X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=5319eab2979525105e2281d0772b40466db34363;hb=a2385e4eb979d9b603c4c35453d63ed192fd7bc6;hp=99a17269ede8f82eeb1b0cf05d0478bbc5e5c3a4;hpb=8364d3900ad4271d460ae15a245add45c66c2e89;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 99a1726..5319eab 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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;
@@ -21,14 +24,18 @@ 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.beans.PropertyChangeSupport;
+import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
@@ -37,6 +44,7 @@ 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;
@@ -54,9 +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
*
@@ -81,8 +133,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false, aborted = false;
-
/**
* @return the aborted
*/
@@ -100,10 +150,10 @@ 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 +164,38 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
try
{
- Cache.log
- .debug("Waiting around for old discovery thread to finish.");
+ Cache.log.debug(
+ "Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
} catch (Exception e)
{
}
}
+ aborted = false;
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
- changeSupport.firePropertyChange("services", services, new Vector());
+
+ // first set up exclusion list if needed
+ final Set ignoredServices = new HashSet();
+ for (String ignored : Cache
+ .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+ changeSupport.firePropertyChange("services", services,
+ new Vector());
oldthread = Thread.currentThread();
try
{
- Class foo = getClass().getClassLoader().loadClass(
- "compbio.ws.client.Jws2Client");
+ Class foo = getClass().getClassLoader()
+ .loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
- System.err
- .println("Not enabling JABA Webservices : client jar is not available."
+ System.err.println(
+ "Not enabling JABA Webservices : client jar is not available."
+ "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
@@ -159,16 +220,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
ArrayList svctypes = new ArrayList();
List qrys = new ArrayList();
- for (final String jwsservers : getServiceUrls())
+ for (final String jwsserver : getServiceUrls())
{
- JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+ 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)
{
- svctypes.add(sv.toString());
+ if (!ignoredServices.contains(sv.toString()))
+ {
+ svctypes.add(sv.toString());
+ }
}
}
@@ -188,12 +252,15 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
;
for (JabaWsServerQuery squery : qrys)
{
- finished = finished && !squery.isRunning();
+ if (squery.isRunning())
+ {
+ finished = false;
+ }
}
if (aborted)
{
- Cache.log.debug("Aborting " + qrys.size()
- + " JABAWS discovery threads.");
+ Cache.log.debug(
+ "Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
squery.setQuit(true);
@@ -203,14 +270,14 @@ 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.
+ // 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();
+ List svcUrls = getServiceUrls();
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
@@ -221,13 +288,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
services = new Vector();
for (Jws2Instance svc : svcs)
{
- services.add(svc);
+ if (!ignoredServices.contains(svc.serviceType))
+ {
+ services.add(svc);
+ }
}
}
}
oldthread = null;
running = false;
- changeSupport.firePropertyChange("services", new Vector(), services);
+ changeSupport.firePropertyChange("services", new Vector(),
+ services);
}
/**
@@ -243,14 +314,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
services = new Vector();
}
- System.out.println("Discovered service: " + jwsservers + " "
- + service.toString());
+ 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();
+ ParamDatastoreI pds = service.getParamStore();
if (pds != null)
{
pds.getPresets();
@@ -258,20 +329,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
service.hasParameters();
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
*/
+ @Override
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
// dynamically regenerate service list.
@@ -290,8 +357,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
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.
@@ -361,15 +427,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
Desktop.showUrl(service.getHost());
}
});
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+ hitm.setToolTipText(JvSwingUtils.wrapTooltip(false,
+ MessageManager.getString("label.open_jabaws_web_page")));
service.attachWSMenuEntry(atpoint, alignFrame);
if (alternates.containsKey(service.serviceType))
{
- atpoint.add(hitm = new JMenu("Switch server"));
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Choose a server for running this service"));
+ 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;
@@ -383,27 +450,19 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
setPreferredServiceFor(alignFrame, sv.serviceType,
sv.action, sv);
changeSupport.firePropertyChange("services",
- new Vector(), 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(); } });
- */
}
}
}
@@ -413,16 +472,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* submenus to index by host and service program type
*/
private void addEnumeratedServices(final JMenu jws2al,
- final AlignFrame alignFrame, List enumerableServices)
+ final AlignFrame alignFrame,
+ List enumerableServices)
{
- boolean byhost = Cache.getDefault("WSMENU_BYHOST", false), bytype = Cache
- .getDefault("WSMENU_BYTYPE", false);
+ 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>();
@@ -441,8 +501,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
// now add hosts in order of the given array
for (String host : hostlist)
{
- Jws2Instance orderedsvcs[] = hosts.get(host).toArray(
- new Jws2Instance[1]);
+ Jws2Instance orderedsvcs[] = hosts.get(host)
+ .toArray(new Jws2Instance[1]);
String sortbytype[] = new String[orderedsvcs.length];
for (int i = 0; i < sortbytype.length; i++)
{
@@ -458,7 +518,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host);
if (atpoint.getToolTipText() == null)
{
- atpoint.setToolTipText("Services at " + host);
+ atpoint.setToolTipText(MessageManager
+ .formatMessage("label.services_at", new String[]
+ { host }));
}
}
if (bytype)
@@ -469,9 +531,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
atpoint.setToolTipText(service.getActionText());
}
}
- if (!byhost
- && !hostLabels.contains(host + service.serviceType
- + service.getActionText()))
+ if (!byhost && !hostLabels.contains(
+ host + service.serviceType + service.getActionText()))
// !hostLabels.contains(host + (bytype ?
