webservices/compbio/ws/server/MafftWS.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0  \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.MsaWS;\r
  29 import compbio.data.sequence.Alignment;\r
  30 import compbio.data.sequence.FastaSequence;\r
  31 import compbio.engine.AsyncExecutor;\r
  32 import compbio.engine.Configurator;\r
  33 import compbio.engine.client.ConfiguredExecutable;\r
  34 import compbio.metadata.ChunkHolder;\r
  35 import compbio.metadata.JobStatus;\r
  36 import compbio.metadata.JobSubmissionException;\r
  37 import compbio.metadata.Limit;\r
  38 import compbio.metadata.LimitsManager;\r
  39 import compbio.metadata.Option;\r
  40 import compbio.metadata.Preset;\r
  41 import compbio.metadata.PresetManager;\r
  42 import compbio.metadata.ResultNotAvailableException;\r
  43 import compbio.metadata.RunnerConfig;\r
  44 import compbio.metadata.WrongParameterException;\r
  45 import compbio.runner.Util;\r
  46 import compbio.runner.msa.Mafft;\r
  47 \r
  48 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")\r
  49 public class MafftWS implements MsaWS<Mafft> {\r
  50 \r
  51         private static Logger log = Logger.getLogger(MafftWS.class);\r
  52 \r
  53         private static final RunnerConfig<Mafft> mafftOptions = Util\r
  54                         .getSupportedOptions(Mafft.class);\r
  55 \r
  56         private static final PresetManager<Mafft> mafftPresets = Util\r
  57                         .getPresets(Mafft.class);\r
  58 \r
  59         private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util\r
  60                         .getLimits(new Mafft().getType());\r
  61 \r
  62         @Override\r
  63         public String align(List<FastaSequence> sequences)\r
  64                         throws JobSubmissionException {\r
  65                 WSUtil.validateFastaInput(sequences);\r
  66                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
  67                 return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));\r
  68         }\r
  69 \r
  70         ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
  71                         throws JobSubmissionException {\r
  72                 Mafft mafft = new Mafft();\r
  73                 return Configurator.configureExecutable(mafft, dataSet);\r
  74         }\r
  75 \r
  76         @Override\r
  77         public String customAlign(List<FastaSequence> sequences,\r
  78                         List<Option<Mafft>> options) throws JobSubmissionException,\r
  79                         WrongParameterException {\r
  80                 WSUtil.validateFastaInput(sequences);\r
  81                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
  82                 List<String> params = WSUtil.getCommands(options,\r
  83                                 Mafft.KEY_VALUE_SEPARATOR);\r
  84                 log.info("Setting parameters: " + params);\r
  85                 confMafft.addParameters(params);\r
  86                 return WSUtil.align(sequences, confMafft, null, "customAlign",\r
  87                                 getLimit(""));\r
  88         }\r
  89 \r
  90         @Override\r
  91         public String presetAlign(List<FastaSequence> sequences,\r
  92                         Preset<Mafft> preset) throws JobSubmissionException,\r
  93                         WrongParameterException {\r
  94                 WSUtil.validateFastaInput(sequences);\r
  95                 if (preset == null) {\r
  96                         throw new WrongParameterException("Preset must be provided!");\r
  97                 }\r
  98                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
  99                 confMafft.addParameters(preset.getOptions());\r
 100                 // This will return default limit if a specific the limit for a\r
 101                 // particular preset is not found\r
 102                 Limit<Mafft> limit = getLimit(preset.getName());\r
 103 \r
 104                 return WSUtil.align(sequences, confMafft, null, "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<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine\r
 113                                 .getResults(jobId);\r
 114                 Alignment al = mafft.getResults();\r
 115                 // log(jobId, "getResults");\r
 116                 return al;\r
 117         }\r
 118 \r
 119         @Override\r
 120         public Limit<Mafft> 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<Mafft> 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                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 137                                 + new Mafft().getError();\r
 138                 return WSUtil.pullFile(file, position);\r
 139         }\r
 140 \r
 141         @Override\r
 142         public boolean cancelJob(String jobId) {\r
 143                 WSUtil.validateJobId(jobId);\r
 144                 return WSUtil.cancelJob(jobId);\r
 145         }\r
 146 \r
 147         @Override\r
 148         public JobStatus getJobStatus(String jobId) {\r
 149                 WSUtil.validateJobId(jobId);\r
 150                 return WSUtil.getJobStatus(jobId);\r
 151         }\r
 152 \r
 153         @Override\r
 154         public PresetManager<Mafft> getPresets() {\r
 155                 return mafftPresets;\r
 156         }\r
 157 \r
 158         @Override\r
 159         public RunnerConfig<Mafft> getRunnerOptions() {\r
 160                 return mafftOptions;\r
 161         }\r
 162 \r
 163 }\r