Add tests for functionality with no network requirement

Author: Mark Robinson

src/main/java/org/commonwl/view/docker/DockerService.java

@@ -20,8 +20,8 @@ public class DockerService {
     public static String getDockerHubURL(String dockerPull) {
         Matcher m = dockerhubPattern.matcher(dockerPull);
         if (m.find()) {
-            if (m.group(1).isEmpty()) {
-                return "https://hub.docker.com/r/_/" + m.group(2);
+            if (m.group(2) == null) {
+                return "https://hub.docker.com/r/_/" + m.group(1);
             } else {
                 return "https://hub.docker.com/r/" + m.group(1) + "/" + m.group(2);
             }

src/main/java/org/commonwl/view/github/GithubDetails.java

@@ -97,7 +97,7 @@ public String getURL() {
      */
     public String getURL(String ref) {
         String url = "https://github.com/" + owner + "/" + repoName + "/tree/" + ref;
-        if (path != null) {
+        if (path != null && path != "/") {
             url += "/" + this.path;
         }
         return url;

src/main/resources/templates/workflow.html

@@ -216,7 +216,7 @@ <h2>Steps</h2>
                                 (<span th:text="${step.value.runType}">Workflow</span>)
                             </div>
                             <div th:if="${step.value.run != null and step.value.runType == null}">
-                                <span th:text="${step.value.run} + '(?)'" class="notFound" data-tooltip="true" title="Not Found - Must be somewhere within this repository">workflow.cwl (?)</span>
+                                <span th:text="${step.value.run} + ' (?)'" class="notFound" data-tooltip="true" title="Not Found - Must be somewhere within this repository">workflow.cwl (?)</span>
                             </div>
                         </td>
                         <td th:text="${step.value.label}">Label</td>

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

@@ -0,0 +1,32 @@
+package org.commonwl.view.cwl;
+
+import org.junit.Test;
+
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+public class CWLElementTest {
+
+    /**
+     * Test addition and retrieval of source IDs from a node
+     * null values should not be added to the list
+     */
+    @Test
+    public void testSourceIDList() throws Exception {
+
+        CWLElement element = new CWLElement();
+
+        element.addSourceID("sourceID1");
+        element.addSourceID("sourceID2");
+        element.addSourceID(null);
+        element.addSourceID("sourceID3");
+
+        List<String> sourceIDs = element.getSourceIDs();
+
+        assertEquals(3, sourceIDs.size());
+        assertEquals("sourceID3", sourceIDs.get(2));
+
+    }
+
+}

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

@@ -0,0 +1,19 @@
+package org.commonwl.view.cwl;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class CWLProcessTest {
+
+    /**
+     * Test toString method for enum
+     */
+    @Test
+    public void testToString() throws Exception {
+        assertEquals("Workflow", CWLProcess.WORKFLOW.toString());
+        assertEquals("Commandlinetool", CWLProcess.COMMANDLINETOOL.toString());
+        assertEquals("Expressiontool", CWLProcess.EXPRESSIONTOOL.toString());
+    }
+
+}

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

@@ -0,0 +1,26 @@
+package org.commonwl.view.docker;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class DockerServiceTest {
+
+    /**
+     * Test conversion from docker pull tag to dockerhub URL
+     */
+    @Test
+    public void getDockerHubURL() throws Exception {
+
+        String test1 = DockerService.getDockerHubURL("stain/cwlviewer");
+        assertEquals("https://hub.docker.com/r/stain/cwlviewer", test1);
+
+        String test2 = DockerService.getDockerHubURL("rabix/lobSTR");
+        assertEquals("https://hub.docker.com/r/rabix/lobSTR", test2);
+
+        String test3 = DockerService.getDockerHubURL("ubuntu");
+        assertEquals("https://hub.docker.com/r/_/ubuntu", test3);
+
+    }
+
+}

