bug-fix in sending SBOLDocument to BOOST API

Author: eoberortner

src/main/java/gov/doe/jgi/boost/client/RequestBuilder.java

@@ -464,16 +464,24 @@ public static JSONObject buildSequenceData(final SBOLDocument designSequences, S
 		// sequence information
 		JSONObject sequenceData = new JSONObject();
 
-		// reading from SBOL document
-		ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
-		SBOLWriter.write(designSequences,  outputStream);
-		String designDoc = outputStream.toString("UTF-8");
-		
-		// put its content into the JSON object
-		if(designDoc != null && !designDoc.isEmpty()) {
-			sequenceData.put(JSONKeys.TEXT, designSequences);
-		}
+		// write the SBOLDocument to a String
+		try (
+				ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+			) {
 
+			SBOLWriter.write(designSequences,  outputStream);
+			String designDoc = outputStream.toString("UTF-8");
+			
+			System.out.println(designDoc);
+			
+			// put its content into the JSON object
+			if(designDoc != null && !designDoc.isEmpty()) {
+				sequenceData.put(JSONKeys.TEXT, designDoc);
+			}
+			
+		} catch(Exception e) {
+			throw new BOOSTClientException(e.getMessage());
+		}
 
 		// sequence type
 		JSONArray types = new JSONArray();

src/main/java/gov/doe/jgi/boost/client/constants/BOOSTResources.java

@@ -9,7 +9,7 @@ public class BOOSTResources {
 //	// BOOST prod
 //    public static String BOOST_REST_URL = "https://boost.jgi.doe.gov/rest";
 
-	// BOOST dev
+//	// BOOST dev
     public static String BOOST_REST_URL = "https://boost.jgi.doe.gov/Dev/rest";
 
     // local

src/test/java/gov/doe/jgi/boost/client/DemoClient.java

@@ -41,6 +41,7 @@ public static void main(String[] args)
 			System.out.println(jsonPredefinedHosts.toString(4));
 		}catch(NullPointerException e) {
 			System.out.println(e.getMessage() + " Error in jsonPredefinedHosts");
+			System.exit(1);
 		}
 
 		// set the target namespace
@@ -62,16 +63,16 @@ public static void main(String[] args)
 //		
 //
 		// codon juggle
-//		String codonJuggleJobUUID = client.codonJuggle(
-//				"./data/codon_juggle.sbol.xml",		// input sequences 
-//				false,					 			// exclusively 5'-3' coding sequences 
-//				Strategy.MostlyUsed,		  			// codon selection strategy
-//				"Saccharomyces cerevisiae",   		// predefined host
-//				FileFormat.SBOL);		  			// output format
-//		if(null != codonJuggleJobUUID) {
-//			jobUUIDs.add(codonJuggleJobUUID);
-//			System.out.println("Data for codon Juggling :" + codonJuggleJobUUID );
-//		}
+		String codonJuggleJobUUID = client.codonJuggle(
+				"./data/codon_juggle.sbol.xml",		// input sequences 
+				false,					 			// exclusively 5'-3' coding sequences 
+				Strategy.Balanced,		  			// codon selection strategy
+				"Saccharomyces cerevisiae",   		// predefined host
+				FileFormat.SBOL);		  			// output format
+		if(null != codonJuggleJobUUID) {
+			jobUUIDs.add(codonJuggleJobUUID);
+			System.out.println("Data for codon Juggling :" + codonJuggleJobUUID );
+		}
 
 //    	// verify against DNA synthesis constraints and sequence patterns
 //		String dnaVarificationJobUUID = client.dnaVarification(