Fix compilation issues

Author: kinow

src/test/java/org/commonwl/view/CwlViewerApplicationTests.java

@@ -19,12 +19,12 @@
 
 package org.commonwl.view;
 
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.context.junit4.SpringRunner;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-@RunWith(SpringRunner.class)
+@ExtendWith(SpringExtension.class)
 @SpringBootTest
 public class CwlViewerApplicationTests {
 

src/test/java/org/commonwl/view/PageControllerTest.java

@@ -19,8 +19,8 @@
 
 package org.commonwl.view;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 import org.springframework.test.web.servlet.MockMvc;
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 import org.springframework.web.servlet.view.InternalResourceViewResolver;
@@ -34,7 +34,7 @@ public class PageControllerTest {
 
     private MockMvc mockMvc;
 
-    @Before
+    @BeforeEach
     public void setup() {
         InternalResourceViewResolver viewResolver = new InternalResourceViewResolver();
         viewResolver.setPrefix("/src/main/resources/templates/");

src/test/java/org/commonwl/view/cwl/CWLElementTest.java

@@ -19,11 +19,11 @@
 
 package org.commonwl.view.cwl;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import java.util.List;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class CWLElementTest {
 

src/test/java/org/commonwl/view/cwl/CWLProcessTest.java

@@ -19,9 +19,9 @@
 
 package org.commonwl.view.cwl;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class CWLProcessTest {
 

src/test/java/org/commonwl/view/cwl/CWLServiceTest.java

@@ -19,22 +19,28 @@
 
 package org.commonwl.view.cwl;
 
-import org.apache.jena.query.*;
+import org.apache.jena.query.Dataset;
+import org.apache.jena.query.DatasetFactory;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.query.ResultSetFactory;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowOverview;
-import org.junit.Before;
-import org.junit.Rule;
-import org.junit.Test;
-import org.junit.rules.ExpectedException;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mockito;
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.context.junit4.SpringRunner;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
 import java.io.ByteArrayInputStream;
 import java.io.File;
@@ -44,12 +50,15 @@
 import java.util.Map;
 
 import static org.apache.commons.io.FileUtils.readFileToString;
-import static org.junit.Assert.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Matchers.anyObject;
 import static org.mockito.Matchers.anyString;
 import static org.mockito.Mockito.when;
 
-@RunWith(SpringRunner.class)
+@ExtendWith(SpringExtension.class)
 @SpringBootTest
 public class CWLServiceTest {
 
@@ -58,7 +67,7 @@ public class CWLServiceTest {
      */
     private RDFService rdfService;
 
-    @Before
+    @BeforeEach
     public void setUp() throws Exception {
         File packedWorkflowRdf = new File("src/test/resources/cwl/make_to_cwl/dna.ttl");
         Model workflowModel = ModelFactory.createDefaultModel();
@@ -82,12 +91,6 @@ public ResultSet answer(InvocationOnMock invocation) throws Throwable {
         Mockito.doReturn(true).when(rdfService).graphExists(anyString());
     }
 
-    /**
-     * Used for expected IOExceptions for filesize limits
-     */
-    @Rule
-    public ExpectedException thrown = ExpectedException.none();
-
     @Test
     public void parsePackedWorkflowNativePath() throws Exception {
         CWLService cwlService = new CWLService(rdfService, Mockito.mock(CWLTool.class), 5242880);
@@ -180,13 +183,12 @@ public void parseWorkflowWithCwltool() throws Exception {
     public void workflowOverSingleFileSizeLimitThrowsIOException() throws Exception {
 
