X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=5e8cb98a351e656cdfb5f52794c3099b1d9d05d6;hb=057f733ab390518a3641f1dedebd36c028bf03d6;hp=393f4751c9f848dd2af639d49357fbf0fc29e294;hpb=1081321a1184686cebd3ccfe3f255ed82af3e5c1;p=jalview.git
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 393f475..5e8cb98 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,27 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.jws2;
import java.util.*;
import compbio.data.msa.MsaWS;
-import compbio.data.sequence.AlignmentMetadata;
-import compbio.data.sequence.Program;
import compbio.metadata.Argument;
import compbio.metadata.ChunkHolder;
import compbio.metadata.JobStatus;
@@ -31,6 +32,7 @@ import jalview.analysis.*;
import jalview.bin.*;
import jalview.datamodel.*;
import jalview.gui.*;
+import jalview.util.MessageManager;
import jalview.ws.AWsJob;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
@@ -108,8 +110,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
int nseqs = 0;
if (minlen < 0)
{
- throw new Error(
- "Implementation error: minlen must be zero or more.");
+ throw new Error(MessageManager.getString("error.implementation_error_minlen_must_be_greater_zero"));
}
for (int i = 0; i < seqs.length; i++)
{
@@ -516,7 +517,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
try
{
boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
- if (cancelledJob || true)
+ if (true) // cancelledJob || true)
{
// CANCELLED_JOB
// if the Jaba server indicates the job can't be cancelled, its
@@ -547,6 +548,14 @@ class MsaWSThread extends AWS2Thread implements WSClientI
wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader
+ cancelledMessage + "\n");
}
+ else
+ {
+ // if we hadn't submitted then just mark the job as cancelled.
+ jobs[job].setSubjobComplete(true);
+ wsInfo.setStatus(jobs[job].getJobnum(),
+ WebserviceInfo.STATE_CANCELLED_OK);
+
+ }
}
if (cancelled)
{
@@ -586,7 +595,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
StringBuffer response = j.jobProgress;
long lastchunk = j.getLastChunk();
- boolean changed=false;
+ boolean changed = false;
do
{
j.setLastChunk(lastchunk);
@@ -594,9 +603,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI
.pullExecStatistics(j.getJobId(), lastchunk);
if (chunk != null)
{
- changed=chunk.getChunk().length()>0;
+ changed |= chunk.getChunk().length() > 0;
response.append(chunk.getChunk());
lastchunk = chunk.getNextPosition();
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ ;
}
;
} while (lastchunk >= 0 && j.getLastChunk() != lastchunk);
@@ -609,8 +625,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
// boiler plate template
if (!(job instanceof MsaWSJob))
{
- throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "
- + job.getClass());
+ throw new Error(MessageManager.formatMessage("error.implementation_error_msawbjob_called", new String[]{job.getClass().toString()}));
}
MsaWSJob j = (MsaWSJob) job;
if (j.isSubmitted())
@@ -628,7 +643,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
// special case - selection consisted entirely of empty sequences...
j.setjobStatus(JobStatus.FINISHED);
- j.setStatus("Empty Alignment Job");
+ j.setStatus(MessageManager.getString("label.empty_alignment_job"));
}
try
{
@@ -640,7 +655,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
else if (j.hasArguments())
{
- j.setJobId(server.customAlign(j.seqs,j.getJabaArguments()));
+ j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
}
else
{
@@ -656,35 +671,28 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
else
{
- throw new Exception(
- "Server at "
- + WsUrl
- + " returned null string for job id, it probably cannot be contacted. Try again later ?");
+ throw new Exception(MessageManager.formatMessage("exception.web_service_returned_null_try_later", new String[]{WsUrl}));
}
} catch (compbio.metadata.UnsupportedRuntimeException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because the server doesn't support this program.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Service not supported!");
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_server_doesnt_support_program", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.service_not_supported"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
wsInfo.setStatus(j.getJobnum(),
WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (compbio.metadata.LimitExceededException _lex)
{
lex = _lex;
- wsInfo.appendProgressText("Job could not be run because it exceeded a hard limit on the server.\n"
- + _lex.getMessage());
- wsInfo.warnUser(_lex.getMessage(), "Input is too big!");
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_exceeded_hard_limit", new String[]{_lex.getMessage()}));
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.input_is_too_big"));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (compbio.metadata.WrongParameterException _lex)
{
lex = _lex;
- wsInfo.warnUser(_lex.getMessage(), "Invalid job parameter set!");
- wsInfo.appendProgressText("Job could not be run because some of the parameter settings are not supported by the server.\n"
- + _lex.getMessage()
- + "\nPlease check to make sure you have used the correct parameter set for this service!\n");
+ wsInfo.warnUser(_lex.getMessage(), MessageManager.getString("warn.invalid_job_param_set"));
+ wsInfo.appendProgressText(MessageManager.formatMessage("info.job_couldnt_be_run_incorrect_param_setting", new String[]{_lex.getMessage()}));
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
} catch (Error e)
@@ -718,16 +726,15 @@ class MsaWSThread extends AWS2Thread implements WSClientI
j.setAllowedServerExceptions(0);
wsInfo.appendProgressText(j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "Just close the window\n");
+ MessageManager.getString("info.failed_to_submit_sequences_for_alignment"));
}
}
}
public void parseResult()
{
- long progbar=System.currentTimeMillis();
- wsInfo.setProgressBar("Collecting job results.", progbar);
+ long progbar = System.currentTimeMillis();
+ wsInfo.setProgressBar(MessageManager.getString("status.collecting_job_results"), progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
@@ -737,40 +744,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
if (jobs[j].isFinished() && msjob.alignment == null)
{
- boolean jpchanged=false,jpex=false;
- do {
+ int nunchanged = 3, nexcept = 3;
+ boolean jpchanged = false, jpex = false;
+ do
+ {
try
{
jpchanged = updateJobProgress(msjob);
- jpex=false;
+ jpex = false;
+ if (jpchanged)
+ {
+ nexcept = 3;
+ }
} catch (Exception e)
{
-
+
Cache.log
.warn("Exception when retrieving remaining Job progress data for job "
+ msjob.getJobId() + " on server " + WsUrl);
e.printStackTrace();
- if (jpex) {
- // give up polling after two consecutive exceptions
- jpchanged=false;
- } else {
- jpchanged=true;
- }
+ nexcept--;
+ nunchanged = 3;
// set flag remember that we've had an exception.
- jpex=true;
+ jpex = true;
+ jpchanged = false;
}
- if (jpchanged)
+ if (!jpchanged)
{
try
{
- Thread.sleep(jpex ? 400 : 200); // wait a bit longer if we experienced an exception.
+ Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+ // experienced an exception.
} catch (Exception ex)
{
}
;
+ nunchanged--;
}
- } while (jpchanged);
-
+ } while (nunchanged > 0 && nexcept > 0);
+
if (Cache.log.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
@@ -789,6 +801,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
Cache.log
.debug("Results not available for finished job - marking as broken job.",
e);
+ msjob.jobProgress
+ .append("\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
+ + e.getLocalizedMessage());
msjob.setjobStatus(JobStatus.FAILED);
} catch (Exception e)
{
@@ -845,9 +860,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
else
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
wsInfo.setProgressBar(null, progbar);
}