X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FRNAalifoldWS.java;h=ed94c23cdc071f3617cf1910dd5f87bdc8a0b3e5;hb=184bf3dce9500c599b5257140ec49edd80f8cea1;hp=83d7c93ec45f2a59112adc2a559e3779689ca221;hpb=a966c1a63f4365f34a0567514dee6d1bc4d3af91;p=jabaws.git

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index 83d7c93..ed94c23 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -1,130 +1,70 @@
-package compbio.ws.server;
-
-import java.io.File;
-import java.util.List;
-
-import javax.jws.WebParam;
-import javax.jws.WebService;
-
-import org.apache.log4j.Logger;
-
-import compbio.data.msa.JABAService;
-import compbio.data.msa.JManagement;
-import compbio.data.msa.Metadata;
-import compbio.data.msa.MsaWS;
-import compbio.data.sequence.Alignment;
-import compbio.data.sequence.FastaSequence;
-import compbio.engine.AsyncExecutor;
-import compbio.engine.Configurator;
-import compbio.engine.client.ConfiguredExecutable;
-import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.ChunkHolder;
-import compbio.metadata.JobStatus;
-import compbio.metadata.JobSubmissionException;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
-import compbio.metadata.Option;
-import compbio.metadata.Preset;
-import compbio.metadata.PresetManager;
-import compbio.metadata.ResultNotAvailableException;
-import compbio.metadata.RunnerConfig;
-import compbio.metadata.WrongParameterException;
-import compbio.runner.Util;
-import compbio.runner.msa.ClustalW;
-import compbio.runner.structure.RNAalifold;
-
-@WebService(targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
-public class RNAalifoldWS implements JABAService, JManagement, Metadata<RNAalifold> {
-
-	private static Logger log = Logger.getLogger(ClustalWS.class);
-	
-	private static final RunnerConfig<RNAalifold> rnaalifoldOptions = Util.
-			getSupportedOptions(RNAalifold.class);
-	
-	private static final PresetManager<RNAalifold> rnaalifoldPresets = Util
-			.getPresets(RNAalifold.class);
-
-	private static final LimitsManager<RNAalifold> limitMan = compbio.engine.client.Util
-			.getLimits(new RNAalifold().getType());
-	
-	//public String fold()
-	
-	
-	ConfiguredExecutable<RNAalifold> init() throws JobSubmissionException {
-		RNAalifold rnaalifold = new RNAalifold();
-		rnaalifold.setInput(SkeletalExecutable.INPUT)
-				.setOutput(SkeletalExecutable.OUTPUT)
-				.setError(SkeletalExecutable.ERROR);
-		ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
-				.configureExecutable(rnaalifold);
-		return confRNAalifold;
-	}
-		
-	@Override
-	public RunnerConfig<RNAalifold> getRunnerOptions() {
-		return rnaalifoldOptions;
-	}
-	
-	@SuppressWarnings("unchecked")
-	public String getResult(@WebParam(name = "jobId") String jobId) throws ResultNotAvailableException {
-		
-		WSUtil.validateJobId(jobId);
-		AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
-		ConfiguredExecutable<RNAalifold> rnaalifold = (ConfiguredExecutable<RNAalifold>) asyncEngine
-				.getResults(jobId);
-		return rnaalifold.getResults();
-	}
-	
-	@Override
-	public boolean cancelJob(String jobId) {
-		WSUtil.validateJobId(jobId);
-		boolean result = WSUtil.cancelJob(jobId);
-		return result;
-	}
-	
-	@Override
-	public JobStatus getJobStatus(String jobId) {
-		WSUtil.validateJobId(jobId);
-		JobStatus status = WSUtil.getJobStatus(jobId);
-		return status;
-	}
-	
-	@Override
-	public Limit<RNAalifold> getLimit(String presetName) {
-		if (limitMan == null) {
-			// No limit is configured
-			return null;
-		}
-		Limit<RNAalifold> limit = limitMan.getLimitByName(presetName);
-		return limit;
-	}
-	
-	@Override
-	public LimitsManager<RNAalifold> getLimits() {
-		return limitMan;
-	}
-	
-	@Override 
-	// PlaceHolder
-	public PresetManager<RNAalifold> getPresets() {
-		if (rnaalifoldPresets == null) {
-			// No presets are configured
-			return null;
-		}
-		return rnaalifoldPresets;
-	}
-
-	@Override
-	// PlaceHolder 
-	public ChunkHolder pullExecStatistics(String jobId, long position) {
-
-//		WSUtil.validateJobId(jobId);
-//		String file = Configurator.getWorkDirectory(jobId) + File.separator
-//				+ RNAalifold.getStatFile();
-//		ChunkHolder cholder = WSUtil.pullFile(file, position);
-//		return cholder;
-		return new ChunkHolder("", -1);
-	}
-}
-	
-	
+package compbio.ws.server;
+
+import java.util.List;
+
+import javax.jws.WebService;
+
+import org.apache.log4j.Logger;
+
+import compbio.data.msa.JABAService;
+import compbio.data.msa.SequenceAnnotation;
+import compbio.data.sequence.FastaSequence;
+import compbio.engine.client.ConfiguredExecutable;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Option;
+import compbio.metadata.Preset;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+import compbio.runner.conservation.AACon;
+import compbio.runner.structure.RNAalifold;
+
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RNAalifoldWS")
+public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold> implements SequenceAnnotation<RNAalifold> {
+
+	private static Logger log = Logger.getLogger(RNAalifoldWS.class);
+	
+	public RNAalifoldWS() {
+		super (new RNAalifold(), log);
+	}
+	
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
+	@Override
+	public String analize(List<FastaSequence> sequences)
+			throws UnsupportedRuntimeException, LimitExceededException,
+			JobSubmissionException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<RNAalifoldWS> confRNAalifold = init(sequences);
+		return WSUtil.fold(sequences, confRNAalifold, log, "analize", getLimit(""));
+	}
+
+	// Only purpose is to replace "analize" with "fold" method 
+	// so that a clustal input file and not fasta will be generated
+	@SuppressWarnings("unchecked")
+	@Override
+	public String customAnalize(List<FastaSequence> sequences,
+			List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException {
+		WSUtil.validateFastaInput(sequences);
+		ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);
+		List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);
+		confRNAalifold.addParameters(params);
+		return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));
+	}
+	
+	
+	/*
+	 * No presets are supported, thus the result of this call will be as simple
+	 * call to analize without parameters
+	 */
+	@Override
+	public String presetAnalize(List<FastaSequence> sequences,
+			Preset<RNAalifold> preset) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException {
+		return analize(sequences);
+	}
+}