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