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Merge branch 'develop' into improvement/JAL-3594_BG_and_UoD_logos_added
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
MsaWSThread.java
diff --git
a/src/jalview/ws/jws2/MsaWSThread.java
b/src/jalview/ws/jws2/MsaWSThread.java
index
db6e03f
..
ee0fbc5
100644
(file)
--- a/
src/jalview/ws/jws2/MsaWSThread.java
+++ b/
src/jalview/ws/jws2/MsaWSThread.java
@@
-21,7
+21,7
@@
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
package jalview.ws.jws2;
import jalview.analysis.AlignSeq;
-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;
@@
-574,7
+574,7
@@
class MsaWSThread extends AWS2Thread 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);
}
@@
-667,9
+667,9
@@
class MsaWSThread extends AWS2Thread 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;
@@
-811,7
+811,7
@@
class MsaWSThread extends AWS2Thread 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();
@@
-835,7
+835,7
@@
class MsaWSThread extends AWS2Thread 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);
@@
-850,7
+850,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
{
// job has failed for some reason - probably due to invalid
// parameters
{
// job has failed for some reason - probably due to invalid
// parameters
- Cache.log.debug(
+ Console.debug(
"Results not available for finished job - marking as broken job.",
e);
msjob.jobProgress.append(
"Results not available for finished job - marking as broken job.",
e);
msjob.jobProgress.append(
@@
-859,7
+859,7
@@
class MsaWSThread extends AWS2Thread implements WSClientI
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
- 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.setjobStatus(JobStatus.UNDEFINED);
}
// TODO: Increment count and retry ?
msjob.setjobStatus(JobStatus.UNDEFINED);
}
@@
-887,7
+887,7
@@
class MsaWSThread extends AWS2Thread 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);