Merge pull request #74 from EBISPOT/2.x-dev

2.x dev
EBISPOT · May 14, 2021 · c0a87d0 · c0a87d0
2 parents b05f7df + da45f1b
commit c0a87d0
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Showing 38 changed files with 447 additions and 351 deletions.
diff --git a/pom.xml b/pom.xml
@@ -15,6 +15,8 @@
         <org.springframework.version>4.1.2.RELEASE</org.springframework.version>
         <org.springframework.security.version>3.2.5.RELEASE</org.springframework.security.version>
         <org.slf4j.version>1.7.5</org.slf4j.version>
+        <junit.jupiter.version>5.7.1</junit.jupiter.version>
+        <maven.surefire.version>3.0.0-M5</maven.surefire.version>
     </properties>
 
     <build>
@@ -23,8 +25,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>2.3.2</version>
                 <configuration>
-                    <source>1.7</source>
-                    <target>1.7</target>
+                    <source>1.8</source>
+                    <target>1.8</target>
                 </configuration>
             </plugin>
             <plugin>
@@ -236,12 +238,14 @@
         </dependency>
 
         <!-- testing dependencies -->
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.10</version>
-            <scope>test</scope>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>junit</groupId>-->
+<!--            <artifactId>junit</artifactId>-->
+<!--            <version>4.10</version>-->
+<!--            <scope>test</scope>-->
+<!--        </dependency>-->
+
+
 
         <dependency>
             <groupId>org.slf4j</groupId>
@@ -396,6 +400,19 @@
                 <version>1.9.0</version>
                 <scope>test</scope>
             </dependency>
+
+            <dependency>
+                <groupId>org.junit.jupiter</groupId>
+                <artifactId>junit-jupiter</artifactId>
+                <version>${junit.jupiter.version}</version>
+                <scope>test</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>${maven.surefire.version}</version>
+            </dependency>
         </dependencies>
     </dependencyManagement>
 
@@ -455,6 +472,18 @@
                             </execution>
                         </executions>
                     </plugin>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <version>${maven.surefire.version}</version>
+                        <dependencies>
+                            <dependency>
+                                <groupId>org.junit.jupiter</groupId>
+                                <artifactId>junit-jupiter-engine</artifactId>
+                                <version>${junit.jupiter.version}</version>
+                            </dependency>
+                        </dependencies>
+                    </plugin>
                 </plugins>
             </build>
         </profile>

diff --git a/zooma-api/pom.xml b/zooma-api/pom.xml
@@ -15,6 +15,7 @@
 
     <properties>
         <zooma.version>2.1.11-SNAPSHOT</zooma.version>
+        <junit.jupiter.version>5.7.1</junit.jupiter.version>
     </properties>
 
     <dependencies>
@@ -30,5 +31,10 @@
             <groupId>org.mockito</groupId>
             <artifactId>mockito-core</artifactId>
         </dependency>
+
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+        </dependency>
     </dependencies>
 </project>
diff --git a/zooma-api/src/main/java/uk/ac/ebi/fgpt/zooma/util/CollectionUtils.java b/zooma-api/src/main/java/uk/ac/ebi/fgpt/zooma/util/CollectionUtils.java
@@ -1,5 +1,8 @@
 package uk.ac.ebi.fgpt.zooma.util;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 import java.util.Collection;
 
 /**
@@ -9,15 +12,19 @@
  * @date 28/05/12
  */
 public class CollectionUtils {
+    private static Logger logger = LoggerFactory.getLogger(CollectionUtils.class);
+
     public static <C extends Collection> boolean compareCollectionContents(C c1, C c2) {
         if (c1.size() != c2.size()) {
+            logger.trace("Size of c1=" + c1.size() + " does not match size of c2=" + c2.size());
             return false;
         }
         else {
             boolean allMatched = true;
             // make sure c2 contains all elements in c1
             for (Object o : c1) {
                 if (!c2.contains(o)) {
+                    logger.trace(c2 + " does not contain o=" + o);
                     allMatched = false;
                     break;
                 }
@@ -26,6 +33,7 @@ public static <C extends Collection> boolean compareCollectionContents(C c1, C c
             // and make sure c1 contains all elements in c2
             for (Object o : c2) {
                 if (!c1.contains(o)) {
+                    logger.trace(c1 + " does not contain o=" + o);
                     allMatched = false;
                     break;
                 }

diff --git a/zooma-api/src/test/java/uk/ac/ebi/fgpt/zooma/util/TestCollectionUtils.java b/zooma-api/src/test/java/uk/ac/ebi/fgpt/zooma/util/TestCollectionUtils.java
@@ -1,8 +1,8 @@
 package uk.ac.ebi.fgpt.zooma.util;
 
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -12,8 +12,7 @@
 import java.util.List;
 import java.util.Set;
 
-import static junit.framework.Assert.assertFalse;
-import static junit.framework.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.*;
 
 /**
  * Javadocs go here!
@@ -22,6 +21,8 @@
  * @date 18/02/13
  */
 public class TestCollectionUtils {
+    private Logger logger = LoggerFactory.getLogger(getClass());
+
     private Object item1;
     private Object item2;
 
