webservices/compbio/ws/server/WSUtil.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\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.List;\r
  23 \r
  24 import org.apache.log4j.Logger;\r
  25 \r
  26 import compbio.data.sequence.FastaSequence;\r
  27 import compbio.engine.AsyncExecutor;\r
  28 import compbio.engine.Configurator;\r
  29 import compbio.engine.ProgressGetter;\r
  30 import compbio.engine.client.ConfiguredExecutable;\r
  31 import compbio.metadata.ChunkHolder;\r
  32 import compbio.metadata.JobStatus;\r
  33 import compbio.metadata.JobSubmissionException;\r
  34 import compbio.metadata.Limit;\r
  35 import compbio.metadata.LimitExceededException;\r
  36 import compbio.metadata.Option;\r
  37 import compbio.util.Timer;\r
  38 \r
  39 public final class WSUtil {\r
  40 \r
  41         private static Logger log = Logger.getLogger(WSUtil.class);\r
  42 \r
  43         public static final void validateJobId(String jobId)\r
  44                         throws InvalidParameterException {\r
  45                 if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
  46                         throw new InvalidParameterException(\r
  47                                         "JobId is not provided or cannot be recognised! Given value: "\r
  48                                                         + jobId);\r
  49                 }\r
  50         }\r
  51 \r
  52         public static final void validateFastaInput(List<FastaSequence> sequences)\r
  53                         throws InvalidParameterException {\r
  54                 if (sequences == null || sequences.isEmpty()) {\r
  55                         throw new InvalidParameterException(\r
  56                                         "List of fasta sequences required but not provided! ");\r
  57                 }\r
  58         }\r
  59 \r
  60         public static JobStatus getJobStatus(String jobId) {\r
  61                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  62                 return asyncEngine.getJobStatus(jobId);\r
  63         }\r
  64 \r
  65         public static ChunkHolder pullFile(String file, long position) {\r
  66                 return ProgressGetter.pull(file, position);\r
  67         }\r
  68 \r
  69         public static byte getProgress(String jobId) {\r
  70                 throw new UnsupportedOperationException();\r
  71         }\r
  72 \r
  73         public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
  74                 assert confClustal != null;\r
  75                 return Configurator.getAsyncEngine(confClustal);\r
  76         }\r
  77 \r
  78         public static boolean cancelJob(String jobId) {\r
  79                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  80                 return asyncEngine.cancelJob(jobId);\r
  81         }\r
  82 \r
  83         public static <T> String align(List<FastaSequence> sequences,\r
  84                         ConfiguredExecutable<T> confExec, WSLogger logger,\r
  85                         String callingMethod, Limit<T> limit)\r
  86                         throws LimitExceededException, JobSubmissionException {\r
  87                 Timer timer = Timer.getMilliSecondsTimer();\r
  88                 if (limit != null && limit.isExceeded(sequences)) {\r
  89                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
  90                 }\r
  91                 compbio.runner.Util.writeInput(sequences, confExec);\r
  92                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
  93                 String jobId = engine.submitJob(confExec);\r
  94                 if (logger != null) {\r
  95                         logger.log(timer, callingMethod, jobId);\r
  96                 }\r
  97                 return jobId;\r
  98         }\r
  99 \r
 100         /*\r
 101          * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
 102          */\r
 103         public static final <T> List<String> getCommands(List<Option<T>> options,\r
 104                         String keyValueSeparator) {\r
 105                 List<String> oList = new ArrayList<String>();\r
 106                 for (Option<T> o : options) {\r
 107                         oList.add(o.toCommand(keyValueSeparator));\r
 108                 }\r
 109                 return oList;\r
 110         }\r
 111 \r
 112 }\r