src/jalview/ws/jws2/jabaws2/JabawsMsaInstance.java

   1 package jalview.ws.jws2.jabaws2;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.Sequence;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.WebserviceInfo;
   8 import jalview.util.MessageManager;
   9 import jalview.ws.api.CancellableI;
  10 import jalview.ws.api.JobId;
  11 import jalview.ws.api.MultipleSequenceAlignmentI;
  12 import jalview.ws.gui.WsJob;
  13 import jalview.ws.gui.WsJob.JobState;
  14 import jalview.ws.jws2.JabaParamStore;
  15 import jalview.ws.jws2.JabaPreset;
  16 import jalview.ws.jws2.dm.JabaWsParamSet;
  17 import jalview.ws.params.ArgumentI;
  18 import jalview.ws.params.InvalidArgumentException;
  19 import jalview.ws.params.WsParamSetI;
  20
  21 import java.io.IOError;
  22 import java.rmi.ServerError;
  23 import java.util.ArrayList;
  24 import java.util.HashMap;
  25 import java.util.List;
  26 import java.util.Map;
  27
  28 import compbio.data.msa.MsaWS;
  29 import compbio.data.sequence.Alignment;
  30 import compbio.data.sequence.FastaSequence;
  31 import compbio.metadata.Argument;
  32 import compbio.metadata.ChunkHolder;
  33 import compbio.metadata.JobStatus;
  34 import compbio.metadata.Preset;
  35 import compbio.metadata.ResultNotAvailableException;
  36
  37 public class JabawsMsaInstance
  38         implements MultipleSequenceAlignmentI, CancellableI
  39 {
  40   /**
  41    * our service instance handler generated by the discoverer
  42    */
  43   Jws2Instance our;
  44
  45   MsaWS<?> service;
  46
  47   @Override
  48   public JobId align(List<SequenceI> toalign, WsParamSetI parameters,
  49           List<ArgumentI> arguments) throws Throwable
  50   {
  51     List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
  52     for (SequenceI seq : toalign)
  53     {
  54       seqs.add(new FastaSequence(seq.getName(), seq.getSequenceAsString()));
  55     }
  56     String jobid = null;
  57     if (parameters != null)
  58     {
  59       if (parameters instanceof JabaPreset)
  60       {
  61         jobid = service.presetAlign(seqs,
  62                 ((JabaPreset) parameters).getJabaPreset());
  63       }
  64       else
  65       {
  66         jobid = service.customAlign(seqs, JabaParamStore
  67                 .getJabafromJwsArgs(parameters.getArguments()));
  68       }
  69     }
  70     else if (arguments != null && arguments.size() > 0)
  71     {
  72       jobid = service.customAlign(seqs,
  73               JabaParamStore.getJabafromJwsArgs(arguments));
  74     }
  75     else
  76     {
  77       jobid = service.align(seqs);
  78     }
  79
  80     if (jobid == null)
  81     {
  82       return null;
  83     }
  84     return new JobId(our.getServiceType(), our.getName(), jobid);
  85   }
  86
  87   @Override
  88   public AlignmentI getAlignmentFor(JobId jobId)
  89           throws InvalidArgumentException, ServerError, IOError
  90   {
  91     Alignment alignment = null;
  92     try
  93     {
  94       alignment = service.getResult(jobId.getJobId());
  95     } catch (ResultNotAvailableException rnotav)
  96     {
  97
  98       // TODO - migrate JABA exception
  99       // throw new ServerError("Couldn't get result for job",rnotav);
 100     }
 101     SequenceI[] alseqs;
 102     int alseq_l = 0;
 103     if (alignment.getSequences().size() == 0)
 104     {
 105       return null;
 106     }
 107
 108     alseqs = new SequenceI[alignment.getSequences().size()];
 109     for (compbio.data.sequence.FastaSequence seq : alignment.getSequences())
 110     {
 111       alseqs[alseq_l++] = new Sequence(seq.getId(), seq.getSequence());
 112     }
 113     AlignmentI jv_al = new jalview.datamodel.Alignment(alseqs);
 114     jv_al.setGapCharacter(alignment.getMetadata().getGapchar());
 115     return jv_al;
 116
 117   }
 118
 119   public JabawsMsaInstance(Jws2Instance handle)
 120   {
 121     our = handle;
 122     service = (MsaWS<?>) our.service;
 123   }
 124
 125   @Override
 126   public boolean cancel(WsJob job)
 127   {
 128     service.cancelJob(job.getJobId());
 129     // if the Jaba server indicates the job can't be cancelled, its
 130     // because its running on the server's local execution engine
 131     // so we just close the window anyway.
