/*
* 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.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 compbio.ws.client.Services;
/**
* discoverer for jws2 services. Follows the lightweight service discoverer
* pattern (archetyped by EnfinEnvision2OneWay)
*
* @author JimP
*
*/
public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
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
*
* @param listener
* to be added that consumes new services Hashtable object.
*/
public void addPropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
changeSupport.addPropertyChangeListener(listener);
}
/**
*
*
* @param listener
* to be removed
*/
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
{
changeSupport.removePropertyChangeListener(listener);
}
/**
* @return the aborted
*/
public boolean isAborted()
{
return aborted;
}
/**
* @param aborted
* the aborted to set
*/
public void setAborted(boolean aborted)
{
this.aborted = aborted;
}
@Override
public void run()
{
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
{
return;
}
while (running)
{
try
{
Cache.log.debug(
"Waiting around for old discovery thread to finish.");
// wait around until old discoverer dies
Thread.sleep(100);
} catch (Exception e)
{
}
}
aborted = false;
Cache.log.debug("Old discovery thread has finished.");
}
running = true;
// first set up exclusion list if needed
final Set ignoredServices = new HashSet();
for (String ignored : Cache
.getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
{
ignoredServices.add(ignored);
}
changeSupport.firePropertyChange("services", services,
new Vector());
oldthread = Thread.currentThread();
try
{
Class foo = getClass().getClassLoader()
.loadClass("compbio.ws.client.Jws2Client");
} catch (ClassNotFoundException e)
{
System.err.println(
"Not enabling JABA Webservices : client jar is not available."
+ "\nPlease check that your webstart JNLP file is up to date!");
running = false;
return;
}
// reinitialise records of good and bad service URLs
if (services != null)
{
services.removeAllElements();
}
if (urlsWithoutServices != null)
{
urlsWithoutServices.removeAllElements();
}
if (invalidServiceUrls != null)
{
invalidServiceUrls.removeAllElements();
}
if (validServiceUrls != null)
{
validServiceUrls.removeAllElements();
}
ArrayList svctypes = new ArrayList();
List qrys = new ArrayList();
for (final String jwsserver : getServiceUrls())
{
JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver);
if (svctypes.size() == 0)
{
// TODO: remove this ugly hack to get Canonical JABA service ordering
// for all possible services
for (Services sv : squery.JABAWS2SERVERS)
{
if (!ignoredServices.contains(sv.toString()))
{
svctypes.add(sv.toString());
}
}
}
qrys.add(squery);
new Thread(squery).start();
}
boolean finished = true;
do
{
finished = true;
try
{
Thread.sleep(100);
} catch (Exception e)
{
}
;
for (JabaWsServerQuery squery : qrys)
{
if (squery.isRunning())
{
finished = false;
}
}
if (aborted)
{
Cache.log.debug(
"Aborting " + qrys.size() + " JABAWS discovery threads.");
for (JabaWsServerQuery squery : qrys)
{
squery.setQuit(true);
}
}
} while (!aborted && !finished);
if (!aborted)
{
// resort services according to order found in jabaws service list
// also ensure services for each host are ordered in same way.
if (services != null && services.size() > 0)
{
Jws2Instance[] svcs = new Jws2Instance[services.size()];
int[] spos = new int[services.size()];
int ipos = 0;
List svcUrls = getServiceUrls();
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
spos[ipos++] = 1000 * svcUrls.indexOf(svc.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);
}
/**
* record this service endpoint so we can use it
*
* @param jwsservers
* @param srv
* @param service2
*/
synchronized void addService(String jwsservers, Jws2Instance service)
{
if (services == null)
{
services = new Vector();
}
System.out.println(
"Discovered service: " + jwsservers + " " + service.toString());
// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
// service2);
services.add(service);
// retrieve the presets and parameter set and cache now
ParamDatastoreI pds = service.getParamStore();
if (pds != null)
{
pds.getPresets();
}
service.hasParameters();
if (validServiceUrls == null)
{
validServiceUrls = new Vector();
}
validServiceUrls.add(jwsservers);
}
/**
* 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.
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)
{
if (running || services == null || services.size() == 0)
{
return;
}
/**
* 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(false,
MessageManager.getString("label.open_jabaws_web_page")));
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();
}
});
}
}
}
}
/**
* 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;
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)
{
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(MessageManager
.formatMessage("label.services_at", new String[]
{ 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() : "")))
{
// 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());
}
service.attachWSMenuEntry(atpoint, alignFrame);
}
}
}
public static void main(String[] args)
{
if (args.length > 0)
{
testUrls = new ArrayList();
for (String url : args)
{
testUrls.add(url);
}
;
}
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
{
Thread.sleep(50);
} catch (InterruptedException e)
{
}
;
}
try
{
Thread.sleep(50);
} catch (InterruptedException x)
{
}
}
/**
* Returns the singleton instance of this class.
*
* @return
*/
public static Jws2Discoverer getDiscoverer()
{
if (discoverer == null)
{
discoverer = new Jws2Discoverer();
}
return discoverer;
}
public boolean hasServices()
{
return !running && services != null && services.size() > 0;
}
public boolean isRunning()
{
return running;
}
public void setServiceUrls(List wsUrls)
{
if (wsUrls != null && !wsUrls.isEmpty())
{
StringBuilder urls = new StringBuilder(128);
String sep = "";
for (String url : wsUrls)
{
urls.append(sep);
urls.append(url);
sep = ",";
}
Cache.setProperty(JWS2HOSTURLS, urls.toString());
}
else
{
Cache.removeProperty(JWS2HOSTURLS);
}
}
/**
* Returns web service URLs, in the order in which they should be tried (or an
* empty list).
*
* @return
*/
public List getServiceUrls()
{
if (testUrls != null)
{
// return test urls, if there are any, instead of touching cache
return testUrls;
}
List urls = new ArrayList();
if (this.preferredUrl != null)
{
urls.add(preferredUrl);
}
String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
while (st.hasMoreElements())
{
String url = null;
try
{
url = st.nextToken();
new URL(url);
if (!urls.contains(url))
{
urls.add(url);
}
else
{
Cache.log.warn("Ignoring duplicate url " + url + " in "
+ JWS2HOSTURLS + " list");
}
} catch (MalformedURLException ex)
{
Cache.log.warn("Problem whilst trying to make a URL from '"
+ ((url != null) ? url : "") + "'");
Cache.log.warn(
"This was probably due to a malformed comma separated list"
+ " in the " + JWS2HOSTURLS
+ " entry of $(HOME)/.jalview_properties)");
Cache.log.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
Cache.log.warn("Error parsing comma separated list of urls in "
+ JWS2HOSTURLS + " preference.", ex);
}
return urls;
}
public Vector getServices()
{
return (services == null) ? new Vector()
: new Vector(services);
}
/**
* test the given URL with the JabaWS test code
*
* @param foo
* @return
*/
public static boolean testServiceUrl(URL foo)
{
try
{
compbio.ws.client.WSTester
.main(new String[]
{ "-h=" + foo.toString() });
} catch (Exception e)
{
e.printStackTrace();
return false;
} catch (OutOfMemoryError e)
{
e.printStackTrace();
return false;
} catch (Error e)
{
e.printStackTrace();
return false;
}
return true;
}
public boolean restart()
{
synchronized (this)
{
if (running)
{
aborted = true;
}
else
{
running = true;
}
return aborted;
}
}
/**
* Start a fresh discovery thread and notify the given object when we're
* finished. Any known existing threads will be killed before this one is
* started.
*
* @param changeSupport2
* @return new thread
*/
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;
}
}
}