From 2ea710eca2128ed962434e668bbf51180b6ceab8 Mon Sep 17 00:00:00 2001 From: Mateusz Warowny Date: Wed, 25 Oct 2023 17:43:56 +0200 Subject: [PATCH] JAL-4313 Create utilities to test annotations --- test/jalview/testutils/AnnotationsMatcher.java | 78 +++++++++++ test/jalview/testutils/AnnotationsMatcherTest.java | 136 ++++++++++++++++++++ test/jalview/testutils/Matchers.java | 21 +++ 3 files changed, 235 insertions(+) create mode 100644 test/jalview/testutils/AnnotationsMatcher.java create mode 100644 test/jalview/testutils/AnnotationsMatcherTest.java diff --git a/test/jalview/testutils/AnnotationsMatcher.java b/test/jalview/testutils/AnnotationsMatcher.java new file mode 100644 index 0000000..aa86d90 --- /dev/null +++ b/test/jalview/testutils/AnnotationsMatcher.java @@ -0,0 +1,78 @@ +package jalview.testutils; + +import java.util.List; +import java.util.Objects; +import static java.util.Objects.requireNonNullElse; + +import org.hamcrest.Description; +import org.hamcrest.TypeSafeMatcher; + +import jalview.datamodel.Annotation; + +public class AnnotationsMatcher extends TypeSafeMatcher +{ + final List annotations; + + public AnnotationsMatcher(List annotations) + { + this.annotations = annotations; + } + + @Override + public boolean matchesSafely(Annotation[] items) + { + if (annotations.size() != items.length) + return false; + for (int i = 0; i < annotations.size(); i++) + { + var actual = items[i]; + var expected = annotations.get(i); + if (!annotationsEqual(actual, expected)) + return false; + } + return true; + } + + static boolean annotationsEqual(Annotation a, Annotation b) + { + return a.secondaryStructure == b.secondaryStructure && a.value == b.value + && Objects.equals(a.colour, b.colour) + && Objects + .equals(requireNonNullElse(a.displayCharacter, ""), + requireNonNullElse(b.displayCharacter, "")) + && Objects + .equals(requireNonNullElse(a.description, ""), + requireNonNullElse(b.description, "")); + } + + @Override + public void describeTo(Description description) + { + description.appendText("annotations ").appendValue(annotations); + } + + @Override + public void describeMismatchSafely(Annotation[] items, + Description description) + { + if (annotations.size() != items.length) + { + description.appendText("but had length ").appendValue(items.length); + return; + } + boolean first = true; + for (int i = 0; i < annotations.size(); i++) + { + var actual = items[i]; + var expected = annotations.get(i); + if (!annotationsEqual(actual, expected)) + { + description + .appendText(first ? "but " : ", ") + .appendText("element [" + i + "] was ") + .appendValue(items[i]); + first = false; + } + } + } +} diff --git a/test/jalview/testutils/AnnotationsMatcherTest.java b/test/jalview/testutils/AnnotationsMatcherTest.java new file mode 100644 index 0000000..732329b --- /dev/null +++ b/test/jalview/testutils/AnnotationsMatcherTest.java @@ -0,0 +1,136 @@ +package jalview.testutils; + +import org.testng.annotations.DataProvider; +import org.testng.annotations.Test; +import jalview.datamodel.Annotation; + +import static org.hamcrest.MatcherAssert.assertThat; + +import java.awt.Color; +import java.util.*; + +public class AnnotationsMatcherTest +{ + @DataProvider + public Object[][] matchingAnnotationsLists() + { + return new Object[][] { + { + new Annotation[] { + new Annotation("C", "", 'C', 0.0f), + new Annotation("C", "", 'C', 0.1f), + new Annotation("B", "", 'B', 0.2f) }, + new Annotation[] { + new Annotation("C", "", 'C', 0.0f), + new Annotation("C", "", 'C', 0.1f), + new Annotation("B", "", 'B', 0.2f) } }, + { + new Annotation[] { + new Annotation("X", "xxx", 'X', 1.3f), + new Annotation("V", "vvv", 'V', 1.5f), + new Annotation("B", "bbb", 'B', 2.5f) }, + new Annotation[] { + new Annotation("X", "xxx", 'X', 1.3f), + new Annotation("V", "vvv", 'V', 1.5f), + new Annotation("B", "bbb", 'B', 2.5f) } }, + { + new Annotation[] { + new Annotation("A", "", 'A', 0.2f, Color.RED), + new Annotation("A", "", 'A', 0.3f, Color.GREEN), + new Annotation("C", "", 'C', 0.4f, Color.YELLOW), + new