import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
-import jalview.gui.AlignFrame;
import jalview.gui.Jalview2XML;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
-import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.io.StockholmFileTest;
import jalview.ws.jws2.JPred301Client;
import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
import jalview.ws.jws2.SequenceAnnotationWSClient;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Component;
-import java.net.ConnectException;
import java.util.ArrayList;
import java.util.List;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.xml.ws.WebServiceException;
import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-import compbio.data.msa.Category;
-import compbio.data.msa.JABAService;
import compbio.metadata.Argument;
import compbio.metadata.WrongParameterException;
-import compbio.ws.client.Jws2Client;
-import compbio.ws.client.Services;
public class JpredJabaStructExportImport
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static String testseqs = "examples/uniref50.fa";
+ public static String testseqs = "examples/uniref50.fa";
- private static Jws2Instance jpredws;
+ public static Jws2Discoverer disc;
- private static AlignFrame af = null;
+ public static Jws2Instance jpredws;
+
+ jalview.ws.jws2.JPred301Client jpredClient;
+
+ public static jalview.gui.AlignFrame af = null;
@BeforeClass(alwaysRun = true)
- public static void setUpBeforeClass() throws ConnectException,
- WebServiceException
+ public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
- Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("SHOW_QUALITY",
- Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.FALSE.toString());
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.FALSE.toString());
Cache.initLogger();
- getJabaws();
+ disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
- FileLoader fl = new FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, DataSourceType.FILE);
- assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
- }
-
- /**
- * @throws WebServiceException
- * @throws ConnectException
- *
- */
- static void getJabaws() throws ConnectException, WebServiceException
- {
- String jabaws = "http://www.compbio.dundee.ac.uk/jabaws";
- JABAService service = null;
- for (Category category : Category.getCategories())
+ for (Jws2Instance svc : disc.getServices())
{
- for (Services srv : category.getServices())
+ if (svc.getServiceTypeURI().toLowerCase().contains("jpred"))
{
- if ("JpredWS".equals(srv.name()))
- {
- service = Jws2Client.connect(jabaws, srv);
- }
+ jpredws = svc;
}
}
- jpredws = new Jws2Instance(jabaws, "JpredWs",
- "Secondary Structure Prediction",
- "SERVICE: JpredWS version 3.0.3", service);
+
+ System.out.println("State of jpredws: " + jpredws);
Assert.assertNotNull(jpredws, "jpredws is null!");
+ jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
+ af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
+ assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
@AfterClass(alwaysRun = true)
}
}
- @Test(groups = { "Network" })
+ @Test(groups = { "Functional" })
public void testJPredStructOneSeqOnly()
{
af.selectAllSequenceMenuItem_actionPerformed(null);
af.getViewport().getSelectionGroup().getSequenceAt(0),
false);
af.hideSelSequences_actionPerformed(null);
- JPred301Client jpredClient = new JPred301Client(jpredws, af, null, null);
+ jpredClient = new JPred301Client(jpredws, af, null, null);
assertTrue(
"Didn't find any default args to check for. Buggy implementation of hardwired arguments in client.",
}
- /*
- * test disabled pending completion of JAL-1601
- * (JPred301Client is currently hidden in Jalview in
- *
- */
- @Test(groups = { "Network" })
- public void testJPredStructExport() throws InterruptedException
+ @Test(groups = { "Functional" })
+ public void testJPredStructExport()
{
- JPred301Client jpredClient = new JPred301Client(jpredws, af, null, null);
+ jpredClient = new JPred301Client(jpredws, af, null, null);
af.getViewport().getCalcManager().startWorker(jpredClient);
;
} while (af.getViewport().getCalcManager().isWorking());
- synchronized (this)
- {
- wait(2000);
- }
AlignmentI orig_alig = af.getViewport().getAlignment();
- System.out.println("Alignment now has "
- + orig_alig.getAlignmentAnnotation().length + " annotations");
- verifyAnnotationFileIO("Testing JPredWS Annotation IO", orig_alig);
+
+ testAnnotationFileIO("Testing JPredWS Annotation IO", orig_alig);
}
- protected static void verifyAnnotationFileIO(String testname,
- AlignmentI al)
+ public static void testAnnotationFileIO(String testname, AlignmentI al)
{
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = FileFormat.Fasta.getWriter(null).print(
+ String aligfileout = FileFormat.Pfam.getWriter(null).print(
al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
} catch (Exception e)
{
e.printStackTrace();
- Assert.fail("Test "
- + testname
- + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
+ Assert.fail("Test "
+ + testname
+ + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
- @Test(groups = { "Network" }, enabled = false)
+ @Test(groups = { "Functional" })
public void testJpredwsSettingsRecovery()
{
- Assert.fail("not implemented");
+ Assert.fail("not implemnented");
List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
.getRunnerConfig().getArguments())
opts.add(rg);
}
}
- JPred301Client jpredClient = new JPred301Client(jpredws, af, null, opts);
+ jpredClient = new JPred301Client(jpredws, af, null, opts);
af.getViewport().getCalcManager().startWorker(jpredClient);