src/jalview/ws/slivkaws/SlivkaWSInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.gui.WebserviceInfo;
   4 import jalview.ws.api.JalviewServiceEndpointProviderI;
   5 import jalview.ws.api.JalviewWebServiceI;
   6 import jalview.ws.api.ServiceWithParameters;
   7 import jalview.ws.gui.WsJob;
   8 import jalview.ws.params.ParamDatastoreI;
   9 import jalview.ws.params.ParamManager;
  10
  11 import java.io.IOError;
  12 import java.io.IOException;
  13 import java.io.InputStream;
  14 import java.io.InputStreamReader;
  15 import java.util.Arrays;
  16 import java.util.EnumMap;
  17 import java.util.HashSet;
  18 import java.util.Optional;
  19 import java.util.Set;
  20
  21 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  22 import uk.ac.dundee.compbio.slivkaclient.JobState;
  23 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  24 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  25 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  26 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
  27
  28 public abstract class SlivkaWSInstance extends ServiceWithParameters
  29     implements JalviewServiceEndpointProviderI, JalviewWebServiceI
  30 {
  31   protected final SlivkaClient client;
  32
  33   protected final SlivkaService service;
  34
  35   protected SlivkaDatastore store = null;
  36
  37   protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  38   {
  39     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  40     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  41     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  42     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  43     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  44     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  45     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  46   }
  47   protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
  48       WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
  49       WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
  50   ));
  51
  52   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
  53   {
  54     super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
  55     this.client = client;
  56     this.service = service;
  57   }
  58
  59   @Override
  60   public final void updateStatus(WsJob job)
  61   {
  62     try
  63     {
  64       job.setState(stateMap.get(client.getJobState(job.getJobId())));
  65     } catch (IOException e)
  66     {
  67       throw new IOError(e);
  68     }
  69   }
  70
  71   @Override
  72   public final boolean updateJobProgress(WsJob job) throws IOException
  73   {
  74     Optional<RemoteFile> logFile = client.getJobResults(job.getJobId()).stream()
  75         .filter(f -> f.getLabel() == "log").findFirst();
  76     if (logFile.isPresent())
  77     {
  78       InputStream stream = logFile.get().getContent();
  79       long nextChunk = stream.skip(job.getNextChunk());
  80       job.setnextChunk(nextChunk + appendJobStatus(job, stream));
  81     }
  82     if (failedStates.contains(job.getJobState()))
  83     {
  84       Optional<RemoteFile> errLogFile = client.getJobResults(job.getJobId()).stream()
  85           .filter(f -> f.getLabel() == "error-log").findFirst();
  86       if (errLogFile.isPresent())
  87       {
  88         appendJobStatus(job, errLogFile.get().getContent());
  89       }
  90     }
  91     return false;
  92   }
  93
  94   private int appendJobStatus(WsJob job, InputStream stream) throws IOException
  95   {
  96     StringBuilder builder = new StringBuilder(job.getStatus());
  97     InputStreamReader reader = new InputStreamReader(stream);
  98     char[] buffer = new char[4096];
  99     int chunkLen = 0;
 100     int len = 0;
 101     while ((len = reader.read(buffer)) != -1)
 102     {
 103       chunkLen += len;
 104       builder.append(buffer, 0, len);
 105     }
 106     job.setStatus(builder.toString());
 107     return chunkLen;
 108   }
 109
 110   @Override
 111   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
 112   {
 113     if (_lex instanceof FormValidationException)
 114     {
 115       FormValidationException formError = (FormValidationException) _lex;
 116       String[] messages = new String[formError.getErrors().size()];
 117       int i = 0;
 118       for (ValidationException e : formError.getErrors())
 119       {
 120         messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
 121       }
 122       j.setState(WsJob.JobState.INVALID);
 123       j.setStatus(String.join(", ", messages));
 124       return true;
 125     }
 126     return false;
 127   }
 128
 129   @Override
 130   public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
 131   {
 132     // TODO
 133     return false;
 134   }
 135
 136   final SlivkaService getService()
 137   {
 138     return service;
 139   }
 140
 141   @Override
 142   public final Object getEndpoint()
 143   {
 144     return this;
 145   }
 146
 147   @Override
 148   public final void initParamStore(ParamManager userParameterStore)
 149   {
 150     if (store == null)
 151     {
 152       try
 153       {
 154         store = new SlivkaDatastore(service);
 155       } catch (IOException e)
 156       {
 157         throw new IOError(e);
 158       }
 159     }
 160   }
 161
 162   @Override
 163   public boolean hasParameters()
 164   {
 165     return true;
 166   }
 167
 168   @Override
 169   public final ParamDatastoreI getParamStore()
 170   {
 171     if (store == null)
 172     {
 173       initParamStore(null);
 174     }
 175     return store;
 176   }
 177
 178 }