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 final String CACHE_KEY = "LIMITS_CACHE";\r
  42 \r
  43         private static Logger log = Logger.getLogger(WSUtil.class);\r
  44 \r
  45         public static final void validateJobId(String jobId)\r
  46                         throws InvalidParameterException {\r
  47                 if (!compbio.engine.client.Util.isValidJobId(jobId)) {\r
  48                         throw new InvalidParameterException(\r
  49                                         "JobId is not provided or cannot be recognised! Given value: "\r
  50                                                         + jobId);\r
  51                 }\r
  52         }\r
  53 \r
  54         public static final void validateFastaInput(List<FastaSequence> sequences)\r
  55                         throws JobSubmissionException {\r
  56                 if (sequences == null || sequences.isEmpty()) {\r
  57                         throw new JobSubmissionException(\r
  58                                         "List of fasta sequences required but not provided! ");\r
  59                 }\r
  60                 for (FastaSequence fs : sequences) {\r
  61                         if (fs.getLength() == 0) {\r
  62                                 throw new JobSubmissionException(\r
  63                                                 "Sequence must not be empty! Sequence: " + fs.getId()\r
  64                                                                 + " was empty");\r
  65                         }\r
  66                 }\r
  67         }\r
  68 \r
  69         public static JobStatus getJobStatus(String jobId) {\r
  70                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  71                 return asyncEngine.getJobStatus(jobId);\r
  72         }\r
  73 \r
  74         public static ChunkHolder pullFile(String file, long position) {\r
  75                 return ProgressGetter.pull(file, position);\r
  76         }\r
  77 \r
  78         public static byte getProgress(String jobId) {\r
  79                 throw new UnsupportedOperationException();\r
  80         }\r
  81 \r
  82         public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal) {\r
  83                 assert confClustal != null;\r
  84                 return Configurator.getAsyncEngine(confClustal);\r
  85         }\r
  86 \r
  87         public static boolean cancelJob(String jobId) {\r
  88                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  89                 return asyncEngine.cancelJob(jobId);\r
  90         }\r
  91 \r
  92         public static <T> String align(List<FastaSequence> sequences,\r
  93                         ConfiguredExecutable<T> confExec, WSLogger logger,\r
  94                         String callingMethod, Limit<T> limit)\r
  95                         throws LimitExceededException, JobSubmissionException {\r
  96                 Timer timer = Timer.getMilliSecondsTimer();\r
  97                 if (limit != null && limit.isExceeded(sequences)) {\r
  98                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
  99                 }\r
 100                 compbio.runner.Util.writeInput(sequences, confExec);\r
 101                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 102                 String jobId = engine.submitJob(confExec);\r
 103                 if (logger != null) {\r
 104                         logger.log(timer, callingMethod, jobId);\r
 105                 }\r
 106                 return jobId;\r
 107         }\r
 108 \r
 109         /*\r
 110          * TODO Rewrite using purely CommandBuilder. This is breaking encapsulation\r
 111          */\r
 112         public static final <T> List<String> getCommands(List<Option<T>> options,\r
 113                         String keyValueSeparator) {\r
 114                 List<String> oList = new ArrayList<String>();\r
 115                 for (Option<T> o : options) {\r
 116                         oList.add(o.toCommand(keyValueSeparator));\r
 117                 }\r
 118                 return oList;\r
 119         }\r
 120 \r
 121         public static void validateAAConInput(List<FastaSequence> sequences)\r
 122                         throws JobSubmissionException {\r
 123                 validateFastaInput(sequences);\r
 124                 int len = 0;\r
 125                 for (FastaSequence fs : sequences) {\r
 126                         if (len == 0) {\r
 127                                 len = fs.getLength();\r
 128                                 continue;\r
 129                         }\r
 130                         if (fs.getLength() != len) {\r
 131                                 throw new JobSubmissionException(\r
 132                                                 "All sequences must be of the same length. Please align "\r
 133                                                                 + "the sequences prior to submission! The first sequence length is : "\r
 134                                                                 + len + " but the sequence '" + fs.getId()\r
 135                                                                 + "' length is " + fs.getLength());\r
 136                         }\r
 137                 }\r
 138         }\r
 139 \r
 140         /*\r
 141          * UNUSED\r
 142          * \r
 143          * @SuppressWarnings("unchecked") static <T> LimitsManager<T>\r
 144          * getLimits(Class<? extends Executable<T>> clazz, WebServiceContext\r
 145          * wsContext) {\r
 146          * \r
 147          * String LIMIT_KEY = CACHE_KEY + clazz.getCanonicalName(); LimitsManager<T>\r
 148          * limit = (LimitsManager<T>) getObjectFromApplContext( LIMIT_KEY,\r
 149          * wsContext); if (limit == null) { synchronized (WSUtil.class) { limit =\r
 150          * (LimitsManager<T>) getObjectFromApplContext(LIMIT_KEY, wsContext); if\r
 151          * (limit == null) { limit = compbio.runner.Util\r
 152          * .getLimits((Class<Executable<T>>) clazz);\r
 153          * addObjectToApplContext(wsContext, LIMIT_KEY, limit); } } } return limit;\r
 154          * }\r
 155          * \r
 156          * static void addObjectToApplContext(WebServiceContext wsContext, String\r
 157          * objKey, Object obj) { assert !Util.isEmpty(objKey) :\r
 158          * "Key for the object must not be empty! "; assert wsContext != null;\r
 159          * \r
 160          * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
 161          * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); assert ctx !=\r
 162          * null; log.debug("Adding object with key '" + objKey + "' and value '" +\r
 163          * obj + "' to the application context"); ctx.setAttribute(objKey, obj); }\r
 164          * static Object getObjectFromApplContext(String objKey, WebServiceContext\r
 165          * wsContext) { assert !Util.isEmpty(objKey) :\r
 166          * "Key for the object must not be empty! "; assert wsContext != null;\r
 167          * \r
 168          * ServletContext ctx = ((javax.servlet.ServletContext) wsContext\r
 169          * .getMessageContext().get(MessageContext. SERVLET_CONTEXT)); Object obj =\r
 170          * ctx.getAttribute(objKey); log.trace("Retrieving object with key '" +\r
 171          * objKey + "' and value '" + obj + "' from the application context");\r
 172          * return obj; }\r
 173          */\r
 174 }\r