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