Remove unused members of CWLStep

Mark Robinson · Mark Robinson · commit b73616deedf1 · 2017-03-18T23:55:07.000Z
diff --git a/src/main/java/org/commonwl/view/cwl/CWLService.java b/src/main/java/org/commonwl/view/cwl/CWLService.java
@@ -282,7 +282,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
                 // Explicit ID and other fields within each input list
                 for (JsonNode step : steps) {
                     CWLStep stepObject = new CWLStep(extractLabel(step), extractDoc(step),
-                            extractTypes(step), extractRun(step), getInputs(step), getOutputs(step));
+                            extractRun(step), getInputs(step));
                     returnMap.put(extractID(step), stepObject);
                 }
             } else if (steps.getClass() == ObjectNode.class) {
@@ -292,8 +292,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
                     Map.Entry<String, JsonNode> stepNode = iterator.next();
                     JsonNode stepJson = stepNode.getValue();
                     CWLStep stepObject = new CWLStep(extractLabel(stepJson), extractDoc(stepJson),
-                            extractTypes(stepJson), extractRun(stepJson), getInputs(stepJson),
-                            getOutputs(stepJson));
+                            extractRun(stepJson), getInputs(stepJson));
                     returnMap.put(stepNode.getKey(), stepObject);
                 }
             }
diff --git a/src/main/java/org/commonwl/view/cwl/CWLStep.java b/src/main/java/org/commonwl/view/cwl/CWLStep.java
@@ -28,20 +28,16 @@ public class CWLStep {
 
     private String label;
     private String doc;
-    private String type;
     private String run;
     private CWLProcess runType;
-    private Map<String, CWLElement> inputs;
-    private Map<String, CWLElement> outputs;
+    private Map<String, CWLElement> sources;
 
-    public CWLStep(String label, String doc, String type, String run,
-                   Map<String, CWLElement> inputs, Map<String, CWLElement> outputs) {
+    public CWLStep(String label, String doc, String run,
+                   Map<String, CWLElement> sources) {
         this.label = label;
         this.doc = doc;
-        this.type = type;
         this.run = run;
-        this.inputs = inputs;
-        this.outputs = outputs;
+        this.sources = sources;
     }
 
     public String getLabel() {
@@ -60,14 +56,6 @@ public void setDoc(String doc) {
         this.doc = doc;
     }
 
-    public String getType() {
-        return type;
-    }
-
-    public void setType(String type) {
-        this.type = type;
-    }
-
     public String getRun() {
         return run;
     }
@@ -84,20 +72,8 @@ public void setRunType(CWLProcess runType) {
         this.runType = runType;
     }
 
-    public Map<String, CWLElement> getInputs() {
-        return inputs;
-    }
-
-    public void setInputs(Map<String, CWLElement> inputs) {
-        this.inputs = inputs;
-    }
-
-    public Map<String, CWLElement> getOutputs() {
-        return outputs;
-    }
-
-    public void setOutputs(Map<String, CWLElement> outputs) {
-        this.outputs = outputs;
+    public Map<String, CWLElement> getSources() {
+        return sources;
     }
 
 }
diff --git a/src/main/java/org/commonwl/view/graphviz/DotWriter.java b/src/main/java/org/commonwl/view/graphviz/DotWriter.java
@@ -173,8 +173,8 @@ private void writeSteps(Workflow workflow) throws IOException {
         // Write links between the remaining steps
         int defaultCount = 0;
         for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
-            if (step.getValue().getInputs() != null) {
-                for (Map.Entry<String, CWLElement> input : step.getValue().getInputs().entrySet()) {
+            if (step.getValue().getSources() != null) {
+                for (Map.Entry<String, CWLElement> input : step.getValue().getSources().entrySet()) {
                     List<String> sourceIDs = input.getValue().getSourceIDs();
 
                     // Draw the default value on the graph if there are no step inputs (it is a constant)
diff --git a/src/main/java/org/commonwl/view/workflow/WorkflowOverview.java b/src/main/java/org/commonwl/view/workflow/WorkflowOverview.java
@@ -24,9 +24,9 @@
  */
 public class WorkflowOverview {
 
-    private String fileName;
-    private String label;
-    private String doc;
+    private final String fileName;
+    private final String label;
+    private final String doc;
 
     public WorkflowOverview(String fileName, String label, String doc) {
         this.fileName = fileName;
@@ -38,24 +38,12 @@ public String getFileName() {
         return fileName;
     }
 
