*/
package jalview.ws.jabaws;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
-@Test(groups = { "External" })
+/*
+ * All methods in this class are set to the Network group because setUpBeforeClass will fail
+ * if there is no network.
+ */
+@Test(singleThreaded = true)
public class DisorderAnnotExportImport
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
public static String testseqs = "examples/uniref50.fa";
public static Jws2Discoverer disc;
public static jalview.gui.AlignFrame af = null;
- @BeforeClass(inheritGroups = true)
+ @BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.initLogger();
disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+
+ while (disc.isRunning())
+ {
+ // don't get services until discoverer has finished
+ Thread.sleep(100);
+ }
+
iupreds = new ArrayList<Jws2Instance>();
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase().contains("iupredws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
{
iupreds.add(svc);
}
/**
* test for patches to JAL-1294
*/
- @Test
+ @Test(groups = { "External", "Network" })
public void testDisorderAnnotExport()
{
disorderClient = new AADisorderClient(iupreds.get(0), af, null, null);
{
orig_alig.deleteAnnotation(aa);
}
- testAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
+ checkAnnotationFileIO("Testing IUPred Annotation IO", orig_alig);
}
- public static void testAnnotationFileIO(String testname, AlignmentI al)
+ static void checkAnnotationFileIO(String testname, AlignmentI al)
{
try
{
- String aligfileout = new FormatAdapter().formatSequences("PFAM",
- al.getSequencesArray());
+ String aligfileout = FileFormat.Pfam.getWriter(al).print(
+ al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
assertTrue(
DataSourceType.PASTE));
// test for consistency in io
- StockholmFileTest.testAlignmentEquivalence(al, al_new, true);
+ StockholmFileTest.testAlignmentEquivalence(al, al_new, true, false,
+ false);
return;
} catch (Exception e)
{