webservices/compbio/ws/server/ProbconsWS.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 \r
  19 package compbio.ws.server;\r
  20 \r
  21 import java.io.File;\r
  22 import java.util.List;\r
  23 \r
  24 import javax.jws.WebService;\r
  25 \r
  26 import org.apache.log4j.Logger;\r
  27 \r
  28 import compbio.data.msa.JABAService;\r
  29 import compbio.data.msa.MsaWS;\r
  30 import compbio.data.sequence.Alignment;\r
  31 import compbio.data.sequence.FastaSequence;\r
  32 import compbio.engine.AsyncExecutor;\r
  33 import compbio.engine.Configurator;\r
  34 import compbio.engine.client.ConfiguredExecutable;\r
  35 import compbio.engine.client.SkeletalExecutable;\r
  36 import compbio.metadata.ChunkHolder;\r
  37 import compbio.metadata.JobStatus;\r
  38 import compbio.metadata.JobSubmissionException;\r
  39 import compbio.metadata.Limit;\r
  40 import compbio.metadata.LimitsManager;\r
  41 import compbio.metadata.Option;\r
  42 import compbio.metadata.Preset;\r
  43 import compbio.metadata.PresetManager;\r
  44 import compbio.metadata.ResultNotAvailableException;\r
  45 import compbio.metadata.RunnerConfig;\r
  46 import compbio.metadata.WrongParameterException;\r
  47 import compbio.runner.Util;\r
  48 import compbio.runner.msa.Probcons;\r
  49 \r
  50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")\r
  51 public class ProbconsWS implements MsaWS<Probcons> {\r
  52 \r
  53         private static Logger log = Logger.getLogger(ProbconsWS.class);\r
  54 \r
  55         private static final RunnerConfig<Probcons> probconsOptions = Util\r
  56                         .getSupportedOptions(Probcons.class);\r
  57 \r
  58         private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util\r
  59                         .getLimits(new Probcons().getType());\r
  60 \r
  61         @Override\r
  62         public String align(List<FastaSequence> sequences)\r
  63                         throws JobSubmissionException {\r
  64                 WSUtil.validateFastaInput(sequences);\r
  65                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  66                 return WSUtil\r
  67                                 .align(sequences, confProbcons, log, "align", getLimit(""));\r
  68         }\r
  69 \r
  70         ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
  71                         throws JobSubmissionException {\r
  72                 Probcons probcons = new Probcons();\r
  73                 probcons.setInput(SkeletalExecutable.INPUT)\r
  74                                 .setOutput(SkeletalExecutable.OUTPUT)\r
  75                                 .setError(SkeletalExecutable.ERROR);\r
  76                 return Configurator.configureExecutable(probcons, dataSet);\r
  77         }\r
  78 \r
  79         @Override\r
  80         public String customAlign(List<FastaSequence> sequences,\r
  81                         List<Option<Probcons>> options) throws JobSubmissionException,\r
  82                         WrongParameterException {\r
  83                 WSUtil.validateFastaInput(sequences);\r
  84                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  85                 List<String> params = WSUtil.getCommands(options,\r
  86                                 Probcons.KEY_VALUE_SEPARATOR);\r
  87                 log.info("Setting parameters:" + params);\r
  88                 confProbcons.addParameters(params);\r
  89                 return WSUtil.align(sequences, confProbcons, log, "customAlign",\r
  90                                 getLimit(""));\r
  91         }\r
  92 \r
  93         @Override\r
  94         public String presetAlign(List<FastaSequence> sequences,\r
  95                         Preset<Probcons> preset) throws JobSubmissionException,\r
  96                         WrongParameterException {\r
  97                 WSUtil.validateFastaInput(sequences);\r
  98                 if (preset == null) {\r
  99                         throw new WrongParameterException("Preset must be provided!");\r
 100                 }\r
 101                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
 102                 confProbcons.addParameters(preset.getOptions());\r
 103                 Limit<Probcons> limit = getLimit(preset.getName());\r
 104                 return WSUtil.align(sequences, confProbcons, log, "presetAlign", limit);\r
 105         }\r
 106 \r
 107         @SuppressWarnings("unchecked")\r
 108         @Override\r
 109         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 110                 WSUtil.validateJobId(jobId);\r
 111                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 112                 ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
 113                                 .getResults(jobId);\r
 114                 Alignment al = probcons.getResults();\r
 115                 // log(jobId, "getResults");\r
 116                 return al;\r
 117         }\r
 118 \r
 119         @Override\r
 120         public Limit<Probcons> getLimit(String presetName) {\r
 121                 if (limitMan == null) {\r
 122                         // Limit is not defined\r
 123                         return null;\r
 124                 }\r
 125                 return limitMan.getLimitByName(presetName);\r
 126         }\r
 127 \r
 128         @Override\r
 129         public LimitsManager<Probcons> getLimits() {\r
 130                 return limitMan;\r
 131         }\r
 132 \r
 133         @Override\r
 134         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 135                 WSUtil.validateJobId(jobId);\r
 136                 // TODO check if output is the one to return\r
 137                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 138                                 + new Probcons().getError();\r
 139                 return WSUtil.pullFile(file, position);\r
 140         }\r
 141 \r
 142         @Override\r
 143         public boolean cancelJob(String jobId) {\r
 144                 WSUtil.validateJobId(jobId);\r
 145                 return WSUtil.cancelJob(jobId);\r
 146         }\r
 147 \r
 148         @Override\r
 149         public JobStatus getJobStatus(String jobId) {\r
 150                 WSUtil.validateJobId(jobId);\r
 151                 return WSUtil.getJobStatus(jobId);\r
 152         }\r
 153 \r
 154         @Override\r
 155         public PresetManager<Probcons> getPresets() {\r
 156                 return null;\r
 157         }\r
 158 \r
 159         @Override\r
 160         public RunnerConfig<Probcons> getRunnerOptions() {\r
 161                 return probconsOptions;\r
 162         }\r
 163 \r
 164 }\r