X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=2fb8974a858ed299a84118ee0a98283b9de38449;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=1f3eee9d422c119224d0f4faf48e9521963b609b;hpb=dc300f5fce52bddc74ebe18864c12bfdb4beef64;p=jalview.git diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 1f3eee9..2fb8974 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -1,37 +1,56 @@ +/* + * 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.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.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.Arrays; +import java.util.HashMap; 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; import javax.swing.JMenu; import javax.swing.JMenuItem; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; - -import org.apache.log4j.Level; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentView; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.ws.WSMenuEntryProviderI; -import jalview.ws.params.ParamDatastoreI; -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; /** @@ -43,9 +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 * @@ -70,81 +133,171 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI changeSupport.removePropertyChangeListener(listener); } - boolean running = false; + /** + * @return the aborted + */ + public boolean isAborted() + { + return aborted; + } - 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.debug( + "Waiting around for old discovery thread to finish."); + // wait around until old discoverer dies + Thread.sleep(100); + } catch (Exception e) + { + } + } + aborted = false; + Cache.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 { - 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 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.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.getHost()) + 1 + + svctypes.indexOf(svc.serviceType); + } + jalview.util.QuickSort.sort(spos, svcs); + services = new Vector<>(); + for (Jws2Instance svc : svcs) + { + if (!ignoredServices.contains(svc.serviceType)) + { + services.add(svc); + } + } } } oldthread = null; running = false; - changeSupport.firePropertyChange("services", new Vector(), services); + changeSupport.firePropertyChange("services", new Vector(), + services); } /** @@ -154,298 +307,312 @@ 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 + " " - + srv.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); - service.getParamStore(); + // 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); } - public class Jws2Instance + /** + * attach all available web services to the appropriate submenu in the given + * JMenu + */ + @Override + public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) { - public String hosturl; - - public String serviceType; + // dynamically regenerate service list. + populateWSMenuEntry(wsmenu, alignFrame, null); + } - public MsaWS service; + private boolean isRecalculable(String action) + { + return (action != null && action.equalsIgnoreCase("conservation")); + } - public Jws2Instance(String hosturl, String serviceType, MsaWS service) + private void populateWSMenuEntry(JMenu jws2al, + final AlignFrame alignFrame, String typeFilter) + { + if (running || services == null || services.size() == 0) { - super(); - this.hosturl = hosturl; - this.serviceType = serviceType; - this.service = service; + return; } - PresetManager presets = null; - - public JabaParamStore paramStore = null; - /** - * 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. + * eventually, JWS2 services will appear under the same align/etc submenus. + * for moment we keep them separate. */ - public PresetManager getPresets() + JMenu atpoint; + List enumerableServices = new ArrayList<>(); + // jws2al.removeAll(); + Map preferredHosts = new HashMap<>(); + Map> alternates = new HashMap<>(); + for (Jws2Instance service : services.toArray(new Jws2Instance[0])) { - if (presets == null) + if (!isRecalculable(service.action)) { - try + // add 'one shot' services to be displayed using the classic menu + // structure + enumerableServices.add(service); + } + else + { + if (!preferredHosts.containsKey(service.serviceType)) { - presets = service.getPresets(); - } catch (Exception ex) + Jws2Instance preferredInstance = getPreferredServiceFor( + alignFrame, service.serviceType); + if (preferredInstance != null) + { + preferredHosts.put(service.serviceType, preferredInstance); + } + else + { + preferredHosts.put(service.serviceType, service); + } + } + List ph = alternates.get(service.serviceType); + if (preferredHosts.get(service.serviceType) != service) { - System.err - .println("Exception when retrieving presets for service " - + serviceType + " at " + hosturl); + if (ph == null) + { + ph = new ArrayList<>(); + } + ph.add(service); + alternates.put(service.serviceType, ph); } } - return presets; - } - - public String getHost() - { - 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; - */ - } - /** - * @return short description of what the service will do - */ - public String getActionText() - { - return "Align with " + serviceType; - } - - /** - * non-thread safe - blocks whilst accessing service to get complete set of - * available options and parameters - * - * @return - */ - public RunnerConfig getRunnerConfig() - { - return service.getRunnerOptions(); } - @Override - protected void finalize() throws Throwable + // create GUI element for classic services + addEnumeratedServices(jws2al, alignFrame, enumerableServices); + // and the instantaneous services + for (final Jws2Instance service : preferredHosts.values()) { - if (service != null) + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); + JMenuItem hitm; + if (atpoint.getItemCount() > 1) { - try - { - Closeable svc = (Closeable) service; - service = null; - svc.close(); - } catch (Exception e) - { - } - ; + // previous service of this type already present + atpoint.addSeparator(); } - super.finalize(); - } - - public ParamDatastoreI getParamStore() - { - if (paramStore == null) + atpoint.add(hitm = new JMenuItem(service.getHost())); + hitm.setForeground(Color.blue); + hitm.addActionListener(new ActionListener() { - try - { - paramStore = new JabaParamStore(this, - (Desktop.instance != null ? Desktop - .getUserParameterStore() : null)); - } catch (Exception ex) + + @Override + public void actionPerformed(ActionEvent e) { + Desktop.showUrl(service.getHost()); } + }); + hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, + MessageManager.getString("label.open_jabaws_web_page"))); - } - return paramStore; - } - - public String getUri() - { - // this is only valid for Jaba 1.0 - this formula might have to change! - return hosturl+(hosturl.lastIndexOf("/")==(hosturl.length()-1) ? "/" : "") +serviceType; - } - private boolean hasParams=false,lookedForParams=false; - public boolean hasParameters() - { - if (!lookedForParams) - { - lookedForParams=true; - try - { - hasParams = (getRunnerConfig().getArguments().size() > 0); - } catch (Exception e) + service.attachWSMenuEntry(atpoint, alignFrame); + if (alternates.containsKey(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())); + itm.setForeground(Color.blue); + itm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent arg0) + { + new Thread(new Runnable() + { + @Override + public void run() + { + setPreferredServiceFor(alignFrame, sv.serviceType, + sv.action, sv); + changeSupport.firePropertyChange("services", + new Vector(), services); + } + }).start(); + + } + }); + } } - } - return hasParams; } - }; - - /** - * holds list of services. - */ - protected Vector services; + } /** - * find or add a submenu with the given title in the given menu - * - * @param menu - * @param submenu - * @return the new or existing submenu + * 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 JMenu findOrCreateMenu(JMenu menu, String submenu) + private void addEnumeratedServices(final JMenu jws2al, + final AlignFrame alignFrame, + List enumerableServices) { - JMenu submenuinstance = null; - for (int i = 0, iSize = menu.getMenuComponentCount(); i < iSize; i++) + 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; + + List hostLabels = new ArrayList<>(); + Hashtable lasthostFor = new Hashtable<>(); + Hashtable> hosts = new Hashtable<>(); + ArrayList hostlist = new ArrayList<>(); + for (Jws2Instance service : enumerableServices) { - if (menu.getMenuComponent(i) instanceof JMenu - && ((JMenu) menu.getMenuComponent(i)).getText().equals( - submenu)) + ArrayList hostservices = hosts.get(service.getHost()); + if (hostservices == null) { - submenuinstance = (JMenu) menu.getMenuComponent(i); + hosts.put(service.getHost(), + hostservices = new ArrayList<>()); + hostlist.add(service.getHost()); } + hostservices.add(service); } - if (submenuinstance == null) - { - submenuinstance = new JMenu(submenu); - menu.add(submenuinstance); - } - return submenuinstance; - - } - - public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame) - { - // dynamically regenerate service list. - final JMenu jws2al = new JMenu("JABAWS Alignment"); - jws2al.addMenuListener(new MenuListener() + // now add hosts in order of the given array + for (String host : hostlist) { - // TODO: future: add menu listener to parent menu - so submenus are - // populated *before* they are selected. - @Override - public void menuSelected(MenuEvent e) + Jws2Instance orderedsvcs[] = hosts.get(host) + .toArray(new Jws2Instance[1]); + String sortbytype[] = new String[orderedsvcs.length]; + for (int i = 0; i < sortbytype.length; i++) { - populateWSMenuEntry(jws2al, alignFrame); + sortbytype[i] = orderedsvcs[i].serviceType; } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - }); - wsmenu.add(jws2al); - - } - - private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame) - { - if (running || services == null || services.size() == 0) - { - 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; - MsaWSClient msacl = new MsaWSClient(); - Vector hostLabels = new Vector(); - jws2al.removeAll(); - String lasthost=null; - for (final Jws2Instance service : services) - { - atpoint = jws2al; - String host = service.getHost(); - String type = service.serviceType; - if (byhost) + jalview.util.QuickSort.sort(sortbytype, orderedsvcs); + for (final Jws2Instance service : orderedsvcs) { - atpoint = findOrCreateMenu(atpoint, host); - if (atpoint.getToolTipText() == null) + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); + String type = service.serviceType; + if (byhost) { - atpoint.setToolTipText("Services at " + host); + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(MessageManager + .formatMessage("label.services_at", new String[] + { host })); + } } - } - if (bytype) - { - atpoint = findOrCreateMenu(atpoint, type); - if (atpoint.getToolTipText() == null) + if (bytype) { - atpoint.setToolTipText(service.getActionText()); + atpoint = JvSwingUtils.findOrCreateMenu(atpoint, type); + if (atpoint.getToolTipText() == null) + { + atpoint.setToolTipText(service.getActionText()); + } } - } - if (!byhost && !hostLabels.contains(host + 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 (lasthost==null || !lasthost.equals(host)) + if (!byhost && !hostLabels.contains( + host + service.serviceType + service.getActionText())) + // !hostLabels.contains(host + (bytype ? + // service.serviceType+service.getActionText() : ""))) { - atpoint.add(hitm = new JMenuItem(host)); - hitm.setForeground(Color.blue); + // add a marker indicating where this service is hosted + // relies on services from the same host being listed in a + // contiguous + // group + JMenuItem hitm; + if (hostLabels.contains(host)) + { + atpoint.addSeparator(); + } + else + { + hostLabels.add(host); + } + 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(true, MessageManager + .getString("label.open_jabaws_web_page"))); + lasthostFor.put(service.action, host); + } + hostLabels.add( + host + service.serviceType + service.getActionText()); } - hostLabels.addElement(host + service.serviceType+service.getActionText()); + + service.attachWSMenuEntry(atpoint, alignFrame); } - 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); } }); - */ } } + /** + * + * @param args + * @j2sIgnore + */ public static void main(String[] args) { - Thread runner = new Thread(getDiscoverer()); - getDiscoverer().addPropertyChangeListener(new PropertyChangeListener() + if (args.length > 0) { - - public void propertyChange(PropertyChangeEvent evt) + testUrls = new ArrayList<>(); + for (String url : args) { - System.out.println("Changesupport: There are now " - + getDiscoverer().services.size() + " services"); + testUrls.add(url); } - }); - runner.start(); + } + 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) + { + System.out.println("Service " + i++ + " " + + instance.getClass() + "@" + instance.getHost() + + ": " + instance.getActionText()); + } + + } + } + }); while (runner.isAlive()) { try @@ -454,12 +621,20 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } catch (InterruptedException e) { } - ; + } + try + { + Thread.sleep(50); + } catch (InterruptedException x) + { } } - private static Jws2Discoverer discoverer; - + /** + * Returns the singleton instance of this class. + * + * @return + */ public static Jws2Discoverer getDiscoverer() { if (discoverer == null) @@ -471,7 +646,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public boolean hasServices() { - // TODO Auto-generated method stub return !running && services != null && services.size() > 0; } @@ -480,24 +654,19 @@ 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 { @@ -505,11 +674,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } - 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() { - String surls = Cache.getDefault(JWS2HOSTURLS, - "http://www.compbio.dundee.ac.uk/jabaws"); - Vector urls = new Vector(); + 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, ","); @@ -518,46 +703,40 @@ 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.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.warn("Problem whilst trying to make a URL from '" + + ((url != null) ? url : "") + "'"); + Cache.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.debug("Exception was ", ex); } } } catch (Exception ex) { - jalview.bin.Cache.log.warn( - "Error parsing comma separated list of urls in " - + JWS2HOSTURLS + " preference.", ex); + Cache.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() { - return (services == null) ? new Vector() - : new Vector(services); + return (services == null) ? new Vector<>() + : new Vector<>(services); } /** @@ -570,19 +749,318 @@ 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(); 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 + */ + public Thread startDiscoverer(PropertyChangeListener changeSupport2) + { + /* if (restart()) + { + return; + } + else + { + Thread thr = new Thread(this); + thr.start(); + } + */ + if (isRunning()) + { + setAborted(true); + } + addPropertyChangeListener(changeSupport2); + Thread thr = new Thread(this); + thr.start(); + return thr; + } + + /** + * @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 + */ + 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; + } + + public int getServerStatusFor(String url) + { + if (validServiceUrls != null && validServiceUrls.contains(url)) + { + return 1; + } + if (urlsWithoutServices != null && urlsWithoutServices.contains(url)) + { + return 0; + } + if (invalidServiceUrls != null && invalidServiceUrls.contains(url)) + { + return -1; + } + return -2; + } + + /** + * 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. + */ + public Jws2Instance getPreferredServiceFor(String[] serviceURLs) + { + HashSet urls = new HashSet<>(); + urls.addAll(Arrays.asList(serviceURLs)); + Jws2Instance match = null; + if (services != null) + { + for (Jws2Instance svc : services) + { + 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; + } + } + } + } + return match; + } + + 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. + */ + public Jws2Instance getPreferredServiceFor(AlignFrame af, + String serviceType) + { + String serviceurl = null; + synchronized (preferredServiceMap) + { + String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); + Map prefmap = preferredServiceMap.get(afid); + if (afid.length() > 0 && prefmap == null) + { + // recover global setting, if any + prefmap = preferredServiceMap.get(""); + } + if (prefmap != null) + { + serviceurl = prefmap.get(serviceType); + } + + } + Jws2Instance response = null; + for (Jws2Instance svc : services) + { + if (svc.serviceType.equals(serviceType)) + { + if (serviceurl == null || serviceurl.equals(svc.getHost())) + { + response = svc; + break; + } + } + } + return response; + } + + public void setPreferredServiceFor(AlignFrame af, String serviceType, + String serviceAction, Jws2Instance selectedServer) + { + String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); + if (preferredServiceMap == null) + { + preferredServiceMap = new HashMap<>(); + } + Map prefmap = preferredServiceMap.get(afid); + if (prefmap == null) + { + prefmap = new HashMap<>(); + preferredServiceMap.put(afid, prefmap); + } + prefmap.put(serviceType, selectedServer.getHost()); + prefmap.put(serviceAction, selectedServer.getHost()); + } + + public void setPreferredServiceFor(String serviceType, + String serviceAction, Jws2Instance selectedServer) + { + 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; + } + } }