src/test/java/org/commonwl/view/github/GithubDetailsTest.java

@@ -0,0 +1,53 @@
+package org.commonwl.view.github;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+public class GithubDetailsTest {
+
+    /**
+     * Branch getter, should default to "master" if null
+     */
+    @Test
+    public void getBranch() throws Exception {
+        GithubDetails details1 = new GithubDetails("owner", "repoName", "testbranch", "path/within/workflow.cwl");
+        assertEquals("testbranch", details1.getBranch());
+
+        // Null branch should default to master
+        GithubDetails details2 = new GithubDetails("owner", "repoName", null, null);
+        assertEquals("master", details2.getBranch());
+    }
+
+    /**
+     * Path getter, should default to / if null
+     */
+    @Test
+    public void getPath() throws Exception {
+        GithubDetails details1 = new GithubDetails("owner", "repoName", "branch", "subdir/");
+        assertEquals("subdir/", details1.getPath());
+
+        GithubDetails details2 = new GithubDetails("owner", "repoName", "branch", "test/directory/structure.cwl");
+        assertEquals("test/directory/structure.cwl", details2.getPath());
+
+        GithubDetails details3 = new GithubDetails("owner", "repoName", null, null);
+        assertEquals("/", details3.getPath());
+    }
+
+    /**
+     * Construct a URL from Github details
+     */
+    @Test
+    public void getURL() throws Exception {
+        GithubDetails details1 = new GithubDetails("owner", "repoName", "branch", "path/within/structure.cwl");
+        assertEquals("https://github.com/owner/repoName/tree/branch/path/within/structure.cwl", details1.getURL());
+        assertEquals("https://github.com/owner/repoName/tree/overrideBranch/path/within/structure.cwl",
+                details1.getURL("overrideBranch"));
+
+        GithubDetails details2 = new GithubDetails("owner", "repoName", "branch", null);
+        assertEquals("https://github.com/owner/repoName/tree/branch", details2.getURL());
+        assertEquals("https://github.com/owner/repoName/tree/differentBranch", details2.getURL("differentBranch"));
+
+    }
+
+}

src/test/java/org/commonwl/view/graphviz/DotWriterTest.java

@@ -0,0 +1,92 @@
+package org.commonwl.view.graphviz;
+
+import org.apache.commons.io.FileUtils;
+import org.commonwl.view.cwl.CWLElement;
+import org.commonwl.view.cwl.CWLProcess;
+import org.commonwl.view.cwl.CWLStep;
+import org.commonwl.view.workflow.Workflow;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.StringWriter;
+import java.util.HashMap;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+
+public class DotWriterTest {
+
+    private Workflow testWorkflow;
+
+    /**
+     * Manually make a workflow with multiple steps, default value,
+     * nested workflow etc to test DOT generation
+     * TODO: This is a pain, can it be made simpler?
+     */
+    @Before
+    public void setUp() throws Exception {
+
+        // Inputs
+        Map<String, CWLElement> inputs = new HashMap<>();
+        CWLElement input1 = new CWLElement();
+        input1.setLabel("First Input");
+        inputs.put("input1", input1);
+        inputs.put("input2", new CWLElement());
+
+        // Steps
+        Map<String, CWLStep> steps = new HashMap<>();
+
+        CWLElement step1InputElement  = new CWLElement();
+        step1InputElement.addSourceID("input1");
+        step1InputElement.addSourceID("input2");
+        Map<String, CWLElement> step1inputs = new HashMap<>();
+        step1inputs.put("toolinput1", step1InputElement);
+        CWLStep step1 = new CWLStep(null, null, null, null, step1inputs, null);
+        steps.put("step1", step1);
+
+        CWLElement default1InputElement  = new CWLElement();
+        default1InputElement.setDefaultVal("examplefile.jar");
+        Map<String, CWLElement> default1inputs = new HashMap<>();
+        step1inputs.put("defaultInput", default1InputElement);
+        CWLStep default1 = new CWLStep(null, null, null, null, default1inputs, null);
+        steps.put("default1", default1);
+
+        CWLElement step2InputElement  = new CWLElement();
+        step2InputElement.addSourceID("step1");
+        step2InputElement.addSourceID("default1");
+        Map<String, CWLElement> step2inputs = new HashMap<>();
+        step2inputs.put("toolinput1", step2InputElement);
+        CWLStep step2 = new CWLStep(null, null, null, null, step2inputs, null);
+        step2.setRunType(CWLProcess.WORKFLOW);
+        steps.put("step2", step2);
+
+        // Output
+        Map<String, CWLElement> outputs = new HashMap<>();
+        CWLElement output = new CWLElement();
+        output.setLabel("Single Output");
+        output.setDoc("Description");
+        output.addSourceID("step2");
+        outputs.put("output", output);
+
+        // Save workflow model
+        testWorkflow = new Workflow("Example Workflow", "Description", inputs, outputs, steps, null);
+    }
+
+    /**
+     * Test functionality to write a Workflow to DOT format
+     */
+    @Test
+    public void writeGraph() throws Exception {
+
+        StringWriter dotSource = new StringWriter();
+        DotWriter dotWriter = new DotWriter(dotSource);
+
+        dotWriter.writeGraph(testWorkflow);
+
+        File expectedDot = new File("src/test/resources/graphviz/testWorkflow.dot");
+        assertEquals(FileUtils.readFileToString(expectedDot), dotSource.toString());
+
+    }
+
+}

