X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=1c912d89f3f1be41ec5376ff33be88fd75aa8756;hb=0233d3cada9302f2e78d4444de98886431bf4357;hp=8cc39d741e8979ef8fedc19da761cc0da4c7b12a;hpb=43e280af80c060ad0bca76e5025ebabc38a52a21;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 8cc39d7..1c912d8 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. * @@ -22,7 +22,6 @@ 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; @@ -44,13 +43,12 @@ import jalview.datamodel.AlignmentView; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JalviewChangeSupport; +import jalview.gui.JvSwingUtils; import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.params.ParamDatastoreI; -import compbio.data.msa.MsaWS; +import jalview.ws.jws2.jabaws2.Jws2Instance; +import compbio.data.msa.JABAService; 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; @@ -93,6 +91,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI boolean running = false, aborted = false; /** + * @return the aborted + */ + public boolean isAborted() + { + return aborted; + } + + /** * @param aborted * the aborted to set */ @@ -134,15 +140,25 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } catch (ClassNotFoundException e) { System.err - .println("Not enabling Jalview Webservices version 2: client jar is not available." + .println("Not enabling JABA Webservices : client jar is not available." + "\nPlease check that your webstart JNLP file is up to date!"); running = false; return; } + // reinitialise records of good and bad service URLs if (services != null) { services.removeAllElements(); } + if (urlsWithoutServices != null) + { + urlsWithoutServices.removeAllElements(); + } + if (invalidServiceUrls != null) + { + invalidServiceUrls.removeAllElements(); + } + List qrys = new ArrayList(); for (final String jwsservers : getServiceUrls()) { @@ -189,17 +205,16 @@ 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 @@ -207,216 +222,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI 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 (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(); - } - - @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; - } - }; - /** * 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. @@ -426,78 +252,128 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Vector hostLabels = new Vector(); jws2al.removeAll(); String lasthost = null; - for (final Jws2Instance service : services) + Hashtable> hosts = new Hashtable>(); + String[] sorton; + 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()); } - if (bytype) + hostservices.add(service); + } + sorton = hosts.keySet().toArray(new String[1]); + String hostlist[] = sorton.clone(); + jalview.util.QuickSort.sort(sorton, hostlist); + 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 = JvSwingUtils.findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText("Services at " + host); + } + } + if (bytype) { - atpoint.add(hitm = new JMenuItem(host)); - hitm.setForeground(Color.blue); - lasthost = host; + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(service.getActionText()); + } } - hostLabels.addElement(host + service.serviceType - + service.getActionText()); - // hostLabels.addElement(host + (bytype ? - // service.serviceType+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 (lasthost == null || !lasthost.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")); + lasthost = host; + } + 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) { - Thread runner = getDiscoverer().startDiscoverer(new PropertyChangeListener() + if (args.length>0) { - - public void propertyChange(PropertyChangeEvent evt) + testUrls = new Vector(); + for (String url:args) { - if (getDiscoverer().services!=null) - {System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); - - } - } - }); + testUrls.add(url); + }; + } + Thread runner = getDiscoverer().startDiscoverer( + new PropertyChangeListener() + { + + public void propertyChange(PropertyChangeEvent evt) + { + if (getDiscoverer().services != null) + { + System.out.println("Changesupport: There are now " + + getDiscoverer().services.size() + " services"); + + } + } + }); while (runner.isAlive()) { try @@ -557,8 +433,14 @@ 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(); @@ -626,19 +508,26 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { "-h=" + foo.toString() }); } catch (Exception e) { + e.printStackTrace(); return false; } catch (OutOfMemoryError e) { + e.printStackTrace(); return false; } catch (Error e) { + e.printStackTrace(); return false; } + return true; } /** - * Start a fresh discovery thread and notify the given object when we're finished. Any known existing threads will be killed before this one is started. + * Start a fresh discovery thread and notify the given object when we're + * finished. Any known existing threads will be killed before this one is + * started. + * * @param changeSupport2 * @return new thread */ @@ -654,4 +543,110 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } + Vector invalidServiceUrls = null, urlsWithoutServices = null; + + /** + * @return the invalidServiceUrls + */ + public Vector getInvalidServiceUrls() + { + return invalidServiceUrls; + } + + /** + * @return the urlsWithoutServices + */ + public Vector getUrlsWithoutServices() + { + return urlsWithoutServices; + } + + /** + * 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 + */ + public synchronized void addUrlwithnoservices(String jwsservers) + { + if (urlsWithoutServices == null) + { + urlsWithoutServices = new Vector(); + } + + if ((invalidServiceUrls == null || !invalidServiceUrls + .contains(jwsservers)) + && !urlsWithoutServices.contains(jwsservers)) + { + urlsWithoutServices.add(jwsservers); + } + } + + /** + * add a bad URL to the list + * + * @param jwsservers + */ + public synchronized void addInvalidServiceUrl(String jwsservers) + { + if (invalidServiceUrls == null) + { + invalidServiceUrls = new Vector(); + } + if (!invalidServiceUrls.contains(jwsservers)) + { + invalidServiceUrls.add(jwsservers); + } + } + + /** + * + * @return a human readable report of any problems with the service URLs used + * for discovery + */ + public String getErrorMessages() + { + if (!isRunning() && !isAborted()) + { + StringBuffer ermsg = new StringBuffer(); + boolean list = false; + if (getInvalidServiceUrls() != null + && getInvalidServiceUrls().size() > 0) + { + ermsg.append("URLs that could not be contacted: \n"); + for (String svcurl : getInvalidServiceUrls()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n\n"); + } + list = false; + if (getUrlsWithoutServices() != null + && getUrlsWithoutServices().size() > 0) + { + ermsg.append("URLs without any JABA Services : \n"); + for (String svcurl : getUrlsWithoutServices()) + { + if (list) + { + ermsg.append(", "); + } + list = true; + ermsg.append(svcurl); + } + ermsg.append("\n"); + } + if (ermsg.length() > 1) + { + return ermsg.toString(); + } + + } + return null; + } }