/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 <http://www.gnu.org/licenses/>.
+ */
package jalview.ws;
/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
+ * <p>
+ * Title:
+ * </p>
+ *
+ * <p>
+ * Description:
+ * </p>
+ *
+ * <p>
+ * Copyright: Copyright (c) 2004
+ * </p>
+ *
+ * <p>
+ * Company: Dundee University
+ * </p>
+ *
* @author not attributable
* @version 1.0
*/
+import java.util.*;
+
+import javax.swing.*;
+
import ext.vamsas.*;
-import java.util.Vector;
-import java.util.Hashtable;
-import java.util.StringTokenizer;
-public class Discoverer
- extends Thread implements Runnable
+public class Discoverer extends Thread implements Runnable
{
ext.vamsas.IRegistry registry; // the root registry service.
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.
- PropertyChangeSupport(this);
+
+ 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.
+ *
+ * @param listener
+ * to be added that consumes new services Hashtable object.
*/
public void addPropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ java.beans.PropertyChangeListener listener)
{
changeSupport.addPropertyChangeListener(listener);
}
/**
- *
- *
- * @param listener to be removed
+ *
+ *
+ * @param listener
+ * to be removed
*/
public void removePropertyChangeListener(
- java.beans.PropertyChangeListener listener)
+ java.beans.PropertyChangeListener listener)
{
changeSupport.removePropertyChangeListener(listener);
}
/**
* Property change listener firing routine
- *
- * @param prop services
- * @param oldvalue old services hash
- * @param newvalue new services hash
+ *
+ * @param prop
+ * services
+ * @param oldvalue
+ * old services hash
+ * @param newvalue
+ * new services hash
*/
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ public void firePropertyChange(String prop, Object oldvalue,
+ Object newvalue)
{
changeSupport.firePropertyChange(prop, oldvalue, newvalue);
}
/**
* Initializes the server field with a valid service implementation.
- *
+ *
* @return true if service was located.
*/
private IRegistry locateWebService(java.net.URL WsURL)
try
{
server = loc.getRegistryService(WsURL);
- ( (RegistryServiceSoapBindingStub) server).setTimeout(60000); // One minute timeout
- }
- catch (Exception ex)
+ ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
+ // minute
+ // timeout
+ } catch (Exception ex)
{
- jalview.bin.Cache.log.error(
- "Serious! Service location failed\nfor URL :" + WsURL +
- "\n", ex);
+ jalview.bin.Cache.log
+ .error("Serious! Service location failed\nfor URL :" + WsURL
+ + "\n", ex);
return null;
}
}
static private java.net.URL RootServiceURL = null;
+
static public Vector ServiceURLList = null;
+
static private boolean reallyDiscoverServices = true;
- public static java.util.Hashtable services = null; // vectors of services stored by abstractServiceType string
+ public static java.util.Hashtable services = null; // vectors of services
+
+ // stored by
+ // abstractServiceType
+ // string
+
public static java.util.Vector serviceList = null; // flat list of services
- static private Vector getDiscoveryURLS() {
+
+ static private Vector getDiscoveryURLS()
+ {
Vector urls = new Vector();
- String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
+ String RootServiceURLs = jalview.bin.Cache
+ .getDefault("DISCOVERY_URLS",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
- try{
+ try
+ {
StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
while (st.hasMoreElements())
{
{
java.net.URL u = new java.net.URL(url = st.nextToken());
if (!urls.contains(u))
+ {
urls.add(u);
+ }
else
- jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
- }
- catch (Exception ex)
+ {
+ jalview.bin.Cache.log
+ .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ }
+ } catch (Exception 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 DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
- jalview.bin.Cache.log.debug("Exception was ",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 DISCOVERY_URLS 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 DISCOVERY_URLS.",ex);}
- if (urls.size()>0)
+ } catch (Exception ex)
+ {
+ jalview.bin.Cache.log
+ .warn(
+ "Error parsing comma separated list of urls in DISCOVERY_URLS.",
+ ex);
+ }
+ if (urls.size() > 0)
+ {
return urls;
+ }
return null;
}
