/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.
- *
+ *
* 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 <http://www.gnu.org/licenses/>.
+ * 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;
+import compbio.metadata.Preset;
import jalview.analysis.*;
import jalview.bin.*;
import jalview.ws.AWsJob;
import jalview.ws.WSClientI;
import jalview.ws.JobStateSummary;
+import jalview.ws.jws2.dm.JabaWsParamSet;
+import jalview.ws.params.WsParamSetI;
-/**
- * <p>
- * Title:
- * </p>
- *
- * <p>
- * Description:
- * </p>
- *
- * <p>
- * Copyright: Copyright (c) 2004
- * </p>
- *
- * <p>
- * Company: Dundee University
- * </p>
- *
- * @author not attributable
- * @version 1.0
- */
class MsaWSThread extends AWS2Thread implements WSClientI
{
boolean submitGaps = false; // pass sequences including gaps to alignment
class MsaWSJob extends JWs2Job
{
- long lastChunk=0;
-
+ long lastChunk = 0;
+
+ WsParamSetI preset = null;
+
+ List<Argument> arguments = null;
+
/**
- * input
+ * input
*/
ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+
/**
* output
*/
compbio.data.sequence.Alignment alignment;
- // set if the job didn't get run - then the input is simply returned to the user
- private boolean returnInput=false;
-
+
+ // set if the job didn't get run - then the input is simply returned to the
+ // user
+ private boolean returnInput = false;
+
/**
* MsaWSJob
*
}
- Hashtable<String,Map> SeqNames = new Hashtable();
+ Hashtable<String, Map> SeqNames = new Hashtable();
Vector<String[]> emptySeqs = new Vector();
// for
// any
// subjob
- SeqNames.put(newname, jalview.analysis.SeqsetUtils
- .SeqCharacterHash(seqs[i]));
+ SeqNames.put(newname,
+ jalview.analysis.SeqsetUtils.SeqCharacterHash(seqs[i]));
if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
{
// make new input sequence with or without gaps
seq = new compbio.data.sequence.FastaSequence(newname,
(submitGaps) ? seqs[i].getSequenceAsString()
- : AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- seqs[i].getSequenceAsString()));
+ : AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString()));
this.seqs.add(seq);
}
else
if (seqs[i].getEnd() >= seqs[i].getStart())
{
empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq
- .extractGaps(jalview.util.Comparison.GapChars, seqs[i]
- .getSequenceAsString());
+ .extractGaps(jalview.util.Comparison.GapChars,
+ seqs[i].getSequenceAsString());
}
emptySeqs.add(new String[]
{ newname, empty });
*/
public boolean hasResults()
{
- if (subjobComplete && isFinished() && (alignment!=null || (emptySeqs!=null && emptySeqs.size()>0)))
+ if (subjobComplete
+ && isFinished()
+ && (alignment != null || (emptySeqs != null && emptySeqs
+ .size() > 0)))
{
return true;
}
/**
*
- * get the alignment including any empty sequences in the original order with original ids. Caller must access the alignment.getMetadata() object to annotate the final result passsed to the user.
+ * get the alignment including any empty sequences in the original order
+ * with original ids. Caller must access the alignment.getMetadata() object
+ * to annotate the final result passsed to the user.
+ *
* @return { SequenceI[], AlignmentOrder }
*/
public Object[] getAlignment()
SequenceI[] alseqs = null;
char alseq_gapchar = '-';
int alseq_l = 0;
- if (alignment.getSequences().size()>0)
+ if (alignment.getSequences().size() > 0)
{
alseqs = new SequenceI[alignment.getSequences().size()];
- for (compbio.data.sequence.FastaSequence seq: alignment.getSequences())
+ for (compbio.data.sequence.FastaSequence seq : alignment
+ .getSequences())
{
- alseqs[alseq_l++] = new Sequence(seq.getId(),seq.getSequence());
+ alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
}
alseq_gapchar = alignment.getMetadata().getGapchar();
-
+
}
// add in the empty seqs.
if (emptySeqs.size() > 0)
*/
public boolean hasValidInput()
{
- // TODO: get attributes for this MsaWS instance to check if it can do two sequence alignment.
