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                 jronn.setInput("fasta.in").setOutput("jronn.out");\r
  59                 return Configurator.configureExecutable(jronn, sequences);\r
  60         }\r
  61 \r
  62         @Override\r
  63         public ScoreManager getAnnotation(String jobId)\r
  64                         throws ResultNotAvailableException {\r
  65                 WSUtil.validateJobId(jobId);\r
  66                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  67                 ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine\r
  68                                 .getResults(jobId);\r
  69                 ScoreManager mas = jronn.getResults();\r
  70                 log.trace(jobId + " getConservation : " + mas);\r
  71                 return mas;\r
  72         }\r
  73 \r
  74         @Override\r
  75         public Limit<Jronn> getLimit(String presetName) {\r
  76                 return limitMan.getLimitByName(presetName);\r
  77         }\r
  78 \r
  79         @Override\r
  80         public LimitsManager<Jronn> getLimits() {\r
  81                 return limitMan;\r
  82         }\r
  83 \r
  84         @Override\r
  85         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  86                 WSUtil.validateJobId(jobId);\r
  87                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  88                                 + Jronn.getStatFile();\r
  89                 return WSUtil.pullFile(file, position);\r
  90         }\r
  91 \r
  92         @Override\r
  93         public boolean cancelJob(String jobId) {\r
  94                 WSUtil.validateJobId(jobId);\r
  95                 return WSUtil.cancelJob(jobId);\r
  96         }\r
  97 \r
  98         @Override\r
  99         public JobStatus getJobStatus(String jobId) {\r
 100                 WSUtil.validateJobId(jobId);\r
 101                 return WSUtil.getJobStatus(jobId);\r
 102         }\r
 103 \r
 104         @Override\r
 105         public PresetManager<Jronn> getPresets() {\r
 106                 return jronnPresets;\r
 107         }\r
 108 \r
 109         @Override\r
 110         public RunnerConfig<Jronn> getRunnerOptions() {\r
 111                 return jronnOptions;\r
 112         }\r
 113 \r
 114         String analize(List<FastaSequence> sequences,\r
 115                         ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
 116                         Limit<Jronn> limit) throws JobSubmissionException {\r
 117                 if (limit != null && limit.isExceeded(sequences)) {\r
 118                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 119                 }\r
 120 \r
 121                 compbio.runner.Util.writeInput(sequences, confExec);\r
 122                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 123                 String jobId = engine.submitJob(confExec);\r
 124                 return jobId;\r
 125         }\r
 126 \r
 127         @Override\r
 128         public String analize(List<FastaSequence> sequences)\r
 129                         throws UnsupportedRuntimeException, LimitExceededException,\r
 130                         JobSubmissionException {\r
 131                 WSUtil.validateFastaInput(sequences);\r
 132                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 133 \r
 134                 return analize(sequences, confJronn, null, "analize", getLimit(""));\r
 135         }\r
 136 \r
 137         @Override\r
 138         public String customAnalize(List<FastaSequence> sequences,\r
 139                         List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
 140                         LimitExceededException, JobSubmissionException,\r
 141                         WrongParameterException {\r
 142                 WSUtil.validateFastaInput(sequences);\r
 143                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 144 \r
 145                 List<String> params = WSUtil.getCommands(options,\r
 146                                 AACon.KEY_VALUE_SEPARATOR);\r
 147                 confJronn.addParameters(params);\r
 148                 return analize(sequences, confJronn, null, "customAnalize",\r
 149                                 getLimit(""));\r
 150         }\r
 151 \r
 152         @Override\r
 153         public String presetAnalize(List<FastaSequence> sequences,\r
 154                         Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
 155                         LimitExceededException, JobSubmissionException,\r
 156                         WrongParameterException {\r
 157                 WSUtil.validateFastaInput(sequences);\r
 158                 if (preset == null) {\r
 159                         throw new WrongParameterException("Preset must be provided!");\r
 160                 }\r
 161                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 162                 confJronn.addParameters(preset.getOptions());\r
 163                 Limit<Jronn> limit = getLimit(preset.getName());\r
 164                 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
 165         }\r
 166 \r
 167 }\r