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.List;
  19 import java.util.Optional;
  20 import java.util.Set;
  21
  22 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  23 import uk.ac.dundee.compbio.slivkaclient.JobState;
  24 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  25 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  26 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  27 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
  28
  29 public abstract class SlivkaWSInstance extends ServiceWithParameters
  30     implements JalviewServiceEndpointProviderI, JalviewWebServiceI
  31 {
  32   protected final SlivkaClient client;
  33
  34   protected final SlivkaService service;
  35
  36   protected SlivkaDatastore store = null;
  37
  38   protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  39   {
  40     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  41     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  42     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  43     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  44     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  45     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  46     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  47   }
  48   protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
  49       WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
  50       WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
  51   ));
  52
  53   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
  54   {
  55     super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
  56     this.client = client;
  57     this.service = service;
  58   }
  59
  60   @Override
  61   public final void updateStatus(WsJob job)
  62   {
  63     try
  64     {
  65       job.setState(stateMap.get(client.getJobState(job.getJobId())));
  66     } catch (IOException e)
  67     {
  68       throw new IOError(e);
  69     }
  70   }
  71
  72   @Override
  73   public final boolean updateJobProgress(WsJob job) throws IOException
  74   {
  75     List<RemoteFile> files = client.getJobResults(job.getJobId());
  76     Optional<RemoteFile> logFile = files.stream()
  77         .filter(f -> f.getLabel().equals("log")).findFirst();
  78     boolean newContent = false;
  79     if (logFile.isPresent())
  80     {
  81       InputStream stream = logFile.get().getContent();
  82       long nextChunk = stream.skip(job.getNextChunk());
  83       int len = appendJobStatus(job, stream);
  84       job.setnextChunk(nextChunk + len);
  85       newContent |= len > 0;
  86     }
  87     if (failedStates.contains(job.getJobState()))
  88     {
  89       Optional<RemoteFile> errLogFile = files.stream()
  90           .filter(f -> f.getLabel().equals("error-log")).findFirst();
  91       if (errLogFile.isPresent())
  92       {
  93         newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
  94       }
  95     }
  96     return newContent;
  97   }
  98
  99   private int appendJobStatus(WsJob job, InputStream stream) throws IOException
 100   {
 101     StringBuilder builder = new StringBuilder(job.getStatus());
 102     InputStreamReader reader = new InputStreamReader(stream);
 103     char[] buffer = new char[4096];
 104     int chunkLen = 0;
 105     int len = 0;
 106     while ((len = reader.read(buffer)) != -1)
 107     {
 108       chunkLen += len;
 109       builder.append(buffer, 0, len);
 110     }
 111     job.setStatus(builder.toString());
 112     return chunkLen;
 113   }
 114
 115   @Override
 116   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
 117   {
 118     if (_lex instanceof FormValidationException)
 119     {
 120       FormValidationException formError = (FormValidationException) _lex;
 121       String[] messages = new String[formError.getErrors().size()];
 122       int i = 0;
 123       for (ValidationException e : formError.getErrors())
 124       {
 125         messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
 126       }
 127       j.setState(WsJob.JobState.INVALID);
 128       j.setStatus(String.join(", ", messages));
 129       return true;
 130     }
 131     return false;
 132   }
 133
 134   @Override
 135   public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
 136   {
 137     // TODO
 138     return false;
 139   }
 140
 141   final SlivkaService getService()
 142   {
 143     return service;
 144   }
 145
 146   @Override
 147   public final Object getEndpoint()
 148   {
 149     return this;
 150   }
 151
 152   @Override
 153   public final void initParamStore(ParamManager userParameterStore)
 154   {
 155     if (store == null)
 156     {
 157       try
 158       {
 159         store = new SlivkaDatastore(service);
 160       } catch (IOException e)
 161       {
 162         throw new IOError(e);
 163       }
 164     }
 165   }
 166
 167   @Override
 168   public boolean hasParameters()
 169   {
 170     return true;
 171   }
 172
 173   @Override
 174   public final ParamDatastoreI getParamStore()
 175   {
 176     if (store == null)
 177     {
 178       initParamStore(null);
 179     }
 180     return store;
 181   }
 182
 183 }