X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=d2bb8973ecf6fb61322473c90b3dc3b2a24e9049;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=3ecba74d392d4d4ffbdbc6ba44da4cab9cb64c22;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java index 3ecba74..d2bb897 100644 --- a/src/jalview/ws/jws2/MsaWSThread.java +++ b/src/jalview/ws/jws2/MsaWSThread.java @@ -1,42 +1,55 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 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; -import jalview.ws.jws2.dm.JabaWsParamSet; -import jalview.ws.params.WsParamSetI; - class MsaWSThread extends AWS2Thread implements WSClientI { boolean submitGaps = false; // pass sequences including gaps to alignment @@ -108,8 +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++) { @@ -220,7 +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(); @@ -251,7 +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], @@ -473,7 +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++) { @@ -485,6 +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; @@ -495,9 +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; @@ -516,7 +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 @@ -547,6 +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) { @@ -586,7 +621,7 @@ 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 +629,16 @@ 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 +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()) @@ -628,7 +669,7 @@ 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 +681,7 @@ 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 +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) @@ -718,14 +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 @@ -735,40 +770,45 @@ 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: " @@ -787,6 +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) { @@ -843,9 +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)