webservices/compbio/ws/server/DisemblWS.java

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