X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FWSTester.java;h=2f33cb1dd4a3d4166128722ec99eaa949141cdac;hb=652864eebc0ecdeb6f8bfef1700e3b365a0d7227;hp=883890377832fb70363ca9a33782a53cc1a7d108;hpb=1e1c3681ba25ee1797a46f871b8c80f259afe2ca;p=jabaws.git

diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index 8838903..2f33cb1 100644
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@ -32,8 +32,6 @@ import java.util.List;
 
 import javax.xml.ws.WebServiceException;
 
-import org.apache.log4j.Logger;
-
 import compbio.data.msa.JABAService;
 import compbio.data.msa.Metadata;
 import compbio.data.msa.MsaWS;
@@ -62,22 +60,24 @@ import compbio.util.Util;
  */
 public class WSTester {
 
-	private static Logger log = Logger.getLogger(WSTester.class);
 	/**
 	 * Sequences to be used as input for all WS
 	 */
-	static final String fastaInput = ">Foo\n"
+	public static final String fastaInput2records = ">Foo\n"
 			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
 			+ "\n>Bar\n"
-			+ "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA";
+			+ "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";
+	public static final String fastaInput1record = ">Foo\n"
+			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"
+			+ "\n";
 
-	static final String fastaAlignment = ">Foo\r\n"
-			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\r\n"
-			+ ">Bar\r\n"
-			+ "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\r\n"
+	public static final String fastaAlignment = ">Foo\n"
+			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"
+			+ ">Bar\n"
+			+ "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"
 			+ "";
 
-	static final List<FastaSequence> seqs = loadSeqs();
+	static final List<FastaSequence> seqs = loadSeqs(2);
 
 	private static final String FAILED = "FAILED";
 	private static final String OK = "OK";
@@ -89,10 +89,12 @@ public class WSTester {
 	 * 
 	 * @return List of FastaSequence records
 	 */
-	private static List<FastaSequence> loadSeqs() {
+	private static List<FastaSequence> loadSeqs(int nLines) {
 		try {
-			return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput
-					.getBytes()));
+			if (nLines == 1) {
+				return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));
+			}
+			return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));
 		} catch (IOException ignored) {
 			// Should not happen as a source is not a external stream
 			ignored.printStackTrace();
@@ -144,12 +146,10 @@ public class WSTester {
 				+ pseparator + "host_and_context " + "<" + servicekey
 				+ pseparator + "serviceName>");
 		System.out.println();
-		System.out
-				.println(hostkey
+		System.out.println(hostkey
 						+ pseparator
 						+ "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");
-		System.out
-				.println(servicekey
+		System.out.println(servicekey
 						+ pseparator
 						+ "<ServiceName> - optional if unspecified all services are tested otherwise one of "
 						+ Arrays.toString(Services.values()));
@@ -224,8 +224,7 @@ public class WSTester {
 	private <T> boolean checkService(JABAService wservice, Services service) {
 		try {
 			if (wservice == null) {
-				throw new NullPointerException(
-						"JABAService instance must be provided!");
+				throw new NullPointerException("JABAService instance must be provided!");
 			}
 
 			if (wservice instanceof MsaWS) {
@@ -234,8 +233,7 @@ public class WSTester {
 				return testSequenceAnnotationWS(
 						(SequenceAnnotation<T>) wservice, service);
 			} else {
-				throw new UnsupportedOperationException("The service: "
-						+ wservice.getClass() + " is not supported! ");
+				throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");
 			}
 		} catch (Exception e) {
 			reportException(e);
@@ -247,10 +245,13 @@ public class WSTester {
 			SequenceAnnotation<T> wservice, Services service) throws Exception {
 		writer.print("Calling analyse.........");
 
-		List<FastaSequence> input = loadSeqs();
+		List<FastaSequence> input = loadSeqs(2);
 		if (service == Services.AAConWS) {
 			input = loadAlignment();
 		}
+		if (service == Services.JpredWS) {
+			input = loadSeqs(1);
+		}
 		boolean success = testDefaultAnalyse(input, wservice, null, null);
 
 		PresetManager<T> presetman = wservice.getPresets();
@@ -385,8 +386,7 @@ public class WSTester {
 		String host = CmdHelper.getHost(args);
 		String serviceName = CmdHelper.getServiceName(args);
 		if (!Jws2Client.validURL(host)) {
-			System.err
-					.println("<host_and_context> parameter is not provided or is incorrect!");
+			System.err.println("<host_and_context> parameter is not provided or is incorrect!");
 			System.exit(1);
 		}
 		WSTester tester = new WSTester(host, new PrintWriter(System.out, true));
@@ -394,8 +394,7 @@ public class WSTester {
 		if (serviceName != null) {
 			Services service = Services.getService(serviceName);
 			if (service == null) {
-				tester.writer.println("Service '" + serviceName
-						+ "' is not supported. Valid values are: "
+				tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "
 						+ Arrays.toString(Services.values()));
 				tester.writer.println();
 				printUsage();
@@ -405,8 +404,7 @@ public class WSTester {
 			System.exit(0);
 		}
 
-		tester.writer
-				.println("<ServiceName> is not provided checking all known services...");
+		tester.writer.println("<ServiceName> is not provided checking all known services...");
 
 		for (Services serv : Services.values()) {
 			tester.writer.println();
@@ -428,8 +426,8 @@ public class WSTester {
 			WebServiceException {
 		JABAService ws = Jws2Client.connect(hostname, service);
 		if (ws == null) {
-			writer.println("Cannot estabilish the connection to host "
-					+ hostname + " with service " + service.toString());
+			String line = "Cannot estabilish the connection to host " + hostname + " with service ";
+			writer.println(line + service.toString());
 			return false;
 		}
 		boolean succeed = false;
@@ -445,11 +443,9 @@ public class WSTester {
 
 	private void reportResults(Services serv, boolean succeed) {
 		if (succeed) {
-			writer.println("Check is completed. The Service " + serv
-					+ " IS WORKING\n");
+			writer.println("Check is completed. The Service " + serv + " IS WORKING\n");
 		} else {
-			writer.println("Check is aborted. The Service " + serv
-					+ " HAS SOME PROBLEMS\n");
+			writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");
 		}
 	}
 }