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