");
- } catch (UnsupportedEncodingException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
- groupURLLinks
- .addElement(wfname
- + "|"
- + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + urlstub
- + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,"); // #"+description+"#");
- groupURLLinks
- .addElement(wfname
- + "|"
- + "http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow="
- + urlstub
- + "&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,"); // #"+description+"#");
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
- */
- public void characters(char[] ch, int start, int length)
- throws SAXException
- {
- if (description != null)
- {
- for (int i = start; i < start + length; i++)
- {
- description += ch[i];
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String,
- * java.lang.String, java.lang.String, org.xml.sax.Attributes)
- */
- public void startElement(String uri, String localName, String qName,
- Attributes attributes) throws SAXException
- {
- if (qName.equalsIgnoreCase("workflow"))
- {
- description = null;
- wfname = attributes.getValue("name");
- }
- if (qName.equalsIgnoreCase("description"))
- {
- description = "";
- }
-
- // System.err.println("Start element: : '"+uri+" "+localName+" "+qName+" attributes"+attributes);
- // super.startElement(uri,localName,qname,attributes);
- }
-
- private boolean started = false;
-
- private boolean running = false;
-
- private Vector groupURLLinks = null;
-
- private Vector groupURLdescr = null;
-
- private static String[] allowedDb = new String[]
- { "UNIPROT", "EMBL", "PDB" };
-
- public EnfinEnvision2OneWay()
- {
- groupURLLinks = new Vector();
- groupURLdescr = new Vector();
-
- enfinService = Cache.getDefault("ENVISION2_WORKFLOWSERVICE",
- "http://www.ebi.ac.uk/enfin-srv/envision2/pages/workflows.xml");
- new Thread(this).start();
- }
-
- public void run()
- {
- started = true;
- running = true;
- try
- {
- SAXParserFactory spf = SAXParserFactory.newInstance();
- SAXParser sp = spf.newSAXParser();
- sp.parse(new URL(enfinService).openStream(), this);
- } catch (Exception e)
- {
- Cache.log.warn("Exception when discovering One Way services: ", e);
- } catch (Error e)
- {
- Cache.log.warn("Error when discovering One Way services: ", e);
- }
- running = false;
- Cache.log.debug("Finished running.");
- }
-
- /**
- * have we finished running yet ?
- *
- * @return false if we have been run.
- */
- public boolean isRunning()
- {
-
- // TODO Auto-generated method stub
- return !started || running;
- }
-
- public static void main(String[] args)
- {
- Cache.initLogger();
- EnfinEnvision2OneWay ow = new EnfinEnvision2OneWay();
- while (ow.isRunning())
- {
- try
- {
- Thread.sleep(50);
- } catch (Exception e)
- {
- }
- ;
-
- }
- for (int i = 0; i < ow.groupURLLinks.size(); i++)
- {
- System.err.println("Description" + ow.groupURLdescr.elementAt(i)
- + "Service URL: " + ow.groupURLLinks.elementAt(i));
- }
- }
-
- // / Copied from jalview.gui.PopupMenu
- /**
- * add a late bound URL service item to the given menu
- *
- * @param linkMenu
- * @param label
- * - menu label string
- * @param urlgenerator
- * GroupURLLink used to generate URL
- * @param urlstub
- * Object array returned from the makeUrlStubs function.
- */
- private void addshowLink(JMenu linkMenu, String label, String descr,
- String dbname, final GroupUrlLink urlgenerator,
- final Object[] urlstub)
- {
- Component[] jmi = linkMenu.getMenuComponents();
- for (int i = 0; i < jmi.length; i++)
- {
- if (jmi[i] instanceof JMenuItem
- && ((JMenuItem) jmi[i]).getText().equalsIgnoreCase(label))
- {
- // don't add this - its a repeat of an existing URL.
- return;
- }
- }
- try
- {
- // TODO check with Jim if this class (EnfinEnvision) is obsolete
- // descr = HtmlEncoder.encode(descr); // iText removed from Jmol 14.2
- } catch (Exception e)
- {
- }
- ;
-
- boolean seqsorids = (urlgenerator.getGroupURLType() & urlgenerator.SEQUENCEIDS) == 0;
- int i = urlgenerator.getNumberInvolved(urlstub);
- JMenuItem item = new JMenuItem(label);
- //
- if (dbname == null || dbname.trim().length() == 0)
- {
- dbname = "";
- }
- item.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager.formatMessage("label.submit_sequence", new String[]{Integer.valueOf(i).toString(), dbname, (seqsorids ? "sequence" : "sequence id"), (i > 1 ? "s" : "")})));
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- new Thread(new Runnable()
- {
-
- public void run()
- {
- try
- {
- showLink(urlgenerator.constructFrom(urlstub));
- } catch (UrlStringTooLongException ex)
- {
- Cache.log.warn("Not showing link: URL is too long!", ex);
- }
- }
-
- }).start();
- }
- });
-
- linkMenu.add(item);
- }
-
- /**
- * open the given link in a new browser window
- *
- * @param url
- */
- public void showLink(String url)
- {
- try
- {
- jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex)
- {
- JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
- /**
- * called by a web service menu instance when it is opened.
