X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=56a4b775b9fc78a03b39e2148caff9f5a9fabd76;hb=c41398473f1493a06f28da53be50630a0f6e6f6d;hp=c0addfe15af47c67839584f56e5d4558c7574cbe;hpb=ead7c435d61624a226f459a0fca90fc24e94caa9;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index c0addfe..56a4b77 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,47 +1,56 @@
/*
- * 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.bin.Console;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvSwingUtils;
-import jalview.ws.WSMenuEntryProviderI;
+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.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.HashMap;
+import java.util.Collections;
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 java.util.concurrent.CompletableFuture;
+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 compbio.ws.client.Services;
@@ -52,36 +61,80 @@ import compbio.ws.client.Services;
* @author JimP
*
*/
-public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
+public class Jws2Discoverer implements WSDiscovererI, Runnable, ApplicationSingletonI
{
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
- this);
-
/**
- * change listeners are notified of "services" property changes
+ * Returns the singleton instance of this class.
*
- * @param listener
- * to be added that consumes new services Hashtable object.
+ * @return
*/
- public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ public static Jws2Discoverer getInstance()
{
- changeSupport.addPropertyChangeListener(listener);
+ return (Jws2Discoverer) ApplicationSingletonProvider
+ .getInstance(Jws2Discoverer.class);
}
+ 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";
+
+ /*
+ * Override for testing only
+ */
+ private 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;
/**
- *
- *
- * @param listener
- * to be removed
+ * holds list of services.
+ */
+ protected Vector services;
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
*/
- public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ private Jws2Discoverer()
{
- changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false, aborted = false;
+ @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
@@ -100,10 +153,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
this.aborted = aborted;
}
- Thread oldthread = null;
-
+ @Override
public void run()
{
+
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
@@ -114,27 +167,36 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
try
{
- Cache.log
- .debug("Waiting around for old discovery thread to finish.");
+ Console.debug(
+ "Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
} catch (Exception e)
{
}
}
- Cache.log.debug("Old discovery thread has finished.");
+ aborted = false;
+ Console.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);
+ }
+
+ 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 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;
@@ -156,18 +218,22 @@ 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());
+ }
}
}
@@ -177,22 +243,24 @@ 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.");
+ Console.debug(
+ "Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
squery.setQuit(true);
@@ -202,29 +270,34 @@ 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);
+ notifyServiceListeners(services);
}
/**
@@ -238,342 +311,102 @@ 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
+ *
+ * @param args
+ * @j2sIgnore
*/
- public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
- {
- // dynamically regenerate service list.
- populateWSMenuEntry(wsmenu, alignFrame, null);
- }
- private boolean isRecalculable(String action) {
- return (action!=null && action.equalsIgnoreCase("conservation"));
- }
- private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+ public static void main(String[] args)
{
- if (running || services == null || services.size() == 0)
+ Jws2Discoverer instance = getInstance();
+ if (args.length > 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;
- List enumerableServices=new ArrayList();
- //jws2al.removeAll();
- Map preferredHosts=new HashMap();
- Map> alternates = new HashMap>();
- for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
- {
- if (!isRecalculable(service.action)) {
- // add 'one shot' services to be displayed using the classic menu structure
- enumerableServices.add(service);
- } else {
- if (!preferredHosts.containsKey(service.serviceType))
- {
- 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)
- {
- if (ph==null)
- {
- ph=new ArrayList();
- }
- ph.add(service);
- alternates.put(service.serviceType, ph);
- }
- }
-
- }
-
- // create GUI element for classic services
- addEnumeratedServices(jws2al, alignFrame, enumerableServices);
- // and the instantaneous services
- for (final Jws2Instance service : preferredHosts.values())
- {
- atpoint = JvSwingUtils.findOrCreateMenu(jws2al,service.action);
- JMenuItem hitm;
- if (atpoint.getItemCount()>1) {
- // previous service of this type already present
- atpoint.addSeparator();
- }
- atpoint.add(hitm = new JMenuItem(service.getHost()));
- 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"));
-
- service.attachWSMenuEntry(atpoint, alignFrame);
- if (alternates.containsKey(service.serviceType))
+ instance.testUrls = new ArrayList<>();
+ for (String url : args)
{
- atpoint.add(hitm=new JMenu("Switch server"));
- hitm.setToolTipText(JvSwingUtils.wrapTooltip("Choose a server for running this service"));
- for (final Jws2Instance sv:alternates.get(service.serviceType))
- {
- 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() {
- public void run() {
- setPreferredServiceFor(alignFrame, sv.serviceType, sv.action, sv);
- changeSupport.firePropertyChange("services", new Vector(), services);
- };
- }).start();
-
- }
- });
- }
- /*hitm.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent arg0)
- {
- new Thread(new Runnable() {
- @Override
- public void run()
- {
- new SetPreferredServer(alignFrame, service.serviceType, service.action);
- }
- }).start();
- }
- });*/
+ instance.testUrls.add(url);
}
}
- }
- /**
- * add services using the Java 2.5/2.6/2.7 system which optionally creates submenus to index by host and service program type
- */
- private void addEnumeratedServices(final JMenu jws2al, final AlignFrame alignFrame, List enumerableServices)
- {
- 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();
- List hostLabels = new ArrayList();
- Hashtable lasthostFor = new Hashtable();
- Hashtable> hosts = new Hashtable>();
- ArrayList hostlist=new ArrayList();
- for (Jws2Instance service : enumerableServices)
- {
- ArrayList hostservices = hosts.get(service.getHost());
- if (hostservices == null)
