webservices/compbio/ws/server/JronnWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.List;\r
   5 \r
   6 import javax.annotation.Resource;\r
   7 import javax.jws.WebService;\r
   8 import javax.xml.ws.WebServiceContext;\r
   9 \r
  10 import org.apache.log4j.Logger;\r
  11 \r
  12 import compbio.data.msa.SequenceAnnotation;\r
  13 import compbio.data.sequence.FastaSequence;\r
  14 import compbio.data.sequence.ScoreManager;\r
  15 import compbio.engine.AsyncExecutor;\r
  16 import compbio.engine.Configurator;\r
  17 import compbio.engine.client.ConfiguredExecutable;\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.conservation.AACon;\r
  33 import compbio.runner.disorder.Jronn;\r
  34 \r
  35 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
  36 public class JronnWS implements SequenceAnnotation<Jronn> {\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("JronnWS-stats");\r
  43 \r
  44         private static Logger log = Logger.getLogger(JronnWS.class);\r
  45 \r
  46         private static final RunnerConfig<Jronn> jronnOptions = Util\r
  47                         .getSupportedOptions(Jronn.class);\r
  48 \r
  49         private static final PresetManager<Jronn> jronnPresets = Util\r
  50                         .getPresets(Jronn.class);\r
  51 \r
  52         private static final LimitsManager<Jronn> limitMan = compbio.runner.Util\r
  53                         .getLimits(new Jronn().getType());\r
  54 \r
  55         ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
  56                         throws JobSubmissionException {\r
  57                 Jronn jronn = new Jronn();\r
  58                 return Configurator.configureExecutable(jronn, 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<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine\r
  67                                 .getResults(jobId);\r
  68                 ScoreManager mas = jronn.getResults();\r
  69                 log.trace(jobId + " getConservation : " + mas);\r
  70                 return mas;\r
  71         }\r
  72 \r
  73         @Override\r
  74         public Limit<Jronn> getLimit(String presetName) {\r
  75                 if (limitMan == null) {\r
  76                         return null;\r
  77                 }\r
  78                 return limitMan.getLimitByName(presetName);\r
  79         }\r
  80 \r
  81         @Override\r
  82         public LimitsManager<Jronn> getLimits() {\r
  83                 return limitMan;\r
  84         }\r
  85 \r
  86         @Override\r
  87         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  88                 WSUtil.validateJobId(jobId);\r
  89                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  90                                 + Jronn.getStatFile();\r
  91                 return WSUtil.pullFile(file, position);\r
  92         }\r
  93 \r
  94         @Override\r
  95         public boolean cancelJob(String jobId) {\r
  96                 WSUtil.validateJobId(jobId);\r
  97                 return WSUtil.cancelJob(jobId);\r
  98         }\r
  99 \r
 100         @Override\r
 101         public JobStatus getJobStatus(String jobId) {\r
 102                 WSUtil.validateJobId(jobId);\r
 103                 return WSUtil.getJobStatus(jobId);\r
 104         }\r
 105 \r
 106         @Override\r
 107         public PresetManager<Jronn> getPresets() {\r
 108                 return jronnPresets;\r
 109         }\r
 110 \r
 111         @Override\r
 112         public RunnerConfig<Jronn> getRunnerOptions() {\r
 113                 return jronnOptions;\r
 114         }\r
 115 \r
 116         String analize(List<FastaSequence> sequences,\r
 117                         ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
 118                         Limit<Jronn> limit) throws JobSubmissionException {\r
 119                 if (limit != null && limit.isExceeded(sequences)) {\r
 120                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 121                 }\r
 122 \r
 123                 compbio.runner.Util.writeInput(sequences, confExec);\r
 124                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 125                 String jobId = engine.submitJob(confExec);\r
 126                 return jobId;\r
 127         }\r
 128 \r
 129         @Override\r
 130         public String analize(List<FastaSequence> sequences)\r
 131                         throws UnsupportedRuntimeException, LimitExceededException,\r
 132                         JobSubmissionException {\r
 133                 WSUtil.validateFastaInput(sequences);\r
 134                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 135 \r
 136                 return analize(sequences, confJronn, null, "analize", getLimit(""));\r
 137         }\r
 138 \r
 139         @Override\r
 140         public String customAnalize(List<FastaSequence> sequences,\r
 141                         List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
 142                         LimitExceededException, JobSubmissionException,\r
 143                         WrongParameterException {\r
 144                 WSUtil.validateFastaInput(sequences);\r
 145                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 146 \r
 147                 List<String> params = WSUtil.getCommands(options,\r
 148                                 AACon.KEY_VALUE_SEPARATOR);\r
 149                 confJronn.addParameters(params);\r
 150                 return analize(sequences, confJronn, null, "customAnalize",\r
 151                                 getLimit(""));\r
 152         }\r
 153 \r
 154         @Override\r
 155         public String presetAnalize(List<FastaSequence> sequences,\r
 156                         Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
 157                         LimitExceededException, JobSubmissionException,\r
 158                         WrongParameterException {\r
 159                 WSUtil.validateFastaInput(sequences);\r
 160                 if (preset == null) {\r
 161                         throw new WrongParameterException("Preset must be provided!");\r
 162                 }\r
 163                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 164                 confJronn.addParameters(preset.getOptions());\r
 165                 Limit<Jronn> limit = getLimit(preset.getName());\r
 166                 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
 167         }\r
 168 \r
 169 }\r