 132
 133     return true;
 134   }
 135
 136   Map<JobStatus, JobState> jwsState = new HashMap<>();
 137   {
 138     jwsState.put(JobStatus.CANCELLED, JobState.CANCELLED);
 139     jwsState.put(JobStatus.COLLECTED, JobState.FINISHED);
 140     jwsState.put(JobStatus.FAILED, JobState.FAILED);
 141     jwsState.put(JobStatus.FINISHED, JobState.FINISHED);
 142     jwsState.put(JobStatus.PENDING, JobState.QUEUED);
 143     jwsState.put(JobStatus.RUNNING, JobState.RUNNING);
 144     jwsState.put(JobStatus.STARTED, JobState.RUNNING);
 145     jwsState.put(JobStatus.SUBMITTED, JobState.SUBMITTED);
 146     jwsState.put(JobStatus.UNDEFINED, JobState.UNKNOWN);
 147   }
 148   @Override
 149   public void updateStatus(WsJob job)
 150   {
 151     JobStatus jwsstatus = service.getJobStatus(job.getJobId());
 152     job.setState(jwsState.get(jwsstatus));
 153   }
 154
 155   @Override
 156   public boolean updateJobProgress(WsJob job) throws Exception
 157   {
 158     StringBuilder response = new StringBuilder(job.getStatus());
 159     long lastchunk = job.getNextChunk();
 160     boolean changed = false;
 161     do
 162     {
 163       ChunkHolder chunk = service.pullExecStatistics(job.getJobId(),
 164               lastchunk);
 165       if (chunk != null)
 166       {
 167         changed |= chunk.getChunk().length() > 0;
 168         response.append(chunk.getChunk());
 169         lastchunk = chunk.getNextPosition();
 170         try
 171         {
 172           Thread.sleep(50);
 173         } catch (InterruptedException x)
 174         {
 175         }
 176         ;
 177       }
 178       ;
 179       job.setnextChunk(lastchunk);
 180     } while (lastchunk >= 0 && job.getNextChunk() != lastchunk);
 181     if (job instanceof WsJob)
 182     {
 183       // TODO decide if WsJob will be the bean for all ng-webservices
 184       job.setStatus(response.toString());
 185     }
 186     return changed;
 187   }
 188
 189   public boolean isPresetJob(WsJob job)
 190   {
 191     return job.getPreset() != null && job.getPreset() instanceof JabaPreset;
 192   }
 193
 194   public Preset getServerPreset(WsJob job)
 195   {
 196     return (isPresetJob(job))
 197             ? ((JabaPreset) job.getPreset()).getJabaPreset()
 198             : null;
 199   }
 200
 201   public List<Argument> getJabaArguments(WsParamSetI preset)
 202   {
 203     List<Argument> newargs = new ArrayList<>();
 204     if (preset != null)
 205     {
 206       if (preset instanceof JabaWsParamSet)
 207       {
 208         newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
 209       }
 210       else
 211       {
 212         newargs.addAll(
 213                 JabaParamStore.getJabafromJwsArgs(preset.getArguments()));
 214       }
 215     }
 216     return newargs;
 217   }
 218
 219   @Override
 220   public boolean handleSubmitError(Throwable _lex, WsJob j,
 221           WebserviceInfo wsInfo) throws Exception, Error
 222   {
 223     if (_lex instanceof compbio.metadata.UnsupportedRuntimeException)
 224     {
 225       wsInfo.appendProgressText(MessageManager.formatMessage(
 226               "info.job_couldnt_be_run_server_doesnt_support_program",
 227               new String[]
 228               { _lex.getMessage() }));
 229       wsInfo.warnUser(_lex.getMessage(),
 230               MessageManager.getString("warn.service_not_supported"));
 231       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
 232       wsInfo.setStatus(j.getJobnum(),
 233               WebserviceInfo.STATE_STOPPED_SERVERERROR);
 234       return true;
 235     }
 236     if (_lex instanceof compbio.metadata.LimitExceededException)
 237     {
 238       wsInfo.appendProgressText(MessageManager.formatMessage(
 239               "info.job_couldnt_be_run_exceeded_hard_limit", new String[]
 240               { _lex.getMessage() }));
 241       wsInfo.warnUser(_lex.getMessage(),
 242               MessageManager.getString("warn.input_is_too_big"));
 243       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
 244       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
 245       return true;
 246     }
 247     if (_lex instanceof compbio.metadata.WrongParameterException)
 248     {
 249       wsInfo.warnUser(_lex.getMessage(),
 250               MessageManager.getString("warn.invalid_job_param_set"));
 251       wsInfo.appendProgressText(MessageManager.formatMessage(
 252               "info.job_couldnt_be_run_incorrect_param_setting",
 253               new String[]
 254               { _lex.getMessage() }));
 255       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
 256       wsInfo.setStatus(j.getJobnum(), WebserviceInfo.STATE_STOPPED_ERROR);
 257       return true;
 258     }
 259     // pass on to generic error handler
 260     return false;
 261   }
 262
 263   @Override
 264   public boolean handleCollectionException(Exception ex, WsJob msjob,
 265           WebserviceInfo wsInfo)
 266   {
 267     if (ex instanceof compbio.metadata.ResultNotAvailableException)
 268     {
 269       // job has failed for some reason - probably due to invalid
 270       // parameters
 271       Cache.log.debug(
 272               "Results not available for finished job - marking as broken job.",
 273               ex);
 274       String status = msjob.getStatus();
 275
 276       msjob.setStatus(status
 277               +
 278               "\nResult not available. Probably due to invalid input or parameter settings. Server error message below:\n\n"
 279                       + ex.getLocalizedMessage());
 280       msjob.setState(WsJob.JobState.BROKEN);
 281       return true;
 282     }
 283     return false;
 284   }
 285 }