/* Copyright (c) 2011 Peter Troshin\r
+ * Copyright (c) 2013 Alexander Sherstnev\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0\r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
import java.io.IOException;\r
import java.io.PrintWriter;\r
import java.net.ConnectException;\r
+import java.net.MalformedURLException;\r
+import java.net.URL;\r
import java.util.Arrays;\r
import java.util.List;\r
+import java.util.logging.Level;\r
\r
+import javax.xml.ws.Service;\r
import javax.xml.ws.WebServiceException;\r
\r
import compbio.data.msa.JABAService;\r
* \r
* @author pvtroshin\r
* \r
- * @version 1.0 February 2010\r
+ * @version 1.5 February 2013\r
*/\r
public class WSTester {\r
\r
/**\r
- * Sequences to be used as input for all WS\r
+ * Test sequences to be used as input for WS\r
+ */\r
+ public static final String fastaInput2records = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"\r
+ + ">Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
+ public static final String fastaInput1record = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n";\r
+ public static final String fastaAlignment = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
+ + ">Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n";\r
+ public static final String fastaRNAAlignment = \r
+ ">Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"\r
+ + ">Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";\r
+\r
+ public static final String clustalRNAAlignment = \r
+ "CLUSTAL\n" +\r
+ "Foo C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGA\n" +\r
+ "Bar G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGA\n" +\r
+ "Foo UGGUUG----GCAAC\n" +\r
+ "Bar U-UACGAUUAACCAC";\r
+ /**\r
+ * Status strings\r
*/\r
- public static final String fastaInput = ">Foo\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
- + "\n>Bar\n"\r
- + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
-\r
- public static final String fastaAlignment = ">Foo\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
- + ">Bar\n"\r
- + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"\r
- + "";\r
-\r
- public static final String fastaRNAAlignment = ">Foo\n"\r
- + "C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n"\r
- + ">Bar\n"\r
- + "G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n";\r
-\r
private static final String FAILED = "FAILED";\r
private static final String OK = "OK";\r
-\r
private static final String UNSUPPORTED = "UNSUPPORTED";\r
\r
/**\r
* \r
* @return List of FastaSequence records\r
*/\r
- private static List<FastaSequence> loadSeqs() {\r
+ private static List<FastaSequence> loadSeqs(int nLines) {\r
try {\r
- return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput\r
- .getBytes()));\r
+ if (nLines == 1) {\r
+ return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput1record.getBytes()));\r
+ }\r
+ return SequenceUtil.readFasta(new ByteArrayInputStream(fastaInput2records.getBytes()));\r
} catch (IOException ignored) {\r
// Should not happen as a source is not a external stream\r
ignored.printStackTrace();\r
/**\r
* Converting input to a form accepted by WS\r
* \r
- * @return List of FastaSequence records with aligned protein sequences\r
+ * @return List of FastaSequence records\r
*/\r
private static List<FastaSequence> loadAlignment() {\r
try {\r
+ pseparator + "host_and_context " + "<" + servicekey\r
+ pseparator + "serviceName>");\r
System.out.println();\r
- System.out\r
- .println(hostkey\r
+ System.out.println(hostkey\r
+ pseparator\r
+ "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
- System.out\r
- .println(servicekey\r
+ System.out.println(servicekey\r
+ pseparator\r
+ "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
+ Arrays.toString(Services.values()));\r
writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
Alignment al = null;\r
try {\r
- String taskId = msaws.presetAlign(loadSeqs(), preset);\r
+ String taskId = msaws.presetAlign(loadSeqs(2), preset);\r
al = msaws.getResult(taskId);\r
if (al != null) {\r
writer.println(OK);\r
return succeed;\r
}\r
\r
- private <T> boolean testMsaWS(MsaWS<T> msaws) throws Exception {\r
+ private <T> boolean testMsaWS(MsaWS<T> msaws, Services service) throws Exception {\r
assert msaws != null;\r
\r
- boolean succeed = testDefaultAlignment(msaws);\r
+ boolean succeed = testDefaultAlignment(msaws, service);\r
// If exception above is thrown than the tests below is not run\r
\r
PresetManager<T> pmanager = msaws.getPresets();\r
testMetadata(msaws);\r
return succeed;\r
}\r
- \r
/**\r
* Call most of web services functions and check the output\r
* \r
private <T> boolean checkService(JABAService wservice, Services service) {\r
try {\r
if (wservice == null) {\r
- throw new NullPointerException(\r
- "JABAService instance must be provided!");\r
+ throw new NullPointerException("JABAService instance must be provided!");\r
}\r
\r
if (wservice instanceof MsaWS) {\r
- return testMsaWS((MsaWS<T>) wservice);\r
