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