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list.");
+ jalview.bin.Cache.log
+ .debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
+ reallyDiscoverServices = jalview.bin.Cache.getDefault(
+ "DISCOVERY_START", false);
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
jalview.bin.Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
- ServiceHandle[] defServices = {
+ ServiceHandle[] defServices =
+ {
new ServiceHandle(
- "MsaWS",
- "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " +
- "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
- "Muscle Multiple Protein Sequence Alignment"
-),
+ "MsaWS",
+ "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment "
+ + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS",
+ "Muscle Multiple Protein Sequence Alignment"),
new ServiceHandle(
- "MsaWS",
- "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" +
- " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." +
- " Nucleic Acids Research, 22 4673-4680",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
- "ClustalW Multiple Sequence Alignment"),
+ "MsaWS",
+ "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) "
+ + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\""
+ + " Nucleic Acids Research, 33 511-518",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS",
+ "MAFFT Multiple Sequence Alignment"),
new ServiceHandle(
- "SecStrPred",
- "Cuff J. A and Barton G.J (2000) Application of " +
- "multiple sequence alignment profiles to improve protein secondary structure prediction, " +
- "Proteins 40:502-511",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
- )};
+ "MsaWS",
+ "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple"
+ + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice."
+ + " Nucleic Acids Research, 22 4673-4680",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS",
+ "ClustalW Multiple Sequence Alignment"),
+ new ServiceHandle(
+ "SecStrPred",
+ "Cole C., Barber J. D., Barton G.J (2008) "
+ + "The Jpred 3 secondary structure prediction server "
+ + "Nucleic Acids Research, 36 W197-W201",
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred",
+ "JNet Secondary Structure Prediction") };
services = new Hashtable();
serviceList = new Vector();
buildServiceLists(defServices, serviceList, services);
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.err.println(
- "jalview.rootRegistry is not a proper url!\nWas set to " +
- RootServiceURL + "\n" + e);
+ System.err
+ .println("jalview.rootRegistry is not a proper url!\nWas set to "
+ + RootServiceURL + "\n" + e);
}
}
+
// TODO: JBPNote : make this discover more services based on list of
// discovery service urls, break cyclic references to the same url and
// duplicate service entries (same endpoint *and* same interface)
{
jalview.bin.Cache.log.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
- }
- catch (Exception e)
+ } catch (org.apache.axis.AxisFault f)
{
- jalview.bin.Cache.log.debug("No Discovery service at " +
- location);
- jalview.bin.Cache.log.debug(e);
-
+ // JBPNote - should do this a better way!
+ if (f.getFaultReason().indexOf("(407)") > -1)
+ {
+ if (jalview.gui.Desktop.desktop != null)
+ {
+ JOptionPane
+ .showMessageDialog(
+ jalview.gui.Desktop.desktop,
+ "Please set up your proxy settings in the 'Connections' tab of the Preferences window",
+ "Proxy Authorization Failed",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ jalview.bin.Cache.log.warn("No Discovery service at " + location);
+ jalview.bin.Cache.log.debug("Axis Fault", f);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.warn("No Discovery service at " + location);
+ jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
}
- if ( (shs != null) && shs.getServices().length > 0)
+ if ((shs != null) && shs.getServices().length > 0)
{
return shs.getServices();
}
/**
* Adds a list of services to the service catalog and categorised catalog
* returns true if ServiceURLList was modified with a new DiscoveryService URL
- * @param sh ServiceHandle[]
- * @param cat Vector
- * @param sscat Hashtable
+ *
+ * @param sh
+ * ServiceHandle[]
+ * @param cat
+ * Vector
+ * @param sscat
+ * Hashtable
* @return boolean
*/
static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
- Hashtable sscat)
+ Hashtable sscat)
{
