X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=b440de8f8909011b2fef16d31960c23bb68621d0;hb=e9aa1cee679000405c5549829ee08e1c08b2ffd5;hp=8089e1a584cbfe41ffb4dcf157e941d0194e53bc;hpb=4674dbf3f27eee61a7e21174649aa4c9ec7a04dd;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 8089e1a..b440de8 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -17,16 +17,20 @@ */ package jalview.ws.jws2; +import jalview.bin.Cache; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.JvSwingUtils; +import jalview.ws.WSMenuEntryProviderI; +import jalview.ws.jws2.jabaws2.Jws2Instance; + import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; -import java.io.Closeable; -import java.net.ConnectException; import java.net.URL; import java.util.ArrayList; -import java.util.HashSet; import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; @@ -34,24 +38,7 @@ import java.util.Vector; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; -import org.apache.log4j.Level; - -import jalview.bin.Cache; -import jalview.datamodel.AlignmentView; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.JalviewChangeSupport; -import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.params.ParamDatastoreI; -import compbio.data.msa.MsaWS; -import compbio.metadata.Option; -import compbio.metadata.Preset; -import compbio.metadata.PresetManager; -import compbio.metadata.RunnerConfig; -import compbio.ws.client.Jws2Client; import compbio.ws.client.Services; /** @@ -134,6 +121,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Cache.log.debug("Old discovery thread has finished."); } running = true; + changeSupport.firePropertyChange("services", services, new Vector()); oldthread = Thread.currentThread(); try { @@ -160,17 +148,32 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { invalidServiceUrls.removeAllElements(); } + if (validServiceUrls != null) + { + validServiceUrls.removeAllElements(); + } + ArrayList svctypes=new ArrayList(); List qrys = new ArrayList(); for (final String jwsservers : getServiceUrls()) { JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + if (svctypes.size()==0) + { + // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services + for (Services sv:squery.JABAWS2SERVERS) + { + svctypes.add(sv.toString()); + } + + } qrys.add(squery); new Thread(squery).start(); } - boolean finished = false; + boolean finished = true; do { + finished=true; try { Thread.sleep(100); @@ -180,7 +183,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished |= !squery.isRunning(); + finished = finished && !squery.isRunning(); } if (aborted) { @@ -192,12 +195,32 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } } while (!aborted && !finished); - oldthread = null; - running = false; if (!aborted) { - changeSupport.firePropertyChange("services", new Vector(), services); + // resort services according to order found in jabaws service list + // also ensure servics for each host are ordered in same way. + + if (services!=null && services.size()>0) + { + Jws2Instance[] svcs=new Jws2Instance[services.size()]; + int[] spos=new int[services.size()]; + int ipos=0; + Vector svcUrls = getServiceUrls(); + for (Jws2Instance svc:services) + { + svcs[ipos]=svc; + spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType); + } + jalview.util.QuickSort.sort(spos, svcs); + services=new Vector(); + for (Jws2Instance svc:svcs) { + services.add(svc); + } + } } + oldthread = null; + running = false; + changeSupport.firePropertyChange("services", new Vector(), services); } /** @@ -207,234 +230,49 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - synchronized void addService(String jwsservers, Services srv, - MsaWS service2) + synchronized void addService(String jwsservers, Jws2Instance service) { if (services == null) { services = new Vector(); } System.out.println("Discovered service: " + jwsservers + " " - + srv.toString()); - Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), - service2); + + service.toString()); +// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), +// service2); services.add(service); // retrieve the presets and parameter set and cache now service.getParamStore().getPresets(); service.hasParameters(); - } - - public class Jws2Instance - { - public String hosturl; - - public String serviceType; - - public MsaWS service; - - public Jws2Instance(String hosturl, String serviceType, MsaWS service) - { - super(); - this.hosturl = hosturl; - this.serviceType = serviceType; - this.service = service; - } - - PresetManager presets = null; - - public JabaParamStore paramStore = null; - - /** - * non thread safe - gets the presets for this service (blocks whilst it - * calls the service to get the preset set) - * - * @return service presets or null if exceptions were raised. - */ - public PresetManager getPresets() + if (validServiceUrls==null) { - if (presets == null) - { - try - { - presets = service.getPresets(); - } catch (Exception ex) - { - System.err - .println("Exception when retrieving presets for service " - + serviceType + " at " + hosturl); - } - } - return presets; - } - - public String getHost() - { - return hosturl; - /* - * try { URL serviceurl = new URL(hosturl); if (serviceurl.getPort()!