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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[jalview.git]
/
src
/
jalview
/
ws
/
gui
/
MsaWSThread.java
diff --git
a/src/jalview/ws/gui/MsaWSThread.java
b/src/jalview/ws/gui/MsaWSThread.java
index
48846ef
..
9298fb5
100644
(file)
--- a/
src/jalview/ws/gui/MsaWSThread.java
+++ b/
src/jalview/ws/gui/MsaWSThread.java
@@
-21,6
+21,7
@@
package jalview.ws.gui;
import jalview.bin.Cache;
package jalview.ws.gui;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
@@
-58,6
+59,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
// order
// order
+
String alTitle; // name which will be used to form new alignment window.
AlignmentI dataset; // dataset to which the new alignment will be
String alTitle; // name which will be used to form new alignment window.
AlignmentI dataset; // dataset to which the new alignment will be
@@
-199,7
+201,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
{
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
- Cache.log.warn(
+ Console.warn(
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
"Exception whilst cancelling " + jobs[job].getJobId(),
exc);
}
@@
-258,9
+260,9
@@
public class MsaWSThread extends AWSThread implements WSClientI
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
{
- Cache.log.debug(
+ Console.debug(
"Tried to submit an already submitted job " + j.getJobId());
}
return;
"Tried to submit an already submitted job " + j.getJobId());
}
return;
@@
-288,7
+290,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
} catch (Throwable throwable)
{
} catch (Throwable throwable)
{
- Cache.log.error("failed to send the job to the alignment server", throwable);
+ Console.error("failed to send the job to the alignment server", throwable);
if (!server.handleSubmitError(throwable, j, wsInfo))
{
if (throwable instanceof Exception)
if (!server.handleSubmitError(throwable, j, wsInfo))
{
if (throwable instanceof Exception)
@@
-302,6
+304,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
}
}
///// generic
}
}
///// generic
+
if (j.getJobId() != null)
{
j.setSubmitted(true);
if (j.getJobId() != null)
{
j.setSubmitted(true);
@@
-385,7
+388,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
} catch (Exception e)
{
} catch (Exception e)
{
- Cache.log.warn(
+ Console.warn(
"Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
"Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
@@
-409,7
+412,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
}
} while (nunchanged > 0 && nexcept > 0);
}
} while (nunchanged > 0 && nexcept > 0);
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
+ msjob.getJobId() + " on server " + WsUrl);
{
System.out.println("Job Execution file for job: "
+ msjob.getJobId() + " on server " + WsUrl);
@@
-425,7
+428,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
{
if (!server.handleCollectionException(e, msjob, wsInfo))
{
{
if (!server.handleCollectionException(e, msjob, wsInfo))
{
- Cache.log.error("Couldn't get Alignment for job.", e);
+ Console.error("Couldn't get Alignment for job.", e);
// TODO: Increment count and retry ?
msjob.setState(JobState.SERVERERROR);
}
// TODO: Increment count and retry ?
msjob.setState(JobState.SERVERERROR);
}
@@
-441,7
+444,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
} catch (Exception ex)
{
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
"Unexpected exception when processing results for " + alTitle,
ex);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
@@
-535,6
+538,7
@@
public class MsaWSThread extends AWSThread implements WSClientI
if (newFrame)
{
displayInNewFrame(al, alorders, hidden);
if (newFrame)
{
displayInNewFrame(al, alorders, hidden);
+
}
else
{
}
else
{