webservices/compbio/ws/server/GenericMetadataService.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.ws.server;\r
  19 \r
  20 import java.util.List;\r
  21 \r
  22 import org.apache.log4j.Logger;\r
  23 \r
  24 import compbio.data.sequence.FastaSequence;\r
  25 import compbio.engine.Configurator;\r
  26 import compbio.engine.client.ConfiguredExecutable;\r
  27 import compbio.engine.client.Executable;\r
  28 import compbio.engine.client.SkeletalExecutable;\r
  29 import compbio.metadata.ChunkHolder;\r
  30 import compbio.metadata.JobStatus;\r
  31 import compbio.metadata.JobSubmissionException;\r
  32 import compbio.metadata.Limit;\r
  33 import compbio.metadata.LimitsManager;\r
  34 import compbio.metadata.PresetManager;\r
  35 import compbio.metadata.RunnerConfig;\r
  36 import compbio.runner.Util;\r
  37 \r
  38 public abstract class GenericMetadataService<T> {\r
  39 \r
  40         private final RunnerConfig<T> aaconOptions;\r
  41         private final PresetManager<T> aaconPresets;\r
  42         private final LimitsManager<T> limitMan;\r
  43         private SkeletalExecutable<T> exec;\r
  44         final Logger log;\r
  45 \r
  46         /*\r
  47          * FIXME - instances of the Runner (?) and their types should be defined in\r
  48          * Executable IF\r
  49          */\r
  50         GenericMetadataService(SkeletalExecutable<T> exec, Logger log) {\r
  51                 assert log != null;\r
  52                 assert exec != null;\r
  53                 this.log = log;\r
  54                 this.exec = exec;\r
  55                 this.limitMan = compbio.engine.client.Util.getLimits(exec.getType());\r
  56                 this.aaconOptions = Util\r
  57                                 .getSupportedOptions((Class<? extends Executable<T>>) exec\r
  58                                                 .getType());\r
  59                 this.aaconPresets = Util\r
  60                                 .getPresets((Class<? extends Executable<T>>) exec.getType());\r
  61         }\r
  62 \r
  63         ConfiguredExecutable<T> init(List<FastaSequence> sequences)\r
  64                         throws JobSubmissionException {\r
  65                 // FIXME\r
  66                 try {\r
  67                         exec = (SkeletalExecutable<T>) exec.getType().newInstance();\r
  68                 } catch (InstantiationException e) {\r
  69                         log.error(e.getLocalizedMessage(), e);\r
  70                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  71                 } catch (IllegalAccessException e) {\r
  72                         log.error(e.getLocalizedMessage(), e);\r
  73                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  74                 }\r
  75                 exec.setInput(SkeletalExecutable.INPUT)\r
  76                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  77                                 .setError(SkeletalExecutable.ERROR);\r
  78                 return Configurator.configureExecutable(exec, sequences);\r
  79         }\r
  80 \r
  81         public boolean cancelJob(String jobId) {\r
  82                 WSUtil.validateJobId(jobId);\r
  83                 return WSUtil.cancelJob(jobId);\r
  84         }\r
  85 \r
  86         public JobStatus getJobStatus(String jobId) {\r
  87                 WSUtil.validateJobId(jobId);\r
  88                 return WSUtil.getJobStatus(jobId);\r
  89         }\r
  90 \r
  91         public Limit<T> getLimit(String presetName) {\r
  92                 if (limitMan == null) {\r
  93                         // Limit is not defined\r
  94                         return null;\r
  95                 }\r
  96                 return limitMan.getLimitByName(presetName);\r
  97         }\r
  98 \r
  99         public LimitsManager<T> getLimits() {\r
 100                 return limitMan;\r
 101         }\r
 102 \r
 103         public PresetManager<T> getPresets() {\r
 104                 return aaconPresets;\r
 105         }\r
 106 \r
 107         public RunnerConfig<T> getRunnerOptions() {\r
 108                 return aaconOptions;\r
 109         }\r
 110 \r
 111         /**\r
 112          * Assume statistics is not supported\r
 113          * \r
 114          * @param jobId\r
 115          * @param position\r
 116          * @return ChunkHolder\r
 117          */\r
 118         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 119                 // Execution stat is not supported\r
 120                 return new ChunkHolder("", -1);\r
 121         }\r
 122 \r
 123 }\r