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