+/*
+* 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
+*/
package jalview.ws;
/**
import ext.vamsas.*;
import java.util.Vector;
import java.util.Hashtable;
-import java.util.ArrayList;
+import java.util.StringTokenizer;
public class Discoverer
extends Thread implements Runnable
}
catch (Exception ex)
{
- jalview.bin.Jalview.log.error(
+ jalview.bin.Cache.log.error(
"Serious! Service location failed\nfor URL :" + WsURL +
"\n", ex);
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;
+ }
static
{
reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
- RootServiceURL = new java.net.URL(
- "http://webservices.compbio.dundee.ac.uk:8080/jalTestWS/services/ServiceRegistry");
- if (ServiceURLList == null)
- {
- ServiceURLList = new Vector();
- }
- if (!ServiceURLList.contains(RootServiceURL))
- {
- ServiceURLList.add(RootServiceURL);
- }
+ ServiceURLList = getDiscoveryURLS();
}
else
{
- jalview.bin.Jalview.log.debug("Setting default services");
+ jalview.bin.Cache.log.debug("Setting default services");
services = new Hashtable();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = {
"Cuff J. A and Barton G.J (1999) Application of enhanced " +
"multiple sequence alignment profiles to improve protein secondary structure prediction, " +
"Proteins 40:502-511",
- "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JPred Secondary Structure Prediction"
+ "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction"
)};
services = new Hashtable();
serviceList = new Vector();
ServiceHandles shs = null;
try
{
- jalview.bin.Jalview.log.debug("Discovering services using " + location);
+ jalview.bin.Cache.log.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
}
catch (Exception e)
{
- System.err.println("failed to locate Services through URL : " +
- location + "\n");
- e.printStackTrace();
+ jalview.bin.Cache.log.debug("No Discovery service at " +
+ location);
+ jalview.bin.Cache.log.debug(e);
}
if ( (shs != null) && shs.getServices().length > 0)
{
if (!cat.contains(sh[i]))
{
- jalview.bin.Jalview.log.debug("A " + sh[i].getAbstractName() +
+ jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() +
" service called " +
sh[i].getName() + " exists at " +
sh[i].getEndpointURL() + "\n");
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Jalview.log.debug(
+ jalview.bin.Cache.log.debug(
"Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
catch (Exception e)
{
- jalview.bin.Jalview.log.debug(
+ jalview.bin.Cache.log.debug(
"Ignoring bad discovery service URL " + sh[i].getEndpointURL(),
e);
}
int s_url = 0;
if (ServiceURLList==null)
{
- jalview.bin.Jalview.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())
{
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++;
}
// 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;
+ //Vector oldServicelist = serviceList;
services = sscat;
serviceList = cat;
firePropertyChange("services", oldServices, services);
git://source.jalview.org / jalview.git / blobdiff