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.Score;\r
  17 import compbio.engine.AsyncExecutor;\r
  18 import compbio.engine.Configurator;\r
  19 import compbio.engine.client.ConfiguredExecutable;\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.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
  37 public class AAConWS implements Annotation<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         ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)\r
  54                         throws JobSubmissionException {\r
  55                 AACon aacon = new AACon();\r
  56                 aacon.setInput("fasta.in").setOutput("aacon.out");\r
  57                 return Configurator.configureExecutable(aacon, sequences);\r
  58         }\r
  59 \r
  60         @Override\r
  61         public HashSet<Score> getAnnotation(String jobId)\r
  62                         throws ResultNotAvailableException {\r
  63                 WSUtil.validateJobId(jobId);\r
  64                 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
  65                 ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
  66                                 .getResults(jobId);\r
  67                 HashSet<Score> mas = aacon.getResults();\r
  68                 log.trace(jobId + " getConservation : " + mas);\r
  69                 return mas;\r
  70         }\r
  71         /*\r
  72          * @SuppressWarnings("unchecked") public JalviewAnnotation\r
  73          * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
  74          * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
  75          * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
  76          */\r
  77 \r
  78         @Override\r
  79         public Limit<AACon> getLimit(String presetName) {\r
  80                 return new AACon().getLimit(presetName);\r
  81         }\r
  82 \r
  83         @Override\r
  84         public LimitsManager<AACon> getLimits() {\r
  85                 return new AACon().getLimits();\r
  86         }\r
  87 \r
  88         @Override\r
  89         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  90                 WSUtil.validateJobId(jobId);\r
  91                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  92                                 + AACon.getStatFile();\r
  93                 return WSUtil.pullFile(file, position);\r
  94         }\r
  95 \r
  96         @Override\r
  97         public boolean cancelJob(String jobId) {\r
  98                 WSUtil.validateJobId(jobId);\r
  99                 return WSUtil.cancelJob(jobId);\r
 100         }\r
 101 \r
 102         @Override\r
 103         public JobStatus getJobStatus(String jobId) {\r
 104                 WSUtil.validateJobId(jobId);\r
 105                 return WSUtil.getJobStatus(jobId);\r
 106         }\r
 107 \r
 108         @Override\r
 109         public PresetManager<AACon> getPresets() {\r
 110                 return aaconPresets;\r
 111         }\r
 112 \r
 113         @Override\r
 114         public RunnerConfig<AACon> getRunnerOptions() {\r
 115                 return aaconOptions;\r
 116         }\r
 117 \r
 118         String analize(List<FastaSequence> sequences,\r
 119                         ConfiguredExecutable<AACon> confExec, Logger log, String method,\r
 120                         Limit<AACon> limit) throws JobSubmissionException {\r
 121                 if (limit != null && limit.isExceeded(sequences)) {\r
 122                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 123                 }\r
 124 \r
 125                 compbio.runner.Util.writeInput(sequences, confExec);\r
 126                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 127                 String jobId = engine.submitJob(confExec);\r
 128                 return jobId;\r
 129         }\r
 130 \r
 131         @Override\r
 132         public String analize(List<FastaSequence> sequences)\r
 133                         throws UnsupportedRuntimeException, LimitExceededException,\r
 134                         JobSubmissionException {\r
 135                 WSUtil.validateFastaInput(sequences);\r
 136                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 137 \r
 138                 // set default conservation method to fastest - SHENKIN\r
 139                 // TODO: This violates encapsulation, should be moved to the runners\r
 140                 // level.\r
 141                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
 142                 return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
 143         }\r
 144 \r
 145         @Override\r
 146         public String customAnalize(List<FastaSequence> sequences,\r
 147                         List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
 148                         LimitExceededException, JobSubmissionException,\r
 149                         WrongParameterException {\r
 150                 WSUtil.validateFastaInput(sequences);\r
 151                 ConfiguredExecutable<AACon> confAACon = init(sequences);\r
 152                 // Could not do that! Space separated values\r
 153                 // will all be treated as keys! thus duplicates removed\r
 154                 // String params = cbuilder.getCommand();\r
 155                 List<String> params = WSUtil.getCommands(options,\r
 156                                 AACon.KEY_VALUE_SEPARATOR);\r
 157                 confAACon.addParameters(params);\r
 158                 return analize(sequences, confAACon, null, "customAnalize",\r
 159                                 getLimit(""));\r
 160         }\r
 161 \r
 162         @Override\r
 163         public String presetAnalize(List<FastaSequence> sequences,\r
 164                         Preset<AACon> preset) throws UnsupportedRuntimeException,\r
 165                         LimitExceededException, JobSubmissionException,\r
 166                         WrongParameterException {\r
 167                 WSUtil.validateFastaInput(sequences);\r
 168                 if (preset == null) {\r
 169                         throw new WrongParameterException("Preset must be provided!");\r
 170                 }\r
 171                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 172                 confAAcon.addParameters(preset.getOptions());\r
 173                 Limit<AACon> limit = getLimit(preset.getName());\r
 174                 return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);\r
 175         }\r
 176 \r
 177 }\r