Fix unit tests

Author: kinow

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

@@ -22,14 +22,18 @@
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.context.ApplicationContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
+import static org.assertj.core.api.Assertions.assertThat;
+
 @ExtendWith(SpringExtension.class)
-@SpringBootTest
+@SpringBootTest(classes={WebConfig.class})
 public class CwlViewerApplicationTests {
 
 	@Test
-	public void contextLoads() {
+	public void contextLoads(ApplicationContext context) {
+		assertThat(context).isNotNull();
 	}
 
 }

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

@@ -35,12 +35,9 @@
 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.junit.jupiter.SpringExtension;
 
 import java.io.ByteArrayInputStream;
 import java.io.File;
@@ -54,12 +51,9 @@
 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.ArgumentMatchers.any;
 import static org.mockito.Mockito.when;
 
-@ExtendWith(SpringExtension.class)
-@SpringBootTest
 public class CWLServiceTest {
 
     /**
@@ -87,8 +81,8 @@ public ResultSet answer(InvocationOnMock invocation) throws Throwable {
         };
 
         this.rdfService = Mockito.spy(new RDFService("http://localhost:3030/cwlviewer/"));
-        Mockito.doAnswer(queryRdf).when(rdfService).runQuery(anyObject());
-        Mockito.doReturn(true).when(rdfService).graphExists(anyString());
+        Mockito.doAnswer(queryRdf).when(rdfService).runQuery(any());
+        Mockito.doReturn(true).when(rdfService).graphExists(any(String.class));
     }
 
     @Test
@@ -149,7 +143,7 @@ public void parseWorkflowWithCwltool() throws Exception {
         // Mock CWLTool
         CWLTool mockCwlTool = Mockito.mock(CWLTool.class);
         File packedWorkflowRdf = new File("src/test/resources/cwl/make_to_cwl/dna.ttl");
-        when(mockCwlTool.getRDF(anyString()))
+        when(mockCwlTool.getRDF(any(String.class)))
                 .thenReturn(readFileToString(packedWorkflowRdf));
 
         // CWLService to test

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

@@ -19,6 +19,9 @@
 
 package org.commonwl.view.cwl;
 
+import org.commonwl.view.CwlViewerApplication;
+import org.commonwl.view.MongoConfig;
+import org.commonwl.view.WebConfig;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -28,7 +31,7 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @ExtendWith(SpringExtension.class)
-@SpringBootTest
+@SpringBootTest(classes=RDFService.class)
 public class RDFServiceTest {
 
     /**

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

@@ -23,6 +23,7 @@
 import java.io.IOException;
 
 import org.eclipse.jgit.api.CheckoutCommand;
+import org.eclipse.jgit.api.CloneCommand;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefNotFoundException;
@@ -62,6 +63,7 @@ public void setup() throws GitAPIException {
         when(this.mockGit.checkout()).thenReturn(this.mockCheckoutCommand);
         when(this.mockBranchNotFoundCommand.call()).thenThrow(branchNotFoundException);
         when(this.mockTagNotFoundCommand.call()).thenThrow(tagNotFoundException);
+        doReturn(this.mockGit).when(this.spyGitService).cloneRepo(Mockito.any(), Mockito.any());
     }
 
     @Test

src/test/java/org/commonwl/view/researchobject/ROBundleFactoryTest.java

@@ -19,6 +19,7 @@
 
 package org.commonwl.view.researchobject;
 
+import org.apache.taverna.robundle.Bundle;
 import org.commonwl.view.git.GitDetails;
 import org.commonwl.view.workflow.Workflow;
 import org.commonwl.view.workflow.WorkflowRepository;
@@ -29,7 +30,7 @@
 import java.util.HashMap;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.mockito.Matchers.anyObject;
+import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.when;
 
 /**
@@ -49,12 +50,12 @@ public void bundleForValidWorkflow() throws Exception {
 
         // Mocked path to a RO bundle
         ROBundleService mockROBundleService = Mockito.mock(ROBundleService.class);
-        when(mockROBundleService.saveToFile(anyObject()))
+        when(mockROBundleService.saveToFile(any()))
                 .thenReturn(Paths.get("test/path/to/check/for.zip"));
 
