X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=d2bb8973ecf6fb61322473c90b3dc3b2a24e9049;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=6f06731f1d704d35cbf764a9f89908573384fbfe;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 6f06731..d2bb897 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,60 +1,55 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * 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 jalview.analysis.AlignSeq;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.WebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.AWsJob;
+import jalview.ws.JobStateSummary;
+import jalview.ws.WSClientI;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
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;
import compbio.metadata.Preset;
-import jalview.analysis.*;
-import jalview.bin.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.ws.AWsJob;
-import jalview.ws.WSClientI;
-import jalview.ws.JobStateSummary;
-
-/**
- *
- * Title:
- *
- *
- *
- * Description:
- *
- *
- *
- * Copyright: Copyright (c) 2004
- *
- *
- *
- * Company: Dundee University
- *
- *
- * @author not attributable
- * @version 1.0
- */
class MsaWSThread extends AWS2Thread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
@@ -69,7 +64,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
long lastChunk = 0;
- Preset preset = null;
+ WsParamSetI preset = null;
List arguments = null;
@@ -126,8 +121,7 @@ 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++)
{
@@ -238,7 +232,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
int ow = w, nw = w;
for (i = 0, w = emptySeqs.size(); i < w; i++)
{
- String[] es = (String[]) emptySeqs.get(i);
+ String[] es = emptySeqs.get(i);
if (es != null && es[1] != null)
{
int sw = es[1].length();
@@ -269,7 +263,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
for (i = 0, w = emptySeqs.size(); i < w; i++)
{
- String[] es = (String[]) emptySeqs.get(i);
+ String[] es = emptySeqs.get(i);
if (es[1] == null)
{
t_alseqs[i + alseq_l] = new jalview.datamodel.Sequence(es[0],
@@ -373,6 +367,67 @@ class MsaWSThread extends AWS2Thread implements WSClientI
return alignmentProgram;
}
+ public boolean hasArguments()
+ {
+ return (arguments != null && arguments.size() > 0)
+ || (preset != null && preset instanceof JabaWsParamSet);
+ }
+
+ public List getJabaArguments()
+ {
+ List newargs = new ArrayList();
+ if (preset != null && preset instanceof JabaWsParamSet)
+ {
+ newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ newargs.addAll(arguments);
+ }
+ return newargs;
+ }
+
+ /**
+ * add a progess header to status string containing presets/args used
+ */
+ public void addInitialStatus()
+ {
+ if (preset != null)
+ {
+ jobProgress.append("Using "
+ + (preset instanceof JabaPreset ? "Server" : "User")
+ + "Preset: " + preset.getName());
+ if (preset instanceof JabaWsParamSet)
+ {
+ for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments())
+ {
+ jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+ + "\n");
+ }
+ }
+ }
+ if (arguments != null && arguments.size() > 0)
+ {
+ jobProgress.append("With custom parameters : \n");
+ // merge arguments with preset's own arguments.
+ for (Argument opt : arguments)
+ {
+ jobProgress.append(opt.getName() + " " + opt.getDefaultValue()
+ + "\n");
+ }
+ }
+ jobProgress.append("\nJob Output:\n");
+ }
+
+ public boolean isPresetJob()
+ {
+ return preset != null && preset instanceof JabaPreset;
+ }
+
+ public Preset getServerPreset()
+ {
+ return (isPresetJob()) ? ((JabaPreset) preset).p : null;
+ }
}
String alTitle; // name which will be used to form new alignment window.
