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.getSupportedOptions((Class<? extends Executable<T>>) exec.getType());\r
  57                 this.aaconPresets = Util.getPresets((Class<? extends Executable<T>>) exec.getType());\r
  58         }\r
  59 \r
  60         ConfiguredExecutable<T> init(List<FastaSequence> sequences)\r
  61                         throws JobSubmissionException {\r
  62                 // FIXME\r
  63                 try {\r
  64                         exec = (SkeletalExecutable<T>) exec.getType().newInstance();\r
  65                 } catch (InstantiationException e) {\r
  66                         log.error(e.getLocalizedMessage(), e);\r
  67                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  68                 } catch (IllegalAccessException e) {\r
  69                         log.error(e.getLocalizedMessage(), e);\r
  70                         throw new JobSubmissionException(e.getLocalizedMessage(), e);\r
  71                 }\r
  72                 exec.setInput(SkeletalExecutable.INPUT)\r
  73                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  74                                 .setError(SkeletalExecutable.ERROR);\r
  75                 return Configurator.configureExecutable(exec, sequences);\r
  76         }\r
  77 \r
  78         public boolean cancelJob(String jobId) {\r
  79                 WSUtil.validateJobId(jobId);\r
  80                 return WSUtil.cancelJob(jobId);\r
  81         }\r
  82 \r
  83         public JobStatus getJobStatus(String jobId) {\r
  84                 WSUtil.validateJobId(jobId);\r
  85                 return WSUtil.getJobStatus(jobId);\r
  86         }\r
  87 \r
  88         public Limit<T> getLimit(String presetName) {\r
  89                 if (limitMan == null) {\r
  90                         // Limit is not defined\r
  91                         return null;\r
  92                 }\r
  93                 return limitMan.getLimitByName(presetName);\r
  94         }\r
  95 \r
  96         public LimitsManager<T> getLimits() {\r
  97                 return limitMan;\r
  98         }\r
  99 \r
 100         public PresetManager<T> getPresets() {\r
 101                 return aaconPresets;\r
 102         }\r
 103 \r
 104         public RunnerConfig<T> getRunnerOptions() {\r
 105                 return aaconOptions;\r
 106         }\r
 107 \r
 108         /**\r
 109          * Assume statistics is not supported\r
 110          * \r
 111          * @param jobId\r
 112          * @param position\r
 113          * @return ChunkHolder\r
 114          */\r
 115         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 116                 // Execution stat is not supported\r
 117                 return new ChunkHolder("", -1);\r
 118         }\r
 119 }\r