+ var discoverer = getInstance();
+ discoverer.addServiceChangeListener((_discoverer, _services) -> {
+ if (discoverer.services != 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() : "")))
+ System.out.println("Changesupport: There are now "
+ + discoverer.services.size() + " services");
+ int i = 1;
+ for (ServiceWithParameters s_instance : discoverer.services)
{
- // 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("Opens the JABAWS server's homepage in web browser"));
- lasthostFor.put(service.action,host);
- }
- hostLabels.add(host + service.serviceType
- + service.getActionText());
+ System.out.println(
+ "Service " + i++ + " " + s_instance.getClass()
+ + "@" + s_instance.getHostURL() + ": "
+ + s_instance.getActionText());
}
-
- service.attachWSMenuEntry(atpoint, alignFrame);
+
}
- }
- }
- public static void main(String[] args)
- {
- if (args.length>0)
+ });
+ try
{
- testUrls = new Vector();
- for (String url:args)
- {
- testUrls.add(url);
- };
- }
- Thread runner = getDiscoverer().startDiscoverer(
- new PropertyChangeListener()
- {
-
- 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())
+ discoverer.startDiscoverer().get();
+ } catch (InterruptedException | ExecutionException e)
{
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
- }
- ;
}
- try {
+ try
+ {
Thread.sleep(50);
- } catch (InterruptedException x) {}
- }
-
- private static Jws2Discoverer discoverer;
-
- public static Jws2Discoverer getDiscoverer()
- {
- if (discoverer == null)
+ } catch (InterruptedException x)
{
- discoverer = new Jws2Discoverer();
}
- return discoverer;
}
+
+ @Override
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
+ @Override
public boolean isRunning()
{
return running;
}
- /**
- * the jalview .properties entry for JWS2 URLS
- */
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
- public static void setServiceUrls(Vector urls)
+ @Override
+ public void setServiceUrls(List wsUrls)
{
- if (urls != null)
+ if (wsUrls != null && !wsUrls.isEmpty())
{
- StringBuffer urlbuffer = new StringBuffer();
+ StringBuilder urls = new StringBuilder(128);
String sep = "";
- for (String url : urls)
+ for (String url : wsUrls)
{
- urlbuffer.append(sep);
- urlbuffer.append(url);
+ urls.append(sep);
+ urls.append(url);
sep = ",";
}
- Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ Cache.setProperty(JWS2HOSTURLS, urls.toString());
}
else
{
@@ -581,17 +414,28 @@ 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
+ */
+ @Override
+ public List getServiceUrls()
{
- if (testUrls!=null)
+ if (testUrls != null)
{
// return test urls, if there are any, instead of touching cache
return testUrls;
}
- String surls = Cache.getDefault(JWS2HOSTURLS,
- "http://www.compbio.dundee.ac.uk/jabaws");
- Vector urls = new Vector();
+ List urls = new ArrayList<>();
+
+ if (this.preferredUrl != null)
+ {
+ urls.add(preferredUrl);
+ }
+
+ String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
@@ -600,46 +444,40 @@ 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 "
+ Console.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
+ Console.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "") + "'");
+ Console.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);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
- "Error parsing comma separated list of urls in "
- + JWS2HOSTURLS + " preference.", ex);
- }
- if (urls.size() >= 0)
- {
- return urls;
+ Console.warn("Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
}
- return null;
+ return urls;
}
- public Vector getServices()
+ @Override
+ public Vector getServices()
{
- return (services == null) ? new Vector()
- : new Vector(services);
+ return (services == null) ? new Vector<>() : new Vector<>(services);
}
/**
@@ -648,12 +486,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* @param foo
* @return
*/
- public static boolean testServiceUrl(URL foo)
+ @Override
+ public boolean testServiceUrl(URL foo)
{
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();
@@ -671,6 +511,22 @@ 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
@@ -679,20 +535,31 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* @param changeSupport2
* @return new thread
*/
- public Thread startDiscoverer(PropertyChangeListener changeSupport2)
+ @Override
+ public CompletableFuture startDiscoverer()
{
+ /* 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;
+ CompletableFuture task = CompletableFuture
+ .supplyAsync(() -> {
+ run();
+ return Jws2Discoverer.this;
+ });
+ return task;
}
- Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
-
/**
* @return the invalidServiceUrls
*/
@@ -719,11 +586,11 @@ 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);
@@ -739,7 +606,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
if (invalidServiceUrls == null)
{
- invalidServiceUrls = new Vector();
+ invalidServiceUrls = new Vector<>();
}
if (!invalidServiceUrls.contains(jwsservers))
{
@@ -752,6 +619,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* @return a human readable report of any problems with the service URLs used
* for discovery
*/
+ @Override
public String getErrorMessages()
{
if (!isRunning() && !isAborted())
@@ -761,7 +629,8 @@ 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)
@@ -777,7 +646,8 @@ 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)
@@ -798,114 +668,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return null;
}
+ @Override
public int getServerStatusFor(String url)
{
- if (validServiceUrls!=null && validServiceUrls.contains(url))
+ if (validServiceUrls != null && validServiceUrls.contains(url))
{
- return 1;
+ return STATUS_OK;
}
- if (urlsWithoutServices!=null && urlsWithoutServices.contains(url))
- return 0;
- if (invalidServiceUrls!=null && invalidServiceUrls.contains(url))
+ if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
{
- return -1;
+ return STATUS_NO_SERVICES;
}
- 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;
- for (Jws2Instance svc:services)
+ if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
- 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 STATUS_INVALID;
}
- return match;
+ return STATUS_UNKNOWN;
}
-
- 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.
+ * 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 Jws2Instance getPreferredServiceFor(AlignFrame af,
- String serviceType)
+ public void setPreferredUrl(String value) throws MalformedURLException
{
- String serviceurl = null;
- synchronized (preferredServiceMap)
+ if (value != null && value.trim().length() > 0)
{
- 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);
- }
-
+ new URL(value);
+ preferredUrl = value;
}
- 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);
}
}