X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=db6e03f2e511d9502a43a45df7c6c15b6821d185;hb=efb5cfa00ee832a62dfdf59f5fb847a0e16424d9;hp=bd86bf0f39c158d88f888b9f6f9a1504629920cd;hpb=bf16f469383285628cdae9743c008095f9662605;p=jalview.git
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index bd86bf0..db6e03f 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -1,62 +1,59 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
- * 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 @@ -128,8 +125,8 @@ 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++) { @@ -164,12 +161,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI String empty = null; if (seqs[i].getEnd() >= seqs[i].getStart()) { - empty = (submitGaps) ? seqs[i].getSequenceAsString() : AlignSeq - .extractGaps(jalview.util.Comparison.GapChars, + empty = (submitGaps) ? seqs[i].getSequenceAsString() + : AlignSeq.extractGaps(jalview.util.Comparison.GapChars, seqs[i].getSequenceAsString()); } - emptySeqs.add(new String[] - { newname, empty }); + emptySeqs.add(new String[] { newname, empty }); } } return valid; @@ -179,12 +175,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI * * @return true if getAlignment will return a valid alignment result. */ + @Override 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; } @@ -213,7 +208,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI 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(); @@ -240,7 +236,7 @@ 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(); @@ -271,7 +267,7 @@ 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], @@ -300,8 +296,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI jalview.analysis.AlignmentSorter.recoverOrder(alseqs); // account for any missing sequences jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs); - return new Object[] - { alseqs, msaorder }; + return new Object[] { alseqs, msaorder }; } return null; } @@ -320,6 +315,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI * * @return boolean true if job can be submitted. */ + @Override public boolean hasValidInput() { // TODO: get attributes for this MsaWS instance to check if it can do two @@ -409,8 +405,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI { for (Argument opt : ((JabaWsParamSet) preset).getjabaArguments()) { - jobProgress.append(opt.getName() + " " + opt.getDefaultValue() - + "\n"); + jobProgress.append( + opt.getName() + " " + opt.getDefaultValue() + "\n"); } } } @@ -420,8 +416,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI // merge arguments with preset's own arguments. for (Argument opt : arguments) { - jobProgress.append(opt.getName() + " " + opt.getDefaultValue() - + "\n"); + jobProgress.append( + opt.getName() + " " + opt.getDefaultValue() + "\n"); } } jobProgress.append("\nJob Output:\n"); @@ -440,7 +436,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI String alTitle; // name which will be used to form new alignment window. - Alignment dataset; // dataset to which the new alignment will be + AlignmentI dataset; // dataset to which the new alignment will be // associated. @@ -455,7 +451,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI * @param presorder * boolean */ - MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo, + private MsaWSThread(MsaWS server, String wsUrl, WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, AlignmentView alview, String wsname, boolean subgaps, boolean presorder) { @@ -483,7 +479,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI String wsUrl, WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, String wsname, String title, AlignmentView _msa, boolean subgaps, boolean presorder, - Alignment seqset) + AlignmentI seqset) { this(server2, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder); OutputHeader = wsInfo.getProgressText(); @@ -493,7 +489,7 @@ 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++) { @@ -505,6 +501,10 @@ 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; @@ -515,14 +515,28 @@ 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; + } + + @Override public boolean isCancellable() { return true; } + @Override public void cancelJob() { if (!jobComplete && jobs != null) @@ -536,7 +550,7 @@ 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 @@ -564,8 +578,16 @@ class MsaWSThread extends AWS2Thread implements WSClientI "Exception whilst cancelling " + jobs[job].getJobId(), exc); } - wsInfo.setProgressText(jobs[job].getJobnum(), OutputHeader - + cancelledMessage + "\n"); + 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) @@ -585,6 +607,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI } } + @Override public void pollJob(AWsJob job) throws Exception { // TODO: investigate if we still need to cast here in J1.6 @@ -596,40 +619,58 @@ 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); - ChunkHolder chunk = server - .pullExecStatistics(j.getJobId(), 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; } + @Override public void StartJob(AWsJob job) { Exception lex = null; // 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()) { if (Cache.log.isDebugEnabled()) { - Cache.log.debug("Tried to submit an already submitted job " - + j.getJobId()); + Cache.log.debug( + "Tried to submit an already submitted job " + j.getJobId()); } return; } @@ -639,7 +680,7 @@ 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 { @@ -651,7 +692,7 @@ 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 { @@ -667,44 +708,50 @@ 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) { // 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"); + 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(), @@ -712,10 +759,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI } catch (Exception 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"); + 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(), @@ -728,15 +774,19 @@ class MsaWSThread extends AWS2Thread implements WSClientI // TODO: JBPNote catch timeout or other fault types explicitly j.setAllowedServerExceptions(0); - wsInfo.appendProgressText(j.getJobnum(), - "Failed to submit sequences for alignment.\n" - + "Just close the window\n"); + wsInfo.appendProgressText(j.getJobnum(), MessageManager.getString( + "info.failed_to_submit_sequences_for_alignment")); } } } + @Override 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 @@ -746,16 +796,45 @@ 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: " @@ -771,9 +850,12 @@ class MsaWSThread extends AWS2Thread implements WSClientI { // 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); + 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) { @@ -794,7 +876,8 @@ class MsaWSThread extends AWS2Thread implements WSClientI // wsInfo.appendProgressText(jobs[j].getJobnum(), // "\nAlignment Object Method Notes\n"); // wsInfo.appendProgressText(jobs[j].getJobnum(), - // "Calculated with "+alignment.getMetadata().getProgram().toString()); + // "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 @@ -804,8 +887,9 @@ class MsaWSThread extends AWS2Thread implements WSClientI } catch (Exception ex) { - Cache.log.error("Unexpected exception when processing results for " - + alTitle, ex); + Cache.log.error( + "Unexpected exception when processing results for " + alTitle, + ex); wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); } if (results > 0) @@ -813,6 +897,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI wsInfo.showResultsNewFrame .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(true); @@ -821,6 +906,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI wsInfo.mergeResults .addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(java.awt.event.ActionEvent evt) { displayResults(false); @@ -830,15 +916,22 @@ class MsaWSThread extends AWS2Thread implements WSClientI } else { - wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR); wsInfo.setFinishedNoResults(); } + updateGlobalStatus(finalState); + wsInfo.setProgressBar(null, progbar); } + /** + * Display alignment results in a new frame (or - not currently supported - + * added to an existing alignment). + * + * @param newFrame + */ void displayResults(boolean newFrame) { // view input or result data for each block - Vector alorders = new Vector(); + List