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