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