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