         // Test method retries multiple times to get workflow model before success
         WorkflowRepository mockRepository = Mockito.mock(WorkflowRepository.class);
-        when(mockRepository.findByRetrievedFrom(anyObject()))
+        when(mockRepository.findByRetrievedFrom(any(GitDetails.class)))
                 .thenReturn(null)
                 .thenReturn(null)
                 .thenReturn(validWorkflow);

src/test/java/org/commonwl/view/researchobject/ROBundleServiceTest.java

@@ -19,24 +19,6 @@
 
 package org.commonwl.view.researchobject;
 
-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.any;
-import static org.mockito.Matchers.anyBoolean;
-import static org.mockito.Matchers.anyObject;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.io.File;
-import java.net.URI;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
 import org.apache.jena.query.ResultSet;
 import org.apache.taverna.robundle.Bundle;
 import org.apache.taverna.robundle.Bundles;
@@ -59,6 +41,21 @@
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
 
+import java.io.File;
+import java.net.URI;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+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.ArgumentMatchers.any;
+import static org.mockito.Mockito.when;
+
 public class ROBundleServiceTest {
 
     private static ROBundleService roBundleService;
@@ -75,36 +72,36 @@ public void setUp() throws Exception {
 
         // Get mock Git service
         GitService mockGitService = Mockito.mock(GitService.class);
-        when(mockGitService.getRepository(anyObject(), anyBoolean())).thenReturn(gitRepo);
+        when(mockGitService.getRepository(any(GitDetails.class), any(Boolean.class))).thenReturn(gitRepo);
 
         Set<HashableAgent> authors = new HashSet<>();
         authors.add(new HashableAgent("Mark Robinson", null, new URI("mailto:[email protected]")));
-        when(mockGitService.getAuthors(anyObject(), anyObject()))
+        when(mockGitService.getAuthors(any(Git.class), any(String.class)))
                 .thenReturn(authors);
 
         // Mock Graphviz service
         GraphVizService mockGraphvizService = Mockito.mock(GraphVizService.class);
-        when(mockGraphvizService.getGraphPath(anyString(), anyString(), anyString()))
+        when(mockGraphvizService.getGraphPath(any(String.class), any(String.class), any(String.class)))
                 .thenReturn(Paths.get("src/test/resources/graphviz/testVis.png"))
                 .thenReturn(Paths.get("src/test/resources/graphviz/testVis.svg"));
-        when(mockGraphvizService.getGraphStream(anyString(), anyString()))
+        when(mockGraphvizService.getGraphStream(any(), any(String.class)))
         .thenReturn(getClass().getResourceAsStream("/graphviz/testVis.png"))
         .thenReturn(getClass().getResourceAsStream("/graphviz/testVis.svg"));
 
 
         // Mock CWLTool
         CWLTool mockCwlTool = Mockito.mock(CWLTool.class);
-        when(mockCwlTool.getPackedVersion(anyString()))
+        when(mockCwlTool.getPackedVersion(any(String.class)))
                 .thenReturn("cwlVersion: v1.0");
 
         // Mock RDF Service
         ResultSet emptyResult = Mockito.mock(ResultSet.class);
         when(emptyResult.hasNext()).thenReturn(false);
         RDFService mockRdfService = Mockito.mock(RDFService.class);
-        when(mockRdfService.getAuthors(anyString(), anyString())).thenReturn(emptyResult);
-        when(mockRdfService.graphExists(anyString()))
+        when(mockRdfService.getAuthors(any(String.class), any(String.class))).thenReturn(emptyResult);
+        when(mockRdfService.graphExists(any(String.class)))
                 .thenReturn(true);
-        when(mockRdfService.getModel(anyObject(), anyObject()))
+        when(mockRdfService.getModel(any(String.class), any(String.class)))
                 .thenReturn("@prefix cwl: <https://w3id.org/cwl/cwl#> .".getBytes());
 
         // Create new RO bundle

src/test/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryTest.java

@@ -1,17 +1,17 @@
 package org.commonwl.view.workflow;
 
+import org.commonwl.view.MongoConfig;
 import org.commonwl.view.git.GitDetails;
 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.autoconfigure.data.mongo.DataMongoTest;
-import org.springframework.test.context.junit.jupiter.SpringExtension;
+import org.springframework.test.context.ContextConfiguration;
 
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertNull;
 
 @DataMongoTest
-@ExtendWith(SpringExtension.class)
+@ContextConfiguration(classes={MongoConfig.class})
 public class QueuedWorkflowRepositoryTest {
 
     @Autowired