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                 disembl.setInput("fasta.in").setOutput("disembl.out");\r
  57                 return Configurator.configureExecutable(disembl, sequences);\r
  58         }\r
  59 \r
  60         @Override\r
  61         public ScoreManager getAnnotation(String jobId)\r
  62                         throws ResultNotAvailableException {\r
  63                 WSUtil.validateJobId(jobId);\r
  64                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  65                 ConfiguredExecutable<Disembl> disembl = (ConfiguredExecutable<Disembl>) asyncEngine\r
  66                                 .getResults(jobId);\r
  67                 ScoreManager mas = disembl.getResults();\r
  68                 log.trace(jobId + " getDisorder : " + mas);\r
  69                 return mas;\r
  70         }\r
  71 \r
  72         @Override\r
  73         public Limit<Disembl> getLimit(String presetName) {\r
  74                 if (limitMan == null) {\r
  75                         // Limit is not defined\r
  76                         return null;\r
  77                 }\r
  78                 return limitMan.getLimitByName(presetName);\r
  79         }\r
  80 \r
  81         @Override\r
  82         public LimitsManager<Disembl> getLimits() {\r
  83                 return limitMan;\r
  84         }\r
  85 \r
  86         @Override\r
  87         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  88                 // Execution stat is not supported\r
  89                 return new ChunkHolder("", -1);\r
  90         }\r
  91 \r
  92         @Override\r
  93         public boolean cancelJob(String jobId) {\r
  94                 WSUtil.validateJobId(jobId);\r
  95                 return WSUtil.cancelJob(jobId);\r
  96         }\r
  97 \r
  98         @Override\r
  99         public JobStatus getJobStatus(String jobId) {\r
 100                 WSUtil.validateJobId(jobId);\r
 101                 return WSUtil.getJobStatus(jobId);\r
 102         }\r
 103 \r
 104         @Override\r
 105         public PresetManager<Disembl> getPresets() {\r
 106                 return disemblPresets;\r
 107         }\r
 108 \r
 109         @Override\r
 110         public RunnerConfig<Disembl> getRunnerOptions() {\r
 111                 return disemblOptions;\r
 112         }\r
 113 \r
 114         String analize(List<FastaSequence> sequences,\r
 115                         ConfiguredExecutable<Disembl> confExec, Logger log, String method,\r
 116                         Limit<Disembl> limit) throws JobSubmissionException {\r
 117                 if (limit != null && limit.isExceeded(sequences)) {\r
 118                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 119                 }\r
 120 \r
 121                 compbio.runner.Util.writeInput(sequences, confExec);\r
 122                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 123                 String jobId = engine.submitJob(confExec);\r
 124                 return jobId;\r
 125         }\r
 126 \r
 127         @Override\r
 128         public String analize(List<FastaSequence> sequences)\r
 129                         throws UnsupportedRuntimeException, LimitExceededException,\r
 130                         JobSubmissionException {\r
 131                 WSUtil.validateFastaInput(sequences);\r
 132                 ConfiguredExecutable<Disembl> confDisembl = init(sequences);\r
 133 \r
 134                 return analize(sequences, confDisembl, null, "analize", getLimit(""));\r
 135         }\r
 136 \r
 137         /*\r
 138          * No options are supported, thus the result of this call will be as simple\r
 139          * call to analize without parameters\r
 140          */\r
 141         @Override\r
 142         public String customAnalize(List<FastaSequence> sequences,\r
 143                         List<Option<Disembl>> options) throws UnsupportedRuntimeException,\r
 144                         LimitExceededException, JobSubmissionException,\r
 145                         WrongParameterException {\r
 146                 return analize(sequences);\r
 147         }\r
 148 \r
 149         /*\r
 150          * No presets are supported, thus the result of this call will be as simple\r
 151          * call to analize without parameters\r
 152          */\r
 153         @Override\r
 154         public String presetAnalize(List<FastaSequence> sequences,\r
 155                         Preset<Disembl> preset) throws UnsupportedRuntimeException,\r
 156                         LimitExceededException, JobSubmissionException,\r
 157                         WrongParameterException {\r
 158 \r
 159                 return analize(sequences);\r
 160         }\r
 161 \r
 162 }\r