From 42d82f347c559914cc57499c43daa49aed0573b8 Mon Sep 17 00:00:00 2001
From: Daniel Barton <daluke.barton@gmail.com>
Date: Fri, 16 Aug 2013 16:25:31 +0100
Subject: [PATCH] Webservice working with ScoreManager

---
 testsrc/compbio/ws/client/TestRNAalifoldWS.java |   18 ++++++++++++------
 webservices/compbio/ws/server/RNAalifoldWS.java |   12 ------------
 webservices/compbio/ws/server/WSUtil.java       |    5 +++--
 3 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index 5e66f43..c5f3f6d 100644
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -1,4 +1,4 @@
-package compbio.ws.client;
+	package compbio.ws.client;
 
 import compbio.metadata.AllTestSuit;
 import static org.testng.Assert.assertEquals;
@@ -45,7 +45,7 @@ import compbio.ws.server.RNAalifoldWS;
 
 public class TestRNAalifoldWS {
 	
-	FoldWS<RNAalifoldWS> foldws;
+	SequenceAnnotation<RNAalifoldWS> foldws;
 	
 	@BeforeTest(groups = {AllTestSuit.test_group_webservices})
 	void initConnection() {
@@ -53,7 +53,7 @@ public class TestRNAalifoldWS {
 		try {
 			JABAService client = Jws2Client.connect(
 					"http://localhost:8080/jabaws", Services.RNAalifoldWS);
-			foldws = (FoldWS<RNAalifoldWS>) client;
+			foldws = (SequenceAnnotation<RNAalifoldWS>) client;
 		} catch (ConnectException e) {
 			e.printStackTrace();
 			fail(e.getMessage());
@@ -74,14 +74,20 @@ public class TestRNAalifoldWS {
 		Alignment aln = ClustalAlignmentUtil.readClustalFile(new FileInputStream(
 				AllTestSuit.test_input_aln));
 		
+		List<FastaSequence> fsl = aln.getSequences();
+		
 		try {
 			List<Option<RNAalifoldWS>> options  = new ArrayList<Option<RNAalifoldWS>>();
 			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--mis"));
+			options.add(foldws.getRunnerOptions().getArgumentByOptionName("-p"));
+			options.add(foldws.getRunnerOptions().getArgumentByOptionName("--MEA"));
+			
 			System.out.println("TestRNAalifoldWS: print options: " + options.toString());
-			String jobId = foldws.customFold(aln, options);
+			
+			String jobId = foldws.customAnalize(fsl, options);
 			System.out.println("J: " + jobId);
-			String result = foldws.getResult(jobId);
-			System.out.println("fold results: \n" + result);
+			ScoreManager result = foldws.getAnnotation(jobId);
+			System.out.println("fold results: \n" + result.asRNAStruct().toString());
 			assertNotNull(result);
 			
 		} catch (UnsupportedRuntimeException e) {
diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index b05c973..34f0aaf 100644
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -48,18 +48,6 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
 		super (new RNAalifold(), log);
 	}
 
-	/*
-	 * No options are supported, thus the result of this call will be as simple
-	 * call to analize without parameters
-	 */
-	@Override
-	public String customAnalize(List<FastaSequence> sequences,
-			List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,
-			LimitExceededException, JobSubmissionException,
-			WrongParameterException {
-		
-		return analize(sequences);
-	}
 
 	/*
 	 * No presets are supported, thus the result of this call will be as simple
diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 9d81a6a..7646747 100644
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -153,8 +153,9 @@ public final class WSUtil {
 			throw LimitExceededException.newLimitExceeded(limit, sequences);
 		}
 		log.debug("Method: " + method + " with task: " + confExec.getTaskId());
-
-		compbio.runner.Util.writeInput(sequences, confExec);
+		// Change this line for RNAalifold testing
+		// compbio.runner.Util.writeInput(sequences, confExec);
+		compbio.runner.Util.writeClustalInput(sequences, confExec, '-');
 		AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
 		String jobId = engine.submitJob(confExec);
 		reportUsage(confExec, log);
-- 
1.7.10.2