/* * 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. * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.jws2; import jalview.bin.Cache; import jalview.gui.AlignFrame; import jalview.util.MessageManager; import jalview.ws.ServiceChangeListener; import jalview.ws.WSDiscovererI; import jalview.ws.api.ServiceWithParameters; import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.ParamDatastoreI; 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.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.StringTokenizer; import java.util.Vector; import java.util.concurrent.CopyOnWriteArraySet; import java.util.concurrent.ExecutionException; import java.util.concurrent.Future; import java.util.concurrent.FutureTask; import javax.swing.JMenu; import compbio.ws.client.Services; /** * discoverer for jws2 services. Follows the lightweight service discoverer * pattern (archetyped by EnfinEnvision2OneWay) * * @author JimP * */ public class Jws2Discoverer implements WSDiscovererI, Runnable { 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 Set serviceListeners = new CopyOnWriteArraySet<>(); private Vector invalidServiceUrls = null; private Vector urlsWithoutServices = null; private Vector validServiceUrls = null; private volatile boolean running = false; private volatile boolean aborted = false; private volatile Thread oldthread = null; /** * holds list of services. */ protected Vector services; /** * Private constructor enforces use of singleton via getDiscoverer() */ private Jws2Discoverer() { } @Override public void addServiceChangeListener(ServiceChangeListener listener) { serviceListeners.add(listener); } @Override public void removeServiceChangeListener(ServiceChangeListener listener) { serviceListeners.remove(listener); } private void notifyServiceListeners(List services) { if (services == null) services = this.services; for (var listener : serviceListeners) { listener.servicesChanged(this, services); } } /** * @return the aborted */ public boolean isAborted() { return aborted; } /** * @param aborted * the aborted to set */ public void setAborted(boolean aborted) { this.aborted = aborted; } @Override public void run() { if (running && oldthread != null && oldthread.isAlive()) { if (!aborted) { return; } while (running) { try { 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; // first set up exclusion list if needed final Set ignoredServices = new HashSet<>(); for (String ignored : Cache .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|")) { ignoredServices.add(ignored); } notifyServiceListeners(Collections.emptyList()); oldthread = Thread.currentThread(); try { getClass().getClassLoader().loadClass("compbio.ws.client.Jws2Client"); } catch (ClassNotFoundException e) { 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; } // reinitialise records of good and bad service URLs if (services != null) { services.removeAllElements(); } if (urlsWithoutServices != null) { urlsWithoutServices.removeAllElements(); } if (invalidServiceUrls != null) { invalidServiceUrls.removeAllElements(); } if (validServiceUrls != null) { validServiceUrls.removeAllElements(); } ArrayList svctypes = new ArrayList<>(); List qrys = new ArrayList<>(); for (final String jwsserver : getServiceUrls()) { 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) { if (!ignoredServices.contains(sv.toString())) { svctypes.add(sv.toString()); } } } qrys.add(squery); new Thread(squery).start(); } boolean finished = true; do { finished = true; try { Thread.sleep(100); } catch (Exception e) { } for (JabaWsServerQuery squery : qrys) { if (squery.isRunning()) { finished = false; } } if (aborted) { Cache.log.debug( "Aborting " + qrys.size() + " JABAWS discovery threads."); for (JabaWsServerQuery squery : qrys) { squery.setQuit(true); } } } while (!aborted && !finished); if (!aborted) { // resort services according to order found in jabaws service list // 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; List svcUrls = getServiceUrls(); for (Jws2Instance svc : services) { 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) { if (!ignoredServices.contains(svc.getName())) { services.add(svc); } } } } oldthread = null; running = false; notifyServiceListeners(services); } /** * record this service endpoint so we can use it * * @param jwsservers * @param srv * @param service2 */ synchronized void addService(String jwsservers, Jws2Instance service) { if (services == null) { services = new Vector<>(); } 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 ParamDatastoreI pds = service.getParamStore(); if (pds != null) { pds.getPresets(); } service.hasParameters(); if (validServiceUrls == null) { validServiceUrls = new Vector<>(); } validServiceUrls.add(jwsservers); } /** * * @param args * @j2sIgnore */ public static void main(String[] args) { if (args.length > 0) { testUrls = new ArrayList<>(); for (String url : args) { testUrls.add(url); } } var discoverer = getDiscoverer(); discoverer.addServiceChangeListener((_discoverer, _services) -> { if (discoverer.services != null) { System.out.println("Changesupport: There are now " + discoverer.services.size() + " services"); int i = 1; for (ServiceWithParameters instance : discoverer.services) { System.out.println( "Service " + i++ + " " + instance.getClass() + "@" + instance.getHostURL() + ": " + instance.getActionText()); } } }); try { discoverer.startDiscoverer().get(); } catch (InterruptedException | ExecutionException e) { } try { Thread.sleep(50); } catch (InterruptedException x) { } } /** * Returns the singleton instance of this class. * * @return */ public static Jws2Discoverer getDiscoverer() { if (discoverer == null) { discoverer = new Jws2Discoverer(); } return discoverer; } @Override public boolean hasServices() { return !running && services != null && services.size() > 0; } @Override public boolean isRunning() { return running; } @Override public void setServiceUrls(List wsUrls) { if (wsUrls != null && !wsUrls.isEmpty()) { StringBuilder urls = new StringBuilder(128); String sep = ""; for (String url : wsUrls) { urls.append(sep); urls.append(url); sep = ","; } Cache.setProperty(JWS2HOSTURLS, urls.toString()); } else { Cache.removeProperty(JWS2HOSTURLS); } } /** * Returns web service URLs, in the order in which they should be tried (or an * empty list). * * @return */ @Override public List getServiceUrls() { if (testUrls != null) { // return test urls, if there are any, instead of touching cache return testUrls; } List urls = new ArrayList<>(); if (this.preferredUrl != null) { urls.add(preferredUrl); } String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS); try { StringTokenizer st = new StringTokenizer(surls, ","); while (st.hasMoreElements()) { String url = null; try { url = st.nextToken(); new URL(url); if (!urls.contains(url)) { urls.add(url); } else { Cache.log.warn("Ignoring duplicate url " + url + " in " + JWS2HOSTURLS + " list"); } } catch (MalformedURLException ex) { 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)"); Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { Cache.log.warn("Error parsing comma separated list of urls in " + JWS2HOSTURLS + " preference.", ex); } return urls; } @Override public Vector getServices() { return (services == null) ? new Vector<>() : new Vector<>(services); } /** * test the given URL with the JabaWS test code * * @param foo * @return */ @Override public boolean testServiceUrl(URL foo) { try { compbio.ws.client.WSTester .main(new String[] { "-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; } 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 * started. * * @param changeSupport2 * @return new thread */ @Override public FutureTask startDiscoverer() { /* if (restart()) { return; } else { Thread thr = new Thread(this); thr.start(); } */ if (isRunning()) { setAborted(true); } FutureTask task = new FutureTask<>(this, this); new Thread(task).start(); return task; } /** * @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 */ @Override public String getErrorMessages() { if (!isRunning() && !isAborted()) { StringBuffer ermsg = new StringBuffer(); boolean list = false; if (getInvalidServiceUrls() != null && getInvalidServiceUrls().size() > 0) { ermsg.append(MessageManager.getString("warn.urls_not_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( MessageManager.getString("warn.urls_no_jaba") + ": \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; } @Override public int getServerStatusFor(String url) { if (validServiceUrls != null && validServiceUrls.contains(url)) { return STATUS_OK; } if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) { return STATUS_NO_SERVICES; } if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) { return STATUS_INVALID; } return STATUS_UNKNOWN; } /** * 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; } } }