// service.serviceType+service.getActionText() : "")))
{
@@ -502,12 +563,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
Desktop.showUrl(service.getHost());
}
});
- hitm.setToolTipText(JvSwingUtils
- .wrapTooltip("Opens the JABAWS server's homepage in web browser"));
+ 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.add(
+ host + service.serviceType + service.getActionText());
}
service.attachWSMenuEntry(atpoint, alignFrame);
@@ -519,17 +581,18 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
if (args.length > 0)
{
- testUrls = new Vector();
+ testUrls = new ArrayList();
for (String url : args)
{
testUrls.add(url);
}
;
}
- Thread runner = getDiscoverer().startDiscoverer(
- new PropertyChangeListener()
+ Thread runner = getDiscoverer()
+ .startDiscoverer(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (getDiscoverer().services != null)
@@ -540,9 +603,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
for (Jws2Instance instance : getDiscoverer().services)
{
System.out.println("Service " + i++ + " "
- + instance.getClass() + "@"
- + instance.getHost() + ": "
- + instance.getActionText());
+ + instance.getClass() + "@" + instance.getHost()
+ + ": " + instance.getActionText());
}
}
@@ -566,8 +628,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
}
- private static Jws2Discoverer discoverer;
-
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
public static Jws2Discoverer getDiscoverer()
{
if (discoverer == null)
@@ -579,7 +644,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
@@ -588,24 +652,19 @@ 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
{
@@ -613,18 +672,27 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
}
- private static Vector testUrls = null;
-
- public static Vector getServiceUrls()
+ /**
+ * Returns web service URLs, in the order in which they should be tried (or an
+ * empty list).
+ *
+ * @return
+ */
+ public List getServiceUrls()
{
if (testUrls != null)
{
// 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, ",");
@@ -633,40 +701,34 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
String url = null;
try
{
- java.net.URL u = new java.net.URL(url = st.nextToken());
+ url = st.nextToken();
+ new URL(url);
if (!urls.contains(url))
{
urls.add(url);
}
else
{
- jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ Cache.log.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
- } catch (Exception ex)
+ } catch (MalformedURLException ex)
{
- jalview.bin.Cache.log
- .warn("Problem whilst trying to make a URL from '"
- + ((url != null) ? url : "") + "'");
- jalview.bin.Cache.log
- .warn("This was probably due to a malformed comma separated list"
- + " in the "
- + JWS2HOSTURLS
+ Cache.log.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "") + "'");
+ Cache.log.warn(
+ "This was probably due to a malformed comma separated list"
+ + " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ", ex);
+ Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
- "Error parsing comma separated list of urls in "
- + JWS2HOSTURLS + " preference.", ex);
+ Cache.log.warn("Error parsing comma separated list of urls in "
+ + JWS2HOSTURLS + " preference.", ex);
}
- if (urls.size() >= 0)
- {
- return urls;
- }
- return null;
+ return urls;
}
public Vector getServices()
@@ -685,8 +747,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
try
{
- compbio.ws.client.WSTester.main(new String[]
- { "-h=" + foo.toString() });
+ compbio.ws.client.WSTester
+ .main(new String[]
+ { "-h=" + foo.toString() });
} catch (Exception e)
{
e.printStackTrace();
@@ -704,6 +767,22 @@ 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
@@ -714,6 +793,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
*/
public Thread startDiscoverer(PropertyChangeListener changeSupport2)
{
+ /* if (restart())
+ {
+ return;
+ }
+ else
+ {
+ Thread thr = new Thread(this);
+ thr.start();
+ }
+ */
if (isRunning())
{
setAborted(true);
@@ -724,9 +813,6 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return thr;
}
- Vector invalidServiceUrls = null, urlsWithoutServices = null,
- validServiceUrls = null;
-
/**
* @return the invalidServiceUrls
*/
@@ -756,8 +842,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
urlsWithoutServices = new Vector();
}
- if ((invalidServiceUrls == null || !invalidServiceUrls
- .contains(jwsservers))
+ if ((invalidServiceUrls == null
+ || !invalidServiceUrls.contains(jwsservers))
&& !urlsWithoutServices.contains(jwsservers))
{
urlsWithoutServices.add(jwsservers);
@@ -795,7 +881,8 @@ 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)
@@ -811,7 +898,8 @@ 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)
@@ -839,7 +927,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
return 1;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+ {
return 0;
+ }
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
return -1;
@@ -951,6 +1041,24 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public void setPreferredServiceFor(String serviceType,
String serviceAction, Jws2Instance selectedServer)
{
- setPreferredServiceFor(null, serviceType, serviceAction, 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;
+ }
}
}