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.annotation.Resource;\r
  25 import javax.jws.WebService;\r
  26 import javax.xml.ws.WebServiceContext;\r
  27 \r
  28 import org.apache.log4j.Logger;\r
  29 \r
  30 import compbio.data.msa.MsaWS;\r
  31 import compbio.data.sequence.Alignment;\r
  32 import compbio.data.sequence.FastaSequence;\r
  33 import compbio.engine.AsyncExecutor;\r
  34 import compbio.engine.Configurator;\r
  35 import compbio.engine.client.ConfiguredExecutable;\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.Mafft;\r
  49 \r
  50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")\r
  51 public class MafftWS implements MsaWS<Mafft> {\r
  52 \r
  53         // Ask for resource injection\r
  54         @Resource\r
  55         WebServiceContext wsContext;\r
  56 \r
  57         private static Logger statLog = Logger.getLogger("MafftWS-stats");\r
  58 \r
  59         private static Logger log = Logger.getLogger(MafftWS.class);\r
  60 \r
  61         private static final RunnerConfig<Mafft> mafftOptions = Util\r
  62                         .getSupportedOptions(Mafft.class);\r
  63 \r
  64         private static final PresetManager<Mafft> mafftPresets = Util\r
  65                         .getPresets(Mafft.class);\r
  66 \r
  67         private static final LimitsManager<Mafft> limitMan = compbio.engine.client.Util\r
  68                         .getLimits(new Mafft().getType());\r
  69 \r
  70         @Override\r
  71         public String align(List<FastaSequence> sequences)\r
  72                         throws JobSubmissionException {\r
  73                 WSUtil.validateFastaInput(sequences);\r
  74                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
  75                 return WSUtil.align(sequences, confMafft, null, "align", getLimit(""));\r
  76         }\r
  77 \r
  78         ConfiguredExecutable<Mafft> init(List<FastaSequence> dataSet)\r
  79                         throws JobSubmissionException {\r
  80                 Mafft mafft = new Mafft();\r
  81                 return Configurator.configureExecutable(mafft, dataSet);\r
  82         }\r
  83 \r
  84         @Override\r
  85         public String customAlign(List<FastaSequence> sequences,\r
  86                         List<Option<Mafft>> options) throws JobSubmissionException,\r
  87                         WrongParameterException {\r
  88                 WSUtil.validateFastaInput(sequences);\r
  89                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
  90                 List<String> params = WSUtil.getCommands(options,\r
  91                                 Mafft.KEY_VALUE_SEPARATOR);\r
  92                 log.info("Setting parameters: " + params);\r
  93                 confMafft.addParameters(params);\r
  94                 return WSUtil.align(sequences, confMafft, null, "customAlign",\r
  95                                 getLimit(""));\r
  96         }\r
  97 \r
  98         @Override\r
  99         public String presetAlign(List<FastaSequence> sequences,\r
 100                         Preset<Mafft> preset) throws JobSubmissionException,\r
 101                         WrongParameterException {\r
 102                 WSUtil.validateFastaInput(sequences);\r
 103                 if (preset == null) {\r
 104                         throw new WrongParameterException("Preset must be provided!");\r
 105                 }\r
 106                 ConfiguredExecutable<Mafft> confMafft = init(sequences);\r
 107                 confMafft.addParameters(preset.getOptions());\r
 108                 // This will return default limit if a specific the limit for a\r
 109                 // particular preset is not found\r
 110                 Limit<Mafft> limit = getLimit(preset.getName());\r
 111 \r
 112                 return WSUtil.align(sequences, confMafft, null, "presetAlign", limit);\r
 113         }\r
 114 \r
 115         @SuppressWarnings("unchecked")\r
 116         @Override\r
 117         public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
 118                 WSUtil.validateJobId(jobId);\r
 119                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 120                 ConfiguredExecutable<Mafft> mafft = (ConfiguredExecutable<Mafft>) asyncEngine\r
 121                                 .getResults(jobId);\r
 122                 Alignment al = mafft.getResults();\r
 123                 // log(jobId, "getResults");\r
 124                 return al;\r
 125         }\r
 126 \r
 127         @Override\r
 128         public Limit<Mafft> getLimit(String presetName) {\r
 129                 if (limitMan == null) {\r
 130                         // Limit is not defined\r
 131                         return null;\r
 132                 }\r
 133                 return limitMan.getLimitByName(presetName);\r
 134         }\r
 135 \r
 136         @Override\r
 137         public LimitsManager<Mafft> getLimits() {\r
 138                 return limitMan;\r
 139         }\r
 140 \r
 141         @Override\r
 142         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 143                 WSUtil.validateJobId(jobId);\r
 144                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 145                                 + new Mafft().getError();\r
 146                 return WSUtil.pullFile(file, position);\r
 147         }\r
 148 \r
 149         @Override\r
 150         public boolean cancelJob(String jobId) {\r
 151                 WSUtil.validateJobId(jobId);\r
 152                 return WSUtil.cancelJob(jobId);\r
 153         }\r
 154 \r
 155         @Override\r
 156         public JobStatus getJobStatus(String jobId) {\r
 157                 WSUtil.validateJobId(jobId);\r
 158                 return WSUtil.getJobStatus(jobId);\r
 159         }\r
 160 \r
 161         @Override\r
 162         public PresetManager<Mafft> getPresets() {\r
 163                 return mafftPresets;\r
 164         }\r
 165 \r
 166         @Override\r
 167         public RunnerConfig<Mafft> getRunnerOptions() {\r
 168                 return mafftOptions;\r
 169         }\r
 170 \r
 171 }\r