- *
- * @param enfinServiceMenu
- * @param alignFrame
- */
- private void buildGroupLinkMenu(JMenu enfinServiceMenu,
- AlignFrame alignFrame)
- {
- if (running || !started)
- {
- return;
- }
- SequenceI[] seqs = alignFrame.getViewport().getSelectionAsNewSequence();
- SequenceGroup sg = alignFrame.getViewport().getSelectionGroup();
- if (sg == null)
- {
- // consider visible regions here/
- }
- enfinServiceMenu.removeAll();
- JMenu entries = buildGroupURLMenu(seqs, sg);
- if (entries != null)
- {
- for (int i = 0, iSize = entries.getMenuComponentCount(); i < iSize; i++)
- {
- // transfer - menu component is removed from entries automatically
- enfinServiceMenu.add(entries.getMenuComponent(0));
- }
- // entries.removeAll();
- enfinServiceMenu.setEnabled(true);
- }
- else
- {
- enfinServiceMenu.setEnabled(false);
- }
- }
-
- /**
- * construct a dynamic enfin services menu given a sequence selection
- *
- * @param seqs
- * @param sg
- * @param groupLinks
- * @return
- */
- private JMenu buildGroupURLMenu(SequenceI[] seqs, SequenceGroup sg)
- {
- if (groupURLdescr == null || groupURLLinks == null)
- {
- return null;
- }
- // TODO: usability: thread off the generation of group url content so root
- // menu appears asap
- // sequence only URLs
- // ID/regex match URLs
- JMenu groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
- String[][] idandseqs = GroupUrlLink.formStrings(seqs);
- Hashtable commonDbrefs = new Hashtable();
- for (int sq = 0; sq < seqs.length; sq++)
- {
-
- int start, end;
- if (sg != null)
- {
- start = seqs[sq].findPosition(sg.getStartRes());
- end = seqs[sq].findPosition(sg.getEndRes());
- }
- else
- {
- // get total width of alignment.
- start = seqs[sq].getStart();
- end = seqs[sq].findPosition(seqs[sq].getLength());
- }
- // we skip sequences which do not have any non-gaps in the region of
- // interest
- if (start > end)
- {
- continue;
- }
- // just collect ids from dataset sequence
- // TODO: check if IDs collected from selecton group intersects with the
- // current selection, too
- SequenceI sqi = seqs[sq];
- while (sqi.getDatasetSequence() != null)
- {
- sqi = sqi.getDatasetSequence();
- }
- DBRefEntry[] dbr = sqi.getDBRef();
- if (dbr != null && dbr.length > 0)
- {
- for (int d = 0; d < dbr.length; d++)
- {
- String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
- Object[] sarray = (Object[]) commonDbrefs.get(src);
- if (sarray == null)
- {
- sarray = new Object[2];
- sarray[0] = new int[]
- { 0 };
- sarray[1] = new String[seqs.length];
-
- commonDbrefs.put(src, sarray);
- }
-
- if (((String[]) sarray[1])[sq] == null)
- {
- if (!dbr[d].hasMap()
- || (dbr[d].getMap().locateMappedRange(start, end) != null))
- {
- ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
- ((int[]) sarray[0])[0]++;
- }
- }
- }
- }
- }
- // now create group links for all distinct ID/sequence sets.
- Hashtable<String, JMenu[]> gurlMenus = new Hashtable<String, JMenu[]>();
- /**
- * last number of sequences where URL generation failed
- */
- int[] nsqtype = new int[]
- { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
- for (int i = 0; i < groupURLLinks.size(); i++)
- {
- String link = (String) groupURLLinks.elementAt(i);
- String descr = (String) groupURLdescr.elementAt(i);
-
- // boolean specialCase =
- // additionalPar.elementAt(i).toString().equals(BACKGROUND);
- GroupUrlLink urlLink = null;
- try
- {
- urlLink = new GroupUrlLink(link);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
- + "'", foo);
- continue;
- }
- ;
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- continue;
- }
- final String label = urlLink.getLabel();
- // create/recover the sub menus that might be populated for this link.
- JMenu[] wflinkMenus = gurlMenus.get(label);
- if (wflinkMenus == null)
- {
- // three types of url that might be
- // created.
