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.FoldWS;
  12 import compbio.data.msa.JABAService;
  13 import compbio.data.msa.JManagement;
  14 import compbio.data.msa.Metadata;
  15 import compbio.data.sequence.Alignment;
  16 import compbio.data.sequence.RNAstruct;
  17 import compbio.data.sequence.FastaSequence;
  18 import compbio.engine.AsyncExecutor;
  19 import compbio.engine.Configurator;
  20 import compbio.engine.client.ConfiguredExecutable;
  21 import compbio.engine.client.SkeletalExecutable;
  22 import compbio.metadata.ChunkHolder;
  23 import compbio.metadata.JobStatus;
  24 import compbio.metadata.JobSubmissionException;
  25 import compbio.metadata.Limit;
  26 import compbio.metadata.LimitsManager;
  27 import compbio.metadata.Option;
  28 import compbio.metadata.Preset;
  29 import compbio.metadata.PresetManager;
  30 import compbio.metadata.ResultNotAvailableException;
  31 import compbio.metadata.RunnerConfig;
  32 import compbio.metadata.WrongParameterException;
  33 import compbio.runner.Util;
  34 import compbio.runner.structure.RNAalifold;
  35
  36 @WebService(endpointInterface = "compbio.data.msa.FoldWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
  37 public class RNAalifoldWS implements FoldWS<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
  51         @Override
  52         public String fold(Alignment alignment)
  53                         throws JobSubmissionException {
  54
  55                 // Validate clustal input here?
  56                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
  57                 return WSUtil.fold(alignment, confRNAalifold, log, "fold", getLimit(""));
  58         }
  59
  60
  61         ConfiguredExecutable<RNAalifold> init(Alignment dataset) throws JobSubmissionException {
  62                 RNAalifold rnaalifold = new RNAalifold();
  63                 rnaalifold.setInput(SkeletalExecutable.INPUT)
  64                                 .setOutput(SkeletalExecutable.OUTPUT)
  65                                 .setError(SkeletalExecutable.ERROR);
  66                 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
  67                                 .configureExecutable(rnaalifold, dataset.getSequences());
  68                 return confRNAalifold;
  69         }
  70
  71         @Override
  72         public String presetFold(Alignment alignment,
  73                         Preset<RNAalifold> preset) throws JobSubmissionException,
  74                         WrongParameterException {
  75                 // validate
  76                 if (preset == null) {
  77                         throw new WrongParameterException("Preset must be Provided!");
  78                 }
  79                 Limit<RNAalifold> limit = getLimit(preset.getName());
  80                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
  81                 confRNAalifold.addParameters(preset.getOptions());
  82                 return WSUtil.fold(alignment, confRNAalifold, log, "presetFold", limit);
  83         }
  84
  85         @Override
  86         public String customFold(Alignment alignment,
  87                         List<Option<RNAalifold>> options) throws JobSubmissionException,
  88                         WrongParameterException {
  89                 // validate
  90                 ConfiguredExecutable<RNAalifold> confRNAalifold = init(alignment);
  91                 List<String> params = WSUtil.getCommands(options,
  92                                 RNAalifold.KEY_VALUE_SEPARATOR);
  93                 confRNAalifold.addParameters(params);
  94                 log.info("Setting parameters: " + params);
  95                 return WSUtil.fold(alignment, confRNAalifold, log, "customFold",
  96                                 getLimit(""));
  97         }
  98
  99         @Override
 100         public RunnerConfig<RNAalifold> getRunnerOptions() {
 101                 return rnaalifoldOptions;
 102         }
 103
 104         @SuppressWarnings("unchecked")
 105         public RNAstruct getResult(String jobId) throws ResultNotAvailableException {
 106
 107                 WSUtil.validateJobId(jobId);
 108                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
 109                 ConfiguredExecutable<RNAalifold> rnaalifold = (ConfiguredExecutable<RNAalifold>) asyncEngine
 110                                 .getResults(jobId);
 111                 return rnaalifold.getResults();
 112         }
 113
 114         @Override
 115         public boolean cancelJob(String jobId) {
 116                 WSUtil.validateJobId(jobId);
 117                 boolean result = WSUtil.cancelJob(jobId);
 118                 return result;
 119         }
 120
 121         @Override
 122         public JobStatus getJobStatus(String jobId) {
 123                 WSUtil.validateJobId(jobId);
 124                 JobStatus status = WSUtil.getJobStatus(jobId);
 125                 return status;
 126         }
 127
 128         @Override
 129         public Limit<RNAalifold> getLimit(String presetName) {
 130                 if (limitMan == null) {
 131                         // No limit is configured
 132                         return null;
 133                 }
 134                 Limit<RNAalifold> limit = limitMan.getLimitByName(presetName);
 135                 return limit;
 136         }
 137
 138         @Override
 139         public LimitsManager<RNAalifold> getLimits() {
 140                 return limitMan;
 141         }
 142
 143         @Override
 144         // PlaceHolder
 145         public PresetManager<RNAalifold> getPresets() {
 146                 if (rnaalifoldPresets == null) {
 147                         // No presets are configured
 148                         return null;
 149                 }
 150                 return rnaalifoldPresets;
 151         }
 152
 153         @Override
 154         // PlaceHolder
 155         public ChunkHolder pullExecStatistics(String jobId, long position) {
 156
 157 //              WSUtil.validateJobId(jobId);
 158 //              String file = Configurator.getWorkDirectory(jobId) + File.separator
 159 //                              + RNAalifold.getStatFile();
 160 //              ChunkHolder cholder = WSUtil.pullFile(file, position);
 161 //              return cholder;
 162                 return new ChunkHolder("", -1);
 163         }
 164 }
 165
 166