/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import jalview.bin.Cache;
+import jalview.bin.Console;
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.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.Hashtable;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
*/
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<String> testUrls = null;
+
+ // preferred url has precedence over others
+ private String preferredUrl;
+
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
+ private Vector<String> invalidServiceUrls = null;
+
+ private Vector<String> urlsWithoutServices = null;
+
+ private Vector<String> validServiceUrls = null;
+
+ private volatile boolean running = false;
+
+ private volatile boolean aborted = false;
+
+ private Thread oldthread = null;
+
+ /**
+ * holds list of services.
+ */
+ protected Vector<Jws2Instance> services;
+
+ /**
+ * Private constructor enforces use of singleton via getDiscoverer()
+ */
+ private Jws2Discoverer()
+ {
+ }
+
/**
* change listeners are notified of "services" property changes
*
changeSupport.removePropertyChangeListener(listener);
}
- boolean running = false, aborted = false;
-
/**
* @return the aborted
*/
this.aborted = aborted;
}
- Thread oldthread = null;
-
+ @Override
public void run()
{
+
if (running && oldthread != null && oldthread.isAlive())
{
if (!aborted)
{
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<String> ignoredServices = new HashSet<>();
+ for (String ignored : Cache
+ .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|"))
+ {
+ ignoredServices.add(ignored);
+ }
+
+ changeSupport.firePropertyChange("services", services,
+ new Vector<Jws2Instance>());
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;
{
validServiceUrls.removeAllElements();
}
- ArrayList<String> svctypes = new ArrayList<String>();
+ ArrayList<String> svctypes = new ArrayList<>();
- List<JabaWsServerQuery> qrys = new ArrayList<JabaWsServerQuery>();
- for (final String jwsservers : getServiceUrls())
+ List<JabaWsServerQuery> qrys = new ArrayList<>();
+ 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());
+ }
}
}
qrys.add(squery);
- new Thread(squery).start();
+ new Thread(squery, "JabaQuery").start();
}
boolean finished = true;
do
} catch (Exception e)
{
}
- ;
for (JabaWsServerQuery squery : qrys)
{
- if (squery.isRunning()){
- finished=false;
+ 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);
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<String> svcUrls = getServiceUrls();
for (Jws2Instance svc : services)
{
svcs[ipos] = svc;
+ svctypes.indexOf(svc.serviceType);
}
jalview.util.QuickSort.sort(spos, svcs);
- services = new Vector<Jws2Instance>();
+ 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<Jws2Instance>(),
+ services);
}
/**
{
if (services == null)
{
- services = new Vector<Jws2Instance>();
+ 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);
service.hasParameters();
if (validServiceUrls == null)
{
- validServiceUrls = new Vector();
+ validServiceUrls = new Vector<>();
}
validServiceUrls.add(jwsservers);
}
/**
- * holds list of services.
- */
- protected Vector<Jws2Instance> 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.
{
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<Jws2Instance> enumerableServices = new ArrayList<Jws2Instance>();
+ List<Jws2Instance> enumerableServices = new ArrayList<>();
// jws2al.removeAll();
- Map<String, Jws2Instance> preferredHosts = new HashMap<String, Jws2Instance>();
- Map<String, List<Jws2Instance>> alternates = new HashMap<String, List<Jws2Instance>>();
+ Map<String, Jws2Instance> preferredHosts = new HashMap<>();
+ Map<String, List<Jws2Instance>> alternates = new HashMap<>();
for (Jws2Instance service : services.toArray(new Jws2Instance[0]))
{
if (!isRecalculable(service.action))
{
if (ph == null)
{
- ph = new ArrayList<Jws2Instance>();
+ ph = new ArrayList<>();
}
ph.add(service);
alternates.put(service.serviceType, ph);
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;
{
new Thread(new Runnable()
{
+ @Override
public void run()
{
setPreferredServiceFor(alignFrame, sv.serviceType,
sv.action, sv);
changeSupport.firePropertyChange("services",
- new Vector(), services);
+ new Vector<Jws2Instance>(), services);
};
- }).start();
-
+ }, "LoadPreferredService").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(); } });
- */
}
}
}
* submenus to index by host and service program type
*/
private void addEnumeratedServices(final JMenu jws2al,
- final AlignFrame alignFrame, List<Jws2Instance> enumerableServices)
+ final AlignFrame alignFrame,
+ List<Jws2Instance> 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<String> hostLabels = new ArrayList<String>();
- Hashtable<String, String> lasthostFor = new Hashtable<String, String>();
- Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<String, ArrayList<Jws2Instance>>();
- ArrayList<String> hostlist = new ArrayList<String>();
+
+ List<String> hostLabels = new ArrayList<>();
+ Hashtable<String, String> lasthostFor = new Hashtable<>();
+ Hashtable<String, ArrayList<Jws2Instance>> hosts = new Hashtable<>();
+ ArrayList<String> hostlist = new ArrayList<>();
for (Jws2Instance service : enumerableServices)
{
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
{
- hosts.put(service.getHost(),
- hostservices = new ArrayList<Jws2Instance>());
+ 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]);
+ Jws2Instance orderedsvcs[] = hosts.get(host)
+ .toArray(new Jws2Instance[1]);
String sortbytype[] = new String[orderedsvcs.length];
for (int i = 0; i < sortbytype.length; i++)
{
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)
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() : "")))
{
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);
}
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
if (args.length > 0)
{
- testUrls = new Vector<String>();
+ 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)
for (Jws2Instance instance : getDiscoverer().services)
{
System.out.println("Service " + i++ + " "
- + instance.getClass() + "@"
- + instance.getHost() + ": "
- + instance.getActionText());
+ + instance.getClass() + "@" + instance.getHost()
+ + ": " + instance.getActionText());
}
}
} catch (InterruptedException e)
{
}
- ;
}
try
{
}
}
- private static Jws2Discoverer discoverer;
-
+ /**
+ * Returns the singleton instance of this class.
