webservices/compbio/ws/server/WSUtil.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 package compbio.ws.server;\r
  19 \r
  20 import java.security.InvalidParameterException;\r
  21 import java.util.ArrayList;\r
  22 import java.util.HashSet;\r
  23 import java.util.List;\r
  24 import java.util.Set;\r
  25 \r
  26 import org.apache.log4j.Logger;\r
  27 \r
  28 import compbio.data.sequence.FastaSequence;\r
  29 import compbio.data.sequence.ScoreManager;\r
  30 import compbio.engine.AsyncExecutor;\r
  31 import compbio.engine.Configurator;\r
  32 import compbio.engine.ProgressGetter;\r
  33 import compbio.engine.client.ConfiguredExecutable;\r
  34 import compbio.engine.client.EngineUtil;\r
  35 import compbio.metadata.ChunkHolder;\r
  36 import compbio.metadata.JobStatus;\r
  37 import compbio.metadata.JobSubmissionException;\r
  38 import compbio.metadata.Limit;\r
  39 import compbio.metadata.LimitExceededException;\r
  40 import compbio.metadata.Option;\r
  41 import compbio.metadata.ResultNotAvailableException;\r
  42 import compbio.ws.client.Services;\r
  43 import compbio.ws.client.ServicesUtil;\r
  44 \r
  45 public final class WSUtil {\r
  46 \r
  47         public static final void validateJobId(String jobId)\r
  48                         throws InvalidParameterException {\r
  49                 if (!EngineUtil.isValidJobId(jobId)) {\r
  50                         throw new InvalidParameterException("JobId is not provided or cannot be recognised! Given value: " + jobId);\r
  51                 }\r
  52         }\r
  53 \r
  54         public static final void validateFastaInput(List<FastaSequence> sequences)\r
  55                         throws JobSubmissionException {\r
  56                 if (sequences == null || sequences.isEmpty()) {\r
  57                         throw new JobSubmissionException("List of fasta sequences required but not provided! ");\r
  58                 }\r
  59                 Set<String> names = new HashSet<String>();\r
  60                 for (FastaSequence fs : sequences) {\r
  61                         boolean unique = names.add(fs.getId());\r
  62                         if (!unique) {\r
  63                                 throw new JobSubmissionException(\r
  64                                                 "Input sequences must have unique names! \nSequence " + fs.getId() + " is a duplicate!");\r
  65                         }\r
  66                         if (fs.getLength() == 0) {\r
  67                                 throw new JobSubmissionException("Sequence must not be empty! Sequence: " + fs.getId() + " was empty");\r
  68                         }\r
  69                 }\r
  70         }\r
  71 \r
  72         public static JobStatus getJobStatus(String jobId) {\r
  73                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  74                 return asyncEngine.getJobStatus(jobId);\r
  75         }\r
  76 \r
  77         public static ChunkHolder pullFile(String file, long position) {\r
  78                 return ProgressGetter.pull(file, position);\r
  79         }\r
  80 \r
  81         public static byte getProgress(String jobId) {\r
  82                 throw new UnsupportedOperationException();\r
  83         }\r
  84 \r
  85         public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
  86                 assert confClustal != null;\r
  87                 return Configurator.getAsyncEngine(confClustal);\r
  88         }\r
  89 \r
  90         public static boolean cancelJob(String jobId) {\r
  91                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  92                 return asyncEngine.cancelJob(jobId);\r
  93         }\r
  94 \r
  95         public static <T> String align(List<FastaSequence> sequences,\r
  96                         ConfiguredExecutable<T> confExec, Logger logger,\r
  97                         String callingMethod, Limit<T> limit)\r
  98                         throws LimitExceededException, JobSubmissionException {\r
  99 \r
 100                 if (limit != null && limit.isExceeded(sequences)) {\r
 101                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 102                 }\r
 103                 compbio.runner.RunnerUtil.writeInput(sequences, confExec);\r
 104                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 105                 String jobId = engine.submitJob(confExec);\r
 106                 reportUsage(confExec, logger);\r
 107                 return jobId;\r
 108         }\r
 109         \r
 110 \r
 111         static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
 112                 if (GAUtils.IS_GA_ENABLED) {\r
 113                         Services service = ServicesUtil.getServiceByRunner(confExec.getExecutable().getClass());\r
 114                         GAUtils.reportUsage(service);\r
 115                         logger.info("Reporting GA usage for " + service);\r
 116                 }\r
 117         }\r
 118 \r
 119         public static <T> String analize(List<FastaSequence> sequences,\r
