X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJws2Discoverer.java;h=b440de8f8909011b2fef16d31960c23bb68621d0;hb=3f72d101fbeb83a7526a3c4f8f62cfe8e8a0189d;hp=2d8eaa6e9e1559c609a2ec6b5141d359b41c07a6;hpb=b793de8470fd1824f60169477a00cc3282f58907;p=jalview.git
diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java
index 2d8eaa6..b440de8 100644
--- a/src/jalview/ws/jws2/Jws2Discoverer.java
+++ b/src/jalview/ws/jws2/Jws2Discoverer.java
@@ -1,22 +1,45 @@
+/*
+ * 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
+ *
+ * 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 .
+ */
package jalview.ws.jws2;
+import jalview.bin.Cache;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvSwingUtils;
+import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+
+import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.HashSet;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.StringTokenizer;
import java.util.Vector;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import org.apache.log4j.Level;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentView;
-import jalview.gui.AlignFrame;
-import jalview.ws.WSMenuEntryProviderI;
-import compbio.data.msa.MsaWS;
-import compbio.ws.client.Jws2Base;
-import compbio.ws.client.Jws2Base.Services;
+import compbio.ws.client.Services;
/**
* discoverer for jws2 services. Follows the lightweight service discoverer
@@ -27,56 +50,177 @@ import compbio.ws.client.Jws2Base.Services;
*/
public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
{
- compbio.data.msa.MsaWS service;
- boolean running=false;
- @Override
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
+
+ /**
+ * 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);
+ }
+
+ boolean running = false, aborted = false;
+
+ /**
+ * @return the aborted
+ */
+ public boolean isAborted()
+ {
+ return aborted;
+ }
+
+ /**
+ * @param aborted
+ * the aborted to set
+ */
+ public void setAborted(boolean aborted)
+ {
+ this.aborted = aborted;
+ }
+
+ Thread oldthread = null;
+
public void run()
{
- if (running)
+ if (running && oldthread != null && oldthread.isAlive())
{
- return;
+ 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)
+ {
+ }
+ }
+ Cache.log.debug("Old discovery thread has finished.");
}
- running=true;
-// Cache.initLogger();
-// Cache.log.setLevel(Level.DEBUG);
- // TODO: Document and PACK JWS2
- String jwsservers = Cache.getDefault("JWS2HOSTURLS",
- "http://webservices.compbio.dundee.ac.uk:8084/jws2");
+ running = true;
+ changeSupport.firePropertyChange("services", services, new Vector());
+ oldthread = Thread.currentThread();
try
{
- if (Jws2Base.validURL(jwsservers))
+ 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 jwsservers : getServiceUrls())
+ {
+ JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsservers);
+ if (svctypes.size()==0)
{
- // look for services
- for (Services srv : Jws2Base.Services.values())
+ // TODO: remove this ugly hack to get Canonical JABA service ordering for all possible services
+ for (Services sv:squery.JABAWS2SERVERS)
{
- MsaWS service = null;
- try
- {
- service = Jws2Base.connect(jwsservers, srv);
- } catch (Exception e)
- {
- }
- ;
- if (service != null)
- {
- addService(jwsservers, srv, service);
- }
+ svctypes.add(sv.toString());
}
}
- else
+ qrys.add(squery);
+ new Thread(squery).start();
+ }
+ boolean finished = true;
+ do
+ {
+ finished=true;
+ try
+ {
+ Thread.sleep(100);
+ } catch (Exception e)
{
- Cache.log.info("Ignoring invalid Jws2 service url " + jwsservers);
}
- } catch (Exception e)
- {
- Cache.log.warn("Exception when discovering Jws2 services.", e);
- } catch (Error e)
+ ;
+ for (JabaWsServerQuery squery : qrys)
+ {
+ finished = finished && !squery.isRunning();
+ }
+ if (aborted)
+ {
+ Cache.log.debug("Aborting " + qrys.size()
+ + " JABAWS discovery threads.");
+ for (JabaWsServerQuery squery : qrys)
+ {
+ squery.setQuit(true);
+ }
+ }
+ } while (!aborted && !finished);
+ if (!aborted)
{
