Remove test requirement on sparql endpoint

Author: MarkRobbo

src/main/java/org/commonwl/view/cwl/RDFService.java

@@ -305,7 +305,7 @@ public String labelFromName(String name) {
      * @param queryString The query to be run
      * @return The result set of the query
      */
-    private ResultSet runQuery(ParameterizedSparqlString queryString) {
+    ResultSet runQuery(ParameterizedSparqlString queryString) {
         Query query = QueryFactory.create(queryString.toString());
         try (QueryExecution qexec = QueryExecutionFactory.createServiceRequest(rdfService, query)) {
             return ResultSetFactory.copyResults(qexec.execSelect());

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

@@ -19,21 +19,25 @@
 
 package org.commonwl.view.cwl;
 
+import org.apache.jena.query.*;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
 import org.commonwl.view.github.GitHubService;
 import org.commonwl.view.github.GithubDetails;
 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.mockito.Mockito;
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.test.context.junit4.SpringRunner;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
 import java.util.Map;
@@ -51,9 +55,32 @@ public class CWLServiceTest {
     /**
      * RDFService for testing
      */
-    @Autowired
     private RDFService rdfService;
 
+    @Before
+    public void setUp() throws Exception {
+        File packedWorkflowRdf = new File("src/test/resources/cwl/make_to_cwl/dna.ttl");
+        Model workflowModel = ModelFactory.createDefaultModel();
+        workflowModel.read(new ByteArrayInputStream(readFileToString(packedWorkflowRdf).getBytes()), null, "TURTLE");
+        Dataset workflowDataset = DatasetFactory.create();
+        workflowDataset.addNamedModel("http://madeup.endpoint/github.com/common-workflow-language/workflows/master/workflows/make-to-cwl/dna.cwl", workflowModel);
+
+        Answer queryRdf = new Answer<ResultSet>() {
+            @Override
+            public ResultSet answer(InvocationOnMock invocation) throws Throwable {
+                Object[] args = invocation.getArguments();
+                Query query = QueryFactory.create(args[0].toString());
+                try (QueryExecution qexec = QueryExecutionFactory.create(query, workflowDataset)) {
+                    return ResultSetFactory.copyResults(qexec.execSelect());
+                }
+            }
+        };
+
+        this.rdfService = Mockito.spy(new RDFService("http://madeup.endpoint/"));
+        Mockito.doAnswer(queryRdf).when(rdfService).runQuery(anyObject());
+        Mockito.doReturn(true).when(rdfService).graphExists(anyString());
+    }
+
     /**
      * Used for expected IOExceptions for filesize limits
      */

src/test/resources/cwl/make_to_cwl/visualisation.dot

@@ -41,16 +41,16 @@ digraph workflow {
   "combine_sequences" [label="combine_sequences"];
   "get_sequences" [label="get_sequences"];
   "translate_sequences" [label="translate_sequences"];
-  "get_sequences" -> "combine_sequences" [label="sequences"];
   "default1" -> "combine_sequences" [label="catfilename"];
   "default1" [label="\"database.dna\"", fillcolor="#D5AEFC"];
+  "get_sequences" -> "combine_sequences" [label="sequences"];
   "rna" -> "get_sequences" [label="sequence"];
+  "default2" -> "translate_sequences" [label="filename"];
+  "default2" [label="\"database.dna\"", fillcolor="#D5AEFC"];
+  "default3" -> "translate_sequences" [label="from"];
+  "default3" [label="\"U\"", fillcolor="#D5AEFC"];
+  "default4" -> "translate_sequences" [label="to"];
+  "default4" [label="\"T\"", fillcolor="#D5AEFC"];
   "combine_sequences" -> "translate_sequences" [label="trinput"];
-  "default2" -> "translate_sequences" [label="to"];
-  "default2" [label="\"T\"", fillcolor="#D5AEFC"];
-  "default3" -> "translate_sequences" [label="filename"];
-  "default3" [label="\"database.dna\"", fillcolor="#D5AEFC"];
-  "default4" -> "translate_sequences" [label="from"];
-  "default4" [label="\"U\"", fillcolor="#D5AEFC"];
   "translate_sequences" -> "outfile";
 }