+ return testMsaWS((MsaWS<T>) wservice, service);\r
} else if (wservice instanceof SequenceAnnotation) {\r
return testSequenceAnnotationWS(\r
(SequenceAnnotation<T>) wservice, service);\r
} else {\r
- throw new UnsupportedOperationException("The service: "\r
- + wservice.getClass() + " is not supported! ");\r
+ throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");\r
}\r
} catch (Exception e) {\r
reportException(e);\r
\r
private <T> boolean testSequenceAnnotationWS(\r
SequenceAnnotation<T> wservice, Services service) throws Exception {\r
- writer.print("Calling analyse.........");\r
+ writer.print("Calling annotation test.........");\r
\r
- List<FastaSequence> input = loadSeqs();\r
+ List<FastaSequence> input = loadSeqs(2);\r
if (service == Services.AAConWS ) {\r
input = loadAlignment();\r
} else if (service == Services.RNAalifoldWS) {\r
\r
private void reportException(Exception e) {\r
writer.println(FAILED);\r
- writer.println("Exception while waiting for results. "\r
- + "Exception details are below:");\r
+ writer.println("Exception while waiting for results. Exception details are below:");\r
writer.println(e.getLocalizedMessage());\r
e.printStackTrace(writer);\r
}\r
* @param msaws\r
* @throws UnsupportedRuntimeException\r
*/\r
- private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {\r
+ private <T> boolean testDefaultAlignment(MsaWS<T> msaws, Services service) throws Exception {\r
writer.print("Testing alignment with default parameters:");\r
Alignment al = null;\r
boolean succeed = false;\r
+ String taskId;\r
\r
- String taskId = msaws.align(loadSeqs());\r
+ if (service == Services.JpredWS) {\r
+ taskId = msaws.align(loadAlignment());\r
+ } else {\r
+ taskId = msaws.align(loadSeqs(2));\r
+ }\r
writer.print("\nQuerying job status...");\r
JobStatus status = msaws.getJobStatus(taskId);\r
while (status != JobStatus.FINISHED) {\r
}\r
return succeed;\r
}\r
- \r
/**\r
* Test JWS2 web services\r
* \r
String host = CmdHelper.getHost(args);\r
String serviceName = CmdHelper.getServiceName(args);\r
if (!Jws2Client.validURL(host)) {\r
- System.err\r
- .println("<host_and_context> parameter is not provided or is incorrect!");\r
+ System.err.println("<host_and_context> parameter is not provided or is incorrect!");\r
System.exit(1);\r
}\r
WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
if (serviceName != null) {\r
Services service = Services.getService(serviceName);\r
if (service == null) {\r
- tester.writer.println("Service '" + serviceName\r
- + "' is not supported. Valid values are: "\r
+ tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "\r
+ Arrays.toString(Services.values()));\r
tester.writer.println();\r
printUsage();\r
System.exit(0);\r
}\r
\r
- tester.writer\r
- .println("<ServiceName> is not provided checking all known services...");\r
+ tester.writer.println("<ServiceName> is not provided checking all known services...");\r
\r
for (Services serv : Services.values()) {\r
tester.writer.println();\r
tester.checkService(serv);\r
}\r
+\r
+ }\r
+ \r
+ /**\r
+ * Connects to a web service by the host and the service name web service type\r
+ * \r
+ * @param host\r
+ * the fully qualified name of JABAWS server including JABAWS\r
+ * context name e.g\r
+ * http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
+ * @param service\r
+ * the name of the JABAWS service to connect to\r
+ * @return JABAService<T>\r
+ * @throws WebServiceException\r
+ * @throws ConnectException\r
+ * if fails to connect to the service on the host\r
+ */\r
+ private JABAService connect(String host, Services service)\r
+ throws WebServiceException, ConnectException {\r
+ URL url = null;\r
+ System.out.println ("Attempting to connect with " + service.toString() + "...");\r
+ try {\r
+ url = new URL(host + "/" + service.toString() + "?wsdl");\r
+ System.out.println ("URL: " + url.toString());\r
+ } catch (MalformedURLException e) {\r
+ e.printStackTrace();\r
+ }\r
+ Service serv = null;\r
+ try {\r
+ serv = service.getService(url, service.getServiceNamespace());\r
+ } catch (WebServiceException wse) {\r
+ wse.printStackTrace();\r
+ }\r
+ if (serv == null) {\r
+ throw new ConnectException("Could not connect to " + url + ". Is the server down?");\r
+ }\r
+ JABAService srv = service.getInterface(serv);\r
+ System.out.println ("Connected successfully!");\r
+ return srv;\r
}\r
\r
/**\r
*/\r
public boolean checkService(Services service) throws ConnectException,\r
WebServiceException {\r
- JABAService ws = Jws2Client.connect(hostname, service);\r
+ JABAService ws = connect(hostname, service);\r
if (ws == null) {\r
- writer.println("Cannot estabilish the connection to host "\r
- + hostname + " with service " + service.toString());\r
+ String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
+ writer.println(line + service.toString());\r
return false;\r
}\r
boolean succeed = false;\r
git://source.jalview.org / jabaws.git / blobdiff