Add test for main CWL service

Gets workflows from community repo by commit ID to test

Author: Mark Robinson

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

@@ -668,7 +668,7 @@ private String extractTypes(JsonNode typeNode) {
                 }
 
                 // Add optional if null was included in the multiple types
-                if (optional) typeDetails.append(" (Optional)");
+                if (optional) typeDetails.append("?");
 
                 // Set the type to the constructed string
                 return typeDetails.toString();

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

@@ -0,0 +1,124 @@
+package org.commonwl.view.cwl;
+
+import org.commonwl.view.github.GithubDetails;
+import org.commonwl.view.workflow.Workflow;
+import org.commonwl.view.workflow.WorkflowOverview;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import java.util.Map;
+
+import static org.junit.Assert.*;
+
+@RunWith(SpringRunner.class)
+@SpringBootTest
+public class CWLServiceTest {
+
+    private final Logger logger = LoggerFactory.getLogger(this.getClass());
+
+    /**
+     * Create a service to test
+     */
+    @Autowired
+    private CWLService cwlService;
+
+    /**
+     * Test main parsing of a the LobSTR workflow CWL version draft-3
+     */
+    @Test
+    public void parseLobSTRDraft3Workflow() throws Exception {
+
+        // Get workflow from community repo by commit ID so it will not change
+        GithubDetails lobSTRDraft3Details = new GithubDetails("common-workflow-language",
+                "workflows", null, "workflows/lobSTR/lobSTR-workflow.cwl");
+        Workflow lobSTRDraft3 = cwlService.parseWorkflow(lobSTRDraft3Details, "920c6be45f08e979e715a0018f22c532b024074f");
+
+        testLobSTRWorkflow(lobSTRDraft3);
+
+        // Extra docker requirement test
+        assertEquals("true", lobSTRDraft3.getDockerLink());
+    }
+
+    /**
+     * Test main parsing of a the LobSTR workflow CWL version 1.0
+     */
+    @Test
+    public void parseLobSTRv1Workflow() throws Exception {
+
+        // Get workflow from community repo by commit ID so it will not change
+        GithubDetails lobSTRv1Details = new GithubDetails("common-workflow-language",
+                "workflows", null, "workflows/lobSTR/lobSTR-workflow.cwl");
+        Workflow lobSTRv1 = cwlService.parseWorkflow(lobSTRv1Details, "933bf2a1a1cce32d88f88f136275535da9df0954");
+
+        testLobSTRWorkflow(lobSTRv1);
+
+        // Extra docker requirement test
+        assertEquals("https://hub.docker.com/r/rabix/lobstr", lobSTRv1.getDockerLink());
+
+    }
+
+    /**
+     * Validate a LobSTR workflow
+     * See: https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR
+     */
+    private void testLobSTRWorkflow(Workflow lobSTR) throws Exception {
+
+        // Overall not null
+        assertNotNull(lobSTR);
+
+        // Input Tests
+        Map<String, CWLElement> inputs = lobSTR.getInputs();
+        assertNotNull(inputs);
+        assertEquals(8, inputs.size());
+        assertNotNull(inputs.get("strinfo"));
+        assertEquals("File", inputs.get("strinfo").getType());
+        assertNotNull(inputs.get("p2"));
+        assertEquals("File[]?", inputs.get("p2").getType());
+        assertNotNull(inputs.get("rg-sample"));
+        assertEquals("Use this in the read group SM tag", inputs.get("rg-sample").getDoc());
+
+        // Step tests
+        Map<String, CWLStep> steps = lobSTR.getSteps();
+        assertNotNull(steps);
+        assertEquals(4, steps.size());
+        assertNotNull(steps.get("lobSTR"));
+        assertEquals("lobSTR-tool.cwl", steps.get("lobSTR").getRun());
+        assertEquals(CWLProcess.COMMANDLINETOOL, steps.get("lobSTR").getRunType());
+        assertNotNull(steps.get("samindex"));
+        assertTrue(steps.get("samindex").getInputs().get("input").getSourceIDs().contains("samsort"));
+
+        // Output tests
+        Map<String, CWLElement> outputs = lobSTR.getOutputs();
+        assertNotNull(outputs);
+        assertEquals(4, outputs.size());
+        assertNotNull(outputs.get("bam_stats"));
+        assertEquals("File", outputs.get("bam_stats").getType());
+        assertTrue(outputs.get("bam").getSourceIDs().contains("samindex"));
+
+    }
+
+    /**
+     * Test retrieval of a workflow overview for hello world example in cwl
+     */
+    @Test
+    public void getHelloWorkflowOverview() throws Exception {
+
+        // Get workflow from community repo by commit ID so it will not change
+        GithubDetails helloDetails = new GithubDetails("common-workflow-language",
+                "workflows", "8296e92d358bb5da4dc3c6e7aabefa89726e3409", "workflows/hello/hello.cwl");
+        WorkflowOverview hello = cwlService.getWorkflowOverview(helloDetails);
+        assertNotNull(hello);
+
+        // No docs for this workflow
+        assertEquals("Hello World", hello.getLabel());
+        assertEquals("Puts a message into a file using echo", hello.getDoc());
+        assertEquals("hello.cwl", hello.getFileName());
+
+    }
+
+}

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

@@ -3,6 +3,7 @@
 import org.junit.Test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
 
 public class DockerServiceTest {
 
@@ -21,6 +22,9 @@ public void getDockerHubURL() throws Exception {
         String test3 = DockerService.getDockerHubURL("ubuntu");
         assertEquals("https://hub.docker.com/r/_/ubuntu", test3);
 
+        String test4 = DockerService.getDockerHubURL(null);
+        assertNull(test4);
+
     }
 
 }