         // Should throw IOException due to oversized files
-        thrown.expect(IOException.class);
-        thrown.expectMessage("File 'lobSTR-workflow.cwl' is over singleFileSizeLimit - 2 KB/0 bytes");
-
-        CWLService cwlService = new CWLService(rdfService, Mockito.mock(CWLTool.class), 0);
-        cwlService.parseWorkflowNative(
-                Paths.get("src/test/resources/cwl/lobstr-draft3/lobSTR-workflow.cwl"), null);
-
+        Exception thrown = Assertions.assertThrows(IOException.class, () -> {
+            CWLService cwlService = new CWLService(rdfService, Mockito.mock(CWLTool.class), 0);
+            cwlService.parseWorkflowNative(
+                    Paths.get("src/test/resources/cwl/lobstr-draft3/lobSTR-workflow.cwl"), null);
+        });
+        assertEquals("File 'lobSTR-workflow.cwl' is over singleFileSizeLimit - 2 KB/0 bytes", thrown.getMessage());
     }
 
     /**
@@ -216,19 +218,17 @@ public void getHelloWorkflowOverview() throws Exception {
      */
     @Test
     public void workflowOverviewOverSingleFileSizeLimitThrowsIOException() throws Exception {
-
-        // Test cwl service
-        CWLService cwlService = new CWLService(Mockito.mock(RDFService.class),
-                Mockito.mock(CWLTool.class), 0);
-
         // File to test
         File helloWorkflow = new File("src/test/resources/cwl/hello/hello.cwl");
 
-        // Should throw IOException due to oversized file
-        thrown.expect(IOException.class);
-        thrown.expectMessage(String.format("File 'hello.cwl' is over singleFileSizeLimit - %s bytes/0 bytes", 
-                helloWorkflow.length()));
-        cwlService.getWorkflowOverview(helloWorkflow);
+        // Test cwl service
+        Exception thrown = Assertions.assertThrows(IOException.class, () -> {
+            CWLService cwlService = new CWLService(Mockito.mock(RDFService.class),
+                    Mockito.mock(CWLTool.class), 0);
+            cwlService.getWorkflowOverview(helloWorkflow);
+        });
+        assertEquals(String.format("File 'hello.cwl' is over singleFileSizeLimit - %s bytes/0 bytes",
+                helloWorkflow.length()), thrown.getMessage());
 
     }
 

src/test/java/org/commonwl/view/cwl/RDFServiceTest.java

@@ -19,15 +19,15 @@
 
 package org.commonwl.view.cwl;
 
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.test.context.junit4.SpringRunner;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
-@RunWith(SpringRunner.class)
+@ExtendWith(SpringExtension.class)
 @SpringBootTest
 public class RDFServiceTest {
 

src/test/java/org/commonwl/view/docker/DockerServiceTest.java

@@ -19,11 +19,11 @@
 
 package org.commonwl.view.docker;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 public class DockerServiceTest {
 
@@ -32,7 +32,7 @@ public class DockerServiceTest {
     /**
      * New instance of DockerService
      */
-    @Before
+    @BeforeEach
     public void setUp() throws Exception {
         dockerService = new DockerService();
     }

src/test/java/org/commonwl/view/git/GitDetailsTest.java

@@ -19,10 +19,10 @@
 
 package org.commonwl.view.git;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import static org.commonwl.view.git.GitDetails.normaliseUrl;
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class GitDetailsTest {
 

src/test/java/org/commonwl/view/git/GitSemaphoreTest.java

@@ -19,10 +19,10 @@
 
 package org.commonwl.view.git;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
-import static junit.framework.TestCase.assertFalse;
-import static junit.framework.TestCase.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class GitSemaphoreTest {
 

src/test/java/org/commonwl/view/git/GitServiceTest.java

@@ -26,13 +26,13 @@
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 import org.mockito.Mockito;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.doReturn;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.spy;
@@ -50,7 +50,7 @@ public class GitServiceTest {
     private CheckoutCommand mockTagNotFoundCommand;
     private CheckoutCommand mockCheckoutCommand;
 
-    @Before
+    @BeforeEach
     public void setup() throws GitAPIException {
         GitService gitService = new GitService(null, false);
         this.spyGitService = spy(gitService);