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