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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
ws
/
jws1
/
Discoverer.java
diff --git
a/src/jalview/ws/jws1/Discoverer.java
b/src/jalview/ws/jws1/Discoverer.java
index
9a6c445
..
a5b73da
100644
(file)
--- a/
src/jalview/ws/jws1/Discoverer.java
+++ b/
src/jalview/ws/jws1/Discoverer.java
@@
-20,6
+20,7
@@
*/
package jalview.ws.jws1;
*/
package jalview.ws.jws1;
+
import java.net.URL;
import java.util.Hashtable;
import java.util.StringTokenizer;
import java.net.URL;
import java.util.Hashtable;
import java.util.StringTokenizer;
@@
-31,6
+32,7
@@
import ext.vamsas.RegistryServiceSoapBindingStub;
import ext.vamsas.ServiceHandle;
import ext.vamsas.ServiceHandles;
import jalview.bin.Cache;
import ext.vamsas.ServiceHandle;
import ext.vamsas.ServiceHandles;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.JvOptionPane;
import jalview.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.gui.JvOptionPane;
@@
-38,7
+40,6
@@
import jalview.util.MessageManager;
public class Discoverer implements Runnable, ApplicationSingletonI
{
public class Discoverer implements Runnable, ApplicationSingletonI
{
-
public static Discoverer getInstance()
{
return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
public static Discoverer getInstance()
{
return (Discoverer) ApplicationSingletonProvider.getInstance(Discoverer.class);
@@
-48,7
+49,6
@@
public class Discoverer implements Runnable, ApplicationSingletonI
{
// use getInstance()
}
{
// use getInstance()
}
-
ext.vamsas.IRegistry registry; // the root registry service.
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
ext.vamsas.IRegistry registry; // the root registry service.
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
@@
-111,7
+111,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
// timeout
} catch (Exception ex)
{
// timeout
} catch (Exception ex)
{
- jalview.bin.Cache.log.error(
+ Console.error(
"Serious! Service location failed\nfor URL :" + WsURL + "\n",
ex);
"Serious! Service location failed\nfor URL :" + WsURL + "\n",
ex);
@@
-143,7
+143,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
- String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS",
+ String RootServiceURLs = Cache.getDefault("DISCOVERY_URLS",
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
"http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry");
try
@@
-161,23
+161,21
@@
public class Discoverer implements Runnable, ApplicationSingletonI
}
else
{
}
else
{
- jalview.bin.Cache.log
- .info("Ignoring duplicate url in DISCOVERY_URLS list");
+ Console.info("Ignoring duplicate url in DISCOVERY_URLS list");
}
} catch (Exception ex)
{
}
} 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(
+ Console.warn("Problem whilst trying to make a URL from '"
+ + ((url != null) ? url : "<null>") + "'");
+ Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
"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);
+ Console.debug("Exception was ", ex);
}
}
} catch (Exception ex)
{
}
}
} catch (Exception ex)
{
- jalview.bin.Cache.log.warn(
+ Console.warn(
"Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
"Error parsing comma separated list of urls in DISCOVERY_URLS.",
ex);
}
@@
-198,12
+196,12
@@
public class Discoverer implements Runnable, ApplicationSingletonI
private void discovery()
{
private void discovery()
{
- jalview.bin.Cache.log
+ Console
.debug("(Re)-Initialising the discovery URL list.");
try
{
Discoverer d = getInstance();
.debug("(Re)-Initialising the discovery URL list.");
try
{
Discoverer d = getInstance();
- reallyDiscoverServices = jalview.bin.Cache
+ reallyDiscoverServices = Cache
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
@@
-211,7
+209,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
}
else
{
}
else
{
- jalview.bin.Cache.log.debug("Setting default services");
+ Console.debug("Setting default services");
services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
services = new Hashtable<>();
// Muscle, Clustal and JPred.
ServiceHandle[] defServices = { new ServiceHandle("MsaWS",
@@
-262,7
+260,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
ServiceHandles shs = null;
try
{
ServiceHandles shs = null;
try
{
- jalview.bin.Cache.log.debug("Discovering services using " + location);
+ Console.debug("Discovering services using " + location);
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
shs = locateWebService(location).getServices();
} catch (org.apache.axis.AxisFault f)
{
@@
-280,13
+278,13
@@
public class Discoverer implements Runnable, ApplicationSingletonI
}
else
{
}
else
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Axis Fault", f);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Axis Fault", f);
}
} catch (Exception e)
{
}
} catch (Exception e)
{
- jalview.bin.Cache.log.warn("No Discovery service at " + location);
- jalview.bin.Cache.log.debug("Discovery Service General Exception", e);
+ Console.warn("No Discovery service at " + location);
+ Console.debug("Discovery Service General Exception", e);
}
if ((shs != null) && shs.getServices().length > 0)
{
}
if ((shs != null) && shs.getServices().length > 0)
{
@@
-316,9
+314,9
@@
public class Discoverer implements Runnable, ApplicationSingletonI
{
if (!cat.contains(sh[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");
+ Console.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<>());
if (!sscat.containsKey(sh[i].getAbstractName()))
{
sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
@@
-338,16
+336,15
@@
public class Discoverer implements Runnable, ApplicationSingletonI
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
disc_serv = new java.net.URL(sh[i].getEndpointURL());
if (!ServiceURLList.contains(disc_serv))
{
- jalview.bin.Cache.log.debug(
+ Console.debug(
"Adding new discovery service at " + disc_serv);
ServiceURLList.add(disc_serv);
seenNewDiscovery = true;
}
} catch (Exception e)
{
"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);
+ Console.debug("Ignoring bad discovery service URL "
+ + sh[i].getEndpointURL(), e);
}
}
}
}
}
}
@@
-364,8
+361,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
int s_url = 0;
if (ServiceURLList == null)
{
int s_url = 0;
if (ServiceURLList == null)
{
- jalview.bin.Cache.log
- .debug("No service endpoints to use for service discovery.");
+ Console.debug("No service endpoints to use for service discovery.");
return;
}
while (s_url < ServiceURLList.size())
return;
}
while (s_url < ServiceURLList.size())
@@
-378,8
+374,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
}
else
{
}
else
{
- jalview.bin.Cache.log.warn("No services at "
- + (ServiceURLList.get(s_url))
+ Console.warn("No services at " + (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
@@
-402,7
+397,7
@@
public class Discoverer implements Runnable, ApplicationSingletonI
@Override
public void run()
{
@Override
public void run()
{
- Cache.log.info("Discovering jws1 services");
+ Console.info("Discovering jws1 services");
Discoverer.doDiscovery();
discoverServices();
}
Discoverer.doDiscovery();
discoverServices();
}
@@
-458,7
+453,6
@@
public class Discoverer implements Runnable, ApplicationSingletonI
}
return instance;
}
}
return instance;
}
-
public static Hashtable<String, Vector<ServiceHandle>> getServices()
{
return getInstance().services;
public static Hashtable<String, Vector<ServiceHandle>> getServices()
{
return getInstance().services;