@@ -31,8 +32,9 @@ public class TestCollectionUtils {
     private Object unequalItem1;
     private Object unequalItem2;
 
-    @Before
+    @BeforeEach
     public void setup() {
+        logger.trace("Initializing item1");
         item1 = new Object() {
             @Override public int hashCode() {
                 return 1;
@@ -77,7 +79,7 @@ public void setup() {
         unequalItem2 = new Object();
     }
 
-    @After
+    @AfterEach
     public void teardown() {
         item1 = null;
         item2 = null;
@@ -90,52 +92,46 @@ public void teardown() {
     @Test
     public void testSame() {
         Collection coll = Arrays.asList(item1, item2);
-        assertTrue("Comparing identical collections should be return true",
-                   CollectionUtils.compareCollectionContents(coll, coll));
+        assertTrue(CollectionUtils.compareCollectionContents(coll, coll), "Comparing identical collections should be return true");
     }
 
     @Test
     public void testAllEqual() {
         Collection coll1 = Arrays.asList(item1, item2);
         Collection coll2 = Arrays.asList(equalItem1, equalItem2);
-        assertTrue("Comparing equal collections should be return true",
-                   CollectionUtils.compareCollectionContents(coll1, coll2));
+        assertTrue(CollectionUtils.compareCollectionContents(coll1, coll2), "Comparing equal collections should be return true");
 
         Collection coll3 = Arrays.asList(item1, item2);
-        Collection coll4 = Arrays.asList(equalItem1, equalItem2);
-        assertTrue("Comparing equal but differently ordered collections should be return true",
-                   CollectionUtils.compareCollectionContents(coll3, coll4));
+        Collection coll4 = Arrays.asList(equalItem2, equalItem1);
+        assertTrue(CollectionUtils.compareCollectionContents(coll3, coll4), "Comparing equal but differently ordered collections should be return true");
 
         List<Object> coll5 = new ArrayList<>();
         coll5.add(item1);
         coll5.add(item2);
         Set<Object> coll6 = new HashSet<>();
         coll6.add(equalItem1);
         coll6.add(equalItem2);
-        assertTrue("Comparing differently typed collections with same elements should be return true",
-                   CollectionUtils.compareCollectionContents(coll5, coll6));
+        assertTrue(CollectionUtils.compareCollectionContents(coll5, coll6), "Comparing differently typed collections with same elements should be return true");
     }
 
     @Test
     public void testNotAllEqual() {
         Collection coll1 = Arrays.asList(item1, item2);
         Collection coll2 = Arrays.asList(equalItem1, unequalItem2);
-        assertFalse("Comparing unequal collections should be return false",
-                    CollectionUtils.compareCollectionContents(coll1, coll2));
+        assertFalse(CollectionUtils.compareCollectionContents(coll1, coll2), "Comparing unequal collections should be return false");
     }
 
     @Test
     public void testAllDifferent() {
         Collection coll1 = Arrays.asList(item1, item2);
         Collection coll2 = Arrays.asList(unequalItem1, unequalItem2);
-        assertFalse("Comparing unequal collections should be return false",
-                    CollectionUtils.compareCollectionContents(coll1, coll2));
+        assertFalse(CollectionUtils.compareCollectionContents(coll1, coll2), "Comparing unequal collections should be return false");
     }
 
     @Test
     public void testEmpty() {
         Collection coll1 = Collections.emptyList();
         Collection coll2 = Collections.emptyList();
-        assertTrue("Empty collections should be equal", CollectionUtils.compareCollectionContents(coll1, coll2));
+        assertTrue(CollectionUtils.compareCollectionContents(coll1, coll2), "Empty collections should be equal");
     }
 }
diff --git a/zooma-api/src/test/java/uk/ac/ebi/fgpt/zooma/util/TestLabelUtils.java b/zooma-api/src/test/java/uk/ac/ebi/fgpt/zooma/util/TestLabelUtils.java
@@ -1,16 +1,14 @@
 package uk.ac.ebi.fgpt.zooma.util;
 
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.BeforeEach;
 import uk.ac.ebi.fgpt.zooma.datasource.OntologyDAO;
 
 import java.net.URI;
 import java.util.Collections;
 
-import static junit.framework.Assert.assertEquals;
-import static junit.framework.Assert.assertNotNull;
-import static junit.framework.Assert.fail;
+import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -35,7 +33,7 @@ public class TestLabelUtils {
 
     private OntologyDAO ontologyDAO;
 
-    @Before
+    @BeforeEach
     public void setup() {
         testLabel1 = "label one";
         testLabel2 = "label two";
@@ -55,7 +53,7 @@ public void setup() {
         when(ontologyDAO.getSemanticTagSynonyms(entity1)).thenReturn(Collections.singleton(testSynonym));
     }
 
-    @After
+    @AfterEach
     public void teardown() {
         ontologyDAO = null;
         LabelUtils utils = new LabelUtils();