import ext.vamsas.*;
import java.util.Vector;
import java.util.Hashtable;
-import java.util.ArrayList;
import java.util.StringTokenizer;
+import javax.swing.JOptionPane;
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);
if (!urls.contains(u))
urls.add(u);
else
- jalview.bin.Jalview.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
+ jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
catch (Exception ex)
{
- jalview.bin.Jalview.log.warn(
+ jalview.bin.Cache.log.warn(
"Problem whilst trying to make a URL from '" +
( (url != null) ? url : "<null>")+"'");
- jalview.bin.Jalview.log.warn("This was probably due to a malformed comma separated list"
+ 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.Jalview.log.debug("Exception was ",ex);
+ jalview.bin.Cache.log.debug("Exception was ",ex);
}
}
}catch(Exception ex)
- {jalview.bin.Jalview.log.warn("Error parsing comma separated list of urls in DISCOVERY_URLS.",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
- {
+ /**
+ * 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);
}
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 = {
),
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",
"ClustalW Multiple Sequence Alignment"),
new ServiceHandle(
"SecStrPred",
- "Cuff J. A and Barton G.J (1999) Application of enhanced " +
+ "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"
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)
- {
- jalview.bin.Jalview.log.debug("No Discovery service at " +
- location);
- jalview.bin.Jalview.log.debug(e);
-
+ 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)
{
{
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.Jalview.log.warn(
+ jalview.bin.Cache.log.warn(
"No services at "
+((java.net.URL) ServiceURLList.get(s_url))
+" - check DISCOVERY_URLS property in .jalview_properties");
// 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);
}
+ /**
+ * creates a new thread to call discoverServices()
+ */
public void run()
{
- discoverServices();
+ final Discoverer discoverer = this;
+ Thread discoverThread = new Thread() {
+ public void run() {
+ discoverer.doDiscovery();
+ discoverer.discoverServices();
+ }
+ };
+ discoverThread.start();
}
}
git://source.jalview.org / jalview.git / blobdiff