X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=73d37009638232a079a1d74883d11ef02aa8fba1;hb=2facc0e2aee62c60c28cc59277805194b306f6f9;hp=9897d7968b53617374d837ca9d4b00890cbe3352;hpb=f6cdb4ac43a8e703f8f76feaf4cf195b8b4fe772;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 9897d79..73d3700 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,33 +1,53 @@ +/* + * 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 java.awt.Color; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; +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.io.Closeable; -import java.net.ConnectException; +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.Hashtable; +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 javax.swing.JMenuItem; - -import org.apache.log4j.Level; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentView; -import jalview.gui.AlignFrame; -import jalview.ws.WSMenuEntryProviderI; -import compbio.data.msa.MsaWS; -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; /** @@ -37,111 +57,237 @@ import compbio.ws.client.Services; * @author JimP * */ -public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI +public class Jws2Discoverer implements WSDiscovererI, Runnable { - private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport( - this); + 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; /** - * change listeners are notified of "services" property changes - * - * @param listener - * to be added that consumes new services Hashtable object. + * holds list of services. + */ + protected Vector services; + + /** + * Private constructor enforces use of singleton via getDiscoverer() */ - public void addPropertyChangeListener( - java.beans.PropertyChangeListener listener) + private Jws2Discoverer() + { + } + + + @Override + public void addServiceChangeListener(ServiceChangeListener listener) + { + serviceListeners.add(listener); + } + + @Override + public void removeServiceChangeListener(ServiceChangeListener listener) { - changeSupport.addPropertyChangeListener(listener); + serviceListeners.remove(listener); + } + + private void notifyServiceListeners(List services) + { + if (services == null) services = this.services; + for (var listener : serviceListeners) { + listener.servicesChanged(this, services); + } } /** - * - * - * @param listener - * to be removed + * @return the aborted */ - public void removePropertyChangeListener( - java.beans.PropertyChangeListener listener) + public boolean isAborted() { - changeSupport.removePropertyChangeListener(listener); + return aborted; } - boolean running = false; - - Thread oldthread = null; + /** + * @param aborted + * the aborted to set + */ + public void setAborted(boolean aborted) + { + this.aborted = aborted; + } @Override public void run() { + if (running && oldthread != null && oldthread.isAlive()) { - return; + 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 { - Class foo = getClass().getClassLoader().loadClass( - "compbio.ws.client.Jws2Client"); + getClass().getClassLoader().loadClass("compbio.ws.client.Jws2Client"); } catch (ClassNotFoundException e) { - System.err - .println("Not enabling Jalview Webservices version 2: 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; } + // reinitialise records of good and bad service URLs if (services != null) { services.removeAllElements(); } - for (String jwsservers : getServiceUrls()) + if (urlsWithoutServices != null) { - try + 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) { - if (Jws2Client.validURL(jwsservers)) + // TODO: remove this ugly hack to get Canonical JABA service ordering + // for all possible services + for (Services sv : squery.JABAWS2SERVERS) { - // look for services - for (Services srv : Services.values()) + if (!ignoredServices.contains(sv.toString())) { - MsaWS service = null; - try - { - service = Jws2Client.connect(jwsservers, srv); - } catch (Exception e) - { - System.err.println("Jws2 Discoverer: Problem on " - + jwsservers + " with service " + srv + ":\n" - + e.getMessage()); - if (!(e instanceof javax.xml.ws.WebServiceException)) - { - e.printStackTrace(); - } - } - ; - if (service != null) - { - addService(jwsservers, srv, service); - } + svctypes.add(sv.toString()); } - } - else + + } + 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()) { - Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers); + finished = false; } - } catch (Exception e) + } + if (aborted) { - e.printStackTrace(); - Cache.log.warn("Exception when discovering Jws2 services.", e); - } catch (Error e) + 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) { - Cache.log.error("Exception when discovering Jws2 services.", e); + 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; - changeSupport.firePropertyChange("services", new Vector(), services); + notifyServiceListeners(services); } /** @@ -151,335 +297,408 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * @param srv * @param service2 */ - private void addService(String jwsservers, Services srv, MsaWS service2) + synchronized void addService(String jwsservers, Jws2Instance service) { 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); + + services.add(service); + // retrieve the presets and parameter set and cache now + ParamDatastoreI pds = service.getParamStore(); + if (pds != null) + { + pds.getPresets(); } - System.out.println("Discovered