X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=1c912d89f3f1be41ec5376ff33be88fd75aa8756;hb=0233d3cada9302f2e78d4444de98886431bf4357;hp=9b4c008af388f248bc782bc4867ad7eaecdff6e0;hpb=f149a335b5467a4802eded5da0ca2fc732d7caf7;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 9b4c008..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; @@ -46,13 +45,10 @@ import jalview.gui.Desktop; import jalview.gui.JalviewChangeSupport; import jalview.gui.JvSwingUtils; import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.jws2.Jws2Discoverer.Jws2Instance; -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; @@ -209,17 +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 @@ -227,188 +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; - + /** + * attach all available web services to the appropriate submenu in the given JMenu + */ public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { // dynamically regenerate service list. - final JMenu jws2al = wsmenu; // 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. @@ -445,7 +279,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI jalview.util.QuickSort.sort(sortbytype, orderedsvcs); for (final Jws2Instance service : orderedsvcs) { - atpoint = jws2al; + atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); String type = service.serviceType; if (byhost) { @@ -497,7 +331,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // hostLabels.addElement(host + (bytype ? // service.serviceType+service.getActionText() : "")); } - msacl.attachWSMenuEntry(atpoint, service, alignFrame); + + service.attachWSMenuEntry(atpoint, alignFrame); /* * JMenuItem sitem = new JMenuItem(service.serviceType); * sitem.setToolTipText("Hosted at " + service.hosturl); @@ -517,6 +352,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI 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() { @@ -590,8 +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(); @@ -800,5 +649,4 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } return null; } - }