 120                         ConfiguredExecutable<T> confExec, Logger log, String method,\r
 121                         Limit<T> limit) throws JobSubmissionException {\r
 122                 if (limit != null && limit.isExceeded(sequences)) {\r
 123                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 124                 }\r
 125                 compbio.runner.RunnerUtil.writeInput(sequences, confExec);\r
 126                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 127                 String jobId = engine.submitJob(confExec);\r
 128                 reportUsage(confExec, log);\r
 129                 return jobId;\r
 130         }\r
 131 \r
 132         // Same as analize(...) but RNAalifold takes clustal input not fasta\r
 133         // An if condition in the above method might be a better solution but \r
 134         // you need a way of finding out the type of confExec at runtime\r
 135         \r
 136         public static <T> String fold(List<FastaSequence> sequences,\r
 137                         ConfiguredExecutable<T> confExec, Logger log, String method,\r
 138                         Limit<T> limit) throws JobSubmissionException {\r
 139                 if (limit != null && limit.isExceeded(sequences)) {\r
 140                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 141                 }\r
 142                 compbio.runner.RunnerUtil.writeClustalInput(sequences, confExec, '-');\r
 143                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 144                 String jobId = engine.submitJob(confExec);\r
 145                 reportUsage(confExec, log);\r
 146                 return jobId;\r
 147         }\r
 148 \r
 149         /*\r
 150          * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
 151          */\r
 152         public static final <T> List<String> getCommands(List<Option<T>> options,\r
 153                         String keyValueSeparator) {\r
 154                 List<String> oList = new ArrayList<String>();\r
 155                 for (Option<T> o : options) {\r
 156                         oList.add(o.toCommand(keyValueSeparator));\r
 157                 }\r
 158                 return oList;\r
 159         }\r
 160 \r
 161         public static void validateAAConInput(List<FastaSequence> sequences)\r
 162                         throws JobSubmissionException {\r
 163                 validateFastaInput(sequences);\r
 164                 int len = 0;\r
 165                 for (FastaSequence fs : sequences) {\r
 166                         if (len == 0) {\r
 167                                 len = fs.getLength();\r
 168                                 continue;\r
 169                         }\r
 170                         if (fs.getLength() != len) {\r
 171                                 throw new JobSubmissionException(\r
 172                                                 "All sequences must be of the same length. Please align the sequences " + \r
 173                                                 " prior to submission! The first sequence length is : " + len + \r
 174                                                 " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
 175                         }\r
 176                 }\r
 177         }\r
 178 \r
 179         public static void validateJpredInput(List<FastaSequence> sequences)\r
 180                         throws JobSubmissionException {\r
 181                 validateFastaInput(sequences);\r
 182                 int len = 0;\r
 183                 for (FastaSequence fs : sequences) {\r
 184                         if (len == 0) {\r
 185                                 len = fs.getLength();\r
 186                                 continue;\r
 187                         }\r
 188                         if (fs.getLength() != len) {\r
 189                                 System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());\r
 190                                 throw new JobSubmissionException(\r
 191                                                 "All sequences must be of the same length. Please align the sequences " + \r
 192                                                 " prior to submission! The first sequence length is : " + len + \r
 193                                                 " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
 194                         }\r
 195                 }\r
 196         }\r
 197 \r
 198         public static <T> ScoreManager getAnnotation(String jobId, Logger log)\r
 199                         throws ResultNotAvailableException {\r
 200                 WSUtil.validateJobId(jobId);\r
 201                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 202                 ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);\r
 203                 ScoreManager mas = aacon.getResults();\r
 204                 log.trace(jobId + " getConservation : " + mas);\r
 205                 return mas;\r
 206         }\r
 207 \r
 208 }\r