X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=f1f8690c5d4fe704a3bc08bbe56f512c582ceaab;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=96a6f6bf0a57e7e595ae2d7c41d7317d7ca5c03d;hpb=b0b2035ac995961a10d420f337a91a08a3014298;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 96a6f6b..f1f8690 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,45 +1,46 @@ /* - * 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 ($$Version-Rel$$) + * 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; 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.api.ServiceWithParameters; 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; import java.util.HashSet; -import java.util.Hashtable; import java.util.List; +import java.util.Set; import java.util.StringTokenizer; import java.util.Vector; import javax.swing.JMenu; -import javax.swing.JMenuItem; import compbio.ws.client.Services; @@ -52,9 +53,53 @@ 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 * @@ -79,8 +124,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false, aborted = false; - /** * @return the aborted */ @@ -98,10 +141,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI this.aborted = aborted; } - Thread oldthread = null; - + @Override public void run() { + if (running && oldthread != null && oldthread.isAlive()) { if (!aborted) @@ -112,27 +155,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { try { - Cache.log - .debug("Waiting around for old discovery thread to finish."); + Cache.log.debug( + "Waiting around for old discovery thread to finish."); // wait around until old discoverer dies Thread.sleep(100); } catch (Exception e) { } } + 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 { - Class foo = getClass().getClassLoader().loadClass( - "compbio.ws.client.Jws2Client"); + Class foo = getClass().getClassLoader() + .loadClass("compbio.ws.client.Jws2Client"); } catch (ClassNotFoundException e) { - System.err - .println("Not enabling JABA Webservices : client jar is not available." + System.err.println( + "Not enabling JABA Webservices : client jar is not available." + "\nPlease check that your webstart JNLP file is up to date!"); running = false; return; @@ -154,18 +208,22 @@ 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()) + List qrys = new ArrayList<>(); + 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()); + } } } @@ -175,22 +233,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI boolean finished = true; do { - finished=true; + finished = true; try { Thread.sleep(100); } catch (Exception e) { } - ; for (JabaWsServerQuery squery : qrys) { - finished = finished && !squery.isRunning(); + if (squery.isRunning()) + { + finished = false; + } } if (aborted) { - Cache.log.debug("Aborting " + qrys.size() - + " JABAWS discovery threads."); + Cache.log.debug( + "Aborting " + qrys.size() + " JABAWS discovery threads."); for (JabaWsServerQuery squery : qrys) { squery.setQuit(true); @@ -200,29 +260,35 @@ 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. - - if (services!=null && services.size()>0) + // 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(); - 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.getHostURL()) + 1 + + svctypes.indexOf(svc.getName()); } 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.getName())) + { + services.add(svc); + } } } } oldthread = null; running = false; - changeSupport.firePropertyChange("services", new Vector(), services); + changeSupport.firePropertyChange("services", new Vector(), + services); } /** @@ -236,175 +302,85 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (services == null) { - services = new Vector(); + services = new Vector<>(); } - System.out.println("Discovered service: " + jwsservers + " " - + service.toString()); -// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(), -// service2); + System.out.println( + "Discovered service: " + jwsservers + " " + 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(); + 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 */ + @Override public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { - // dynamically regenerate service list. - populateWSMenuEntry(wsmenu, alignFrame, null); - } - - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter) - { if (running || services == null || services.size() == 0) { 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. - */ - JMenu atpoint; - MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); - //jws2al.removeAll(); - Hashtable lasthostFor = new Hashtable(); - Hashtable> hosts = new Hashtable>(); - ArrayList hostlist=new ArrayList(); - for (Jws2Instance service : services) - { - ArrayList hostservices = hosts.get(service.getHost()); - if (hostservices == null) - { - hosts.put(service.getHost(), - hostservices = new ArrayList()); - hostlist.add(service.getHost()); - } - 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++) - { - sortbytype[i] = orderedsvcs[i].serviceType; - } - jalview.util.QuickSort.sort(sortbytype, orderedsvcs); - for (final Jws2Instance service : orderedsvcs) - { - 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 = 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() : "")); - } - - 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); } - * }); - */ - } - } + // dynamically regenerate service list. + populateWSMenuEntry(wsmenu, alignFrame, null); + } + private void populateWSMenuEntry(JMenu jws2al, + final AlignFrame alignFrame, String typeFilter) + { + PreferredServiceRegistry.getRegistry().populateWSMenuEntry( + getServices(), + changeSupport, jws2al, + alignFrame, typeFilter); } + /** + * + * @param args + * @j2sIgnore + */ 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() + Thread runner = getDiscoverer() + .startDiscoverer(new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (getDiscoverer().services != null) { System.out.println("Changesupport: There are now " + getDiscoverer().services.size() + " services"); - int i=1; - for (Jws2Instance instance:getDiscoverer().services) + int i = 1; + for (ServiceWithParameters instance : getDiscoverer().services) { - System.out.println("Service "+i+++" "+instance.getClass()+"@"+instance.getHost()+": "+instance.getActionText()); + System.out.println("Service " + i++ + " " + + instance.getClass() + "@" + + instance.getHostURL() + + ": " + instance.getActionText()); } } @@ -418,15 +394,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } catch (InterruptedException e) { } - ; } - 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) @@ -438,7 +419,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { - // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } @@ -447,24 +427,19 @@ 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 { @@ -472,17 +447,27 @@ 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, ","); @@ -491,46 +476,40 @@ 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 - .warn("This was probably due to a malformed comma separated list" - + " in the " - + JWS2HOSTURLS + 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); + 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() + public Vector getServices() { - return (services == null) ? new Vector() - : new Vector(services); + return (services == null) ? new Vector<>() + : new Vector<>(services); } /** @@ -543,8 +522,9 @@ 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(); @@ -562,6 +542,22 @@ 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 @@ -572,6 +568,16 @@ 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); @@ -582,8 +588,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return thr; } - Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null; - /** * @return the invalidServiceUrls */ @@ -610,11 +614,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (urlsWithoutServices == null) { - urlsWithoutServices = new Vector(); + urlsWithoutServices = new Vector<>(); } - if ((invalidServiceUrls == null || !invalidServiceUrls - .contains(jwsservers)) + if ((invalidServiceUrls == null + || !invalidServiceUrls.contains(jwsservers)) && !urlsWithoutServices.contains(jwsservers)) { urlsWithoutServices.add(jwsservers); @@ -630,7 +634,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (invalidServiceUrls == null) { - invalidServiceUrls = new Vector(); + invalidServiceUrls = new Vector<>(); } if (!invalidServiceUrls.contains(jwsservers)) { @@ -652,7 +656,8 @@ 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) @@ -668,7 +673,8 @@ 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) @@ -691,13 +697,15 @@ 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; } @@ -705,31 +713,19 @@ 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) + * 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 serviceURL - * @return null or best match for given uri/ls. + * @param value + * @throws MalformedURLException */ - public Jws2Instance getPreferredServiceFor(String[] serviceURLs) + public void setPreferredUrl(String value) throws MalformedURLException { - HashSet urls=new HashSet(); - urls.addAll(Arrays.asList(serviceURLs)); - Jws2Instance match=null; - for (Jws2Instance svc:services) + if (value != null && value.trim().length() > 0) { - if (urls.contains(svc.getServiceTypeURI())) - { - if (match==null) { - // for moment we always pick service from server ordered first in user's preferences - match=svc; - } - if (urls.contains(svc.getUri())) - { - // stop and return - we've matched type URI and URI for service endpoint - return svc; - } - } + new URL(value); + preferredUrl = value; } - return match; } }