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         ConfiguredExecutable<RNAalifold> init() throws JobSubmissionException {
  51                 RNAalifold rnaalifold = new RNAalifold();
  52                 rnaalifold.setInput(SkeletalExecutable.INPUT)
  53                                 .setOutput(SkeletalExecutable.OUTPUT)
  54                                 .setError(SkeletalExecutable.ERROR);
  55                 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
  56                                 .configureExecutable(rnaalifold);
  57                 return confRNAalifold;
  58         }
  59
  60         @Override
  61         public RunnerConfig<RNAalifold> getRunnerOptions() {
  62                 return rnaalifoldOptions;
  63         }
  64
  65         @SuppressWarnings("unchecked")
  66         public String getResult(@WebParam(name = "jobId") String jobId) throws ResultNotAvailableException {
  67
  68                 WSUtil.validateJobId(jobId);
  69                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
  70                 ConfiguredExecutable<RNAalifold> rnaalifold = (ConfiguredExecutable<RNAalifold>) asyncEngine
  71                                 .getResults(jobId);
  72                 return rnaalifold.getResults();
  73         }
  74
  75         @Override
  76         public boolean cancelJob(String jobId) {
  77                 WSUtil.validateJobId(jobId);
  78                 boolean result = WSUtil.cancelJob(jobId);
  79                 return result;
  80         }
  81
  82         @Override
  83         public JobStatus getJobStatus(String jobId) {
  84                 WSUtil.validateJobId(jobId);
  85                 JobStatus status = WSUtil.getJobStatus(jobId);
  86                 return status;
  87         }
  88
  89         @Override
  90         public Limit<RNAalifold> getLimit(String presetName) {
  91                 if (limitMan == null) {
  92                         // No limit is configured
  93                         return null;
  94                 }
  95                 Limit<RNAalifold> limit = limitMan.getLimitByName(presetName);
  96                 return limit;
  97         }
  98
  99         @Override
 100         public LimitsManager<RNAalifold> getLimits() {
 101                 return limitMan;
 102         }
 103
 104         @Override
 105         // PlaceHolder
 106         public PresetManager<RNAalifold> getPresets() {
 107                 if (rnaalifoldPresets == null) {
 108                         // No presets are configured
 109                         return null;
 110                 }
 111                 return rnaalifoldPresets;
 112         }
 113
 114         @Override
 115         // PlaceHolder
 116         public ChunkHolder pullExecStatistics(String jobId, long position) {
 117
 118                 WSUtil.validateJobId(jobId);
 119 //              String file = Configurator.getWorkDirectory(jobId) + File.separator
 120 //                              + RNAalifold.getStatFile();
 121 //              ChunkHolder cholder = WSUtil.pullFile(file, position);
 122 //              return cholder;
 123                 return null;
 124         }
 125 }
 126
 127