X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=12a08a0e0e547b8ca59f49e2223e829084881e7b;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=99a17269ede8f82eeb1b0cf05d0478bbc5e5c3a4;hpb=8364d3900ad4271d460ae15a245add45c66c2e89;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 99a1726..12a08a0 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,19 +1,22 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * 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. + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.jws2; @@ -21,14 +24,18 @@ import jalview.bin.Cache; import jalview.gui.AlignFrame; import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; +import jalview.util.MessageManager; import jalview.ws.WSMenuEntryProviderI; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ParamDatastoreI; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.beans.PropertyChangeEvent; import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; +import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; @@ -37,6 +44,7 @@ import java.util.HashSet; import java.util.Hashtable; import java.util.List; import java.util.Map; +import java.util.Set; import java.util.StringTokenizer; import java.util.Vector; @@ -54,9 +62,53 @@ import compbio.ws.client.Services; */ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( + public static final String COMPBIO_JABAWS = "http://www.compbio.dundee.ac.uk/jabaws"; + + /* + * the .jalview_properties entry for JWS2 URLS + */ + private final static String JWS2HOSTURLS = "JWS2HOSTURLS"; + + /* + * Singleton instance + */ + private static Jws2Discoverer discoverer; + + /* + * Override for testing only + */ + private static List testUrls = null; + + // preferred url has precedence over others + private String preferredUrl; + + private PropertyChangeSupport changeSupport = new PropertyChangeSupport( this); + private Vector invalidServiceUrls = null; + + private Vector urlsWithoutServices = null; + + private Vector validServiceUrls = null; + + private volatile boolean running = false; + + private volatile boolean aborted = false; + + private Thread oldthread = null; + + /** + * holds list of services. + */ + protected Vector services; + + /** + * Private constructor enforces use of singleton via getDiscoverer() + */ + private Jws2Discoverer() + { + } + /** * change listeners are notified of "services" property changes * @@ -81,8 +133,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false, aborted = false; - /** * @return the aborted */ @@ -100,10 +150,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI this.aborted = aborted; } - Thread oldthread = null; - + @Override public void run() { + if (running && oldthread != null && oldthread.isAlive()) { if (!aborted) @@ -122,10 +172,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { } } + aborted = false; Cache.log.debug("Old discovery thread has finished."); } running = true; - changeSupport.firePropertyChange("services", services, new Vector()); + + // first set up exclusion list if needed + final Set ignoredServices = new HashSet(); + for (String ignored : Cache.getDefault("IGNORED_JABAWS_SERVICETYPES", + "").split("\\|")) + { + ignoredServices.add(ignored); + } + + changeSupport.firePropertyChange("services", services, + new Vector()); oldthread = Thread.currentThread(); try { @@ -159,16 +220,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ArrayList svctypes = new ArrayList(); List qrys = new ArrayList(); - for (final String jwsservers : getServiceUrls()) + for (final String jwsserver : getServiceUrls()) { - JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); + JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver); 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()); + if (!ignoredServices.contains(sv.toString())) + { + svctypes.add(sv.toString()); + } } } @@ -188,7 +252,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished = finished && !squery.isRunning(); + if (squery.isRunning()) + { + finished = false; + } } if (aborted) { @@ -203,14 +270,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI if (!aborted) { // resort services according to order found in jabaws service list - // also ensure servics for each host are ordered in same way. + // also ensure services 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(); + List svcUrls = getServiceUrls(); for (Jws2Instance svc : services) { svcs[ipos] = svc; @@ -221,13 +288,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI services = new Vector(); for (Jws2Instance svc : svcs) { - services.add(svc); + if (!ignoredServices.contains(svc.serviceType)) + { + services.add(svc); + } } } } oldthread = null; running = false; - changeSupport.firePropertyChange("services", new Vector(), services); + changeSupport.firePropertyChange("services", + new Vector(), services); } /** @@ -250,7 +321,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI services.add(service); // retrieve the presets and parameter set and cache now - ParamDataStoreI pds = service.getParamStore(); + ParamDatastoreI pds = service.getParamStore(); if (pds != null) { pds.getPresets(); @@ -258,20 +329,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI service.hasParameters(); if (validServiceUrls == null) { - validServiceUrls = new Vector(); + validServiceUrls = new Vector(); } validServiceUrls.add(jwsservers); } /** - * holds list of services. - */ - protected Vector services; - - /** * attach all available web services to the appropriate submenu in the given * JMenu */ + @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { // dynamically regenerate service list. @@ -290,8 +357,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { return; } - 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. @@ -361,15 +427,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Desktop.showUrl(service.getHost()); } }); - hitm.setToolTipText(JvSwingUtils - .wrapTooltip("Opens the JABAWS server's homepage in web browser")); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, + MessageManager.getString("label.open_jabaws_web_page"))); service.attachWSMenuEntry(atpoint, alignFrame); if (alternates.containsKey(service.serviceType)) { - atpoint.add(hitm = new JMenu("Switch server")); - hitm.setToolTipText(JvSwingUtils - .wrapTooltip("Choose a server for running this service")); + atpoint.add(hitm = new JMenu(MessageManager + .getString("label.switch_server"))); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, + MessageManager.getString("label.choose_jabaws_server"))); for (final Jws2Instance sv : alternates.get(service.serviceType)) { JMenuItem itm; @@ -383,27 +450,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { new Thread(new Runnable() { + @Override public void run() { setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv); changeSupport.firePropertyChange("services", - new Vector(), services); + new Vector(), services); }; }).start(); } }); } - /* - * hitm.addActionListener(new ActionListener() { - * - * @Override public void actionPerformed(ActionEvent arg0) { new - * Thread(new Runnable() { - * - * @Override public void run() { new SetPreferredServer(alignFrame, - * service.serviceType, service.action); } }).start(); } }); - */ } } } @@ -422,7 +481,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * for moment we keep them separate. */ JMenu atpoint; - MsaWSClient msacl = new MsaWSClient(); + List hostLabels = new ArrayList(); Hashtable lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); @@ -458,7 +517,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); if (atpoint.getToolTipText() == null) { - atpoint.setToolTipText("Services at " + host); + atpoint.setToolTipText(MessageManager.formatMessage( + "label.services_at", new String[] { host })); } } if (bytype) @@ -502,8 +562,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Desktop.showUrl(service.getHost()); } }); - hitm.setToolTipText(JvSwingUtils - .wrapTooltip("Opens the JABAWS server's homepage in web browser")); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(true, + MessageManager.getString("label.open_jabaws_web_page"))); lasthostFor.put(service.action, host); } hostLabels.add(host + service.serviceType @@ -519,7 +579,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (args.length > 0) { - testUrls = new Vector(); + testUrls = new ArrayList(); for (String url : args) { testUrls.add(url); @@ -530,6 +590,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (getDiscoverer().services != null) @@ -566,8 +627,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } - private static Jws2Discoverer discoverer; - + /** + * Returns the singleton instance of this class. + * + * @return + */ public static Jws2Discoverer getDiscoverer() { if (discoverer == null) @@ -579,7 +643,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { - // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } @@ -588,24 +651,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return running; } - /** - * the jalview .properties entry for JWS2 URLS - */ - final static String JWS2HOSTURLS = "JWS2HOSTURLS"; - - public static void setServiceUrls(Vector urls) + public void setServiceUrls(List wsUrls) { - if (urls != null) + if (wsUrls != null && !wsUrls.isEmpty()) { - StringBuffer urlbuffer = new StringBuffer(); + StringBuilder urls = new StringBuilder(128); String