- Cache.log.error("Exception when discovering Jws2 services.", e);
+ // 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)
+ {
+ Jws2Instance[] svcs=new Jws2Instance[services.size()];
+ int[] spos=new int[services.size()];
+ int ipos=0;
+ Vector 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) {
+ services.add(svc);
+ }
+ }
}
- running=false;
-
+ oldthread = null;
+ running = false;
+ changeSupport.firePropertyChange("services", new Vector(), services);
}
/**
@@ -86,82 +230,184 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
* @param srv
* @param service2
*/
- private void addService(String jwsservers, Services srv, MsaWS service2)
+ synchronized void addService(String jwsservers, Jws2Instance service)
{
- Cache.log.info("Discovered service: " + jwsservers + " "
- + srv.toString());
- if (services==null) {
+ if (services == null)
+ {
services = new Vector();
}
- services.add(new Jws2Instance(jwsservers, "Align with "
- + srv.toString(), service2));
- }
-
- public class Jws2Instance
- {
- String hosturl;
-
- String serviceType;
+ System.out.println("Discovered service: " + jwsservers + " "
+ + service.toString());
+// Jws2Instance service = new Jws2Instance(jwsservers, srv.toString(),
+// service2);
- MsaWS service;
-
- public Jws2Instance(String hosturl, String serviceType, MsaWS service)
+ services.add(service);
+ // retrieve the presets and parameter set and cache now
+ service.getParamStore().getPresets();
+ service.hasParameters();
+ if (validServiceUrls==null)
{
- super();
- this.hosturl = hosturl;
- this.serviceType = serviceType;
- this.service = service;
+ validServiceUrls=new Vector();
}
-
- };
+ validServiceUrls.add(jwsservers);
+ }
/**
* holds list of services.
*/
- Vector services;
-
- @Override
+ protected Vector services;
+ /**
+ * attach all available web services to the appropriate submenu in the given JMenu
+ */
public void attachWSMenuEntry(JMenu wsmenu, final AlignFrame alignFrame)
{
- if (running || services==null || services.size() == 0)
+ // dynamically regenerate service list.
+ populateWSMenuEntry(wsmenu, alignFrame, null);
+ }
+
+ private void populateWSMenuEntry(JMenu jws2al, final AlignFrame alignFrame, String typeFilter)
+ {
+ if (running || services == null || services.size() == 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 jws2 = new JMenu("JWS2 Alignment");
+ JMenu atpoint;
MsaWSClient msacl = new MsaWSClient();
- for (final Jws2Instance service : services)
+ Vector hostLabels = new Vector();
+ jws2al.removeAll();
+ Hashtable lasthostFor = new Hashtable();
+ Hashtable> hosts = new Hashtable>();
+ ArrayList hostlist=new ArrayList();
+ for (Jws2Instance service : services)
{
- msacl.attachWSMenuEntry(jws2, service, alignFrame);
- /*JMenuItem sitem = new JMenuItem(service.serviceType);
- sitem.setToolTipText("Hosted at " + service.hosturl);
- sitem.addActionListener(new ActionListener()
+ ArrayList hostservices = hosts.get(service.getHost());
+ if (hostservices == null)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- AlignmentView msa = alignFrame.gatherSequencesForAlignment();
- MsaWSClient client = new MsaWSClient(service,
- "JWS2 Alignment of " + alignFrame.getTitle(), msa, false,
- true, alignFrame.getViewport().getAlignment().getDataset(),
- alignFrame);
- }
- });*/
+ hosts.put(service.getHost(),
+ hostservices = new ArrayList());
+ hostlist.add(service.getHost());
+ }
+ hostservices.add(service);
}
- if (services.size()>0)
+ // now add hosts in order of the given array
+ for (String host : hostlist)
{
- wsmenu.add(jws2);
+ 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() : "")))
+ {
+ // add a marker indicating where this service is hosted
+ // relies on services from the same host being listed in a
+ // contiguous
+ // group
+ JMenuItem hitm;
+ atpoint.addSeparator();
+ 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.addElement(host + service.serviceType
+ + service.getActionText());
+ // hostLabels.addElement(host + (bytype ?
