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