service: " + jwsservers + " " - + srv.toString()); - services.add(new Jws2Instance(jwsservers, srv.toString(), service2)); + service.hasParameters(); + if (validServiceUrls == null) + { + validServiceUrls = new Vector<>(); + } + validServiceUrls.add(jwsservers); } - public class Jws2Instance + /** + * + * @param args + * @j2sIgnore + */ + public static void main(String[] args) { - public String hosturl; - - public String serviceType; + 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()); + } - public MsaWS service; + } + }); + try + { + discoverer.startDiscoverer().get(); + } catch (InterruptedException | ExecutionException e) + { + } + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { + } + } - public Jws2Instance(String hosturl, String serviceType, MsaWS service) + /** + * Returns the singleton instance of this class. + * + * @return + */ + public static Jws2Discoverer getDiscoverer() + { + if (discoverer == null) { - super(); - this.hosturl = hosturl; - this.serviceType = serviceType; - this.service = service; + discoverer = new Jws2Discoverer(); } + return discoverer; + } - PresetManager presets = null; + @Override + public boolean hasServices() + { + return !running && services != null && services.size() > 0; + } + + @Override + public boolean isRunning() + { + return running; + } - /** - * 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() + @Override + public void setServiceUrls(List wsUrls) + { + if (wsUrls != null && !wsUrls.isEmpty()) { - if (presets == null) + StringBuilder urls = new StringBuilder(128); + String sep = ""; + for (String url : wsUrls) { - try - { - presets = service.getPresets(); - } catch (Exception ex) - { - System.err - .println("Exception when retrieving presets for service " - + serviceType + " at " + hosturl); - } + urls.append(sep); + urls.append(url); + sep = ","; } - return presets; + Cache.setProperty(JWS2HOSTURLS, urls.toString()); } - - public String getHost() + else { - 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; - */ + Cache.removeProperty(JWS2HOSTURLS); } + } - /** - * @return short description of what the service will do - */ - public String getActionText() + /** + * 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 "Align with " + serviceType; + // return test urls, if there are any, instead of touching cache + return testUrls; } + List urls = new ArrayList<>(); - /** - * non-thread safe - blocks whilst accessing service to get complete set of - * available options and parameters - * - * @return - */ - public RunnerConfig getRunnerConfig() + if (this.preferredUrl != null) { - return service.getRunnerOptions(); + urls.add(preferredUrl); } - @Override - protected void finalize() throws Throwable + String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS); + try { - if (service != null) + StringTokenizer st = new StringTokenizer(surls, ","); + while (st.hasMoreElements()) { + String url = null; try { - Closeable svc = (Closeable) service; - service = null; - svc.close(); - } catch (Exception e) + 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); } - ; } - super.finalize(); + } catch (Exception ex) + { + Cache.log.warn("Error parsing comma separated list of urls in " + + JWS2HOSTURLS + " preference.", ex); } - }; + return urls; + } - /** - * holds list of services. - */ - protected Vector services; + @Override + public Vector getServices() + { + return (services == null) ? new Vector<>() : new Vector<>(services); + } /** - * find or add a submenu with the given title in the given menu + * test the given URL with the JabaWS test code * - * @param menu - * @param submenu - * @return the new or existing submenu + * @param foo + * @return */ - private JMenu findOrCreateMenu(JMenu menu, String submenu) + @Override + public boolean testServiceUrl(URL foo) { - JMenu submenuinstance = null; - for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++) + try { - if (menu.getMenuComponent(i) instanceof JMenu - && ((JMenu) menu.getMenuComponent(i)).getText().equals( - submenu)) - { - submenuinstance = (JMenu) menu.getMenuComponent(i); - } - } - if (submenuinstance == null) + compbio.ws.client.WSTester + .main(new String[] + { "-h=" + foo.toString() }); + } catch (Exception e) { - submenuinstance = new JMenu(submenu); - menu.add(submenuinstance); - } - return submenuinstance; - - } - - @Override - public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) - { - if (running || services == null || services.size() == 0) + e.printStackTrace(); + return false; + } catch (OutOfMemoryError e) { - return; - } - boolean byhost = Cache.getDefault("WSMENU_BYHOST", true), bytype = Cache - .getDefault("WSMENU_BYTYPE", true); - /** - * eventually, JWS2 services will appear under the same align/etc submenus. - * for moment we keep them separate. - */ - JMenu atpoint, jws2al = new JMenu("JABA Alignment"); - MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); - for (final Jws2Instance service : services) - { - atpoint = jws2al; - String host = service.getHost(); - String type = service.serviceType; - if (byhost) - { - atpoint = findOrCreateMenu(atpoint, host); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText("Services at " + host); - } - } - if (bytype) - { - atpoint = findOrCreateMenu(atpoint, type); - if (atpoint.getToolTipText() == null) - { - atpoint.setToolTipText(service.getActionText()); - } - } - if (!byhost && !hostLabels.contains(host + 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(); - atpoint.add(hitm = new JMenuItem(host)); - hitm.setForeground(Color.blue); - hostLabels.addElement(host); - } - msacl.attachWSMenuEntry(atpoint, service, 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); } }); - */ - } - if (services.size() > 0) + e.printStackTrace(); + return false; + } catch (Error e) { - wsmenu.add(jws2al); + e.printStackTrace(); + return false; } + return true; } - public static void main(String[] args) + public boolean restart() { - Thread runner = new Thread(getDiscoverer()); - getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() + synchronized (this) { - - @Override - public void propertyChange(PropertyChangeEvent evt) + if (running) { - System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); + aborted = true; } - }); - runner.start(); - while (runner.isAlive()) - { - try - { - Thread.sleep(50); - } catch (InterruptedException e) + else { + running = true; } - ; + return aborted; } } - private static Jws2Discoverer discoverer; - - public static Jws2Discoverer getDiscoverer() + /** + * 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 (discoverer == null) + /* if (restart()) + { + return; + } + else + { + Thread thr = new Thread(this); + thr.start(); + } + */ + if (isRunning()) { - discoverer = new Jws2Discoverer(); + setAborted(true); } - return discoverer; + FutureTask task = new FutureTask<>(this, this); + new Thread(task).start(); + return task; } - public boolean hasServices() + /** + * @return the invalidServiceUrls + */ + public Vector getInvalidServiceUrls() { - // TODO Auto-generated method stub - return !running && services != null && services.size() > 0; + return invalidServiceUrls; } - public boolean isRunning() + /** + * @return the urlsWithoutServices + */ + public Vector getUrlsWithoutServices() { - return running; + return urlsWithoutServices; } /** - * the jalview .properties entry for JWS2 URLS + * 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 */ - final static String JWS2HOSTURLS = "JWS2HOSTURLS"; + public synchronized void addUrlwithnoservices(String jwsservers) + { + if (urlsWithoutServices == null) + { + urlsWithoutServices = new Vector<>(); + } + + if ((invalidServiceUrls == null + || !invalidServiceUrls.contains(jwsservers)) + && !urlsWithoutServices.contains(jwsservers)) + { + urlsWithoutServices.add(jwsservers); + } + } - public static void setServiceUrls(Vector urls) + /** + * add a bad URL to the list + * + * @param jwsservers + */ + public synchronized void addInvalidServiceUrl(String jwsservers) { - if (urls != null) + if (invalidServiceUrls == null) { - StringBuffer urlbuffer = new StringBuffer(); - String sep = ""; - for (String url : urls) - { - urlbuffer.append(sep); - urlbuffer.append(url); - sep = ","; - } - Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString()); + invalidServiceUrls = new Vector<>(); } - else + if (!invalidServiceUrls.contains(jwsservers)) { - Cache.removeProperty(JWS2HOSTURLS); + invalidServiceUrls.add(jwsservers); } } - public static Vector getServiceUrls() + /** + * + * @return a human readable report of any problems with the service URLs used + * for discovery + */ + @Override + public String getErrorMessages() { - String surls = Cache.getDefault(JWS2HOSTURLS, - "http://www.compbio.dundee.ac.uk/jabaws"); - Vector urls = new Vector(); - try + if (!isRunning() && !isAborted()) { - StringTokenizer st = new StringTokenizer(surls, ","); - while (st.hasMoreElements()) + StringBuffer ermsg = new StringBuffer(); + boolean list = false; + if (getInvalidServiceUrls() != null + && getInvalidServiceUrls().size() > 0) { - String url = null; - try + ermsg.append(MessageManager.getString("warn.urls_not_contacted") + + ": \n"); + for (String svcurl : getInvalidServiceUrls()) { - java.net.URL u = new java.net.URL(url = st.nextToken()); - if (!urls.contains(url)) + if (list) { - urls.add(url); + ermsg.append(", "); } - else + 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) { - jalview.bin.Cache.log.info("Ignoring duplicate url in " - + JWS2HOSTURLS + " list"); + ermsg.append(", "); } - } catch (Exception 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 - + " entry of $(HOME)/.jalview_properties)"); - jalview.bin.Cache.log.debug("Exception was ", ex); + list = true; + ermsg.append(svcurl); } + ermsg.append("\n"); } - } catch (Exception ex) + if (ermsg.length() > 1) + { + return ermsg.toString(); + } + + } + return null; + } + + @Override + public int getServerStatusFor(String url) + { + if (validServiceUrls != null && validServiceUrls.contains(url)) { - jalview.bin.Cache.log.warn( - "Error parsing comma separated list of urls in " - + JWS2HOSTURLS + " preference.", ex); + return STATUS_OK; } - if (urls.size() >= 0) + if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) { - return urls; + return STATUS_NO_SERVICES; } - return null; + if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) + { + return STATUS_INVALID; + } + return STATUS_UNKNOWN; } - public Vector getServices() + /** + * 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 { - return (services == null) ? new Vector() - : new Vector(services); + if (value != null && value.trim().length() > 0) + { + new URL(value); + preferredUrl = value; + } } - }