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