webservices/compbio/ws/server/GlobPlotWS.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.GlobPlot;\r
  32 \r
  33 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "GlobPlotWS")\r
  34 public class GlobPlotWS implements SequenceAnnotation<GlobPlot> {\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("GlobPlotWS-stats");\r
  41 \r
  42         private static Logger log = Logger.getLogger(GlobPlotWS.class);\r
  43 \r
  44         private static final RunnerConfig<GlobPlot> globPlotOptions = Util\r
  45                         .getSupportedOptions(GlobPlot.class);\r
  46 \r
  47         private static final PresetManager<GlobPlot> globPlotPresets = Util\r
  48                         .getPresets(GlobPlot.class);\r
  49 \r
  50         ConfiguredExecutable<GlobPlot> init(List<FastaSequence> sequences)\r
  51                         throws JobSubmissionException {\r
  52                 GlobPlot globPlot = new GlobPlot();\r
  53                 globPlot.setInput("fasta.in").setOutput("globPlot.out");\r
  54                 return Configurator.configureExecutable(globPlot, sequences);\r
  55         }\r
  56 \r
  57         @Override\r
  58         public ScoreManager getAnnotation(String jobId)\r
  59                         throws ResultNotAvailableException {\r
  60                 WSUtil.validateJobId(jobId);\r
  61                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  62                 ConfiguredExecutable<GlobPlot> globPlot = (ConfiguredExecutable<GlobPlot>) asyncEngine\r
  63                                 .getResults(jobId);\r
  64                 ScoreManager mas = globPlot.getResults();\r
  65                 log.trace(jobId + " getConservation : " + mas);\r
  66                 return mas;\r
  67         }\r
  68 \r
  69         @Override\r
  70         public Limit<GlobPlot> getLimit(String presetName) {\r
  71                 return new GlobPlot().getLimit(presetName);\r
  72         }\r
  73 \r
  74         @Override\r
  75         public LimitsManager<GlobPlot> getLimits() {\r
  76                 return new GlobPlot().getLimits();\r
  77         }\r
  78 \r
  79         @Override\r
  80         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  81                 // Execution stat is not supported\r
  82                 return new ChunkHolder("", -1);\r
  83         }\r
  84 \r
  85         @Override\r
  86         public boolean cancelJob(String jobId) {\r
  87                 WSUtil.validateJobId(jobId);\r
  88                 return WSUtil.cancelJob(jobId);\r
  89         }\r
  90 \r
  91         @Override\r
  92         public JobStatus getJobStatus(String jobId) {\r
  93                 WSUtil.validateJobId(jobId);\r
  94                 return WSUtil.getJobStatus(jobId);\r
  95         }\r
  96 \r
  97         @Override\r
  98         public PresetManager<GlobPlot> getPresets() {\r
  99                 return globPlotPresets;\r
 100         }\r
 101 \r
 102         @Override\r
 103         public RunnerConfig<GlobPlot> getRunnerOptions() {\r
 104                 return globPlotOptions;\r
 105         }\r
 106 \r
 107         String analize(List<FastaSequence> sequences,\r
 108                         ConfiguredExecutable<GlobPlot> confExec, Logger log, String method,\r
 109                         Limit<GlobPlot> limit) throws JobSubmissionException {\r
 110                 if (limit != null && limit.isExceeded(sequences)) {\r
 111                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 112                 }\r
 113 \r
 114                 compbio.runner.Util.writeInput(sequences, confExec);\r
 115                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 116                 String jobId = engine.submitJob(confExec);\r
 117                 return jobId;\r
 118         }\r
 119 \r
 120         @Override\r
 121         public String analize(List<FastaSequence> sequences)\r
 122                         throws UnsupportedRuntimeException, LimitExceededException,\r
 123                         JobSubmissionException {\r
 124                 WSUtil.validateFastaInput(sequences);\r
 125                 ConfiguredExecutable<GlobPlot> confGlobPlot = init(sequences);\r
 126 \r
 127                 return analize(sequences, confGlobPlot, null, "analize", getLimit(""));\r
 128         }\r
 129 \r
 130         /*\r
 131          * No options are supported, thus the result of this call will be as simple\r
 132          * call to analize without parameters\r
 133          */\r
 134         @Override\r
 135         public String customAnalize(List<FastaSequence> sequences,\r
 136                         List<Option<GlobPlot>> options) throws UnsupportedRuntimeException,\r
 137                         LimitExceededException, JobSubmissionException,\r
 138                         WrongParameterException {\r
 139                 return analize(sequences);\r
 140         }\r
 141 \r
 142         /*\r
 143          * No presets are supported, thus the result of this call will be as simple\r
 144          * call to analize without parameters\r
 145          */\r
 146         @Override\r
 147         public String presetAnalize(List<FastaSequence> sequences,\r
 148                         Preset<GlobPlot> preset) throws UnsupportedRuntimeException,\r
 149                         LimitExceededException, JobSubmissionException,\r
 150                         WrongParameterException {\r
 151 \r
 152                 return analize(sequences);\r
 153         }\r
 154 \r
 155 }\r