webservices/compbio/ws/server/AAConWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.List;\r
   5 \r
   6 import javax.annotation.Resource;\r
   7 import javax.jws.WebService;\r
   8 import javax.xml.ws.WebServiceContext;\r
   9 \r
  10 import org.apache.log4j.Logger;\r
  11 \r
  12 import compbio.conservation.Method;\r
  13 import compbio.data.msa.Annotation;\r
  14 import compbio.data.sequence.FastaSequence;\r
  15 import compbio.data.sequence.JalviewAnnotation;\r
  16 import compbio.data.sequence.MultiAnnotatedSequence;\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.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\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("fasta.out");\r
  57                 return Configurator.configureExecutable(aacon, sequences);\r
  58         }\r
  59 \r
  60         @SuppressWarnings("unchecked")\r
  61         public MultiAnnotatedSequence<Method> getResult(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                 MultiAnnotatedSequence<Method> mas = aacon.getResults();\r
  68                 // log(jobId, "getResults");\r
  69                 return mas;\r
  70         }\r
  71 \r
  72         @SuppressWarnings("unchecked")\r
  73         public JalviewAnnotation getJalviewAnnotation(String jobId)\r
  74                         throws ResultNotAvailableException {\r
  75                 MultiAnnotatedSequence<Method> result = getResult(jobId);\r
  76 \r
  77                 // log(jobId, "getResults");\r
  78                 return result.toJalviewAnnotation();\r
  79         }\r
  80 \r
  81         public Limit<AACon> getLimit(String presetName) {\r
  82                 return new AACon().getLimit(presetName);\r
  83         }\r
  84 \r
  85         public LimitsManager<AACon> getLimits() {\r
  86                 return new AACon().getLimits();\r
  87         }\r
  88 \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         public boolean cancelJob(String jobId) {\r
  97                 WSUtil.validateJobId(jobId);\r
  98                 return WSUtil.cancelJob(jobId);\r
  99         }\r
 100 \r
 101         public JobStatus getJobStatus(String jobId) {\r
 102                 WSUtil.validateJobId(jobId);\r
 103                 return WSUtil.getJobStatus(jobId);\r
 104         }\r
 105 \r
 106         public PresetManager<AACon> getPresets() {\r
 107                 return aaconPresets;\r
 108         }\r
 109 \r
 110         public RunnerConfig<AACon> getRunnerOptions() {\r
 111                 return aaconOptions;\r
 112         }\r
 113 \r
 114         @Override\r
 115         public String analize(List<FastaSequence> sequences)\r
 116                         throws UnsupportedRuntimeException, LimitExceededException,\r
 117                         JobSubmissionException {\r
 118                 // TODO Auto-generated method stub\r
 119                 return null;\r
 120         }\r
 121 \r
 122         @Override\r
 123         public String customAnalize(List<FastaSequence> sequences,\r
 124                         List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
 125                         LimitExceededException, JobSubmissionException,\r
 126                         WrongParameterException {\r
 127                 // TODO Auto-generated method stub\r
 128                 return null;\r
 129         }\r
 130 \r
 131         @Override\r
 132         public String presetAnalize(List<FastaSequence> sequences,\r
 133                         Preset<AACon> preset) throws UnsupportedRuntimeException,\r
 134                         LimitExceededException, JobSubmissionException,\r
 135                         WrongParameterException {\r
 136                 // TODO Auto-generated method stub\r
 137                 return null;\r
 138         }\r
 139 \r
 140 }\r