+ *
+ * @return
+ */
public static Jws2Discoverer getDiscoverer()
{
if (discoverer == null)
public boolean hasServices()
{
- // TODO Auto-generated method stub
return !running && services != null && services.size() > 0;
}
return running;
}
- /**
- * the jalview .properties entry for JWS2 URLS
- */
- final static String JWS2HOSTURLS = "JWS2HOSTURLS";
-
- public static void setServiceUrls(Vector<String> urls)
+ public void setServiceUrls(List<String> 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
{
}
}
- private static Vector<String> testUrls = null;
-
- public static Vector<String> getServiceUrls()
+ /**
+ * Returns web service URLs, in the order in which they should be tried (or an
+ * empty list).
+ *
+ * @return
+ */
+ public List<String> 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<String> urls = new Vector<String>();
+ List<String> urls = new ArrayList<>();
+
+ if (this.preferredUrl != null)
+ {
+ urls.add(preferredUrl);
+ }
+
+ String surls = Cache.getDefault(JWS2HOSTURLS, COMPBIO_JABAWS);
try
{
StringTokenizer st = new StringTokenizer(surls, ",");
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 : "<null>") + "'");
- 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 : "<null>") + "'");
+ 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<Jws2Instance> getServices()
{
return (services == null) ? new Vector<Jws2Instance>()
- : new Vector<Jws2Instance>(services);
+ : new Vector<>(services);
}
/**
{
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 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
*/
public Thread startDiscoverer(PropertyChangeListener changeSupport2)
{
+ /* if (restart())
+ {
+ return;
+ }
+ else
+ {
+ Thread thr = new Thread(this);
+ thr.start();
+ }
+ */
if (isRunning())
{
setAborted(true);
return thr;
}
- Vector<String> invalidServiceUrls = null, urlsWithoutServices = null,
- validServiceUrls = null;
-
/**
* @return the invalidServiceUrls
*/
{
if (urlsWithoutServices == null)
{
- urlsWithoutServices = new Vector<String>();
+ urlsWithoutServices = new Vector<>();
}
- if ((invalidServiceUrls == null || !invalidServiceUrls
- .contains(jwsservers))
+ if ((invalidServiceUrls == null
+ || !invalidServiceUrls.contains(jwsservers))
&& !urlsWithoutServices.contains(jwsservers))
{
urlsWithoutServices.add(jwsservers);
{
if (invalidServiceUrls == null)
{
- invalidServiceUrls = new Vector<String>();
+ invalidServiceUrls = new Vector<>();
}
if (!invalidServiceUrls.contains(jwsservers))
{
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)
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)
return 1;
}
if (urlsWithoutServices != null && urlsWithoutServices.contains(url))
+ {
return 0;
+ }
if (invalidServiceUrls != null && invalidServiceUrls.contains(url))
{
return -1;
*/
public Jws2Instance getPreferredServiceFor(String[] serviceURLs)
{
- HashSet<String> urls = new HashSet<String>();
+ HashSet<String> urls = new HashSet<>();
urls.addAll(Arrays.asList(serviceURLs));
Jws2Instance match = null;
if (services != null)
return match;
}
- Map<String, Map<String, String>> preferredServiceMap = new HashMap<String, Map<String, String>>();;
+ Map<String, Map<String, String>> preferredServiceMap = new HashMap<>();
/**
* get current preferred service of the given type, or global default
String afid = (af == null) ? "" : af.getViewport().getSequenceSetId();
if (preferredServiceMap == null)
{
- preferredServiceMap = new HashMap<String, Map<String, String>>();
+ preferredServiceMap = new HashMap<>();
}
Map<String, String> prefmap = preferredServiceMap.get(afid);
if (prefmap == null)
{
- prefmap = new HashMap<String, String>();
+ prefmap = new HashMap<>();
preferredServiceMap.put(afid, prefmap);
}
prefmap.put(serviceType, selectedServer.getHost());
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;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff