webservices/compbio/ws/server/ProbconsWS.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.Probcons;\r
  49 \r
  50 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
  51 public class ProbconsWS implements MsaWS<Probcons> {\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("ProbconsWS-stats");\r
  58 \r
  59         private static Logger log = Logger.getLogger(ProbconsWS.class);\r
  60 \r
  61         private static final RunnerConfig<Probcons> probconsOptions = Util\r
  62                         .getSupportedOptions(Probcons.class);\r
  63 \r
  64         private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util\r
  65                         .getLimits(new Probcons().getType());\r
  66 \r
  67         @Override\r
  68         public String align(List<FastaSequence> sequences)\r
  69                         throws JobSubmissionException {\r
  70                 WSUtil.validateFastaInput(sequences);\r
  71                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  72                 return WSUtil.align(sequences, confProbcons, null, "align",\r
  73                                 getLimit(""));\r
  74         }\r
  75 \r
  76         ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
  77                         throws JobSubmissionException {\r
  78                 Probcons probcons = new Probcons();\r
  79                 return Configurator.configureExecutable(probcons, dataSet);\r
  80         }\r
  81 \r
  82         @Override\r
  83         public String customAlign(List<FastaSequence> sequences,\r
  84                         List<Option<Probcons>> options) throws JobSubmissionException,\r
  85                         WrongParameterException {\r
  86                 WSUtil.validateFastaInput(sequences);\r
  87                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
  88                 List<String> params = WSUtil.getCommands(options,\r
  89                                 Probcons.KEY_VALUE_SEPARATOR);\r
  90                 log.info("Setting parameters:" + params);\r
  91                 confProbcons.addParameters(params);\r
  92                 return WSUtil.align(sequences, confProbcons, null, "customAlign",\r
  93                                 getLimit(""));\r
  94         }\r
  95 \r
  96         @Override\r
  97         public String presetAlign(List<FastaSequence> sequences,\r
  98                         Preset<Probcons> preset) throws JobSubmissionException,\r
  99                         WrongParameterException {\r
 100                 WSUtil.validateFastaInput(sequences);\r
 101                 if (preset == null) {\r
 102                         throw new WrongParameterException("Preset must be provided!");\r
 103                 }\r
 104                 ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
 105                 confProbcons.addParameters(preset.getOptions());\r
 106                 Limit<Probcons> limit = getLimit(preset.getName());\r
 107                 return WSUtil\r
 108                                 .align(sequences, confProbcons, null, "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<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
 117                                 .getResults(jobId);\r
 118                 Alignment al = probcons.getResults();\r
 119                 // log(jobId, "getResults");\r
 120                 return al;\r
 121         }\r
 122 \r
 123         @Override\r
 124         public Limit<Probcons> getLimit(String presetName) {\r
 125                 if (limitMan == null) {\r
 126                         // Limit is not defined\r
 127                         return null;\r
 128                 }\r
 129                 return limitMan.getLimitByName(presetName);\r
 130         }\r
 131 \r
 132         @Override\r
 133         public LimitsManager<Probcons> getLimits() {\r
 134                 return limitMan;\r
 135         }\r
 136 \r
 137         @Override\r
 138         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
 139                 WSUtil.validateJobId(jobId);\r
 140                 // TODO check if output is the one to return\r
 141                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 142                                 + new Probcons().getError();\r
 143                 return WSUtil.pullFile(file, position);\r
 144         }\r
 145 \r
 146         @Override\r
 147         public boolean cancelJob(String jobId) {\r
 148                 WSUtil.validateJobId(jobId);\r
 149                 return WSUtil.cancelJob(jobId);\r
 150         }\r
 151 \r
 152         @Override\r
 153         public JobStatus getJobStatus(String jobId) {\r
 154                 WSUtil.validateJobId(jobId);\r
 155                 return WSUtil.getJobStatus(jobId);\r
 156         }\r
 157 \r
 158         @Override\r
 159         public PresetManager<Probcons> getPresets() {\r
 160                 return null;\r
 161         }\r
 162 \r
 163         @Override\r
 164         public RunnerConfig<Probcons> getRunnerOptions() {\r
 165                 return probconsOptions;\r
 166         }\r
 167 \r
 168 }\r