/**
* Test predict using code directly
*
* @throws XmppException
* @throws XwsException
* @throws InterruptedException
* @throws Xws4jException
*/
@Test
public void testHivpredServiceDirectly()
throws XmppException, XwsException, InterruptedException, Xws4jException {
String sequence =
"PQITLWQRPLVTIKIGCQLKEALLDTGADDTVLEEANLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF";
String predictionServer = "hivpred.ws1.bmc.uu.se";
String predictionFunction = "predictSusceptibility";
XwsManager xmpp = new XwsManager();
// Connect if not connected (requires JID and password in preferences)
if (!(xmpp.isConnected())) xmpp.connect();
// Set up function
IFunction hivFunction = xmpp.getFunction(predictionServer, predictionFunction);
HIVPredInputType in = HivpredFactory.eINSTANCE.createHIVPredInputType();
in.setSequence(sequence);
DocumentRoot root = HivpredFactory.eINSTANCE.createDocumentRoot();
root.setHIVPredInput(in);
// Convert to DOM since inputElement must be this
Element inputElement = EMFDOMConversion.getDomFromEMF(root);
// Invoke sync service
Element result = hivFunction.invokeSync(inputElement, 20000);
assertNotNull("Result from hivpred is null", result);
System.out.println(
"Got good hivpred result from service: " + JavaDOMTools.w3cElementToString(result));
// Convert output DOM to EMF
// EObject emfo = EMFDOMConversion.getEMFfromDOM(result);
// Element el = document.getDocumentElement();
EObject emfo = EMFDOMConversion.getEMFfromDOMusingJavaDOMtools(result);
if (!(emfo instanceof DocumentRoot)) {
fail("Result from hivpred was not a HIVpred DocumentRoot.");
}
DocumentRoot docroot = (DocumentRoot) emfo;
HIVPredOutputType hivOutput = docroot.getHIVPredOutput();
assertNotNull(hivOutput);
assertEquals(7, hivOutput.getResult().size());
}
@Test
public void testPredictFileWithSingleLine()
throws Xws4jException, XmppException, InterruptedException, URISyntaxException,
MalformedURLException, IOException {
URI uri = getClass().getResource("/testFiles/single.seq").toURI();
URL url = FileLocator.toFileURL(uri.toURL());
String path = url.getFile();
System.out.println("Trying to predict file: " + path);
HIVPredOutputType res = hivdrc.predictPI(path);
assertNotNull(res);
// File contains same string as in testPredictString() method
assertEquals("", res.getErrorMessage());
assertEquals(1, res.getMutNotInDataset().size());
assertEquals("P1A", res.getMutNotInDataset().get(0).getName());
assertEquals(2, res.getMutOutsideModelBoundaries().size());
assertEquals("Q2A", res.getMutOutsideModelBoundaries().get(0).getName());
assertEquals("I3A", res.getMutOutsideModelBoundaries().get(1).getName());
assertEquals(7, res.getResult().size());
assertEquals("amprenavir", res.getResult().get(0).getName());
assertEquals(-9.344846031197962, res.getResult().get(0).getResult(), EPSILON);
assertEquals("atazanavir", res.getResult().get(1).getName());
assertEquals(-8.081778845481008, res.getResult().get(1).getResult(), EPSILON);
assertEquals("indinavir", res.getResult().get(2).getName());
assertEquals(-8.306376101045098, res.getResult().get(2).getResult(), EPSILON);
assertEquals("lopinavir", res.getResult().get(3).getName());
assertEquals(-8.789871555954795, res.getResult().get(3).getResult(), EPSILON);
assertEquals("nelfinavir", res.getResult().get(4).getName());
assertEquals(-7.661361493579009, res.getResult().get(4).getResult(), EPSILON);
assertEquals("ritonavir", res.getResult().get(5).getName());
assertEquals(-8.108639981136413, res.getResult().get(5).getResult(), EPSILON);
// assertEquals("saquinavir", res.getResult().get(6).getName());
// TODO: fix misspelling in sus7.jar class PredictionResult
// saquinanvir -> saquinavir
assertEquals(-8.702355550536716, res.getResult().get(6).getResult(), EPSILON);
System.out.println(res);
}
/**
* Test predict using the hivpredmanager
*
* @throws Xws4jException
* @throws XmppException
* @throws InterruptedException
*/
@Test
public void testPredictString() throws Xws4jException, XmppException, InterruptedException {
String seq =
"AAAALWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF";
HIVPredOutputType res = hivdrc.predictPI(seq);
assertNotNull(res);
/*
<?xml version="1.0" encoding="ASCII"?><hivpred:HIVPredOutput xmlns:hivpred="http://www.hivdrc.org/hivpred" errorMessage="">
<hivpred:mutNotInDataset name="P1A"/>
<hivpred:mutOutsideModelBoundaries name="Q2A"/>
<hivpred:mutOutsideModelBoundaries name="I3A"/>
<hivpred:result name="amprenavir" result="-9.344846031197962"/>
<hivpred:result name="atazanavir" result="-8.081778845481008"/>
<hivpred:result name="indinavir" result="-8.306376101045098"/>
<hivpred:result name="lopinavir" result="-8.789871555954795"/>
<hivpred:result name="nelfinavir" result="-7.661361493579009"/>
<hivpred:result name="ritonavir" result="-8.108639981136413"/>
<hivpred:result name="saquinanvir" result="-8.702355550536716"/>
</hivpred:HIVPredOutput>
*/
assertEquals("", res.getErrorMessage());
assertEquals(1, res.getMutNotInDataset().size());
assertEquals("P1A", res.getMutNotInDataset().get(0).getName());
assertEquals(2, res.getMutOutsideModelBoundaries().size());
assertEquals("Q2A", res.getMutOutsideModelBoundaries().get(0).getName());
assertEquals("I3A", res.getMutOutsideModelBoundaries().get(1).getName());
assertEquals(7, res.getResult().size());
assertEquals("amprenavir", res.getResult().get(0).getName());
assertEquals(-9.344846031197962, res.getResult().get(0).getResult(), EPSILON);
assertEquals("atazanavir", res.getResult().get(1).getName());
assertEquals(-8.081778845481008, res.getResult().get(1).getResult(), EPSILON);
assertEquals("indinavir", res.getResult().get(2).getName());
assertEquals(-8.306376101045098, res.getResult().get(2).getResult(), EPSILON);
assertEquals("lopinavir", res.getResult().get(3).getName());
assertEquals(-8.789871555954795, res.getResult().get(3).getResult(), EPSILON);
assertEquals("nelfinavir", res.getResult().get(4).getName());
assertEquals(-7.661361493579009, res.getResult().get(4).getResult(), EPSILON);
assertEquals("ritonavir", res.getResult().get(5).getName());
assertEquals(-8.108639981136413, res.getResult().get(5).getResult(), EPSILON);
// assertEquals("saquinavir", res.getResult().get(6).getName());
// TODO: fix misspelling in sus7.jar class PredictionResult
// saquinanvir -> saquinavir
assertEquals(-8.702355550536716, res.getResult().get(6).getResult(), EPSILON);
System.out.println(res);
}