=80) - * { return serviceurl.getHost()+":"+serviceurl.getPort(); } return - * serviceurl.getHost(); } catch (Exception e) { - * System.err.println("Failed to parse service URL '" + hosturl + - * "' as a valid URL!"); } return null; - */ - } - - /** - * @return short description of what the service will do - */ - public String getActionText() - { - return "Align with " + serviceType; - } - - /** - * non-thread safe - blocks whilst accessing service to get complete set of - * available options and parameters - * - * @return - */ - public RunnerConfig getRunnerConfig() - { - return service.getRunnerOptions(); + validServiceUrls=new Vector(); } - - @Override - protected void finalize() throws Throwable - { - if (service != null) - { - try - { - Closeable svc = (Closeable) service; - service = null; - svc.close(); - } catch (Exception e) - { - } - ; - } - super.finalize(); - } - - public ParamDatastoreI getParamStore() - { - if (paramStore == null) - { - try - { - paramStore = new JabaParamStore(this, - (Desktop.instance != null ? Desktop - .getUserParameterStore() : null)); - } catch (Exception ex) - { - } - - } - return paramStore; - } - - public String getUri() - { - // this is only valid for Jaba 1.0 - this formula might have to change! - return hosturl - + (hosturl.lastIndexOf("/") == (hosturl.length() - 1) ? "/" - : "") + serviceType; - } - - private boolean hasParams = false, lookedForParams = false; - - public boolean hasParameters() - { - if (!lookedForParams) - { - lookedForParams = true; - try - { - hasParams = (getRunnerConfig().getArguments().size() > 0); - } catch (Exception e) - { - - } - } - return hasParams; - } - }; + validServiceUrls.add(jwsservers); + } /** * holds list of services. */ protected Vector services; - /** - * find or add a submenu with the given title in the given menu - * - * @param menu - * @param submenu - * @return the new or existing submenu + * attach all available web services to the appropriate submenu in the given JMenu */ - private JMenu findOrCreateMenu(JMenu menu, String submenu) - { - JMenu submenuinstance = null; - for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++) - { - if (menu.getMenuComponent(i) instanceof JMenu - && ((JMenu) menu.getMenuComponent(i)).getText().equals( - submenu)) - { - submenuinstance = (JMenu) menu.getMenuComponent(i); - } - } - if (submenuinstance == null) - { - submenuinstance = new JMenu(submenu); - menu.add(submenuinstance); - } - return submenuinstance; - - } - public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { // dynamically regenerate service list. - final JMenu jws2al = new JMenu("JABAWS Alignment"); - jws2al.addMenuListener(new MenuListener() - { - // TODO: future: add menu listener to parent menu - so submenus are - // populated *before* they are selected. - @Override - public void menuSelected(MenuEvent e) - { - populateWSMenuEntry(jws2al, alignFrame); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - }); - wsmenu.add(jws2al); - + populateWSMenuEntry(wsmenu, alignFrame, null); } - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) + private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) { if (running || services == null || services.size() == 0) { return; } - boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache - .getDefault("WSMENU_BYTYPE", true); + boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache + .getDefault("WSMENU_BYTYPE", false); /** * eventually, JWS2 services will appear under the same align/etc submenus. * for moment we keep them separate. @@ -443,81 +281,133 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI MsaWSClient msacl = new MsaWSClient(); Vector hostLabels = new Vector(); jws2al.removeAll(); - String lasthost = null; - for (final Jws2Instance service : services) + Hashtable lasthostFor = new Hashtable(); + Hashtable> hosts = new Hashtable>(); + ArrayList hostlist=new ArrayList(); + for (Jws2Instance service : services) { - atpoint = jws2al; - String host = service.getHost(); - String type = service.serviceType; - if (byhost) + ArrayList hostservices = hosts.get(service.getHost()); + if (hostservices == null) { - atpoint = findOrCreateMenu(atpoint, host); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText("Services at " + host); - } + hosts.put(service.getHost(), + hostservices = new ArrayList()); + hostlist.add(service.getHost()); } - if (bytype) + hostservices.add(service); + } + // now add hosts in order of the given array + for (String host : hostlist) + { + Jws2Instance orderedsvcs[] = hosts.get(host).toArray( + new Jws2Instance[1]); + String sortbytype[] = new String[orderedsvcs.length]; + for (int i = 0; i < sortbytype.length; i++) { - atpoint = findOrCreateMenu(atpoint, type); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText(service.getActionText()); - } + sortbytype[i] = orderedsvcs[i].serviceType; } - if (!byhost - && !hostLabels.contains(host + service.serviceType - + service.getActionText())) - // !hostLabels.contains(host + (bytype ? - // service.serviceType+service.getActionText() : ""))) + jalview.util.QuickSort.sort(sortbytype, orderedsvcs); + for (final Jws2Instance service : orderedsvcs) { - // add a marker indicating where this service is hosted - // relies on services from the same host being listed in a contiguous - // group - JMenuItem hitm; - atpoint.addSeparator(); - if (lasthost == null || !lasthost.equals(host)) + atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + String type = service.serviceType; + if (byhost) { - atpoint.add(hitm = new