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JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...
[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
bee9fad
..
d4a2fd4
100644
(file)
--- a/
src/jalview/ws/jws1/Discoverer.java
+++ b/
src/jalview/ws/jws1/Discoverer.java
@@
-20,6
+20,8
@@
*/
package jalview.ws.jws1;
*/
package jalview.ws.jws1;
+import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
import jalview.gui.JvOptionPane;
import jalview.util.MessageManager;
@@
-98,7
+100,7
@@
public class Discoverer implements Runnable
// 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);
@@
-126,7
+128,7
@@
public class Discoverer implements Runnable
static private Vector<URL> getDiscoveryURLS()
{
Vector<URL> urls = new Vector<>();
static 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
@@
-144,23
+146,21
@@
public class Discoverer implements Runnable
}
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);
}
@@
-176,19
+176,17
@@
public class Discoverer implements Runnable
*/
static public void doDiscovery()
{
*/
static public void doDiscovery()
{
- jalview.bin.Cache.log
- .debug("(Re)-Initialising the discovery URL list.");
+ Console.debug("(Re)-Initialising the discovery URL list.");
try
{
try
{
- reallyDiscoverServices = jalview.bin.Cache
- .getDefault("DISCOVERY_START", false);
+ reallyDiscoverServices = Cache.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
}
else
{
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
}
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",
@@
-224,7
+222,7
@@
public class Discoverer implements Runnable
} catch (Exception e)
{
} catch (Exception e)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"jalview.rootRegistry is not a proper url!\nWas set to "
+ RootServiceURL + "\n" + e);
}
"jalview.rootRegistry is not a proper url!\nWas set to "
+ RootServiceURL + "\n" + e);
}
@@
-239,7
+237,7
@@
public class Discoverer implements Runnable
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)
{
@@
-257,13
+255,13
@@
public class Discoverer implements Runnable
}
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)
{
@@
-293,9
+291,9
@@
public class Discoverer implements Runnable
{
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<>());
@@
-315,16
+313,15
@@
public class Discoverer implements Runnable
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);
}
}
}
}
}
}
@@
-341,22
+338,19
@@
public class Discoverer implements Runnable
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())
{
- if ((sh = getServices(
- ServiceURLList.get(s_url))) != null)
+ if ((sh = getServices(ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
}
else
{
{
buildServiceLists(sh, cat, sscat);
}
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++;
@@
-407,11
+401,10
@@
public class Discoverer implements Runnable
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
- WS1Client instance = serviceClientBindings
- .get(sh.getAbstractName());
+ WS1Client instance = serviceClientBindings.get(sh.getAbstractName());
if (instance == null)
{
if (instance == null)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ sh.getAbstractName());
}
"WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for "
+ sh.getAbstractName());
}