- wflinkMenus = new JMenu[]
- { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
- new JMenu(MessageManager.getString("action.ids_sequences")) };
- gurlMenus.put(label, wflinkMenus);
- }
-
- boolean usingNames = false;
- // Now see which parts of the group apply for this URL
- String ltarget;
- String[] seqstr, ids; // input to makeUrl
- for (int t = 0; t < allowedDb.length; t++)
- {
- ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
- Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
- if (idset != null)
- {
- int numinput = ((int[]) idset[0])[0];
- String[] allids = ((String[]) idset[1]);
- seqstr = new String[numinput];
- ids = new String[numinput];
- if (nsqtype[urlLink.getGroupURLType()] > 0
- && numinput >= nsqtype[urlLink.getGroupURLType()])
- {
- continue;
- }
- for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
- {
- if (allids[sq] != null)
- {
- ids[idcount] = allids[sq];
- seqstr[idcount++] = idandseqs[1][sq];
- }
- }
- try
- {
- createAndAddLinks(wflinkMenus, false, urlLink, ltarget, null,
- descr, ids, seqstr);
- } catch (UrlStringTooLongException ex)
- {
- nsqtype[urlLink.getGroupURLType()] = numinput;
- }
- }
- }
- // also do names only.
- seqstr = idandseqs[1];
- ids = idandseqs[0];
- if (nsqtype[urlLink.getGroupURLType()] > 0
- && idandseqs[0].length >= nsqtype[urlLink.getGroupURLType()])
- {
- continue;
- }
-
- try
- {
- createAndAddLinks(wflinkMenus, true, urlLink, "Any", null, descr,
- ids, seqstr);
- } catch (UrlStringTooLongException ex)
- {
- nsqtype[urlLink.getGroupURLType()] = idandseqs[0].length;
- }
- }
- boolean anyadded = false; // indicates if there are any group links to give
- // to user
- for (Map.Entry<String, JMenu[]> menues : gurlMenus.entrySet())
- {
- JMenu grouplinkset = new JMenu(menues.getKey());
- JMenu[] wflinkMenus = menues.getValue();
- for (int m = 0; m < wflinkMenus.length; m++)
- {
- if (wflinkMenus[m] != null
- && wflinkMenus[m].getMenuComponentCount() > 0)
- {
- anyadded = true;
- grouplinkset.add(wflinkMenus[m]);
- }
- }
- groupLinksMenu.add(grouplinkset);
- }
- if (anyadded)
- {
- return groupLinksMenu;
- }
- return null;
- }
-
- private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
- GroupUrlLink urlLink, String label, String ltarget, String descr,
- String[] ids, String[] seqstr) throws UrlStringTooLongException
- {
- Object[] urlset = urlLink.makeUrlStubs(ids, seqstr, "FromJalview"
- + System.currentTimeMillis(), false);
-
- if (urlset != null)
- {
- int type = urlLink.getGroupURLType() & 3;
- // System.out.println(urlLink.getGroupURLType()
- // +" "+((String[])urlset[3])[0]);
- // first two bits ofurlLink type bitfield are sequenceids and sequences
- // TODO: FUTURE: ensure the groupURL menu structure can be generalised
- addshowLink(
- linkMenus[type],
- label
- + " "
- + (ltarget == null ? (((type & 1) == 1 ? "ID"
- : "Sequence") + (urlLink
- .getNumberInvolved(urlset) > 1 ? "s" : ""))
- : (usingNames ? (((type & 1) == 1) ? "(Names)"
- : "")
- : ("(" + ltarget + ")"))), descr,
- usingNames ? null : label, urlLink, urlset);
- return true;
- }
- return false;
- }
-
- // / end of stuff copied from popupmenu
- public void attachWSMenuEntry(final JMenu wsmenu,
- final AlignFrame alignFrame)
- {
- final JMenu enfinServiceMenu = new JMenu("Envision 2");
- wsmenu.add(enfinServiceMenu);
- enfinServiceMenu.setEnabled(false);
- wsmenu.addMenuListener(new MenuListener()
- {
- // this listener remembers when the menu was first selected, and
- // doesn't rebuild the session list until it has been cleared and
- // reselected again.
- boolean refresh = true;
-
- public void menuCanceled(MenuEvent e)
- {
- refresh = true;
- }
-
- public void menuDeselected(MenuEvent e)
- {
- refresh = true;
- }
-
- public void menuSelected(MenuEvent e)
- {
- if (refresh && !isRunning())
- {
- new Thread(new Runnable()
- {
- public void run()
- {
- try
- {
- buildGroupLinkMenu(enfinServiceMenu, alignFrame);
- } catch (OutOfMemoryError ex)
- {
- Cache.log
- .error("Out of memory when calculating the Envision2 links.",
- ex);
- enfinServiceMenu.setEnabled(false);
- }
- }
- }).start();
- refresh = false;
- }
- }
- });
-
- }
-
-}
git://source.jalview.org / jalview.git / commitdiff