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