X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=7a8eee97f13a7268e1d81cb5eb9db07bdf5ed1d8;hb=da53a3eaf1e5c06ff6a2506b7b603086293a887e;hp=c4ef0596fd9ad6ee77377d1257e741fbe52f6665;hpb=7a54eb647645a6be8d09f134f878ef2a03a0ebd9;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index c4ef059..7a8eee9 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 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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 +62,48 @@ 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 + */ + 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); + Vector invalidServiceUrls = null, urlsWithoutServices = null, + validServiceUrls = null; + + boolean running = false, aborted = false; + + 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 +128,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false, aborted = false; - /** * @return the aborted */ @@ -98,12 +143,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public void setAborted(boolean aborted) { this.aborted = aborted; - } - - Thread oldthread = null; + } public void run() { + if (running && oldthread != null && oldthread.isAlive()) { if (!aborted) @@ -125,6 +169,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI Cache.log.debug("Old discovery thread has finished."); } running = true; + + // 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 @@ -156,18 +210,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { validServiceUrls.removeAllElements(); } - ArrayList svctypes=new ArrayList(); + ArrayList svctypes = new ArrayList(); List qrys = new ArrayList(); - for (final String jwsservers : getServiceUrls()) + for (final String jwsserver : getServiceUrls()) { - JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers); - if (svctypes.size()==0) + 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) + // 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()); + } } } @@ -177,7 +235,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI boolean finished = true; do { - finished=true; + finished = true; try { Thread.sleep(100); @@ -187,7 +245,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI ; for (JabaWsServerQuery squery : qrys) { - finished = finished && !squery.isRunning(); + if (squery.isRunning()) + { + finished = false; + } } if (aborted) { @@ -203,22 +264,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { // 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) + + 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) + Jws2Instance[] svcs = new Jws2Instance[services.size()]; + int[] spos = new int[services.size()]; + int ipos = 0; + List svcUrls = getServiceUrls(); + for (Jws2Instance svc : services) { - svcs[ipos]=svc; - spos[ipos++]=1000*svcUrls.indexOf(svc.getHost()) + 1+svctypes.indexOf(svc.serviceType); + 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); + services = new Vector(); + for (Jws2Instance svc : svcs) + { + if (!ignoredServices.contains(svc.serviceType)) + { + services.add(svc); + } } } } @@ -242,36 +308,41 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } System.out.println("Discovered service: " + jwsservers + " " + service.toString()); -// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), -// service2); + // Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), + // service2); services.add(service); // retrieve the presets and parameter set and cache now - service.getParamStore().getPresets(); + ParamDatastoreI pds = service.getParamStore(); + if (pds != null) + { + pds.getPresets(); + } service.hasParameters(); - if (validServiceUrls==null) + 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 + * 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. populateWSMenuEntry(wsmenu, alignFrame, null); } - private boolean isRecalculable(String action) { - return (action!=null && action.equalsIgnoreCase("conservation")); + + private boolean isRecalculable(String action) + { + return (action != null && action.equalsIgnoreCase("conservation")); } - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) + + private void populateWSMenuEntry(JMenu jws2al, + final AlignFrame alignFrame, String typeFilter) { if (running || services == null || services.size() == 0) { @@ -284,20 +355,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * for moment we keep them separate. */ JMenu atpoint; - List enumerableServices=new ArrayList(); - //jws2al.removeAll(); - Map preferredHosts=new HashMap(); + List enumerableServices = new ArrayList(); + // jws2al.removeAll(); + Map preferredHosts = new HashMap(); Map> alternates = new HashMap>(); for (Jws2Instance service : services.toArray(new Jws2Instance[0])) { - if (!isRecalculable(service.action)) { - // add 'one shot' services to be displayed using the classic menu structure + if (!isRecalculable(service.action)) + { + // add 'one shot' services to be displayed using the classic menu + // structure enumerableServices.add(service); - } else { + } + else + { if (!preferredHosts.containsKey(service.serviceType)) { - Jws2Instance preferredInstance = getPreferredServiceFor(alignFrame, - service.serviceType); + Jws2Instance preferredInstance = getPreferredServiceFor( + alignFrame, service.serviceType); if (preferredInstance != null) { preferredHosts.put(service.serviceType, preferredInstance); @@ -307,12 +382,12 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI preferredHosts.put(service.serviceType, service); } } - List ph=alternates.get(service.serviceType); - if (preferredHosts.get(service.serviceType)!=service) + List ph = alternates.get(service.serviceType); + if (preferredHosts.get(service.serviceType) != service) { - if (ph==null) + if (ph == null) { - ph=new ArrayList(); + ph = new ArrayList(); } ph.add(service); alternates.put(service.serviceType, ph); @@ -326,9 +401,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // and the instantaneous services for (final Jws2Instance service : preferredHosts.values()) { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); JMenuItem hitm; - if (atpoint.getItemCount()>1) { + if (atpoint.getItemCount() > 1) + { // previous service of this type already present atpoint.addSeparator(); } @@ -344,17 +420,18 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } }); hitm.setToolTipText(JvSwingUtils - .wrapTooltip("Opens the JABAWS server's homepage in web browser")); + .