JMenuItem(host)); - hitm.setForeground(Color.blue); - lasthost = host; + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText("Services at " + host); + } + } + if (bytype) + { + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(service.getActionText()); + } + } + if (!byhost + && !hostLabels.contains(host + service.serviceType + + service.getActionText())) + // !hostLabels.contains(host + (bytype ? + // service.serviceType+service.getActionText() : ""))) + { + // add a marker indicating where this service is hosted + // relies on services from the same host being listed in a + // contiguous + // group + JMenuItem hitm; + atpoint.addSeparator(); + if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host)) + { + atpoint.add(hitm = new JMenuItem(host)); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + Desktop.showUrl(service.getHost()); + } + }); + hitm.setToolTipText(JvSwingUtils + .wrapTooltip("Opens the JABAWS server's homepage in web browser")); + lasthostFor.put(service.action,host); + } + hostLabels.addElement(host + service.serviceType + + service.getActionText()); + // hostLabels.addElement(host + (bytype ? + // service.serviceType+service.getActionText() : "")); } - hostLabels.addElement(host + service.serviceType - + service.getActionText()); - // hostLabels.addElement(host + (bytype ? - // service.serviceType+service.getActionText() : "")); + + service.attachWSMenuEntry(atpoint, alignFrame); + /* + * JMenuItem sitem = new JMenuItem(service.serviceType); + * sitem.setToolTipText("Hosted at " + service.hosturl); + * sitem.addActionListener(new ActionListener() { + * + * @Override public void actionPerformed(ActionEvent e) { AlignmentView + * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client = + * new MsaWSClient(service, "JWS2 Alignment of " + + * alignFrame.getTitle(), msa, false, true, + * alignFrame.getViewport().getAlignment().getDataset(), alignFrame); } + * }); + */ } - msacl.attachWSMenuEntry(atpoint, service, alignFrame); - /* - * JMenuItem sitem = new JMenuItem(service.serviceType); - * sitem.setToolTipText("Hosted at " + service.hosturl); - * sitem.addActionListener(new ActionListener() { - * - * @Override public void actionPerformed(ActionEvent e) { AlignmentView - * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client = - * new MsaWSClient(service, "JWS2 Alignment of " + alignFrame.getTitle(), - * msa, false, true, alignFrame.getViewport().getAlignment().getDataset(), - * alignFrame); } }); - */ } + } public static void main(String[] args) { + if (args.length>0) + { + testUrls = new Vector(); + for (String url:args) + { + testUrls.add(url); + }; + } Thread runner = getDiscoverer().startDiscoverer( new PropertyChangeListener() - { + { - public void propertyChange(PropertyChangeEvent evt) - { - if (getDiscoverer().services!=null) + public void propertyChange(PropertyChangeEvent evt) + { + if (getDiscoverer().services != null) { System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); - - } - } - }); + + getDiscoverer().services.size() + " services"); + int i=1; + for (Jws2Instance instance:getDiscoverer().services) + { + System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + } + + } + } + }); while (runner.isAlive()) { try @@ -528,6 +418,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } + try { + Thread.sleep(50); + } catch (InterruptedException x) {} } private static Jws2Discoverer discoverer; @@ -577,8 +470,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } + private static Vector testUrls=null; public static Vector getServiceUrls() { + if (testUrls!=null) + { + // return test urls, if there are any, instead of touching cache + return testUrls; + } String surls = Cache.getDefault(JWS2HOSTURLS, "http://www.compbio.dundee.ac.uk/jabaws"); Vector urls = new Vector(); @@ -657,6 +556,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI e.printStackTrace(); return false; } + return true; } @@ -680,7 +580,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null; + Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null; /** * @return the invalidServiceUrls @@ -699,7 +599,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } /** - * add an 'empty' JABA server to the list + * add an 'empty' JABA server to the list. Only servers not already in the + * 'bad URL' list will be added to this list. * * @param jwsservers */ @@ -709,7 +610,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { urlsWithoutServices = new Vector(); } - if (!urlsWithoutServices.contains(jwsservers)) + + if ((invalidServiceUrls == null || !invalidServiceUrls + .contains(jwsservers)) + && !urlsWithoutServices.contains(jwsservers)) { urlsWithoutServices.add(jwsservers); } @@ -746,7 +650,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI if (getInvalidServiceUrls() != null && getInvalidServiceUrls().size() > 0) { - ermsg.append("Invalid Service URLS: \n"); + ermsg.append("URLs that could not be contacted: \n"); for (String svcurl : getInvalidServiceUrls()) { if (list) @@ -783,4 +687,18 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return null; } + public int getServerStatusFor(String url) + { + if (validServiceUrls!=null && validServiceUrls.contains(url)) + { + return 1; + } + if (urlsWithoutServices!=null && urlsWithoutServices.contains(url)) + return 0; + if (invalidServiceUrls!=null && invalidServiceUrls.contains(url)) + { + return -1; + } + return -2; + } }