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

@@ -0,0 +1,28 @@
+package org.commonwl.view.workflow;
+
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+
+
+public class WorkflowFormTest {
+
+    /**
+     * Test for the form stripping unnecessary trailing slashes from directory URLs
+     */
+    @Test
+    public void getGithubURL() throws Exception {
+
+        String unchangedURL = "https://github.com/common-workflow-language/workflows/tree/master/workflows/compile";
+        WorkflowForm testForm = new WorkflowForm(unchangedURL);
+        assertEquals(unchangedURL, testForm.getGithubURL());
+
+        WorkflowForm testForm2 = new WorkflowForm("https://github.com/common-workflow-language/workflows/tree/master/workflows/compile/");
+        assertEquals("https://github.com/common-workflow-language/workflows/tree/master/workflows/compile", testForm2.getGithubURL());
+
+        testForm2.setGithubURL("https://github.com/common-workflow-language/workflows/tree/master/workflows/make-to-cwl/////");
+        assertEquals("https://github.com/common-workflow-language/workflows/tree/master/workflows/make-to-cwl", testForm2.getGithubURL());
+
+    }
+
+}

src/test/resources/graphviz/testWorkflow.dot

@@ -0,0 +1,52 @@
+digraph workflow {
+  graph [
+    bgcolor = "#eeeeee"
+    color = "black"
+    fontsize = "10"
+    labeljust = "left"
+    clusterrank = "local"
+    ranksep = "0.22"
+    nodesep = "0.05"
+  ]
+  node [
+    fontname = "Helvetica"
+    fontsize = "10"
+    fontcolor = "black"
+    shape = "record"
+    height = "0"
+    width = "0"
+    color = "black"
+    fillcolor = "lightgoldenrodyellow"
+    style = "filled"
+  ];
+  edge [
+    fontname="Helvetica"
+    fontsize="8"
+    fontcolor="black"
+    color="black"
+    arrowsize="0.7"
+  ];
+  subgraph cluster_inputs {
+    rank = "same";
+    style = "dashed";
+    label = "Workflow Inputs";
+    "input2" [fillcolor="#94DDF4"];
+    "input1" [fillcolor="#94DDF4",label="First Input";];
+  }
+  subgraph cluster_outputs {
+    rank = "same";
+    style = "dashed";
+    label = "Workflow Outputs";
+    "output" [fillcolor="#94DDF4",label="Single Output";];
+  }
+  "default1";
+  "step2" [fillcolor="#F3CEA1"];
+  "step1";
+  "step2" -> "output";
+  "step1" -> "step2";
+  "default1" -> "step2";
+  "input1" -> "step1";
+  "input2" -> "step1";
+  "default1" [label="examplefile.jar", fillcolor="#D5AEFC"]
+  "default1" -> "step1";
+}