src/jalview/ws/slivkaws/SlivkaWSInstance.java

   1 package jalview.ws.slivkaws;
   2
   3 import jalview.datamodel.SequenceI;
   4 import jalview.gui.WebserviceInfo;
   5 import jalview.ws.api.JalviewServiceEndpointProviderI;
   6 import jalview.ws.api.JalviewWebServiceI;
   7 import jalview.ws.api.JobId;
   8 import jalview.ws.api.ServiceWithParameters;
   9 import jalview.ws.gui.WsJob;
  10 import jalview.ws.params.ArgumentI;
  11 import jalview.ws.params.ParamDatastoreI;
  12 import jalview.ws.params.ParamManager;
  13 import jalview.ws.params.WsParamSetI;
  14
  15 import java.io.ByteArrayInputStream;
  16 import java.io.IOError;
  17 import java.io.IOException;
  18 import java.io.InputStream;
  19 import java.io.InputStreamReader;
  20 import java.util.Arrays;
  21 import java.util.EnumMap;
  22 import java.util.HashSet;
  23 import java.util.List;
  24 import java.util.Optional;
  25 import java.util.Set;
  26
  27 import uk.ac.dundee.compbio.slivkaclient.FieldType;
  28 import uk.ac.dundee.compbio.slivkaclient.FormField;
  29 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  30 import uk.ac.dundee.compbio.slivkaclient.JobState;
  31 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  32 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  33 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  34 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  35 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
  36
  37 public abstract class SlivkaWSInstance extends ServiceWithParameters
  38     implements JalviewServiceEndpointProviderI, JalviewWebServiceI
  39 {
  40   protected final SlivkaClient client;
  41
  42   protected final SlivkaService service;
  43
  44   protected SlivkaDatastore store = null;
  45
  46   protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  47   {
  48     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  49     stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
  50     stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
  51     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  52     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  53     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  54     stateMap.put(JobState.INTERRUPED, WsJob.JobState.CANCELLED);
  55     stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
  56     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  57     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  58     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  59   }
  60   protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
  61       WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
  62       WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
  63   ));
  64
  65   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
  66   {
  67     super(service.getName(), action, service.getLabel(), "Slivka", client.getUrl().toString());
  68     this.client = client;
  69     this.service = service;
  70   }
  71
  72   protected final JobId submit(List<SequenceI> sequences,
  73           WsParamSetI preset, List<ArgumentI> args) throws Throwable
  74   {
  75     SlivkaForm form = service.getForm();
  76     Optional<FormField> inputField = form.getFields().stream()
  77             .filter(f -> f.getType() == FieldType.FILE).findFirst();
  78     if (inputField.isPresent())
  79     {
  80       StringBuilder builder = new StringBuilder();
  81       for (SequenceI seq : sequences)
  82       {
  83         builder.append(">").append(seq.getName()).append("\n")
  84                 .append(seq.getSequence()).append("\n");
  85       }
  86       InputStream stream = new ByteArrayInputStream(
  87               builder.toString().getBytes());
  88       RemoteFile file = client.uploadFile(stream, "input.fa",
  89               "application/fasta");
  90       form.insert(inputField.get().getName(), file);
  91     }
  92     if (args != null)
  93     {
  94       for (ArgumentI arg : args)
  95       {
  96         String fieldName = arg.getName().split("\\$", 2)[0];
  97         FormField field = form.getField(fieldName);
  98         if (field.getType() == FieldType.BOOLEAN)
  99         {
 100           form.insert(fieldName,
 101                   (arg.getValue() != null && !arg.getValue().isBlank())
 102                           ? true
 103                           : false);
 104         }
 105         else
 106         {
 107           form.insert(fieldName, field.valueOf(arg.getValue()));
 108         }
 109       }
 110     }
 111     return new JobId(service.getName(), service.getName(), form.submit());
 112   }
 113
 114   @Override
 115   public final void updateStatus(WsJob job)
 116   {
 117     try
 118     {
 119       job.setState(stateMap.get(client.getJobState(job.getJobId())));
 120     } catch (IOException e)
 121     {
 122       throw new IOError(e);
 123     }
 124   }
 125
 126   @Override
 127   public final boolean updateJobProgress(WsJob job) throws IOException
 128   {
 129     List<RemoteFile> files = client.getJobResults(job.getJobId());
 130     Optional<RemoteFile> logFile = files.stream()
 131         .filter(f -> f.getLabel().equals("log")).findFirst();
 132     boolean newContent = false;
 133     if (logFile.isPresent())
 134     {
 135       InputStream stream = logFile.get().getContent();
 136       long nextChunk = stream.skip(job.getNextChunk());
 137       int len = appendJobStatus(job, stream);
 138       job.setnextChunk(nextChunk + len);
 139       newContent |= len > 0;
 140     }
 141     if (failedStates.contains(job.getJobState()))
 142     {
 143       Optional<RemoteFile> errLogFile = files.stream()
 144           .filter(f -> f.getLabel().equals("error-log")).findFirst();
 145       if (errLogFile.isPresent())
 146       {
 147         newContent |= appendJobStatus(job, errLogFile.get().getContent()) > 0;
 148       }
 149     }
 150     return newContent;
 151   }
 152
 153   private int appendJobStatus(WsJob job, InputStream stream) throws IOException
 154   {
 155     StringBuilder builder = new StringBuilder(job.getStatus());
 156     InputStreamReader reader = new InputStreamReader(stream);
 157     char[] buffer = new char[4096];
 158     int chunkLen = 0;
 159     int len = 0;
 160     while ((len = reader.read(buffer)) != -1)
 161     {
 162       chunkLen += len;
 163       builder.append(buffer, 0, len);
 164     }
 165     job.setStatus(builder.toString());
 166     return chunkLen;
 167   }
 168
 169   @Override
 170   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
 171   {
 172     if (_lex instanceof FormValidationException)
 173     {
 174       FormValidationException formError = (FormValidationException) _lex;
 175       String[] messages = new String[formError.getErrors().size()];
 176       int i = 0;
 177       for (ValidationException e : formError.getErrors())
 178       {
 179         messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
 180       }
 181       j.setState(WsJob.JobState.INVALID);
 182       j.setStatus(String.join(", ", messages));
 183       return true;
 184     }
 185     return false;
 186   }
 187
 188   @Override
 189   public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
 190   {
 191     // TODO
 192     return false;
 193   }
 194
 195   final SlivkaService getService()
 196   {
 197     return service;
 198   }
 199
 200   @Override
 201   public final Object getEndpoint()
 202   {
 203     return this;
 204   }
 205
 206   @Override
 207   public final void initParamStore(ParamManager userParameterStore)
 208   {
 209     if (store == null)
 210     {
 211       try
 212       {
 213         store = new SlivkaDatastore(service);
 214       } catch (IOException e)
 215       {
 216         throw new IOError(e);
 217       }
 218     }
 219   }
 220
 221   @Override
 222   public boolean hasParameters()
 223   {
 224     return true;
 225   }
 226
 227   @Override
 228   public final ParamDatastoreI getParamStore()
 229   {
 230     if (store == null)
 231     {
 232       initParamStore(null);
 233     }
 234     return store;
 235   }
 236
 237 }