Annotation("C", "", 'C', 0.5f) }, + new Annotation[] { + new Annotation("A", "", 'A', 0.2f, Color.RED), + new Annotation("A", "", 'A', 0.3f, Color.GREEN), + new Annotation("C", "", 'C', 0.4f, Color.YELLOW), + new Annotation("C", "", 'C', 0.5f) } }, + { + new Annotation[] { + Annotation.EMPTY_ANNOTATION, Annotation.EMPTY_ANNOTATION }, + new Annotation[] { + Annotation.EMPTY_ANNOTATION, Annotation.EMPTY_ANNOTATION } } }; + } + + @Test(groups = { "Functional" }, dataProvider = "matchingAnnotationsLists") + public void testMatchesSafely_matchingAnnotations(Annotation[] template, + Annotation[] testdata) + { + assert new AnnotationsMatcher(Arrays.asList(template)) + .matchesSafely(testdata); + } + + @DataProvider + public Object[][] matchingAnnotations() + { + return new Object[][] { + { + new Annotation("A", "aaa", 'A', 0.1f), + new Annotation("A", "aaa", 'A', 0.1f) }, + { + new Annotation("A", "abcdef", 'A', 0.1f, Color.RED), + new Annotation("A", "abcdef", 'A', 0.1f, Color.RED) }, + { + new Annotation("", "xxxx", ' ', 0.0f), + new Annotation("", "xxxx", ' ', 0.0f) }, + { + new Annotation("", "", ' ', 0.0f), + new Annotation("", "", ' ', 0.0f) }, + { + new Annotation(null, null, ' ', 0.0f), + new Annotation(null, null, ' ', 0.0f) }, + { + new Annotation(null, "", ' ', 0.0f), + new Annotation("", null, ' ', 0.0f) } }; + } + + @Test(groups = { "Functional" }, dataProvider = "matchingAnnotations") + public void testAnnotationsEqual_matchingAnnotations(Annotation first, + Annotation second) + { + assert AnnotationsMatcher.annotationsEqual(first, second); + } + + @Test(groups = { "Functional" }) + public void testAnnotationsEqual_compareNullDisplayCharToEmpty() + { + assert AnnotationsMatcher + .annotationsEqual(new Annotation("", "description", 'A', 0.1f), + new Annotation(null, "description", 'A', 0.1f)); + assert AnnotationsMatcher + .annotationsEqual(new Annotation(null, "description", 'A', 0.1f), + new Annotation("", "description", 'A', 0.1f)); + } + + @Test(groups = { "Functional" }) + public void testAnnotationsEqual_compareNullDescriptionToEmpty() + { + assert AnnotationsMatcher + .annotationsEqual(new Annotation("A", null, 'A', 0.2f), + new Annotation("A", "", 'A', 0.2f)); + assert AnnotationsMatcher + .annotationsEqual(new Annotation("A", "", 'A', 0.2f), + new Annotation("A", null, 'A', 0.2f)); + } + + @Test(groups = { "Functional" }) + public void testAnnotationsEqual_compareNullDisplayCharToBlank() + { + assert !AnnotationsMatcher + .annotationsEqual(new Annotation(" ", "aaa", 'A', 0.03f), + new Annotation(null, "aaa", 'A', 0.03f)); + assert !AnnotationsMatcher + .annotationsEqual(new Annotation(null, "aaa", 'A', 0.04f), + new Annotation(" ", "aaa", 'A', 0.04f)); + } + + @Test(groups = { "Functional" }) + public void testAnnotationsEqual_compareNullDescriptionToBlank() + { + assert !AnnotationsMatcher + .annotationsEqual(new Annotation("A", null, 'A', 0.0f), + new Annotation("A", " ", 'A', 0.0f)); + assert !AnnotationsMatcher + .annotationsEqual(new Annotation("A", " ", 'A', 0.01f), + new Annotation("A", null, 'A', 0.01f)); + } +} diff --git a/test/jalview/testutils/Matchers.java b/test/jalview/testutils/Matchers.java index ceb07a0..682d1bf 100644 --- a/test/jalview/testutils/Matchers.java +++ b/test/jalview/testutils/Matchers.java @@ -1,7 +1,11 @@ package jalview.testutils; +import java.util.Arrays; +import java.util.List; + import org.hamcrest.Matcher; +import jalview.datamodel.Annotation; import jalview.datamodel.SequenceI; public class Matchers @@ -10,4 +14,21 @@ public class Matchers { return new SequenceStringMatcher(sequence); } + + public static Matcher matchesSequenceString(SequenceI sequence) + { + return new SequenceStringMatcher(sequence.getSequenceAsString()); + } + + public static Matcher matchesAnnotations( + List annotations) + { + return new AnnotationsMatcher(annotations); + } + + public static Matcher matchesAnnotations( + Annotation... annotations) + { + return new AnnotationsMatcher(Arrays.asList(annotations)); + } } -- 1.7.10.2