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.io.FileFormat;
   6 import jalview.io.FormatAdapter;
   7 import jalview.ws.api.JalviewServiceEndpointProviderI;
   8 import jalview.ws.api.JalviewWebServiceI;
   9 import jalview.ws.api.JobId;
  10 import jalview.ws.api.ServiceWithParameters;
  11 import jalview.ws.gui.WsJob;
  12 import jalview.ws.params.ArgumentI;
  13 import jalview.ws.params.ParamDatastoreI;
  14 import jalview.ws.params.ParamManager;
  15 import jalview.ws.params.WsParamSetI;
  16
  17 import java.io.ByteArrayInputStream;
  18 import java.io.ByteArrayOutputStream;
  19 import java.io.IOError;
  20 import java.io.IOException;
  21 import java.io.InputStream;
  22 import java.util.Arrays;
  23 import java.util.EnumMap;
  24 import java.util.HashSet;
  25 import java.util.List;
  26 import java.util.Optional;
  27 import java.util.Set;
  28
  29 import uk.ac.dundee.compbio.slivkaclient.FieldType;
  30 import uk.ac.dundee.compbio.slivkaclient.FileField;
  31 import uk.ac.dundee.compbio.slivkaclient.FormField;
  32 import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
  33 import uk.ac.dundee.compbio.slivkaclient.JobState;
  34 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
  35 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
  36 import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
  37 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
  38 import uk.ac.dundee.compbio.slivkaclient.ValidationException;
  39
  40 public abstract class SlivkaWSInstance extends ServiceWithParameters
  41     implements JalviewServiceEndpointProviderI, JalviewWebServiceI
  42 {
  43   protected final SlivkaClient client;
  44
  45   protected final SlivkaService service;
  46
  47   protected SlivkaDatastore store = null;
  48
  49   protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
  50   {
  51     stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
  52     stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
  53     stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
  54     stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
  55     stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
  56     stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
  57     stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
  58     stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
  59     stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
  60     stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
  61     stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
  62   }
  63   protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
  64       WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
  65       WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
  66   ));
  67
  68   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
  69   {
  70     super(action, action, service.getLabel(), "Slivka", client.getUrl().toString());
  71     this.client = client;
  72     this.service = service;
  73   }
  74
  75   protected final JobId submit(List<SequenceI> sequences,
  76           WsParamSetI preset, List<ArgumentI> args) throws Throwable
  77   {
  78     SlivkaForm form = service.getForm();
  79     for (FormField field : form.getFields())
  80     {
  81       if (field.getType() == FieldType.FILE)
  82       {
  83         FormatAdapter fa = new FormatAdapter();
  84         fa.setNewlineString("\r\n");
  85         FileField fileField = (FileField) field;
  86         FileFormat format;
  87         switch (fileField.getMediaType())
  88         {
  89         case "application/pfam":
  90           format = FileFormat.Pfam;
  91           break;
  92         case "application/stockholm":
  93           format = FileFormat.Stockholm;
  94           break;
  95         default:
  96         case "application/fasta":
  97           format = FileFormat.Fasta;
  98           break;
  99         }
 100         InputStream stream = new ByteArrayInputStream(
 101             fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
 102                 .getBytes());
 103         RemoteFile rf = client.uploadFile(stream, "input",
 104             fileField.getMediaType());
 105         form.insert(field.getName(), rf);
 106       }
 107     }
 108     if (args != null)
 109     {
 110       for (ArgumentI arg : args)
 111       {
 112         // multiple choice field names are name$number to avoid duplications
 113         // the number is stripped here
 114         String fieldName = arg.getName().split("\\$", 2)[0];
 115         FormField field = form.getField(fieldName);
 116         if (field.getType() == FieldType.BOOLEAN)
 117         {
 118           form.insert(fieldName,
 119                   (arg.getValue() != null && !arg.getValue().isBlank())
 120                           ? true
 121                           : false);
 122         }
 123         else
 124         {
 125           form.insert(fieldName, arg.getValue());
 126         }
 127       }
 128     }
 129     return new JobId(service.getName(), service.getName(), form.submit());
 130   }
 131
 132   @Override
 133   public final void updateStatus(WsJob job)
 134   {
 135     try
 136     {
 137       job.setState(stateMap.get(client.getJobState(job.getJobId())));
 138     } catch (IOException e)
 139     {
 140       throw new IOError(e);
 141     }
 142   }
 143
 144   @Override
 145   public final boolean updateJobProgress(WsJob job) throws IOException
 146   {
 147     List<RemoteFile> files = client.getJobResults(job.getJobId());
 148     RemoteFile logFile=null;
 149     for (RemoteFile f : files)
 150     {
 151       if (f.getLabel().equals("log"))
 152       {
 153         logFile = f; break;
 154       }
 155     }
 156
 157     boolean newContent = false;
 158     if (logFile!=null)
 159     {
 160       ByteArrayOutputStream output = new ByteArrayOutputStream();
 161       logFile.writeTo(output);
 162       if (output.size() > job.getNextChunk())
 163       {
 164         newContent = true;
 165         job.setStatus(output.toString("UTF-8"));
 166         job.setnextChunk(output.size());
 167       }
 168     }
 169     if (failedStates.contains(job.getJobState()))
 170     {
 171
 172       RemoteFile errLogFile = null;
 173       for (RemoteFile f : files)
 174       {
 175         if (f.getLabel().equals("error-log"))
 176         {
 177           errLogFile = f;
 178           break;
 179         }
 180       }
 181
 182       if (errLogFile!=null)
 183       {
 184         ByteArrayOutputStream output = new ByteArrayOutputStream();
 185         errLogFile.writeTo(output);
 186         if (output.size() > 0)
 187         {
 188           newContent = true;
 189           job.setStatus(job.getStatus() + "\n" + output.toString("UTF-8"));
 190         }
 191       }
 192     }
 193     return newContent;
 194   }
 195
 196   @Override
 197   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
 198   {
 199     if (_lex instanceof FormValidationException)
 200     {
 201       FormValidationException formError = (FormValidationException) _lex;
 202       String[] messages = new String[formError.getErrors().size()];
 203       int i = 0;
 204       for (ValidationException e : formError.getErrors())
 205       {
 206         messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
 207       }
 208       j.setState(WsJob.JobState.INVALID);
 209       j.setStatus(String.join(", ", messages));
 210       return true;
 211     }
 212     return false;
 213   }
 214
 215   @Override
 216   public final boolean handleCollectionException(Exception e, WsJob msjob, WebserviceInfo wsInfo)
 217   {
 218     // TODO
 219     return false;
 220   }
 221
 222   final SlivkaService getService()
 223   {
 224     return service;
 225   }
 226
 227   @Override
 228   public final Object getEndpoint()
 229   {
 230     return this;
 231   }
 232
 233   @Override
 234   public final void initParamStore(ParamManager userParameterStore)
 235   {
 236     if (store == null)
 237     {
 238       try
 239       {
 240         store = new SlivkaDatastore(service);
 241       } catch (IOException e)
 242       {
 243         throw new IOError(e);
 244       }
 245     }
 246   }
 247
 248   @Override
 249   public boolean hasParameters()
 250   {
 251     return true;
 252   }
 253
 254   @Override
 255   public final ParamDatastoreI getParamStore()
 256   {
 257     if (store == null)
 258     {
 259       initParamStore(null);
 260     }
 261     return store;
 262   }
 263
 264 }