boolean seenNewDiscovery = false;
for (int i = 0, j = sh.length; i < j; i++)
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
- " service called " +
- sh[i].getName() + " exists at " +
- sh[i].getEndpointURL() + "\n");
+ jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName()
+ + " service called " + sh[i].getName() + " exists at "
+ + sh[i].getEndpointURL() + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
{
sscat.put(sh[i].getAbstractName(), cat = new Vector());
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log.debug(
- "Adding new discovery service at " + disc_serv);
+ jalview.bin.Cache.log
+ .debug("Adding new discovery service at "
+ + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
jalview.bin.Cache.log.debug(
- "Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
- e);
+ "Ignoring bad discovery service URL "
+ + sh[i].getEndpointURL(), e);
}
}
}
Vector cat = new Vector();
ServiceHandle sh[] = null;
int s_url = 0;
- if (ServiceURLList==null)
+ if (ServiceURLList == null)
{
- jalview.bin.Cache.log.debug("No service endpoints to use for service discovery.");
+ jalview.bin.Cache.log
+ .debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
{
- if ( (sh = getServices( (java.net.URL) ServiceURLList.get(s_url))) != null)
+ if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
- } else {
- jalview.bin.Cache.log.warn(
- "No services at "
- +((java.net.URL) ServiceURLList.get(s_url))
- +" - check DISCOVERY_URLS property in .jalview_properties");
+ }
+ else
+ {
+ jalview.bin.Cache.log
+ .warn("No services at "
+ + ((java.net.URL) ServiceURLList.get(s_url))
+ + " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
}
// TODO: decide on correct semantics for services list - PropertyChange
// provides a way of passing the new object around
// so no need to access original discovery thread.
- // Curent decision is to change properties then notify listeners with old and new values.
+ // Curent decision is to change properties then notify listeners with old
+ // and new values.
Hashtable oldServices = services;
- //Vector oldServicelist = serviceList;
+ // Vector oldServicelist = serviceList;
services = sscat;
serviceList = cat;
firePropertyChange("services", oldServices, services);
public void run()
{
final Discoverer discoverer = this;
- Thread discoverThread = new Thread() {
- public void run() {
+ Thread discoverThread = new Thread()
+ {
+ public void run()
+ {
discoverer.doDiscovery();
discoverer.discoverServices();
}
};
discoverThread.start();
}
+
+ /**
+ * binding service abstract name to handler class
+ */
+ private static Hashtable serviceClientBindings;
+
+ public static WSClient getServiceClient(ServiceHandle sh)
+ {
+ if (serviceClientBindings == null)
+ {
+ // get a list from Config or create below
+ serviceClientBindings = new Hashtable();
+ serviceClientBindings.put("MsaWS", new MsaWSClient());
+ serviceClientBindings.put("SecStrPred", new JPredClient());
+ serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
+ }
+ WSClient instance = (WSClient) serviceClientBindings.get(sh
+ .getAbstractName());
+ if (instance == null)
+ {
+ System.err
+ .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ + sh.getAbstractName());
+ }
+ else
+ {
+ instance.serviceHandle = sh;
+ }
+ return instance;
+ }
+ /**
+ * notes on discovery service 1. need to allow multiple discovery source urls.
+ * 2. user interface to add/control list of urls in preferences notes on
+ * wsclient discovery 1. need a classpath property with list of additional
+ * plugin directories 2. optional config to cite specific bindings between
+ * class name and Abstract service name. 3. precedence for automatic discovery
+ * by using getAbstractName for WSClient - user added plugins override default
+ * plugins ? notes on wsclient gui code for gui attachment now moved to
+ * wsclient implementation. Needs more abstraction but approach seems to work.
+ * is it possible to 'generalise' the data retrieval calls further ? current
+ * methods are very specific (gatherForMSA or gatherForSeqOrMsaSecStrPred),
+ * new methods for conservation (group or alignment), treecalc (aligned
+ * profile), seqannot (sequences selected from dataset, annotation back to
+ * dataset).
+ *
+ */
}
git://source.jalview.org / jalview.git / blobdiff