- if (seqs != null && seqs.size()>=2) // two or more sequences is valid ?
+ // TODO: get attributes for this MsaWS instance to check if it can do two
+ // sequence alignment.
+ if (seqs != null && seqs.size() >= 2) // two or more sequences is valid ?
{
return true;
}
return false;
}
- StringBuffer jobProgress=new StringBuffer();
+
+ StringBuffer jobProgress = new StringBuffer();
+
public void setStatus(String string)
{
jobProgress.setLength(0);
@Override
public boolean hasStatus()
{
- return jobProgress!=null;
+ return jobProgress != null;
}
/**
}
/**
- * @param lastChunk the lastChunk to set
+ * @param lastChunk
+ * the lastChunk to set
*/
public void setLastChunk(long lastChunk)
{
this.lastChunk = lastChunk;
}
-
+
+ String alignmentProgram = null;
+
+ public String getAlignmentProgram()
+ {
+ return alignmentProgram;
+ }
+
+ public boolean hasArguments()
+ {
+ return (arguments != null && arguments.size() > 0)
+ || (preset != null && preset instanceof JabaWsParamSet);
+ }
+
+ public List<Argument> getJabaArguments()
+ {
+ List<Argument> newargs = new ArrayList<Argument>();
+ 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.
* @param presorder
* boolean
*/
- MsaWSThread(MsaWS server, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
- AlignmentView alview, String wsname, boolean subgaps,
- boolean presorder)
+ MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo,
+ jalview.gui.AlignFrame alFrame, AlignmentView alview,
+ String wsname, boolean subgaps, boolean presorder)
{
super(alFrame, wsinfo, alview, wsname, wsUrl);
this.server = server;
* @param seqset
* Alignment
*/
- MsaWSThread(MsaWS server2, String wsUrl,
- WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
- String wsname, String title, AlignmentView _msa, boolean subgaps,
- boolean presorder, Alignment seqset)
+ MsaWSThread(MsaWS server2, WsParamSetI preset, List<Argument> paramset,
+ String wsUrl, WebserviceInfo wsinfo,
+ jalview.gui.AlignFrame alFrame, String wsname, String title,
+ AlignmentView _msa, boolean subgaps, boolean presorder,
+ Alignment seqset)
{
- this(server2,wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
+ this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
OutputHeader = wsInfo.getProgressText();
alTitle = title;
dataset = seqset;
{
jobs[j] = new MsaWSJob(0, conmsa[j]);
}
+ ((MsaWSJob) jobs[j]).preset = preset;
+ ((MsaWSJob) jobs[j]).arguments = paramset;
+ ((MsaWSJob) jobs[j]).alignmentProgram = wsname;
if (njobs > 0)
{
- wsinfo
- .setProgressName("region " + jobs[j].getJobnum(),
- jobs[j].getJobnum());
+ wsinfo.setProgressName("region " + jobs[j].getJobnum(),
+ jobs[j].getJobnum());
}
wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
}
String cancelledMessage = "";
try
{
- boolean cancelledJob = server
- .cancelJob(jobs[job].getJobId());
- if (cancelledJob)
+ boolean cancelledJob = server.cancelJob(jobs[job].getJobId());
+ if (true) // cancelledJob || true)
{
// CANCELLED_JOB
+ // if the Jaba server indicates the job can't be cancelled, its
+ // because its running on the server's local execution engine
+ // so we just close the window anyway.