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")); - for (final Jws2Instance sv:alternates.get(service.serviceType)) + 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; - hitm.add(itm=new JMenuItem(sv.getHost())); + hitm.add(itm = new JMenuItem(sv.getHost())); itm.setForeground(Color.blue); itm.addActionListener(new ActionListener() { @@ -362,38 +439,39 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI @Override public void actionPerformed(ActionEvent arg0) { - new Thread(new Runnable() { - public void run() { - setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv); - changeSupport.firePropertyChange("services", new Vector(), services); + new Thread(new Runnable() + { + public void run() + { + setPreferredServiceFor(alignFrame, sv.serviceType, + sv.action, sv); + changeSupport.firePropertyChange("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(); - } - });*/ + /* + * 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(); } }); + */ } } } + /** - * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type + * add services using the Java 2.5/2.6/2.7 system which optionally creates + * submenus to index by host and service program type */ - private void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List enumerableServices) + private void addEnumeratedServices(final JMenu jws2al, + final AlignFrame alignFrame, List enumerableServices) { boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache .getDefault("WSMENU_BYTYPE", false); @@ -406,7 +484,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI List hostLabels = new ArrayList(); Hashtable lasthostFor = new Hashtable(); Hashtable> hosts = new Hashtable>(); - ArrayList hostlist=new ArrayList(); + ArrayList hostlist = new ArrayList(); for (Jws2Instance service : enumerableServices) { ArrayList hostservices = hosts.get(service.getHost()); @@ -431,14 +509,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI jalview.util.QuickSort.sort(sortbytype, orderedsvcs); for (final Jws2Instance service : orderedsvcs) { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action); + 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); + atpoint.setToolTipText(MessageManager.formatMessage("label.services_at", new String[]{host})); } } if (bytype) @@ -460,12 +538,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // contiguous // group JMenuItem hitm; - if (hostLabels.contains(host)) { + if (hostLabels.contains(host)) + { atpoint.addSeparator(); - } else { + } + else + { hostLabels.add(host); } - if (lasthostFor.get(service.action) == null || !lasthostFor.get(service.action).equals(host)) + if (lasthostFor.get(service.action) == null + || !lasthostFor.get(service.action).equals(host)) { atpoint.add(hitm = new JMenuItem(host)); hitm.setForeground(Color.blue); @@ -479,26 +561,28 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } }); hitm.setToolTipText(JvSwingUtils - .wrapTooltip("Opens the JABAWS server's homepage in web browser")); - lasthostFor.put(service.action,host); + .wrapTooltip(true, MessageManager.getString("label.open_jabaws_web_page"))); + lasthostFor.put(service.action, host); } hostLabels.add(host + service.serviceType + service.getActionText()); } - + service.attachWSMenuEntry(atpoint, alignFrame); } } } + public static void main(String[] args) { - if (args.length>0) + if (args.length > 0) { - testUrls = new Vector(); - for (String url:args) + testUrls = new ArrayList(); + for (String url : args) { testUrls.add(url); - }; + } + ; } Thread runner = getDiscoverer().startDiscoverer( new PropertyChangeListener() @@ -510,10 +594,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { System.out.println("Changesupport: There are now " + getDiscoverer().services.size() + " services"); - int i=1; - for (Jws2Instance instance:getDiscoverer().services) + int i = 1; + for (Jws2Instance instance : getDiscoverer().services) { - System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + System.out.println("Service " + i++ + " " + + instance.getClass() + "@" + + instance.getHost() + ": " + + instance.getActionText()); } } @@ -529,13 +616,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } ; } - try { + try + { Thread.sleep(50); - } catch (InterruptedException x) {} + } catch (InterruptedException x) + { + } } - private static Jws2Discoverer discoverer; - + /** + * Returns the singleton instance of this class. + * + * @return + */ public static Jws2Discoverer getDiscoverer() { if (discoverer == null) @@ -547,7 +640,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { - // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } @@ -556,24 +648,19 @@ 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 { @@ -581,17 +668,27 @@ 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) + 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, ","); @@ -600,40 +697,37 @@ 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 + Cache.log .warn("Problem whilst trying to make a URL from '" + ((url != null) ? url : "") + "'"); - jalview.bin.Cache.log + 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( + Cache.log.warn( "Error parsing comma separated list of urls in " + JWS2HOSTURLS + " preference.", ex); } - if (urls.size() >= 0) - { - return urls; - } - return null; + return urls; } public Vector getServices() @@ -691,8 +785,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null; - /** * @return the invalidServiceUrls */ @@ -800,13 +892,15 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public int getServerStatusFor(String url) { - if (validServiceUrls!=null && validServiceUrls.contains(url)) + if (validServiceUrls != null && validServiceUrls.contains(url)) { return 1; } - if (urlsWithoutServices!=null && urlsWithoutServices.contains(url)) - return 0; - if (invalidServiceUrls!=null && invalidServiceUrls.contains(url)) + if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) + { + return 0; + } + if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) { return -1; } @@ -814,7 +908,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } /** - * pick the user's preferred service based on a set of URLs (jaba server locations) and service URIs (specifying version and service interface class) + * pick the user's preferred service based on a set of URLs (jaba server + * locations) and service URIs (specifying version and service interface + * class) * * @param serviceURL * @return null or best match for given uri/ls. @@ -847,15 +943,18 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } return match; } - - Map> preferredServiceMap = new HashMap>(); -; + + Map> preferredServiceMap = new HashMap>();; /** * get current preferred service of the given type, or global default - * @param af null or a specific alignFrame - * @param serviceType Jws2Instance.serviceType for service - * @return null if no service of this type is available, the preferred service for the serviceType and af if specified and if defined. + * + * @param af + * null or a specific alignFrame + * @param serviceType + * Jws2Instance.serviceType for service + * @return null if no service of this type is available, the preferred service + * for the serviceType and af if specified and if defined. */ public Jws2Instance getPreferredServiceFor(AlignFrame af, String serviceType) @@ -870,11 +969,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // recover global setting, if any prefmap = preferredServiceMap.get(""); } - if (prefmap != null) - { - serviceurl = prefmap.get(serviceType); - } - + if (prefmap != null) + { + serviceurl = prefmap.get(serviceType); + } + } Jws2Instance response = null; for (Jws2Instance svc : services) @@ -914,4 +1013,21 @@ 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; + } + } }