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.Alignment;\r
  29 import compbio.data.sequence.FastaSequence;\r
  30 import compbio.data.sequence.RNAStructScoreManager;\r
  31 import compbio.data.sequence.ScoreManager;\r
  32 import compbio.engine.AsyncExecutor;\r
  33 import compbio.engine.Configurator;\r
  34 import compbio.engine.ProgressGetter;\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.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 (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
  51                         throw new InvalidParameterException(\r
  52                                         "JobId is not provided or cannot be recognised! Given value: "\r
  53                                                         + jobId);\r
  54                 }\r
  55         }\r
  56 \r
  57         public static final void validateFastaInput(List<FastaSequence> sequences)\r
  58                         throws JobSubmissionException {\r
  59                 if (sequences == null || sequences.isEmpty()) {\r
  60                         throw new JobSubmissionException(\r
  61                                         "List of fasta sequences required but not provided! ");\r
  62                 }\r
  63                 Set<String> names = new HashSet<String>();\r
  64                 for (FastaSequence fs : sequences) {\r
  65                         boolean unique = names.add(fs.getId());\r
  66                         if (!unique) {\r
  67                                 throw new JobSubmissionException(\r
  68                                                 "Input sequences must have unique names! \n"\r
  69                                                                 + "Sequence " + fs.getId() + " is a duplicate!");\r
  70                         }\r
  71                         if (fs.getLength() == 0) {\r
  72                                 throw new JobSubmissionException(\r
  73                                                 "Sequence must not be empty! Sequence: " + fs.getId()\r
  74                                                                 + " was empty");\r
  75                         }\r
  76                 }\r
  77         }\r
  78 \r
  79         public static JobStatus getJobStatus(String jobId) {\r
  80                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  81                 return asyncEngine.getJobStatus(jobId);\r
  82         }\r
  83 \r
  84         public static ChunkHolder pullFile(String file, long position) {\r
  85                 return ProgressGetter.pull(file, position);\r
  86         }\r
  87 \r
  88         public static byte getProgress(String jobId) {\r
  89                 throw new UnsupportedOperationException();\r
  90         }\r
  91 \r
  92         public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
  93                 assert confClustal != null;\r
  94                 return Configurator.getAsyncEngine(confClustal);\r
  95         }\r
  96 \r
  97         public static boolean cancelJob(String jobId) {\r
  98                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  99                 return asyncEngine.cancelJob(jobId);\r
 100         }\r
 101 \r
 102         public static <T> String align(List<FastaSequence> sequences,\r
 103                         ConfiguredExecutable<T> confExec, Logger logger,\r
 104                         String callingMethod, Limit<T> limit)\r
 105                         throws LimitExceededException, JobSubmissionException {\r
 106 \r
 107                 if (limit != null && limit.isExceeded(sequences)) {\r
 108                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 109                 }\r
 110                 compbio.runner.Util.writeInput(sequences, confExec);\r
 111                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 112                 String jobId = engine.submitJob(confExec);\r
 113                 reportUsage(confExec, logger);\r
 114                 return jobId;\r
 115         }\r
 116         \r
 117         // Hardcoded gapchar '-' in this method\r
 118         \r
 119 //      public static <T> String fold(Alignment alignment,\r
 120 //                      ConfiguredExecutable<T> confExec, Logger logger,\r
 121 //                      String callingMethod, Limit<T> limit)\r
 122 //                      throws LimitExceededException, JobSubmissionException {\r
 123 //              \r
 124 //              List<FastaSequence> sequences = alignment.getSequences();\r
 125 //              if (limit != null && limit.isExceeded(sequences)) {\r
 126 //                      throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 127 //              }\r
 128 //              compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
 129 //              System.out.println("WSUtil-fold: Writing the clustal input file on the server: to file: "\r
 130 //                              + confExec.getInput());\r
 131 //              System.out.println("WSUtil-fold: The executable is configured with parameters: " \r
 132 //                              + confExec.getParameters());\r
 133 ////            System.out.println("WSUTil-fold: Dump the configured executable:\n" \r
 134 ////                            + confExec.toString());\r
 135 //              AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 136 //              String jobId = engine.submitJob(confExec);\r
 137 //              reportUsage(confExec, logger);\r
 138 //              return jobId;\r
 139 //      }\r
 140 \r
 141         static <T> void reportUsage(ConfiguredExecutable<T> confExec, Logger logger) {\r
 142                 if (GAUtils.IS_GA_ENABLED) {\r
 143                         Services service = ServicesUtil.getServiceByRunner(confExec\r
 144                                         .getExecutable().getClass());\r
 145                         GAUtils.reportUsage(service);\r
 146                         logger.info("Reporting GA usage for " + service);\r
 147                 }\r
 148         }\r
 149 \r
 150         public static <T> String analize(List<FastaSequence> sequences,\r
 151                         ConfiguredExecutable<T> confExec, Logger log, String method,\r
