webservices/compbio/ws/server/GenericMetadataService.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.util.List;\r
   4 \r
   5 import org.apache.log4j.Logger;\r
   6 \r
   7 import compbio.data.sequence.FastaSequence;\r
   8 import compbio.engine.Configurator;\r
   9 import compbio.engine.client.ConfiguredExecutable;\r
  10 import compbio.engine.client.Executable;\r
  11 import compbio.engine.client.SkeletalExecutable;\r
  12 import compbio.metadata.ChunkHolder;\r
  13 import compbio.metadata.JobStatus;\r
  14 import compbio.metadata.JobSubmissionException;\r
  15 import compbio.metadata.Limit;\r
  16 import compbio.metadata.LimitsManager;\r
  17 import compbio.metadata.PresetManager;\r
  18 import compbio.metadata.RunnerConfig;\r
  19 import compbio.runner.Util;\r
  20 \r
  21 public abstract class GenericMetadataService<T> {\r
  22 \r
  23         private final RunnerConfig<T> aaconOptions;\r
  24         private final PresetManager<T> aaconPresets;\r
  25         private final LimitsManager<T> limitMan;\r
  26         private SkeletalExecutable<T> exec;\r
  27         final Logger log;\r
  28 \r
  29         /*\r
  30          * FIXME - instances of the Runner (?) and their types should be defined in\r
  31          * Executable IF\r
  32          */\r
  33         GenericMetadataService(SkeletalExecutable<T> exec, Logger log) {\r
  34                 assert log != null;\r
  35                 assert exec != null;\r
  36                 this.log = log;\r
  37                 this.exec = exec;\r
  38                 this.limitMan = compbio.engine.client.Util.getLimits(exec.getType());\r
  39                 this.aaconOptions = Util\r
  40                                 .getSupportedOptions((Class<? extends Executable<T>>) exec\r
  41                                                 .getType());\r
  42                 this.aaconPresets = Util\r
  43                                 .getPresets((Class<? extends Executable<T>>) exec.getType());\r
  44         }\r
  45 \r
  46         ConfiguredExecutable<T> init(List<FastaSequence> sequences)\r
  47                         throws JobSubmissionException {\r
  48                 // FIXME\r
  49                 try {\r
  50                         exec = (SkeletalExecutable<T>) exec.getType().newInstance();\r
  51                 } catch (InstantiationException e) {\r
  52                         log.error(e.getLocalizedMessage(), e);\r
  53                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  54                 } catch (IllegalAccessException e) {\r
  55                         log.error(e.getLocalizedMessage(), e);\r
  56                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  57                 }\r
  58                 exec.setInput(SkeletalExecutable.INPUT)\r
  59                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  60                                 .setError(SkeletalExecutable.ERROR);\r
  61                 return Configurator.configureExecutable(exec, sequences);\r
  62         }\r
  63 \r
  64         public boolean cancelJob(String jobId) {\r
  65                 WSUtil.validateJobId(jobId);\r
  66                 return WSUtil.cancelJob(jobId);\r
  67         }\r
  68 \r
  69         public JobStatus getJobStatus(String jobId) {\r
  70                 WSUtil.validateJobId(jobId);\r
  71                 return WSUtil.getJobStatus(jobId);\r
  72         }\r
  73 \r
  74         public Limit<T> getLimit(String presetName) {\r
  75                 if (limitMan == null) {\r
  76                         // Limit is not defined\r
  77                         return null;\r
  78                 }\r
  79                 return limitMan.getLimitByName(presetName);\r
  80         }\r
  81 \r
  82         public LimitsManager<T> getLimits() {\r
  83                 return limitMan;\r
  84         }\r
  85 \r
  86         public PresetManager<T> getPresets() {\r
  87                 return aaconPresets;\r
  88         }\r
  89 \r
  90         public RunnerConfig<T> getRunnerOptions() {\r
  91                 return aaconOptions;\r
  92         }\r
  93 \r
  94         /**\r
  95          * Assume statistics is not supported\r
  96          * \r
  97          * @param jobId\r
  98          * @param position\r
  99          * @return\r
 100          */\r
 101         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 102                 // Execution stat is not supported\r
 103                 return new ChunkHolder("", -1);\r
 104         }\r
 105 \r
 106 }\r