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.SequenceAnnotation;\r
  15 import compbio.data.sequence.FastaSequence;\r
  16 import compbio.data.sequence.Score;\r
  17 import compbio.data.sequence.ScoreManager;\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.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
  38 public class AAConWS implements SequenceAnnotation<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 ScoreManager 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                 // ScoreManager result = new HashMap<String, HashSet<Score>>();\r
  70                 // result.put("Alignment", mas);\r
  71                 log.trace(jobId + " getConservation : " + mas);\r
  72                 // FIXME\r
  73                 return null;\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                 return new AACon().getLimit(presetName);\r
  85         }\r
  86 \r
  87         @Override\r
  88         public LimitsManager<AACon> getLimits() {\r
  89                 return new AACon().getLimits();\r
  90         }\r
  91 \r
  92         @Override\r
  93         public ChunkHolder pullExecStatistics(String jobId, long position) {\r
  94                 WSUtil.validateJobId(jobId);\r
  95                 String file = Configurator.getWorkDirectory(jobId) + File.separator\r
  96                                 + AACon.getStatFile();\r
  97                 return WSUtil.pullFile(file, position);\r
  98         }\r
  99 \r
 100         @Override\r
 101         public boolean cancelJob(String jobId) {\r
 102                 WSUtil.validateJobId(jobId);\r
 103                 return WSUtil.cancelJob(jobId);\r
 104         }\r
 105 \r
 106         @Override\r
 107         public JobStatus getJobStatus(String jobId) {\r
 108                 WSUtil.validateJobId(jobId);\r
 109                 return WSUtil.getJobStatus(jobId);\r
 110         }\r
 111 \r
 112         @Override\r
 113         public PresetManager<AACon> getPresets() {\r
 114                 return aaconPresets;\r
 115         }\r
 116 \r
 117         @Override\r
 118         public RunnerConfig<AACon> getRunnerOptions() {\r
 119                 return aaconOptions;\r
 120         }\r
 121 \r
 122         String analize(List<FastaSequence> sequences,\r
 123                         ConfiguredExecutable<AACon> confExec, Logger log, String method,\r
 124                         Limit<AACon> limit) throws JobSubmissionException {\r
 125                 if (limit != null && limit.isExceeded(sequences)) {\r
 126                         throw LimitExceededException.newLimitExceeded(limit, sequences);\r
 127                 }\r
 128 \r
 129                 compbio.runner.Util.writeInput(sequences, confExec);\r
 130                 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
 131                 String jobId = engine.submitJob(confExec);\r
 132                 return jobId;\r
 133         }\r
 134 \r
 135         @Override\r
 136         public String analize(List<FastaSequence> sequences)\r
 137                         throws UnsupportedRuntimeException, LimitExceededException,\r
 138                         JobSubmissionException {\r
 139                 WSUtil.validateFastaInput(sequences);\r
 140                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 141 \r
 142                 // set default conservation method to fastest - SHENKIN\r
 143                 // TODO: This violates encapsulation, should be moved to the runners\r
 144                 // level.\r
 145                 confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
 146                 return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
 147         }\r
 148 \r
 149         @Override\r
 150         public String customAnalize(List<FastaSequence> sequences,\r
 151                         List<Option<AACon>> options) throws UnsupportedRuntimeException,\r
 152                         LimitExceededException, JobSubmissionException,\r
 153                         WrongParameterException {\r
 154                 WSUtil.validateFastaInput(sequences);\r
 155                 ConfiguredExecutable<AACon> confAACon = init(sequences);\r
 156                 // Could not do that! Space separated values\r
 157                 // will all be treated as keys! thus duplicates removed\r
 158                 // String params = cbuilder.getCommand();\r
 159                 List<String> params = WSUtil.getCommands(options,\r
 160                                 AACon.KEY_VALUE_SEPARATOR);\r
 161                 confAACon.addParameters(params);\r
 162                 return analize(sequences, confAACon, null, "customAnalize",\r
 163                                 getLimit(""));\r
 164         }\r
 165 \r
 166         @Override\r
 167         public String presetAnalize(List<FastaSequence> sequences,\r
 168                         Preset<AACon> preset) throws UnsupportedRuntimeException,\r
 169                         LimitExceededException, JobSubmissionException,\r
 170                         WrongParameterException {\r
 171                 WSUtil.validateFastaInput(sequences);\r
 172                 if (preset == null) {\r
 173                         throw new WrongParameterException("Preset must be provided!");\r
 174                 }\r
 175                 ConfiguredExecutable<AACon> confAAcon = init(sequences);\r
 176                 confAAcon.addParameters(preset.getOptions());\r
 177                 Limit<AACon> limit = getLimit(preset.getName());\r
 178                 return WSUtil.align(sequences, confAAcon, null, "presetAnalize", limit);\r
 179         }\r
 180 \r
 181 }\r