 152                         Limit<T> limit) throws JobSubmissionException {\r
 153                 if (limit != null && limit.isExceeded(sequences)) {\r
 154                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 155                 }\r
 156                 log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
 157                 compbio.runner.Util.writeInput(sequences, confExec);\r
 158                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 159                 String jobId = engine.submitJob(confExec);\r
 160                 reportUsage(confExec, log);\r
 161                 return jobId;\r
 162         }\r
 163         \r
 164         // Same as analize but Alifold takes clustal input not fasta\r
 165         \r
 166         public static <T> String fold(List<FastaSequence> sequences,\r
 167                         ConfiguredExecutable<T> confExec, Logger log, String method,\r
 168                         Limit<T> limit) throws JobSubmissionException {\r
 169                 if (limit != null && limit.isExceeded(sequences)) {\r
 170                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 171                 }\r
 172                 log.debug("Method: " + method + " with task: " + confExec.getTaskId());\r
 173                 // This line is different from the above method\r
 174                 compbio.runner.Util.writeClustalInput(sequences, confExec, '-');\r
 175                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 176                 String jobId = engine.submitJob(confExec);\r
 177                 reportUsage(confExec, log);\r
 178                 return jobId;\r
 179         }\r
 180 \r
 181         /*\r
 182          * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
 183          */\r
 184         public static final <T> List<String> getCommands(List<Option<T>> options,\r
 185                         String keyValueSeparator) {\r
 186                 List<String> oList = new ArrayList<String>();\r
 187                 for (Option<T> o : options) {\r
 188                         oList.add(o.toCommand(keyValueSeparator));\r
 189                 }\r
 190                 return oList;\r
 191         }\r
 192 \r
 193         public static void validateAAConInput(List<FastaSequence> sequences)\r
 194                         throws JobSubmissionException {\r
 195                 validateFastaInput(sequences);\r
 196                 int len = 0;\r
 197                 for (FastaSequence fs : sequences) {\r
 198                         if (len == 0) {\r
 199                                 len = fs.getLength();\r
 200                                 continue;\r
 201                         }\r
 202                         if (fs.getLength() != len) {\r
 203                                 throw new JobSubmissionException(\r
 204                                                 "All sequences must be of the same length. Please align "\r
 205                                                                 + "the sequences prior to submission! The first sequence length is : "\r
 206                                                                 + len + " but the sequence '" + fs.getId()\r
 207                                                                 + "' length is " + fs.getLength());\r
 208                         }\r
 209                 }\r
 210         }\r
 211 \r
 212         public static <T> ScoreManager getAnnotation(String jobId, Logger log)\r
 213                         throws ResultNotAvailableException {\r
 214                 WSUtil.validateJobId(jobId);\r
 215                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
 216                 ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine\r
 217                                 .getResults(jobId);\r
 218                 \r
 219                 ScoreManager mas = aacon.getResults();\r
 220                 \r
 221                 log.trace(jobId + " getConservation : " + mas);\r
 222                 return mas;\r
 223         }\r
 224         \r
 225 \r
 226         /*\r
 227          * UNUSED\r
 228          * \r
 229          * @SuppressWarnings("unchecked") static <T> LimitsManager<T>\r
 230          * getLimits(Class<? extends Executable<T>> clazz, WebServiceContext\r
 231          * wsContext) {\r
 232          * \r
 233          * String LIMIT_KEY = CACHE_KEY + clazz.getCanonicalName(); LimitsManager<T>\r
 234          * limit = (LimitsManager<T>) getObjectFromApplContext( LIMIT_KEY,\r
 235          * wsContext); if (limit == null) { synchronized (WSUtil.class) { limit =\r
 236          * (LimitsManager<T>) getObjectFromApplContext(LIMIT_KEY, wsContext); if\r
 237          * (limit == null) { limit = compbio.runner.Util\r
 238          * .getLimits((Class<Executable<T>>) clazz);\r
 239          * addObjectToApplContext(wsContext, LIMIT_KEY, limit); } } } return limit;\r
 240          * }\r
 241          * \r
 242          * static void addObjectToApplContext(WebServiceContext wsContext, String\r
 243          * objKey, Object obj) { assert !Util.isEmpty(objKey) :\r
 244          * "Key for the object must not be empty! "; assert wsContext != null;\r
 245          * \r
 246          * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
 247          * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); assert ctx !=\r
 248          * null; log.debug("Adding object with key '" + objKey + "' and value '" +\r
 249          * obj + "' to the application context"); ctx.setAttribute(objKey, obj); }\r
 250          * static Object getObjectFromApplContext(String objKey, WebServiceContext\r
 251          * wsContext) { assert !Util.isEmpty(objKey) :\r
 252          * "Key for the object must not be empty! "; assert wsContext != null;\r
 253          * \r
 254          * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
 255          * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); Object obj =\r
 256          * ctx.getAttribute(objKey); log.trace("Retrieving object with key '" +\r
 257          * objKey + "' and value '" + obj + "' from the application context");\r
 258          * return obj; }\r
 259          */\r
 260 }\r