+++ /dev/null
-/*
- * 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>
- *
- * @author not attributable
- * @version 1.0
- */
-import java.util.*;
-
-import javax.swing.*;
-
-import ext.vamsas.*;
-
-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);
-
- /**
- * 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);
- }
-
- /**
- * Property change listener firing routine
- *
- * @param prop
- * services
- * @param oldvalue
- * old services hash
- * @param newvalue
- * new services hash
- */
- 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)
- {
- IRegistryServiceLocator loc = new IRegistryServiceLocator(); // Default
- IRegistry server = null;
- try
- {
- server = loc.getRegistryService(WsURL);
- ((RegistryServiceSoapBindingStub) server).setTimeout(60000); // One
- // minute
- // timeout
- } catch (Exception ex)
- {
- jalview.bin.Cache.log
- .error("Serious! Service location failed\nfor URL :" + WsURL
- + "\n", ex);
-
- return null;
- }
-
- loc.getEngine().setOption("axis", "1");
-
- return server;
- }
-
- 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.Vector serviceList = null; // flat list of services
-
- 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");
-
- try
- {
- StringTokenizer st = new StringTokenizer(RootServiceURLs, ",");
- while (st.hasMoreElements())
- {
- String url = null;
- try
- {
- 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
- .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)
- {
- return urls;
- }
- return null;
- }
-
- /**
- * fetch new services or reset to hardwired defaults depending on preferences.
- */
- static public void doDiscovery()
- {
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
- try
- {
- reallyDiscoverServices = jalview.bin.Cache.getDefault(
- "DISCOVERY_START", false);
- if (reallyDiscoverServices)
- {
- ServiceURLList = getDiscoveryURLS();
- }
- else
- {
- jalview.bin.Cache.log.debug("Setting default services");
- services = new Hashtable();
- // Muscle, Clustal and JPred.
- 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"),
- new ServiceHandle(
- "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(
- "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)
- {
- 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)
- private ServiceHandle[] getServices(java.net.URL location)
- {
- ServiceHandles shs = null;
- try
- {
- jalview.bin.Cache.log.debug("Discovering services using " + location);
- shs = locateWebService(location).getServices();
- } catch (org.apache.axis.AxisFault f)
- {
- // 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)
- {
- return shs.getServices();
- }
- return null;
- }
-
- /**
- * 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
- * @return boolean
- */
- static private boolean buildServiceLists(ServiceHandle[] sh, Vector cat,
- 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");
- if (!sscat.containsKey(sh[i].getAbstractName()))
- {
- sscat.put(sh[i].getAbstractName(), cat = new Vector());
- }
- else
- {
- cat = (Vector) sscat.get(sh[i].getAbstractName());
- }
- cat.add(sh[i]);
- if (sh[i].getAbstractName().equals("Registry"))
- {
- for (int s = 0, sUrls = ServiceURLList.size(); s < sUrls; s++)
- {
- java.net.URL disc_serv = null;
- try
- {
- 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);
- ServiceURLList.add(disc_serv);
- seenNewDiscovery = true;
- }
- } catch (Exception e)
- {
- jalview.bin.Cache.log.debug(
- "Ignoring bad discovery service URL "
- + sh[i].getEndpointURL(), e);
- }
- }
- }
- }
- }
- return seenNewDiscovery;
- }
-
- public void discoverServices()
- {
- Hashtable sscat = new Hashtable();
- Vector cat = new Vector();
- ServiceHandle sh[] = null;
- int s_url = 0;
- if (ServiceURLList == null)
- {
- 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)
- {
-
- 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");
- }
- 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.
- Hashtable oldServices = services;
- // Vector oldServicelist = serviceList;
- services = sscat;
- serviceList = cat;
- firePropertyChange("services", oldServices, services);
- }
-
- /**
- * creates a new thread to call discoverServices()
- */
- public void run()
- {
- final Discoverer discoverer = this;
- 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 WS1Client 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());
- }
- WS1Client instance = (WS1Client) 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