X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=f1430f673a50f64c60d830051928aee94ba94e97;hb=95ebbef7b78bf266a8252bd479510be3c80cd234;hp=1475b4e4dd6cdc5a59118719d1515bcffbaeef55;hpb=fe9cea784bed23e4fe5507714bf945b4ca67c077;p=jalview.git diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java index 1475b4e..f1430f6 100644 --- a/test/jalview/ws/jabaws/RNAStructExportImport.java +++ b/test/jalview/ws/jabaws/RNAStructExportImport.java @@ -20,13 +20,17 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; +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.Jalview2XML; +import jalview.gui.JvOptionPane; import jalview.io.AnnotationFile; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.io.StockholmFileTest; import jalview.ws.jws2.Jws2Discoverer; @@ -36,21 +40,33 @@ import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.AutoCalcSetting; import java.awt.Component; +import java.io.File; import java.util.ArrayList; import java.util.List; import javax.swing.JMenu; import javax.swing.JMenuItem; -import org.junit.AfterClass; -import org.junit.Assert; -import org.junit.BeforeClass; -import org.junit.Test; +import org.testng.Assert; +import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; +import compbio.metadata.Argument; import compbio.metadata.WrongParameterException; public class RNAStructExportImport { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + private static final String JAR_FILE_NAME = "testRnalifold_param.jar"; + public static String testseqs = "examples/RF00031_folded.stk"; public static Jws2Discoverer disc; @@ -61,11 +77,11 @@ public class RNAStructExportImport public static jalview.gui.AlignFrame af = null; - @BeforeClass + @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - - jalview.bin.Cache.initLogger(); + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + Cache.initLogger(); disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false); for (Jws2Instance svc : disc.getServices()) @@ -81,12 +97,12 @@ public class RNAStructExportImport if (rnaalifoldws == null) { - fail("no web service"); + Assert.fail("no web service"); } jalview.io.FileLoader fl = new jalview.io.FileLoader(false); - af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE); + af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE); assertNotNull("Couldn't load test data ('" + testseqs + "')", af); @@ -108,17 +124,22 @@ public class RNAStructExportImport // public? } - @AfterClass + @AfterClass(alwaysRun = true) public static void tearDownAfterClass() throws Exception { if (af != null) { af.setVisible(false); af.dispose(); + File f = new File(JAR_FILE_NAME); + if (f.exists()) + { + f.delete(); + } } } - @Test + @Test(groups = { "Functional" }) public void testRNAAliFoldValidStructure() { @@ -134,23 +155,24 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); AlignmentI orig_alig = af.getViewport().getAlignment(); - for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation()) + for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation()) { if (alifoldClient.involves(aa)) { if (aa.isRNA()) { - Assert.assertTrue("Did not create valid structure from RNAALiFold prediction", aa.isValidStruc()); + assertTrue( + "Did not create valid structure from RNAALiFold prediction", + aa.isValidStruc()); } } } } - @Test + @Test(groups = { "Functional" }) public void testRNAStructExport() { @@ -166,7 +188,6 @@ public class RNAStructExportImport } catch (InterruptedException x) { } - ; } while (af.getViewport().getCalcManager().isWorking()); AlignmentI orig_alig = af.getViewport().getAlignment(); @@ -180,16 +201,16 @@ public class RNAStructExportImport try { // what format would be appropriate for RNAalifold annotations? - String aligfileout = new FormatAdapter().formatSequences("PFAM", - al.getSequencesArray()); + String aligfileout = FileFormat.Pfam.getWriter(null).print( + al.getSequencesArray(), true); String anfileout = new AnnotationFile() .printAnnotationsForAlignment(al); - assertTrue( + assertNotNull( "Test " + testname + "\nAlignment annotation file was not regenerated. Null string", - anfileout != null); + anfileout); assertTrue( "Test " + testname @@ -201,13 +222,13 @@ public class RNAStructExportImport // again what format would be appropriate? AlignmentI al_new = new FormatAdapter().readFile(aligfileout, - FormatAdapter.PASTE, "PFAM"); + DataSourceType.PASTE, FileFormat.Pfam); assertTrue( "Test " + testname + "\nregenerated annotation file did not annotate alignment.", new AnnotationFile().readAnnotationFile(al_new, anfileout, - FormatAdapter.PASTE)); + DataSourceType.PASTE)); // test for consistency in io StockholmFileTest.testAlignmentEquivalence(al, al_new, false); @@ -216,17 +237,17 @@ public class RNAStructExportImport { e.printStackTrace(); } - fail("Test " + Assert.fail("Test " + testname + "\nCouldn't complete Annotation file roundtrip input/output/input test."); } - @Test + @Test(groups = { "Functional" }) public void testRnaalifoldSettingsRecovery() { - List opts = new ArrayList(); - for (compbio.metadata.Argument rg : (List) rnaalifoldws - .getRunnerConfig().getArguments()) + List opts = new ArrayList(); + for (Argument rg : (List) rnaalifoldws.getRunnerConfig() + .getArguments()) { if (rg.getDescription().contains("emperature")) { @@ -235,7 +256,7 @@ public class RNAStructExportImport rg.setValue("292"); } catch (WrongParameterException q) { - fail("Couldn't set the temperature parameter " + Assert.fail("Couldn't set the temperature parameter " + q.getStackTrace()); } opts.add(rg); @@ -265,10 +286,10 @@ public class RNAStructExportImport // write out parameters jalview.gui.AlignFrame nalf = null; assertTrue("Couldn't write out the Jar file", - new Jalview2XML(false).saveAlignment(af, - "testRnalifold_param.jar", "trial parameter writeout")); + new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME, + "trial parameter writeout")); assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML( - false).loadJalviewAlign("testRnalifold_param.jar")) != null); + false).loadJalviewAlign(JAR_FILE_NAME)) != null); if (nalf != null) { AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(