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