-    public void setFileName(String fileName) {
-        this.fileName = fileName;
-    }
-
     public String getLabel() {
         return label;
     }
 
-    public void setLabel(String label) {
-        this.label = label;
-    }
-
     public String getDoc() {
         return doc;
     }
 
-    public void setDoc(String doc) {
-        this.doc = doc;
-    }
-
 }
diff --git a/src/test/java/org/commonwl/view/cwl/CWLServiceTest.java b/src/test/java/org/commonwl/view/cwl/CWLServiceTest.java
@@ -137,7 +137,7 @@ private void testLobSTRWorkflow(Workflow lobSTR) throws Exception {
         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"));
+        assertTrue(steps.get("samindex").getSources().get("input").getSourceIDs().contains("samsort"));
 
         // Output tests
         Map<String, CWLElement> outputs = lobSTR.getOutputs();
diff --git a/src/test/java/org/commonwl/view/graphviz/DotWriterTest.java b/src/test/java/org/commonwl/view/graphviz/DotWriterTest.java
@@ -61,23 +61,24 @@ public void setUp() throws Exception {
         step1InputElement.addSourceID("input2");
         Map<String, CWLElement> step1inputs = new HashMap<>();
         step1inputs.put("toolinput1", step1InputElement);
-        CWLStep step1 = new CWLStep(null, null, null, null, step1inputs, null);
+        CWLStep step1 = new CWLStep(null, null, null, step1inputs);
         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);
+        CWLStep default1 = new CWLStep(null, null, null, default1inputs);
         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);
+        CWLStep step2 = new CWLStep(null, null, null, step2inputs);
         step2.setRunType(CWLProcess.WORKFLOW);
+        step2.setRun("subworkflow.cwl");
         steps.put("step2", step2);
 
         // Output
diff --git a/src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java b/src/test/java/org/commonwl/view/workflow/WorkflowControllerTest.java
@@ -103,6 +103,32 @@ public void newWorkflowFromGithubURL() throws Exception {
 
     }
 
+    /**
+     * Endpoint for displaying workflows and directories of workflows
+     */
+    @Test
+    public void getWorkflowByGithubDetails() throws Exception {
+
+        // Mock service to return a bundle file and then throw ROBundleNotFoundException
+        WorkflowService mockWorkflowService = Mockito.mock(WorkflowService.class);
+
+
+        // Mock controller/MVC
+        WorkflowController workflowController = new WorkflowController(
+                Mockito.mock(WorkflowFormValidator.class),
+                mockWorkflowService,
+                Mockito.mock(GraphVizService.class));
+        MockMvc mockMvc = MockMvcBuilders
+                .standaloneSetup(workflowController)
+                .build();
+
+        // Redirect with error
+        mockMvc.perform(get("/workflows/github.com/owner/reponame/tree/branch/path/within"))
+                .andExpect(status().isFound())
+                .andExpect(redirectedUrl("/?url=https://github.com/owner/reponame/tree/branch/path/within"));
+
+    }
+
     /**
      * Endpoint for downloading RO bundle for a workflow
      */

Original file line number	Diff line number	Diff line change
`@@ -282,7 +282,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {`
`282`	`282`	`// Explicit ID and other fields within each input list`
`283`	`283`	`for (JsonNode step : steps) {`
`284`	`284`	`CWLStep stepObject = new CWLStep(extractLabel(step), extractDoc(step),`
`285`		`- extractTypes(step), extractRun(step), getInputs(step), getOutputs(step));`
	`285`	`+ extractRun(step), getInputs(step));`
`286`	`286`	`returnMap.put(extractID(step), stepObject);`
`287`	`287`	`}`
`288`	`288`	`} else if (steps.getClass() == ObjectNode.class) {`
`@@ -292,8 +292,7 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {`
`292`	`292`	`Map.Entry<String, JsonNode> stepNode = iterator.next();`
`293`	`293`	`JsonNode stepJson = stepNode.getValue();`
`294`	`294`	`CWLStep stepObject = new CWLStep(extractLabel(stepJson), extractDoc(stepJson),`
`295`		`- extractTypes(stepJson), extractRun(stepJson), getInputs(stepJson),`
`296`		`- getOutputs(stepJson));`
	`295`	`+ extractRun(stepJson), getInputs(stepJson));`
`297`	`296`	`returnMap.put(stepNode.getKey(), stepObject);`
`298`	`297`	`}`
`299`	`298`	`}`