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