webservices/compbio/ws/server/SAService.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.data.sequence.ScoreManager;\r
   9 import compbio.engine.Configurator;\r
  10 import compbio.engine.client.ConfiguredExecutable;\r
  11 import compbio.engine.client.Executable;\r
  12 import compbio.engine.client.SkeletalExecutable;\r
  13 import compbio.metadata.ChunkHolder;\r
  14 import compbio.metadata.JobStatus;\r
  15 import compbio.metadata.JobSubmissionException;\r
  16 import compbio.metadata.Limit;\r
  17 import compbio.metadata.LimitExceededException;\r
  18 import compbio.metadata.LimitsManager;\r
  19 import compbio.metadata.Option;\r
  20 import compbio.metadata.Preset;\r
  21 import compbio.metadata.PresetManager;\r
  22 import compbio.metadata.ResultNotAvailableException;\r
  23 import compbio.metadata.RunnerConfig;\r
  24 import compbio.metadata.UnsupportedRuntimeException;\r
  25 import compbio.metadata.WrongParameterException;\r
  26 import compbio.runner.Util;\r
  27 import compbio.runner.conservation.AACon;\r
  28 \r
  29 /**\r
  30  * Common methods for all SequenceAnnotation web services\r
  31  * \r
  32  * @author pvtroshin\r
  33  * \r
  34  * @param <T>\r
  35  * \r
  36  * @version 1.0 June 2011\r
  37  * @since 2.0\r
  38  */\r
  39 public abstract class SAService<T> {\r
  40 \r
  41         private final RunnerConfig<T> aaconOptions;\r
  42         private final PresetManager<T> aaconPresets;\r
  43         private final LimitsManager<T> limitMan;\r
  44         private SkeletalExecutable<T> exec;\r
  45         private final Logger log;\r
  46 \r
  47         /*\r
  48          * FIXME - instances of the Runner (?) and their types should be defined in\r
  49          * Executable IF\r
  50          */\r
  51         SAService(SkeletalExecutable<T> exec, Logger log) {\r
  52                 assert log != null;\r
  53                 assert exec != null;\r
  54                 this.log = log;\r
  55                 this.exec = exec;\r
  56                 this.limitMan = compbio.engine.client.Util.getLimits(exec.getType());\r
  57                 this.aaconOptions = Util\r
  58                                 .getSupportedOptions((Class<? extends Executable<T>>) exec\r
  59                                                 .getType());\r
  60                 this.aaconPresets = Util\r
  61                                 .getPresets((Class<? extends Executable<T>>) exec.getType());\r
  62         }\r
  63 \r
  64         ConfiguredExecutable<T> init(List<FastaSequence> sequences)\r
  65                         throws JobSubmissionException {\r
  66                 // FIXME\r
  67                 try {\r
  68                         exec = (SkeletalExecutable<T>) exec.getType().newInstance();\r
  69                 } catch (InstantiationException e) {\r
  70                         log.error(e.getLocalizedMessage(), e);\r
  71                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  72                 } catch (IllegalAccessException e) {\r
  73                         log.error(e.getLocalizedMessage(), e);\r
  74                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  75                 }\r
  76                 exec.setInput(SkeletalExecutable.INPUT).setOutput(\r
  77                                 SkeletalExecutable.OUTPUT);\r
  78                 return Configurator.configureExecutable(exec, sequences);\r
  79         }\r
  80 \r
  81         public ScoreManager getAnnotation(String jobId)\r
  82                         throws ResultNotAvailableException {\r
  83                 return WSUtil.getAnnotation(jobId, log);\r
  84         }\r
  85 \r
  86         public boolean cancelJob(String jobId) {\r
  87                 WSUtil.validateJobId(jobId);\r
  88                 return WSUtil.cancelJob(jobId);\r
  89         }\r
  90 \r
  91         public JobStatus getJobStatus(String jobId) {\r
  92                 WSUtil.validateJobId(jobId);\r
  93                 return WSUtil.getJobStatus(jobId);\r
  94         }\r
  95 \r
  96         public Limit<T> getLimit(String presetName) {\r
  97                 if (limitMan == null) {\r
  98                         // Limit is not defined\r
  99                         return null;\r
 100                 }\r
 101                 return limitMan.getLimitByName(presetName);\r
 102         }\r
 103 \r
 104         public LimitsManager<T> getLimits() {\r
 105                 return limitMan;\r
 106         }\r
 107 \r
 108         public PresetManager<T> getPresets() {\r
 109                 return aaconPresets;\r
 110         }\r
 111 \r
 112         public RunnerConfig<T> getRunnerOptions() {\r
 113                 return aaconOptions;\r
 114         }\r
 115 \r
 116         public String analize(List<FastaSequence> sequences)\r
 117                         throws UnsupportedRuntimeException, LimitExceededException,\r
 118                         JobSubmissionException {\r
 119                 WSUtil.validateFastaInput(sequences);\r
 120                 ConfiguredExecutable<T> confIUPred = init(sequences);\r
 121                 return WSUtil.analize(sequences, confIUPred, log, "analize",\r
 122                                 getLimit(""));\r
 123         }\r
 124 \r
 125         public String customAnalize(List<FastaSequence> sequences,\r
 126                         List<Option<T>> options) throws UnsupportedRuntimeException,\r
 127                         LimitExceededException, JobSubmissionException,\r
 128                         WrongParameterException {\r
 129                 WSUtil.validateAAConInput(sequences);\r
 130                 ConfiguredExecutable<T> confAACon = init(sequences);\r
 131                 // Could not do that! Space separated values\r
 132                 // will all be treated as keys! thus duplicates removed\r
 133                 // String params = cbuilder.getCommand();\r
 134                 List<String> params = WSUtil.getCommands(options,\r
 135                                 AACon.KEY_VALUE_SEPARATOR);\r
 136                 confAACon.addParameters(params);\r
 137                 return WSUtil.analize(sequences, confAACon, log, "customAnalize",\r
 138                                 getLimit(""));\r
 139         }\r
 140 \r
 141         public String presetAnalize(List<FastaSequence> sequences, Preset<T> preset)\r
 142                         throws UnsupportedRuntimeException, LimitExceededException,\r
 143                         JobSubmissionException, WrongParameterException {\r
 144                 WSUtil.validateAAConInput(sequences);\r
 145                 if (preset == null) {\r
 146                         throw new WrongParameterException("Preset must be provided!");\r
 147                 }\r
 148                 ConfiguredExecutable<T> confAAcon = init(sequences);\r
 149                 confAAcon.addParameters(preset.getOptions());\r
 150                 Limit<T> limit = getLimit(preset.getName());\r
 151                 return WSUtil\r
 152                                 .analize(sequences, confAAcon, log, "presetAnalize", limit);\r
 153         }\r
 154 \r
 155         /**\r
 156          * Assume statistics is not supported\r
 157          * \r
 158          * @param jobId\r
 159          * @param position\r
 160          * @return\r
 161          */\r
 162         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 163                 // Execution stat is not supported\r
 164                 return new ChunkHolder("", -1);\r
 165         }\r
 166 \r
 167 }\r