cancelledMessage = "Job cancelled.";
- ((MsaWSJob) jobs[job]).cancel(); // TODO: refactor to avoid this ugliness -
+ ((MsaWSJob) jobs[job]).cancel(); // TODO: refactor to avoid this
+ // ugliness -
wsInfo.setStatus(jobs[job].getJobnum(),
WebserviceInfo.STATE_CANCELLED_OK);
- }
- else
+ }
+ else
{
// VALID UNSTOPPABLE JOB
cancelledMessage += "Server cannot cancel this job. just close the window.\n";
cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
+ exc + "\n");
Cache.log.warn(
- "Exception whilst cancelling " + jobs[job].getJobId(), exc);
+ "Exception whilst cancelling " + jobs[job].getJobId(),
+ exc);
}
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)
{
if (!jobComplete)
{
- wsInfo
- .setProgressText(OutputHeader
- + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+ wsInfo.setProgressText(OutputHeader
+ + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
}
}
}
public void pollJob(AWsJob job) throws Exception
{
// TODO: investigate if we still need to cast here in J1.6
- MsaWSJob j=((MsaWSJob) job);
+ MsaWSJob j = ((MsaWSJob) job);
+ // this is standard code, but since the interface doesn't comprise of a
+ // basic one that implements (getJobStatus, pullExecStatistics) we have to
+ // repeat the code for all jw2s services.
j.setjobStatus(server.getJobStatus(job.getJobId()));
+ updateJobProgress(j);
+ }
+
+ /**
+ *
+ * @param j
+ * @return true if more job progress data was available
+ * @throws Exception
+ */
+ protected boolean updateJobProgress(MsaWSJob j) throws Exception
+ {
StringBuffer response = j.jobProgress;
- ChunkHolder chunk = server.pullExecStatistics(job.getJobId(), j.getLastChunk());
- response.append(chunk.getChunk());
- j.setLastChunk(chunk.getNextPosition());
-
+ long lastchunk = j.getLastChunk();
+ boolean changed = false;
+ do
+ {
+ j.setLastChunk(lastchunk);
+ ChunkHolder chunk = server
+ .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)
{
+ Exception lex = null;
// boiler plate template
if (!(job instanceof MsaWSJob))
{
return;
}
// end boilerplate
-
- if (j.seqs == null || j.seqs.size()==0)
+
+ if (j.seqs == null || j.seqs.size() == 0)
{
// special case - selection consisted entirely of empty sequences...
j.setjobStatus(JobStatus.FINISHED);
}
try
{
- // TODO: get the parameters (if any) for this job and submit the job
- j.setJobId(server.align(j.seqs));
+ j.addInitialStatus(); // list the presets/parameters used for the job in
+ // status
+ if (j.isPresetJob())
+ {
+ j.setJobId(server.presetAlign(j.seqs, j.getServerPreset()));
+ }
+ else if (j.hasArguments())
+ {
+ j.setJobId(server.customAlign(j.seqs, j.getJabaArguments()));
+ }
+ else
+ {
+ j.setJobId(server.align(j.seqs));
+ }
- if (j.getJobId()!= null)
+ if (j.getJobId() != null)
{
j.setSubmitted(true);
j.setSubjobComplete(false);
// System.out.println(WsURL + " Job Id '" + jobId + "'");
+ return;
}
else
{
throw new Exception(
- "Server at "
- + WsUrl
- + " returned null string for job id, it probably cannot be contacted. Try again later ?");
- }
+ "Server at "
+ + WsUrl
+ + " returned null string for job id, it probably cannot be contacted. Try again later ?");
+ }
+ } 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.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.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.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+ wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
+ } catch (Error e)
+ {
+ // For unexpected errors
+ System.err
+ .println(WebServiceName
+ + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+ + "When contacting Server:" + WsUrl + "\n");
+ e.printStackTrace(System.err);
+ wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
} catch (Exception e)
{
- // Boilerplate code here
- // TODO: JBPNote catch timeout or other fault types explicitly
// For unexpected errors
System.err
.println(WebServiceName
+ "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
- + "When contacting Server:" + WsUrl + "\n"
- + e.toString() + "\n");