sep = ""; - for (String url : urls) + for (String url : wsUrls) { - urlbuffer.append(sep); - urlbuffer.append(url); + urls.append(sep); + urls.append(url); sep = ","; } - Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString()); + Cache.setProperty(JWS2HOSTURLS, urls.toString()); } else { @@ -613,18 +671,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } - private static Vector testUrls = null; - - public static Vector getServiceUrls() + /** + * Returns web service URLs, in the order in which they should be tried (or an + * empty list). + * + * @return + */ + public List 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(); + List urls = new ArrayList(); + + if (this.preferredUrl != null) + { + urls.add(preferredUrl); + } + + String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS); try { StringTokenizer st = new StringTokenizer(surls, ","); @@ -633,40 +700,35 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI String url = null; try { - java.net.URL u = new java.net.URL(url = st.nextToken()); + url = st.nextToken(); + new URL(url); if (!urls.contains(url)) { urls.add(url); } else { - jalview.bin.Cache.log.info("Ignoring duplicate url in " + Cache.log.warn("Ignoring duplicate url " + url + " in " + JWS2HOSTURLS + " list"); } - } catch (Exception ex) + } catch (MalformedURLException ex) { - jalview.bin.Cache.log - .warn("Problem whilst trying to make a URL from '" - + ((url != null) ? url : "") + "'"); - jalview.bin.Cache.log + Cache.log.warn("Problem whilst trying to make a URL from '" + + ((url != null) ? url : "") + "'"); + Cache.log .warn("This was probably due to a malformed comma separated list" + " in the " + JWS2HOSTURLS + " entry of $(HOME)/.jalview_properties)"); - jalview.bin.Cache.log.debug("Exception was ", ex); + Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { - jalview.bin.Cache.log.warn( - "Error parsing comma separated list of urls in " - + JWS2HOSTURLS + " preference.", ex); - } - if (urls.size() >= 0) - { - return urls; + Cache.log.warn("Error parsing comma separated list of urls in " + + JWS2HOSTURLS + " preference.", ex); } - return null; + return urls; } public Vector getServices() @@ -685,8 +747,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { try { - compbio.ws.client.WSTester.main(new String[] - { "-h=" + foo.toString() }); + compbio.ws.client.WSTester + .main(new String[] { "-h=" + foo.toString() }); } catch (Exception e) { e.printStackTrace(); @@ -704,6 +766,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return true; } + public boolean restart() + { + synchronized (this) + { + if (running) + { + aborted = true; + } + else + { + running = true; + } + return aborted; + } + } + /** * 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 @@ -714,6 +792,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI */ public Thread startDiscoverer(PropertyChangeListener changeSupport2) { + /* if (restart()) + { + return; + } + else + { + Thread thr = new Thread(this); + thr.start(); + } + */ if (isRunning()) { setAborted(true); @@ -724,9 +812,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null, - validServiceUrls = null; - /** * @return the invalidServiceUrls */ @@ -795,7 +880,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI if (getInvalidServiceUrls() != null && getInvalidServiceUrls().size() > 0) { - ermsg.append("URLs that could not be contacted: \n"); + ermsg.append(MessageManager.getString("warn.urls_not_contacted") + + ": \n"); for (String svcurl : getInvalidServiceUrls()) { if (list) @@ -811,7 +897,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI if (getUrlsWithoutServices() != null && getUrlsWithoutServices().size() > 0) { - ermsg.append("URLs without any JABA Services : \n"); + ermsg.append(MessageManager.getString("warn.urls_no_jaba") + ": \n"); for (String svcurl : getUrlsWithoutServices()) { if (list) @@ -839,7 +925,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return 1; } if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) + { return 0; + } if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) { return -1; @@ -953,4 +1041,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { setPreferredServiceFor(null, serviceType, serviceAction, selectedServer); } + + /** + * Set a URL to try before any others. For use with command-line parameter to + * configure a local Jabaws installation without the need to add to property + * files. + * + * @param value + * @throws MalformedURLException + */ + public void setPreferredUrl(String value) throws MalformedURLException + { + if (value != null && value.trim().length() > 0) + { + new URL(value); + preferredUrl = value; + } + } }