webservices/compbio/ws/server/JronnWS.java

   1 package compbio.ws.server;\r
   2 \r
   3 import java.io.File;\r
   4 import java.util.HashSet;\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.Annotation;\r
  14 import compbio.data.sequence.FastaSequence;\r
  15 import compbio.data.sequence.Score;\r
  16 import compbio.engine.AsyncExecutor;\r
  17 import compbio.engine.Configurator;\r
  18 import compbio.engine.client.ConfiguredExecutable;\r
  19 import compbio.metadata.ChunkHolder;\r
  20 import compbio.metadata.JobStatus;\r
  21 import compbio.metadata.JobSubmissionException;\r
  22 import compbio.metadata.Limit;\r
  23 import compbio.metadata.LimitExceededException;\r
  24 import compbio.metadata.LimitsManager;\r
  25 import compbio.metadata.Option;\r
  26 import compbio.metadata.Preset;\r
  27 import compbio.metadata.PresetManager;\r
  28 import compbio.metadata.ResultNotAvailableException;\r
  29 import compbio.metadata.RunnerConfig;\r
  30 import compbio.metadata.UnsupportedRuntimeException;\r
  31 import compbio.metadata.WrongParameterException;\r
  32 import compbio.runner.Util;\r
  33 import compbio.runner.conservation.AACon;\r
  34 import compbio.runner.disorder.Jronn;\r
  35 \r
  36 @WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
  37 public class JronnWS implements Annotation<Jronn> {\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("JronnWS-stats");\r
  44 \r
  45         private static Logger log = Logger.getLogger(JronnWS.class);\r
  46 \r
  47         private static final RunnerConfig<Jronn> aaconOptions = Util\r
  48                         .getSupportedOptions(Jronn.class);\r
  49 \r
  50         private static final PresetManager<Jronn> aaconPresets = Util\r
  51                         .getPresets(Jronn.class);\r
  52 \r
  53         ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
  54                         throws JobSubmissionException {\r
  55                 Jronn jronn = new Jronn();\r
  56                 jronn.setInput("fasta.in").setOutput("aacon.out");\r
  57                 return Configurator.configureExecutable(jronn, 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         @Override\r
  73         public Limit<Jronn> getLimit(String presetName) {\r
  74                 return new Jronn().getLimit(presetName);\r
  75         }\r
  76 \r
  77         @Override\r
  78         public LimitsManager<Jronn> getLimits() {\r
  79                 return new Jronn().getLimits();\r
  80         }\r
  81 \r
  82         @Override\r
  83         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  84                 WSUtil.validateJobId(jobId);\r
  85                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  86                                 + Jronn.getStatFile();\r
  87                 return WSUtil.pullFile(file, position);\r
  88         }\r
  89 \r
  90         @Override\r
  91         public boolean cancelJob(String jobId) {\r
  92                 WSUtil.validateJobId(jobId);\r
  93                 return WSUtil.cancelJob(jobId);\r
  94         }\r
  95 \r
  96         @Override\r
  97         public JobStatus getJobStatus(String jobId) {\r
  98                 WSUtil.validateJobId(jobId);\r
  99                 return WSUtil.getJobStatus(jobId);\r
 100         }\r
 101 \r
 102         @Override\r
 103         public PresetManager<Jronn> getPresets() {\r
 104                 return aaconPresets;\r
 105         }\r
 106 \r
 107         @Override\r
 108         public RunnerConfig<Jronn> getRunnerOptions() {\r
 109                 return aaconOptions;\r
 110         }\r
 111 \r
 112         String analize(List<FastaSequence> sequences,\r
 113                         ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
 114                         Limit<Jronn> limit) throws JobSubmissionException {\r
 115                 if (limit != null && limit.isExceeded(sequences)) {\r
 116                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 117                 }\r
 118 \r
 119                 compbio.runner.Util.writeInput(sequences, confExec);\r
 120                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 121                 String jobId = engine.submitJob(confExec);\r
 122                 return jobId;\r
 123         }\r
 124 \r
 125         @Override\r
 126         public String analize(List<FastaSequence> sequences)\r
 127                         throws UnsupportedRuntimeException, LimitExceededException,\r
 128                         JobSubmissionException {\r
 129                 WSUtil.validateFastaInput(sequences);\r
 130                 ConfiguredExecutable<Jronn> confAAcon = init(sequences);\r
 131 \r
 132                 // set default conservation method to fastest - SHENKIN\r
 133                 return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
 134         }\r
 135 \r
 136         @Override\r
 137         public String customAnalize(List<FastaSequence> sequences,\r
 138                         List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
 139                         LimitExceededException, JobSubmissionException,\r
 140                         WrongParameterException {\r
 141                 WSUtil.validateFastaInput(sequences);\r
 142                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 143                 // Could not do that! Space separated values\r
 144                 // will all be treated as keys! thus duplicates removed\r
 145                 // String params = cbuilder.getCommand();\r
 146                 List<String> params = WSUtil.getCommands(options,\r
 147                                 AACon.KEY_VALUE_SEPARATOR);\r
 148                 confJronn.addParameters(params);\r
 149                 return analize(sequences, confJronn, null, "customAnalize",\r
 150                                 getLimit(""));\r
 151         }\r
 152 \r
 153         @Override\r
 154         public String presetAnalize(List<FastaSequence> sequences,\r
 155                         Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
 156                         LimitExceededException, JobSubmissionException,\r
 157                         WrongParameterException {\r
 158                 WSUtil.validateFastaInput(sequences);\r
 159                 if (preset == null) {\r
 160                         throw new WrongParameterException("Preset must be provided!");\r
 161                 }\r
 162                 ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
 163                 confJronn.addParameters(preset.getOptions());\r
 164                 Limit<Jronn> limit = getLimit(preset.getName());\r
 165                 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
 166         }\r
 167 \r
 168 }\r