@@ -416,7 +471,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, Preset preset, List paramset,
+ MsaWSThread(MsaWS server2, WsParamSetI preset, List paramset,
String wsUrl, WebserviceInfo wsinfo,
jalview.gui.AlignFrame alFrame, String wsname, String title,
AlignmentView _msa, boolean subgaps, boolean presorder,
@@ -430,7 +485,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
SequenceI[][] conmsa = _msa.getVisibleContigs('-');
if (conmsa != null)
{
- int njobs = conmsa.length;
+ int nvalid = 0, njobs = conmsa.length;
jobs = new MsaWSJob[njobs];
for (int j = 0; j < njobs; j++)
{
@@ -442,6 +497,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
+ if (((MsaWSJob) jobs[j]).hasValidInput())
+ {
+ nvalid++;
+ }
((MsaWSJob) jobs[j]).preset = preset;
((MsaWSJob) jobs[j]).arguments = paramset;
((MsaWSJob) jobs[j]).alignmentProgram = wsname;
@@ -452,9 +511,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
}
+ validInput = nvalid > 0;
}
}
+ boolean validInput = false;
+
+ /**
+ *
+ * @return true if the thread will perform a calculation
+ */
+ public boolean hasValidInput()
+ {
+ return validInput;
+ }
public boolean isCancellable()
{
return true;
@@ -473,7 +543,7 @@ 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
@@ -504,6 +574,14 @@ 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)
{
@@ -533,10 +611,17 @@ class MsaWSThread extends AWS2Thread implements WSClientI
updateJobProgress(j);
}
- protected void updateJobProgress(MsaWSJob j) throws Exception
+ /**
+ *
+ * @param j
+ * @return true if more job progress data was available
+ * @throws Exception
+ */
+ protected boolean updateJobProgress(MsaWSJob j) throws Exception
{
StringBuffer response = j.jobProgress;
long lastchunk = j.getLastChunk();
+ boolean changed = false;
do
{
j.setLastChunk(lastchunk);
@@ -544,11 +629,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI
.pullExecStatistics(j.getJobId(), lastchunk);
if (chunk != null)
{
+ 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);
+ return changed;
}
public void StartJob(AWsJob job)
@@ -557,8 +651,7 @@ 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())
@@ -576,25 +669,19 @@ 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
{
- // TODO: get the parameters (if any) for this job and submit the job
- if (j.arguments != null && j.arguments.size() > 0)
+ j.addInitialStatus(); // list the presets/parameters used for the job in
+ // status
+ if (j.isPresetJob())
{
- StringBuffer pset = new StringBuffer();
- for (Argument arg : j.arguments)
- {
- pset.append(arg.getName() + " " + arg.getDefaultValue() + "\n");
- }
- j.setStatus("Custom Parameters:\n" + pset.toString()
- + "\nJob Output:\n");
- j.setJobId(server.customAlign(j.seqs, j.arguments));
+ j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
}
- else if (j.preset != null)
+ else if (j.hasArguments())
{
- j.setJobId(server.presetAlign(j.seqs, j.preset));
+ j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
}
else
{
@@ -610,35 +697,28 @@ 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)
@@ -672,14 +752,15 @@ 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(MessageManager.getString("status.collecting_job_results"), progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
@@ -689,16 +770,45 @@ class MsaWSThread extends AWS2Thread implements WSClientI
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
if (jobs[j].isFinished() && msjob.alignment == null)
{
- try
- {
- updateJobProgress(msjob);
- } catch (Exception e)
+ int nunchanged = 3, nexcept = 3;
+ boolean jpchanged = false, jpex = false;
+ do
{
- Cache.log
- .warn("Exception when retrieving remaining Job progress data for job "
- + msjob.getJobId() + " on server " + WsUrl);
- e.printStackTrace();
- }
+ try
+ {
+ jpchanged = updateJobProgress(msjob);
+ 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();
+ nexcept--;
+ nunchanged = 3;
+ // set flag remember that we've had an exception.
+ jpex = true;
+ jpchanged = false;
+ }
+ if (!jpchanged)
+ {
+ try
+ {
+ Thread.sleep(jpex ? 2400 : 1200); // wait a bit longer if we
+ // experienced an exception.
+ } catch (Exception ex)
+ {
+ }
+ ;
+ nunchanged--;
+ }
+ } while (nunchanged > 0 && nexcept > 0);
+
if (Cache.log.isDebugEnabled())
{
System.out.println("Job Execution file for job: "
@@ -717,6 +827,9 @@ 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)
{
@@ -773,9 +886,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
}
else
{
- wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
+ wsInfo.setProgressBar(null, progbar);
}
void displayResults(boolean newFrame)