/*
* 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.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.AlignFrame;
import jalview.util.MessageManager;
import jalview.ws.ServiceChangeListener;
import jalview.ws.WSDiscovererI;
import jalview.ws.api.ServiceWithParameters;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.ParamDatastoreI;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
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 compbio.ws.client.Services;
/**
* discoverer for jws2 services. Follows the lightweight service discoverer
* pattern (archetyped by EnfinEnvision2OneWay)
*
* @author JimP
*
*/
public class Jws2Discoverer implements WSDiscovererI, Runnable, ApplicationSingletonI
{
/**
* Returns the singleton instance of this class.
*
* @return
*/
public static Jws2Discoverer getInstance()
{
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;
/**
* holds list of services.
*/
protected Vector services;
/**
* Private constructor enforces use of singleton via getDiscoverer()
*/
private Jws2Discoverer()
{
}
@Override
public void addServiceChangeListener(ServiceChangeListener listener)
{
serviceListeners.add(listener);
}
@Override
public void removeServiceChangeListener(ServiceChangeListener listener)
{
serviceListeners.remove(listener);
}
private void notifyServiceListeners(List extends ServiceWithParameters> services)
{
if (services == null) services = this.services;
for (var listener : serviceListeners) {
listener.servicesChanged(this, services);
}
}
/**
* @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);
}
notifyServiceListeners(Collections.emptyList());
oldthread = Thread.currentThread();
try
{
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.getHostURL()) + 1
+ svctypes.indexOf(svc.getName());
}
jalview.util.QuickSort.sort(spos, svcs);
services = new Vector<>();
for (Jws2Instance svc : svcs)
{
if (!ignoredServices.contains(svc.getName()))
{
services.add(svc);
}
}
}
}
oldthread = null;
running = false;
notifyServiceListeners(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);
}
/**
*
* @param args
* @j2sIgnore
*/
public static void main(String[] args)
{
Jws2Discoverer instance = getInstance();
if (args.length > 0)
{
instance.testUrls = new ArrayList<>();
for (String url : args)
{
instance.testUrls.add(url);
}
}
var discoverer = getInstance();
discoverer.addServiceChangeListener((_discoverer, _services) -> {
if (discoverer.services != null)
{
System.out.println("Changesupport: There are now "
+ discoverer.services.size() + " services");
int i = 1;
for (ServiceWithParameters s_instance : discoverer.services)
{
System.out.println(
"Service " + i++ + " " + s_instance.getClass()
+ "@" + s_instance.getHostURL() + ": "
+ s_instance.getActionText());
}
}
});
try
{
discoverer.startDiscoverer().get();
} catch (InterruptedException | ExecutionException e)
{
}
try
{
Thread.sleep(50);
} catch (InterruptedException x)
{
}
}
@Override
public boolean hasServices()
{
return !running && services != null && services.size() > 0;
}
@Override
public boolean isRunning()
{
return running;
}
@Override
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
*/
@Override
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;
}
@Override
public Vector getServices()
{
return (services == null) ? new Vector<>() : new Vector<>(services);
}
/**
* test the given URL with the JabaWS test code
*
* @param foo
* @return
*/
@Override
public 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
*/
@Override
public CompletableFuture startDiscoverer()
{
/* if (restart())
{
return;
}
else
{
Thread thr = new Thread(this);
thr.start();
}
*/
if (isRunning())
{
setAborted(true);
}
CompletableFuture task = CompletableFuture
.supplyAsync(() -> {
run();
return Jws2Discoverer.this;
});
return task;
}
/**
* @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
*/
@Override
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;
}
@Override
public int getServerStatusFor(String url)
{
if (validServiceUrls != null && validServiceUrls.contains(url))
{
return STATUS_OK;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
{
return STATUS_NO_SERVICES;
}
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
return STATUS_INVALID;
}
return STATUS_UNKNOWN;
}
/**
* 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;
}
}
}