webservices/compbio/ws/server/AAConWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.Arrays;\r
   5 import java.util.List;\r
   6 \r
   7 import javax.annotation.Resource;\r
   8 import javax.jws.WebService;\r
   9 import javax.xml.ws.WebServiceContext;\r
  10 \r
  11 import org.apache.log4j.Logger;\r
  12 \r
  13 import compbio.data.msa.SequenceAnnotation;\r
  14 import compbio.data.sequence.FastaSequence;\r
  15 import compbio.data.sequence.ScoreManager;\r
  16 import compbio.engine.AsyncExecutor;\r
  17 import compbio.engine.Configurator;\r
  18 import compbio.engine.client.ConfiguredExecutable;\r
  19 import compbio.engine.client.SkeletalExecutable;\r
  20 import compbio.metadata.ChunkHolder;\r
  21 import compbio.metadata.JobStatus;\r
  22 import compbio.metadata.JobSubmissionException;\r
  23 import compbio.metadata.Limit;\r
  24 import compbio.metadata.LimitExceededException;\r
  25 import compbio.metadata.LimitsManager;\r
  26 import compbio.metadata.Option;\r
  27 import compbio.metadata.Preset;\r
  28 import compbio.metadata.PresetManager;\r
  29 import compbio.metadata.ResultNotAvailableException;\r
  30 import compbio.metadata.RunnerConfig;\r
  31 import compbio.metadata.UnsupportedRuntimeException;\r
  32 import compbio.metadata.WrongParameterException;\r
  33 import compbio.runner.Util;\r
  34 import compbio.runner.conservation.AACon;\r
  35 \r
  36 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
  37 public class AAConWS implements SequenceAnnotation<AACon> {\r
  38 \r
  39         // Ask for resource injection\r
  40         @Resource\r
  41         WebServiceContext wsContext;\r
  42 \r
  43         private static Logger statLog = Logger.getLogger("AAConWS-stats");\r
  44 \r
  45         private static Logger log = Logger.getLogger(AAConWS.class);\r
  46 \r
  47         private static final RunnerConfig<AACon> aaconOptions = Util\r
  48                         .getSupportedOptions(AACon.class);\r
  49 \r
  50         private static final PresetManager<AACon> aaconPresets = Util\r
  51                         .getPresets(AACon.class);\r
  52 \r
  53         private static final LimitsManager<AACon> limitMan = compbio.engine.client.Util\r
  54                         .getLimits(new AACon().getType());\r
  55 \r
  56         ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
  57                         throws JobSubmissionException {\r
  58                 AACon aacon = new AACon();\r
  59                 aacon.setInput(SkeletalExecutable.INPUT).setOutput(\r
  60                                 SkeletalExecutable.OUTPUT);\r
  61                 return Configurator.configureExecutable(aacon, sequences);\r
  62         }\r
  63 \r
  64         @Override\r
  65         public ScoreManager getAnnotation(String jobId)\r
  66                         throws ResultNotAvailableException {\r
  67                 WSUtil.validateJobId(jobId);\r
  68                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  69                 ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
  70                                 .getResults(jobId);\r
  71                 ScoreManager mas = aacon.getResults();\r
  72                 log.trace(jobId + " getConservation : " + mas);\r
  73                 return mas;\r
  74         }\r
  75         /*\r
  76          * @SuppressWarnings("unchecked") public JalviewAnnotation\r
  77          * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
  78          * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
  79          * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
  80          */\r
  81 \r
  82         @Override\r
  83         public Limit<AACon> getLimit(String presetName) {\r
  84                 if (limitMan == null) {\r
  85                         // Limit is not defined\r
  86                         return null;\r
  87                 }\r
  88                 return limitMan.getLimitByName(presetName);\r
  89         }\r
  90 \r
  91         @Override\r
  92         public LimitsManager<AACon> getLimits() {\r
  93                 return limitMan;\r
  94         }\r
  95 \r
  96         @Override\r
  97         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  98                 WSUtil.validateJobId(jobId);\r
  99                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
 100                                 + AACon.getStatFile();\r
 101                 return WSUtil.pullFile(file, position);\r
 102         }\r
 103 \r
 104         @Override\r
 105         public boolean cancelJob(String jobId) {\r
 106                 WSUtil.validateJobId(jobId);\r
 107                 return WSUtil.cancelJob(jobId);\r
 108         }\r
 109 \r
 110         @Override\r
 111         public JobStatus getJobStatus(String jobId) {\r
 112                 WSUtil.validateJobId(jobId);\r
 113                 return WSUtil.getJobStatus(jobId);\r
 114         }\r
 115 \r
 116         @Override\r
 117         public PresetManager<AACon> getPresets() {\r
 118                 return aaconPresets;\r
 119         }\r
 120 \r
 121         @Override\r
 122         public RunnerConfig<AACon> getRunnerOptions() {\r
 123                 return aaconOptions;\r
 124         }\r
 125 \r
 126         private String analize(List<FastaSequence> sequences,\r
 127                         ConfiguredExecutable<AACon> confExec, Logger log, String method,\r
 128                         Limit<AACon> limit) throws JobSubmissionException {\r
 129                 if (limit != null && limit.isExceeded(sequences)) {\r
 130                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 131                 }\r
 132 \r
 133                 compbio.runner.Util.writeInput(sequences, confExec);\r
 134                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 135                 String jobId = engine.submitJob(confExec);\r
 136                 return jobId;\r
 137         }\r
 138 \r
 139         @Override\r
 140         public String analize(List<FastaSequence> sequences)\r
 141                         throws UnsupportedRuntimeException, LimitExceededException,\r
 142                         JobSubmissionException {\r
 143 \r
 144                 WSUtil.validateAAConInput(sequences);\r
 145                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 146 \r
 147                 // set default conservation method to fastest - SHENKIN\r
 148                 // TODO: This violates encapsulation, should be moved to the runners\r
 149                 // level.\r
 150                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
 151                 return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
 152         }\r
 153 \r
 154         @Override\r
 155         public String customAnalize(List<FastaSequence> sequences,\r
 156                         List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
 157                         LimitExceededException, JobSubmissionException,\r
 158                         WrongParameterException {\r
 159                 WSUtil.validateAAConInput(sequences);\r
 160                 ConfiguredExecutable<AACon> confAACon = init(sequences);\r
 161                 // Could not do that! Space separated values\r
 162                 // will all be treated as keys! thus duplicates removed\r
 163                 // String params = cbuilder.getCommand();\r
 164                 List<String> params = WSUtil.getCommands(options,\r
 165                                 AACon.KEY_VALUE_SEPARATOR);\r
 166                 confAACon.addParameters(params);\r
 167                 return analize(sequences, confAACon, null, "customAnalize",\r
 168                                 getLimit(""));\r
 169         }\r
 170 \r
 171         @Override\r
 172         public String presetAnalize(List<FastaSequence> sequences,\r
 173                         Preset<AACon> preset) throws UnsupportedRuntimeException,\r
 174                         LimitExceededException, JobSubmissionException,\r
 175                         WrongParameterException {\r
 176                 WSUtil.validateAAConInput(sequences);\r
 177                 if (preset == null) {\r
 178                         throw new WrongParameterException("Preset must be provided!");\r
 179                 }\r
 180                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 181                 confAAcon.addParameters(preset.getOptions());\r
 182                 Limit<AACon> limit = getLimit(preset.getName());\r
 183                 return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);\r
 184         }\r
 185 \r
 186 }\r