webservices/compbio/ws/server/JronnWS.java

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