From 44f876a4d3b0adfd680ddfa84e14cc7940d6f877 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 24 Jun 2015 14:26:01 +0100 Subject: [PATCH] JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG --- test/jalview/datamodel/SequenceDummyTest.java | 18 +++--- test/jalview/ext/htsjdk/TestHtsContigDb.java | 4 +- test/jalview/io/AnnotatedPDBFileInputTest.java | 6 +- test/jalview/io/Gff3tests.java | 59 ++++++++++---------- test/jalview/io/HtmlFileTest.java | 4 +- test/jalview/ws/jabaws/JalviewJabawsTestUtils.java | 13 ++--- 6 files changed, 53 insertions(+), 51 deletions(-) diff --git a/test/jalview/datamodel/SequenceDummyTest.java b/test/jalview/datamodel/SequenceDummyTest.java index 2fc1934..ca1ac7d 100644 --- a/test/jalview/datamodel/SequenceDummyTest.java +++ b/test/jalview/datamodel/SequenceDummyTest.java @@ -1,15 +1,15 @@ package jalview.datamodel; +import org.testng.Assert; +import org.testng.annotations.Test; -import org.junit.Assert; -import org.junit.Test; +@Test public class SequenceDummyTest { /** * test for become method */ - @Test public void testBecome() { SequenceI seq = new Sequence("OrigSeq", "ASEQUENCE"); @@ -19,10 +19,12 @@ public class SequenceDummyTest SequenceDummy dummySeq = new SequenceDummy("OrigSeq"); dummySeq.addSequenceFeature(ofeat); dummySeq.become(seq); - Assert.assertFalse("Dummy sequence did not become a full sequence", - dummySeq.isDummy()); - Assert.assertTrue("Sequence was not updated from template", seq - .getSequenceAsString().equals(dummySeq.getSequenceAsString())); + Assert.assertFalse(dummySeq.isDummy(), + "Dummy sequence did not become a full sequence"); + Assert.assertTrue( + seq.getSequenceAsString() + .equals(dummySeq.getSequenceAsString()), + "Sequence was not updated from template"); boolean found = false; for (SequenceFeature sf : dummySeq.getSequenceFeatures()) { @@ -32,7 +34,7 @@ public class SequenceDummyTest break; } } - Assert.assertTrue("Didn't retain original sequence feature", found); + Assert.assertTrue(found, "Didn't retain original sequence feature"); // todo - should test all aspect of copy constructor } diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index d168c27..5e0f99a 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -7,8 +7,8 @@ import jalview.datamodel.SequenceI; import java.io.File; -import org.junit.Assert; -import org.junit.Test; +import org.testng.Assert; +import org.testng.annotations.Test; /** * @author jprocter diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java index 1c6a489..c40df35 100644 --- a/test/jalview/io/AnnotatedPDBFileInputTest.java +++ b/test/jalview/io/AnnotatedPDBFileInputTest.java @@ -17,7 +17,7 @@ import jalview.structure.StructureSelectionManager; import java.io.File; -import org.junit.Assert; +import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; @@ -61,8 +61,8 @@ public class AnnotatedPDBFileInputTest for (int q = p + 1; q < avec.length; q++) { Assert.assertNotEquals( - "Found a duplicate annotation row " + avec[p].label, - avec[p], avec[q]); +avec[p], avec[q], + "Found a duplicate annotation row " + avec[p].label); } } } diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java index 8df44df..56b57af 100644 --- a/test/jalview/io/Gff3tests.java +++ b/test/jalview/io/Gff3tests.java @@ -8,8 +8,8 @@ import jalview.gui.AlignFrame; import java.io.IOException; -import org.junit.Assert; -import org.junit.Test; +import org.testng.Assert; +import org.testng.annotations.Test; public class Gff3tests { @@ -29,14 +29,15 @@ public class Gff3tests AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs, FormatAdapter.FILE); - Assert.assertEquals("Unexpected number of DNA protein associations", 0, - af.getViewport().getAlignment().getCodonFrames().size()); + Assert.assertEquals(0, af.getViewport().getAlignment().getCodonFrames() + .size(), "Unexpected number of DNA protein associations"); af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null); - Assert.assertNotEquals("Expected at least one DNA protein association", + Assert.assertNotEquals( 0, af.getViewport().getAlignment().getDataset() - .getCodonFrames().size()); + .getCodonFrames().size(), + "Expected at least one DNA protein association"); } @@ -57,7 +58,7 @@ public class Gff3tests FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, false); - Assert.assertTrue("return result should be true", parseResult); + Assert.assertTrue(parseResult, "return result should be true"); checkDatasetfromSimpleGff3(dataset); } @@ -66,9 +67,8 @@ public class Gff3tests { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( simpleGff3file, FormatAdapter.FILE); - Assert.assertTrue( - "Didn't read the alignment into an alignframe from Gff3 File", - af != null); + Assert.assertTrue(af != null, + "Didn't read the alignment into an alignframe from Gff3 File"); checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset()); } @@ -81,8 +81,8 @@ public class Gff3tests FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, true); - Assert.assertTrue("return result (relaxedID matching) should be true", - parseResult); + Assert.assertTrue(parseResult, + "return result (relaxedID matching) should be true"); checkDatasetfromSimpleGff3(dataset); } @@ -98,38 +98,41 @@ public class Gff3tests private void checkDatasetfromSimpleGff3(AlignmentI dataset) { - Assert.assertEquals("no sequences extracted from GFF3 file", 2, - dataset.getHeight()); + Assert.assertEquals(2, dataset.getHeight(), + "no sequences extracted from GFF3 file"); SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset .findName("seq2"); Assert.assertNotNull(seq1); Assert.assertNotNull(seq2); Assert.assertFalse( - "Failed to replace dummy seq1 with real sequence", seq1 instanceof SequenceDummy - && ((SequenceDummy) seq1).isDummy()); + && ((SequenceDummy) seq1).isDummy(), + "Failed to replace dummy seq1 with real sequence"); Assert.assertFalse( - "Failed to replace dummy seq2 with real sequence", seq2 instanceof SequenceDummy - && ((SequenceDummy) seq2).isDummy()); + && ((SequenceDummy) seq2).isDummy(), + "Failed to replace dummy seq2 with real sequence"); String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); - Assert.assertFalse("dummy replacement buggy for seq1", - placeholderseq.equals(seq1.getSequenceAsString())); + Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()), + "dummy replacement buggy for seq1"); Assert.assertNotEquals("dummy replacement buggy for seq2", placeholderseq.equals(seq2.getSequenceAsString())); - Assert.assertNotNull("No features added to seq1", - seq1.getSequenceFeatures());// != null); - Assert.assertEquals("Wrong number of features", 3, - seq1.getSequenceFeatures().length); + Assert.assertNotNull(seq1.getSequenceFeatures(), + "No features added to seq1"); + Assert.assertEquals(seq1.getSequenceFeatures().length, 3, + "Wrong number of features"); Assert.assertNull(seq2.getSequenceFeatures()); - Assert.assertEquals("Wrong number of features", 0, seq2 + Assert.assertEquals( + seq2 .getSequenceFeatures() == null ? 0 - : seq2.getSequenceFeatures().length); + : seq2 + .getSequenceFeatures().length, 0, + "Wrong number of features"); Assert.assertTrue( - "Expected at least one CDNA/Protein mapping for seq1", dataset.getCodonFrame(seq1) != null - && dataset.getCodonFrame(seq1).size() > 0); + && dataset.getCodonFrame(seq1).size() > 0, + "Expected at least one CDNA/Protein mapping for seq1"); } // @Test diff --git a/test/jalview/io/HtmlFileTest.java b/test/jalview/io/HtmlFileTest.java index eca3984..09b8990 100644 --- a/test/jalview/io/HtmlFileTest.java +++ b/test/jalview/io/HtmlFileTest.java @@ -1,7 +1,5 @@ package jalview.io; -import static org.junit.Assert.fail; - import org.testng.annotations.Test; public class HtmlFileTest @@ -10,7 +8,7 @@ public class HtmlFileTest @Test(enabled = false) public void test() { - fail("Not yet implemented"); + org.testng.AssertJUnit.fail("Not yet implemented"); } } diff --git a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java index ec901da..91e9244 100644 --- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java +++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java @@ -20,13 +20,11 @@ */ package jalview.ws.jabaws; -import static org.junit.Assert.assertTrue; -import static org.junit.Assert.fail; - import jalview.ws.jws2.Jws2Discoverer; import java.util.Vector; +import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -54,7 +52,7 @@ public class JalviewJabawsTestUtils @Test(enabled = false) public void testAnnotExport() { - fail("Not yet implemented"); + Assert.fail("Not yet implemented"); } public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer() @@ -84,10 +82,11 @@ public class JalviewJabawsTestUtils } catch (Exception e) { e.printStackTrace(); - fail("Aborting. Problem discovering services. Tried " + svcurls); + Assert.fail("Aborting. Problem discovering services. Tried " + + svcurls); } - assertTrue("Failed to discover any services at ", disc.getServices() - .size() > 0); + Assert.assertTrue(disc.getServices().size() > 0, + "Failed to discover any services at "); return disc; } -- 1.7.10.2