- j.setAllowedServerExceptions(0);
+ + "When contacting Server:" + WsUrl + "\n");
+ e.printStackTrace(System.err);
wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_SERVERERROR);
- wsInfo
- .appendProgressText(
- j.getJobnum(),
- "Failed to submit sequences for alignment.\n"
- + "It is most likely that there is a problem with the server.\n"
- + "Just close the window\n");
+ wsInfo.setStatus(j.getJobnum(),
+ WebserviceInfo.STATE_STOPPED_SERVERERROR);
+ } finally
+ {
+ if (!j.isSubmitted())
+ {
+ // Boilerplate code here
+ // TODO: JBPNote catch timeout or other fault types explicitly
- // e.printStackTrace(); // TODO: JBPNote DEBUG
+ j.setAllowedServerExceptions(0);
+ wsInfo.appendProgressText(j.getJobnum(),
+ "Failed to submit sequences for alignment.\n"
+ + "Just close the window\n");
+ }
}
}
-
public void parseResult()
{
+ long progbar = System.currentTimeMillis();
+ wsInfo.setProgressBar("Collecting job results.", progbar);
int results = 0; // number of result sets received
JobStateSummary finalState = new JobStateSummary();
try
for (int j = 0; j < jobs.length; j++)
{
MsaWSJob msjob = ((MsaWSJob) jobs[j]);
- if (jobs[j].isFinished() && msjob.alignment==null)
+ if (jobs[j].isFinished() && msjob.alignment == null)
{
- try {
- msjob.alignment = server.getResult(msjob.getJobId());
+ int nunchanged = 3, nexcept = 3;
+ boolean jpchanged = false, jpex = false;
+ do
+ {
+ 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: "
+ + msjob.getJobId() + " on server " + WsUrl);
+ System.out.println(msjob.getStatus());
+ System.out.println("*** End of status");
+
}
- catch (Exception e)
+ try
{
- Cache.log.error("Couldn't get Alignment for job.",e);
+ msjob.alignment = server.getResult(msjob.getJobId());
+ } catch (compbio.metadata.ResultNotAvailableException e)
+ {
+ // job has failed for some reason - probably due to invalid
+ // parameters
+ 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)
+ {
+ Cache.log.error("Couldn't get Alignment for job.", e);
+ // TODO: Increment count and retry ?
+ msjob.setjobStatus(JobStatus.UNDEFINED);
}
}
finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
compbio.data.sequence.Alignment alignment = ((MsaWSJob) jobs[j]).alignment;
if (alignment != null)
{
- wsInfo.appendProgressText(jobs[j].getJobnum(),
- "\nAlignment Object Method Notes\n");
- wsInfo.appendProgressText(jobs[j].getJobnum(), "Calculated with "+alignment.getMetadata().getProgram().toString());
+ // server.close(jobs[j].getJobnum());
+ // wsInfo.appendProgressText(jobs[j].getJobnum(),
+ // "\nAlignment Object Method Notes\n");
+ // wsInfo.appendProgressText(jobs[j].getJobnum(),
+ // "Calculated with "+alignment.getMetadata().getProgram().toString());
// JBPNote The returned files from a webservice could be
// hidden behind icons in the monitor window that,
// when clicked, pop up their corresponding data
{
wsInfo.setFinishedNoResults();
}
+ updateGlobalStatus(finalState);
+ wsInfo.setProgressBar(null, progbar);
}
void displayResults(boolean newFrame)
{
if (jobs[j].hasResults())
{
- msjob = (MsaWSJob)jobs[j];
+ msjob = (MsaWSJob) jobs[j];
Object[] res = msjob.getAlignment();
- lastProgram = msjob.alignment.getMetadata().getProgram().name();
+ lastProgram = msjob.getAlignmentProgram();
alorders.add(res[1]);
results[j] = (SequenceI[]) res[0];
orders[j] = (AlignmentOrder) res[1];
ColumnSelection columnselection = (ColumnSelection) newview[1];
Alignment al = new Alignment(alignment);
// TODO: add 'provenance' property to alignment from the method notes
- if (lastProgram!=null) {
+ if (lastProgram != null)
+ {
al.setProperty("Alignment Program", lastProgram);
}
// accompanying each subjob
}
for (int i = 0, l = alorders.size(); i < l; i++)
{
- af.addSortByOrderMenuItem(WebServiceName
- + ((String) names.get(i)) + " Ordering",
+ af.addSortByOrderMenuItem(
+ WebServiceName + ((String) names.get(i)) + " Ordering",
(AlignmentOrder) alorders.get(i));
}
}
git://source.jalview.org / jalview.git / blobdiff