webservices/compbio/ws/server/RNAalifoldWS.java

   1 package compbio.ws.server;
   2
   3 import java.io.File;
   4 import java.util.List;
   5
   6 import javax.jws.WebParam;
   7 import javax.jws.WebService;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import compbio.data.msa.JABAService;
  12 import compbio.data.msa.JManagement;
  13 import compbio.data.msa.Metadata;
  14 import compbio.data.msa.MsaWS;
  15 import compbio.data.sequence.Alignment;
  16 import compbio.data.sequence.FastaSequence;
  17 import compbio.engine.AsyncExecutor;
  18 import compbio.engine.Configurator;
  19 import compbio.engine.client.ConfiguredExecutable;
  20 import compbio.engine.client.SkeletalExecutable;
  21 import compbio.metadata.ChunkHolder;
  22 import compbio.metadata.JobStatus;
  23 import compbio.metadata.JobSubmissionException;
  24 import compbio.metadata.Limit;
  25 import compbio.metadata.LimitsManager;
  26 import compbio.metadata.Option;
  27 import compbio.metadata.Preset;
  28 import compbio.metadata.PresetManager;
  29 import compbio.metadata.ResultNotAvailableException;
  30 import compbio.metadata.RunnerConfig;
  31 import compbio.metadata.WrongParameterException;
  32 import compbio.runner.Util;
  33 import compbio.runner.msa.ClustalW;
  34 import compbio.runner.structure.RNAalifold;
  35
  36 @WebService(targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
  37 public class RNAalifoldWS implements JABAService, JManagement, Metadata<RNAalifold> {
  38
  39         private static Logger log = Logger.getLogger(ClustalWS.class);
  40
  41         private static final RunnerConfig<RNAalifold> rnaalifoldOptions = Util.
  42                         getSupportedOptions(RNAalifold.class);
  43
  44         private static final PresetManager<RNAalifold> rnaalifoldPresets = Util
  45                         .getPresets(RNAalifold.class);
  46
  47         private static final LimitsManager<RNAalifold> limitMan = compbio.engine.client.Util
  48                         .getLimits(new RNAalifold().getType());
  49
  50         //public String fold()
  51
  52
  53         ConfiguredExecutable<RNAalifold> init() throws JobSubmissionException {
  54                 RNAalifold rnaalifold = new RNAalifold();
  55                 rnaalifold.setInput(SkeletalExecutable.INPUT)
  56                                 .setOutput(SkeletalExecutable.OUTPUT)
  57                                 .setError(SkeletalExecutable.ERROR);
  58                 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
  59                                 .configureExecutable(rnaalifold);
  60                 return confRNAalifold;
  61         }
  62
  63         @Override
  64         public RunnerConfig<RNAalifold> getRunnerOptions() {
  65                 return rnaalifoldOptions;
  66         }
  67
  68         @SuppressWarnings("unchecked")
  69         public String getResult(@WebParam(name = "jobId") String jobId) throws ResultNotAvailableException {
  70
  71                 WSUtil.validateJobId(jobId);
  72                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
  73                 ConfiguredExecutable<RNAalifold> rnaalifold = (ConfiguredExecutable<RNAalifold>) asyncEngine
  74                                 .getResults(jobId);
  75                 return rnaalifold.getResults();
  76         }
  77
  78         @Override
  79         public boolean cancelJob(String jobId) {
  80                 WSUtil.validateJobId(jobId);
  81                 boolean result = WSUtil.cancelJob(jobId);
  82                 return result;
  83         }
  84
  85         @Override
  86         public JobStatus getJobStatus(String jobId) {
  87                 WSUtil.validateJobId(jobId);
  88                 JobStatus status = WSUtil.getJobStatus(jobId);
  89                 return status;
  90         }
  91
  92         @Override
  93         public Limit<RNAalifold> getLimit(String presetName) {
  94                 if (limitMan == null) {
  95                         // No limit is configured
  96                         return null;
  97                 }
  98                 Limit<RNAalifold> limit = limitMan.getLimitByName(presetName);
  99                 return limit;
 100         }
 101
 102         @Override
 103         public LimitsManager<RNAalifold> getLimits() {
 104                 return limitMan;
 105         }
 106
 107         @Override
 108         // PlaceHolder
 109         public PresetManager<RNAalifold> getPresets() {
 110                 if (rnaalifoldPresets == null) {
 111                         // No presets are configured
 112                         return null;
 113                 }
 114                 return rnaalifoldPresets;
 115         }
 116
 117         @Override
 118         // PlaceHolder
 119         public ChunkHolder pullExecStatistics(String jobId, long position) {
 120
 121 //              WSUtil.validateJobId(jobId);
 122 //              String file = Configurator.getWorkDirectory(jobId) + File.separator
 123 //                              + RNAalifold.getStatFile();
 124 //              ChunkHolder cholder = WSUtil.pullFile(file, position);
 125 //              return cholder;
 126                 return new ChunkHolder("", -1);
 127         }
 128 }
 129
 130