--- /dev/null
+/**
+ *
+ */
+package jalview.ws;
+
+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.util.GroupUrlLink;
+
+import java.awt.Cursor;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Hashtable;
+import java.util.Vector;
+
+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;
+
+/**
+ * Lightweight runnable to discover dynamic 'one way' group URL services
+ * @author JimP
+ *
+ */
+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)
+ {
+ groupURLdescr.addElement(description);
+ groupURLdescr.addElement(description);
+ 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+"#");
+ 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+"#");
+ }
+ }
+ }
+
+ /* (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;
+
+ 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, final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText("Submit ("+urlgenerator.getNumberInvolved(urlstub)+" seqs) to workflow: "+descr);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ }
+
+ }).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,
+ "Unixers: Couldn't find default web browser."
+ + "\nAdd the full path to your browser in Preferences.",
+ "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)
+ {
+ 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)
+ {
+
+ // 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("Group Link");
+ JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
+ 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.
+ boolean addMenu = false; // indicates if there are any group links to give to user
+ for (int i = 0; i < groupURLLinks.size(); i++) {
+ String link = groupURLLinks.elementAt(i).toString();
+ String descr = groupURLdescr.elementAt(i).toString();
+// 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();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+ String[] seqstr,ids; // input to makeUrl
+ if (idset!=null)
+ {
+ int numinput = ((int[])idset[0])[0];
+ String[] allids = ((String[])idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq=0,idcount=0;sq<seqs.length;sq++)
+ {
+ if (allids[sq]!=null) {
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
+ }
+ }
+ } else {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames=true;
+ }
+ // and try and make the groupURL!
+
+ 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 + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
+ addMenu = true;
+ }
+ }
+ if (addMenu)
+ {
+ groupLinksMenu = new JMenu("Group Links");
+ for (int m=0;m<linkMenus.length; m++)
+ {
+ if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+ {
+ groupLinksMenu.add(linkMenus[m]);
+ }
+ }
+
+ return groupLinksMenu;
+ }
+ return null;
+ }
+
+ /// 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)
+ {
+ try {
+ buildGroupLinkMenu(enfinServiceMenu,alignFrame);
+ } catch (OutOfMemoryError ex)
+ {
+ Cache.log.error("Out of memory when calculating the Envision2 links.",ex);
+ enfinServiceMenu.setEnabled(false);
+ }
+ refresh = false;
+ }
+ }
+ });
+
+
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff