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