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