Remove Annotated and MuptiAnnotated Sequence use Score instead

[jabaws.git] / webservices / compbio / ws / server / JronnWS.java

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
new file mode 100644 (file)
index 0000000..bcb6af5
--- /dev/null
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -0,0 +1,177 @@
+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.HashSet;\r
+import java.util.List;\r
+\r
+import javax.annotation.Resource;\r
+import javax.jws.WebService;\r
+import javax.xml.ws.WebServiceContext;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.Annotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.Util;\r
+import compbio.runner.conservation.AACon;\r
+import compbio.runner.disorder.Jronn;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
+public class JronnWS implements Annotation<Jronn> {\r
+\r
+       // Ask for resource injection\r
+       @Resource\r
+       WebServiceContext wsContext;\r
+\r
+       private static Logger statLog = Logger.getLogger("JronnWS-stats");\r
+\r
+       private static Logger log = Logger.getLogger(JronnWS.class);\r
+\r
+       private static final RunnerConfig<Jronn> aaconOptions = Util\r
+                       .getSupportedOptions(Jronn.class);\r
+\r
+       private static final PresetManager<Jronn> aaconPresets = Util\r
+                       .getPresets(Jronn.class);\r
+\r
+       ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               Jronn jronn = new Jronn();\r
+               jronn.setInput("fasta.in").setOutput("aacon.out");\r
+               return Configurator.configureExecutable(jronn, sequences);\r
+       }\r
+\r
+       @Override\r
+       public HashSet<Score> getAnnotation(String jobId)\r
+                       throws ResultNotAvailableException {\r
+               WSUtil.validateJobId(jobId);\r
+               AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+               ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
+                               .getResults(jobId);\r
+               HashSet<Score> mas = aacon.getResults();\r
+               log.trace(jobId + " getConservation : " + mas);\r
+               return mas;\r
+       }\r
+       /*\r
+        * @SuppressWarnings("unchecked") public JalviewAnnotation\r
+        * getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
+        * MultiAnnotatedSequence<Method> result = getResult(jobId); // TODO //\r
+        * log(jobId, "getResults"); return result.toJalviewAnnotation(); }\r
+        */\r
+\r
+       @Override\r
+       public Limit<Jronn> getLimit(String presetName) {\r
+               return new Jronn().getLimit(presetName);\r
+       }\r
+\r
+       @Override\r
+       public LimitsManager<Jronn> getLimits() {\r
+               return new Jronn().getLimits();\r
+       }\r
+\r
+       @Override\r
+       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+               WSUtil.validateJobId(jobId);\r
+               String file = Configurator.getWorkDirectory(jobId) + File.separator\r
+                               + Jronn.getStatFile();\r
+               return WSUtil.pullFile(file, position);\r
+       }\r
+\r
+       @Override\r
+       public boolean cancelJob(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.cancelJob(jobId);\r
+       }\r
+\r
+       @Override\r
+       public JobStatus getJobStatus(String jobId) {\r
+               WSUtil.validateJobId(jobId);\r
+               return WSUtil.getJobStatus(jobId);\r
+       }\r
+\r
+       @Override\r
+       public PresetManager<Jronn> getPresets() {\r
+               return aaconPresets;\r
+       }\r
+\r
+       @Override\r
+       public RunnerConfig<Jronn> getRunnerOptions() {\r
+               return aaconOptions;\r
+       }\r
+\r
+       String analize(List<FastaSequence> sequences,\r
+                       ConfiguredExecutable<Jronn> confExec, Logger log, String method,\r
+                       Limit<Jronn> limit) throws JobSubmissionException {\r
+               if (limit != null && limit.isExceeded(sequences)) {\r
+                       throw LimitExceededException.newLimitExceeded(limit, sequences);\r
+               }\r
+\r
+               compbio.runner.Util.writeInput(sequences, confExec);\r
+               AsyncExecutor engine = Configurator.getAsyncEngine(confExec);\r
+               String jobId = engine.submitJob(confExec);\r
+               return jobId;\r
+       }\r
+\r
+       @Override\r
+       public String analize(List<FastaSequence> sequences)\r
+                       throws UnsupportedRuntimeException, LimitExceededException,\r
+                       JobSubmissionException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Jronn> confAAcon = init(sequences);\r
+\r
+               // set default conservation method to fastest - SHENKIN\r
+               // TODO: This violates encapsulation, should be moved to the runners\r
+               // level.\r
+               // confAAcon.addParameters(Arrays.asList("-m=SHENKIN"));\r
+               return analize(sequences, confAAcon, null, "analize", getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String customAnalize(List<FastaSequence> sequences,\r
+                       List<Option<Jronn>> options) throws UnsupportedRuntimeException,\r
+                       LimitExceededException, JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
+               // Could not do that! Space separated values\r
+               // will all be treated as keys! thus duplicates removed\r
+               // String params = cbuilder.getCommand();\r
+               List<String> params = WSUtil.getCommands(options,\r
+                               AACon.KEY_VALUE_SEPARATOR);\r
+               confJronn.addParameters(params);\r
+               return analize(sequences, confJronn, null, "customAnalize",\r
+                               getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String presetAnalize(List<FastaSequence> sequences,\r
+                       Preset<Jronn> preset) throws UnsupportedRuntimeException,\r
+                       LimitExceededException, JobSubmissionException,\r
+                       WrongParameterException {\r
+               WSUtil.validateFastaInput(sequences);\r
+               if (preset == null) {\r
+                       throw new WrongParameterException("Preset must be provided!");\r
+               }\r
+               ConfiguredExecutable<Jronn> confJronn = init(sequences);\r
+               confJronn.addParameters(preset.getOptions());\r
+               Limit<Jronn> limit = getLimit(preset.getName());\r
+               return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);\r
+       }\r
+\r
+}\r