webservices/compbio/ws/server/DisemblWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.util.List;\r
   4 \r
   5 import javax.annotation.Resource;\r
   6 import javax.jws.WebService;\r
   7 import javax.xml.ws.WebServiceContext;\r
   8 \r
   9 import org.apache.log4j.Logger;\r
  10 \r
  11 import compbio.data.msa.SequenceAnnotation;\r
  12 import compbio.data.sequence.FastaSequence;\r
  13 import compbio.data.sequence.ScoreManager;\r
  14 import compbio.engine.AsyncExecutor;\r
  15 import compbio.engine.Configurator;\r
  16 import compbio.engine.client.ConfiguredExecutable;\r
  17 import compbio.metadata.ChunkHolder;\r
  18 import compbio.metadata.JobStatus;\r
  19 import compbio.metadata.JobSubmissionException;\r
  20 import compbio.metadata.Limit;\r
  21 import compbio.metadata.LimitExceededException;\r
  22 import compbio.metadata.LimitsManager;\r
  23 import compbio.metadata.Option;\r
  24 import compbio.metadata.Preset;\r
  25 import compbio.metadata.PresetManager;\r
  26 import compbio.metadata.ResultNotAvailableException;\r
  27 import compbio.metadata.RunnerConfig;\r
  28 import compbio.metadata.UnsupportedRuntimeException;\r
  29 import compbio.metadata.WrongParameterException;\r
  30 import compbio.runner.Util;\r
  31 import compbio.runner.disorder.Disembl;\r
  32 \r
  33 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "DisemblWS")\r
  34 public class DisemblWS implements SequenceAnnotation<Disembl> {\r
  35 \r
  36         // Ask for resource injection\r
  37         @Resource\r
  38         WebServiceContext wsContext;\r
  39 \r
  40         private static Logger statLog = Logger.getLogger("DisemblWS-stats");\r
  41 \r
  42         private static Logger log = Logger.getLogger(DisemblWS.class);\r
  43 \r
  44         private static final RunnerConfig<Disembl> disemblOptions = Util\r
  45                         .getSupportedOptions(Disembl.class);\r
  46 \r
  47         private static final PresetManager<Disembl> disemblPresets = Util\r
  48                         .getPresets(Disembl.class);\r
  49 \r
  50         private static final LimitsManager<Disembl> limitMan = compbio.runner.Util\r
  51                         .getLimits(new Disembl().getType());\r
  52 \r
  53         ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)\r
  54                         throws JobSubmissionException {\r
  55                 Disembl disembl = new Disembl();\r
  56                 return Configurator.configureExecutable(disembl, sequences);\r
  57         }\r
  58 \r
  59         @Override\r
  60         public ScoreManager getAnnotation(String jobId)\r
  61                         throws ResultNotAvailableException {\r
  62                 WSUtil.validateJobId(jobId);\r
  63                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  64                 ConfiguredExecutable<Disembl> disembl = (ConfiguredExecutable<Disembl>) asyncEngine\r
  65                                 .getResults(jobId);\r
  66                 ScoreManager mas = disembl.getResults();\r
  67                 log.trace(jobId + " getDisorder : " + mas);\r
  68                 return mas;\r
  69         }\r
  70 \r
  71         @Override\r
  72         public Limit<Disembl> getLimit(String presetName) {\r
  73                 if (limitMan == null) {\r
  74                         // Limit is not defined\r
  75                         return null;\r
  76                 }\r
  77                 return limitMan.getLimitByName(presetName);\r
  78         }\r
  79 \r
  80         @Override\r
  81         public LimitsManager<Disembl> getLimits() {\r
  82                 return limitMan;\r
  83         }\r
  84 \r
  85         @Override\r
  86         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  87                 // Execution stat is not supported\r
  88                 return new ChunkHolder("", -1);\r
  89         }\r
  90 \r
  91         @Override\r
  92         public boolean cancelJob(String jobId) {\r
  93                 WSUtil.validateJobId(jobId);\r
  94                 return WSUtil.cancelJob(jobId);\r
  95         }\r
  96 \r
  97         @Override\r
  98         public JobStatus getJobStatus(String jobId) {\r
  99                 WSUtil.validateJobId(jobId);\r
 100                 return WSUtil.getJobStatus(jobId);\r
 101         }\r
 102 \r
 103         @Override\r
 104         public PresetManager<Disembl> getPresets() {\r
 105                 return disemblPresets;\r
 106         }\r
 107 \r
 108         @Override\r
 109         public RunnerConfig<Disembl> getRunnerOptions() {\r
 110                 return disemblOptions;\r
 111         }\r
 112 \r
 113         String analize(List<FastaSequence> sequences,\r
 114                         ConfiguredExecutable<Disembl> confExec, Logger log, String method,\r
 115                         Limit<Disembl> limit) throws JobSubmissionException {\r
 116                 if (limit != null && limit.isExceeded(sequences)) {\r
 117                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 118                 }\r
 119 \r
 120                 compbio.runner.Util.writeInput(sequences, confExec);\r
 121                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 122                 String jobId = engine.submitJob(confExec);\r
 123                 return jobId;\r
 124         }\r
 125 \r
 126         @Override\r
 127         public String analize(List<FastaSequence> sequences)\r
 128                         throws UnsupportedRuntimeException, LimitExceededException,\r
 129                         JobSubmissionException {\r
 130                 WSUtil.validateFastaInput(sequences);\r
 131                 ConfiguredExecutable<Disembl> confDisembl = init(sequences);\r
 132 \r
 133                 return analize(sequences, confDisembl, null, "analize", getLimit(""));\r
 134         }\r
 135 \r
 136         /*\r
 137          * No options are supported, thus the result of this call will be as simple\r
 138          * call to analize without parameters\r
 139          */\r
 140         @Override\r
 141         public String customAnalize(List<FastaSequence> sequences,\r
 142                         List<Option<Disembl>> options) throws UnsupportedRuntimeException,\r
 143                         LimitExceededException, JobSubmissionException,\r
 144                         WrongParameterException {\r
 145                 return analize(sequences);\r
 146         }\r
 147 \r
 148         /*\r
 149          * No presets are supported, thus the result of this call will be as simple\r
 150          * call to analize without parameters\r
 151          */\r
 152         @Override\r
 153         public String presetAnalize(List<FastaSequence> sequences,\r
 154                         Preset<Disembl> preset) throws UnsupportedRuntimeException,\r
 155                         LimitExceededException, JobSubmissionException,\r
 156                         WrongParameterException {\r
 157 \r
 158                 return analize(sequences);\r
 159         }\r
 160 \r
 161 }\r