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