+ // service.serviceType+service.getActionText() : ""));
+ }
+
+ service.attachWSMenuEntry(atpoint, alignFrame);
+ /*
+ * JMenuItem sitem = new JMenuItem(service.serviceType);
+ * sitem.setToolTipText("Hosted at " + service.hosturl);
+ * sitem.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent e) { AlignmentView
+ * msa = alignFrame.gatherSequencesForAlignment(); MsaWSClient client =
+ * new MsaWSClient(service, "JWS2 Alignment of " +
+ * alignFrame.getTitle(), msa, false, true,
+ * alignFrame.getViewport().getAlignment().getDataset(), alignFrame); }
+ * });
+ */
+ }
}
-
+
}
+
public static void main(String[] args)
{
- Thread runner = new Thread(getDiscoverer());
- runner.start();
+ if (args.length>0)
+ {
+ 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())
{
try
@@ -172,11 +418,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
}
;
}
+ try {
+ Thread.sleep(50);
+ } catch (InterruptedException x) {}
}
+
private static Jws2Discoverer discoverer;
+
public static Jws2Discoverer getDiscoverer()
{
- if (discoverer==null)
+ if (discoverer == null)
{
discoverer = new Jws2Discoverer();
}
@@ -186,7 +437,268 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI
public boolean hasServices()
{
// TODO Auto-generated method stub
- return services!=null && services.size()>0;
+ return !running && services != null && services.size() > 0;
+ }
+
+ public boolean isRunning()
+ {
+ return running;
+ }
+
+ /**
+ * the jalview .properties entry for JWS2 URLS
+ */
+ final static String JWS2HOSTURLS = "JWS2HOSTURLS";
+
+ public static void setServiceUrls(Vector urls)
+ {
+ if (urls != null)
+ {
+ StringBuffer urlbuffer = new StringBuffer();
+ String sep = "";
+ for (String url : urls)
+ {
+ urlbuffer.append(sep);
+ urlbuffer.append(url);
+ sep = ",";
+ }
+ Cache.setProperty(JWS2HOSTURLS, urlbuffer.toString());
+ }
+ else
+ {
+ Cache.removeProperty(JWS2HOSTURLS);
+ }
+ }
+
+ private static Vector testUrls=null;
+ public static Vector 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();
+ try
+ {
+ StringTokenizer st = new StringTokenizer(surls, ",");
+ while (st.hasMoreElements())
+ {
+ String url = null;
+ try
+ {
+ java.net.URL u = new java.net.URL(url = st.nextToken());
+ if (!urls.contains(url))
+ {
+ urls.add(url);
+ }
+ else
+ {
+ jalview.bin.Cache.log.info("Ignoring duplicate url in "
+ + JWS2HOSTURLS + " list");
+ }
+ } catch (Exception 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
+ + " entry of $(HOME)/.jalview_properties)");
+ jalview.bin.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);
+ }
+ if (urls.size() >= 0)
+ {
+ return urls;
+ }
+ return null;
+ }
+
+ 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;
+ }
+
+ /**
+ * 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 (isRunning())
+ {
+ setAborted(true);
+ }
+ addPropertyChangeListener(changeSupport2);
+ Thread thr = new Thread(this);
+ thr.start();
+ return thr;
+ }
+
+ Vector invalidServiceUrls = null, urlsWithoutServices = null, validServiceUrls=null;
+
+ /**
+ * @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("URLs that could not be 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("URLs without any JABA Services : \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;
}
-
}