Add support for source and default parameters within steps

Author: Mark Robinson

src/main/java/org/commonwl/viewer/domain/CWLCollection.java

@@ -173,23 +173,28 @@ public Workflow getWorkflow() {
      * @param cwlDoc The document to get steps for
      * @return A map of step IDs and details related to them
      */
-    private Map<String, CWLElement> getSteps(JsonNode cwlDoc) {
+    private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
         if (cwlDoc != null && cwlDoc.has("steps")) {
-            Map<String, CWLElement> returnMap = new HashMap<>();
+            Map<String, CWLStep> returnMap = new HashMap<>();
 
             JsonNode steps = cwlDoc.get("steps");
             if (steps.getClass() == ArrayNode.class) {
                 // Explicit ID and other fields within each input list
                 for (JsonNode step : steps) {
                     String id = step.get("id").asText();
-                    returnMap.put(id, getDetails(step));
+                    CWLStep stepObject = new CWLStep(extractID(step), extractDoc(step),
+                            extractTypes(step), getInputs(step), getOutputs(step));
+                    returnMap.put(id, stepObject);
                 }
             } else if (steps.getClass() == ObjectNode.class) {
                 // ID is the key of each object
                 Iterator<Map.Entry<String, JsonNode>> iterator = steps.fields();
                 while (iterator.hasNext()) {
                     Map.Entry<String, JsonNode> stepNode = iterator.next();
-                    returnMap.put(stepNode.getKey(), getDetails(stepNode.getValue()));
+                    JsonNode stepJson = stepNode.getValue();
+                    CWLStep stepObject = new CWLStep(extractID(stepJson), extractDoc(stepJson),
+                            extractTypes(stepJson), getInputs(stepJson), getOutputs(stepJson));
+                    returnMap.put(stepNode.getKey(), stepObject);
                 }
             }
 
@@ -263,9 +268,8 @@ private CWLElement getDetails(JsonNode inputOutput) {
             } else {
                 details.setLabel(extractLabel(inputOutput));
                 details.setDoc(extractDoc(inputOutput));
-
-                // OutputSource is only for outputs of the overall workflow
                 details.setSourceID(extractOutputSource(inputOutput));
+                details.setDefaultVal(extractDefault(inputOutput));
 
                 // Type is only for inputs
                 if (inputOutput.has("type")) {
@@ -302,6 +306,18 @@ private String extractLabel(JsonNode node) {
         return null;
     }
 
+    /**
+     * Extract the default value from a node
+     * @param node The node to have the label extracted from
+     * @return The string for the default value of the node
+     */
+    private String extractDefault(JsonNode node) {
+        if (node != null && node.has("default")) {
+            return node.get("default").asText();
+        }
+        return null;
+    }
+
     /**
      * Extract the outputSource from a node
      * @param node The node to have the label extracted from

src/main/java/org/commonwl/viewer/domain/CWLElement.java

@@ -28,6 +28,7 @@ public class CWLElement {
     private String doc;
     private String type;
     private String sourceID;
+    private String defaultVal;
 
     public String getLabel() {
         return label;
@@ -61,4 +62,11 @@ public void setSourceID(String sourceID) {
         this.sourceID = sourceID;
     }
 
+    public String getDefaultVal() {
+        return defaultVal;
+    }
+
+    public void setDefaultVal(String defaultVal) {
+        this.defaultVal = defaultVal;
+    }
 }

src/main/java/org/commonwl/viewer/domain/CWLStep.java

@@ -0,0 +1,84 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.commonwl.viewer.domain;
+
+import java.util.Map;
+
+/**
+ * Represents a step of a workflow
+ */
+public class CWLStep {
+
+    private String label;
+    private String doc;
+    private String type;
+    private Map<String, CWLElement> inputs;
+    private Map<String, CWLElement> outputs;
+
+    public CWLStep(String label, String doc, String type,
+                   Map<String, CWLElement> inputs, Map<String, CWLElement> outputs) {
+        this.label = label;
+        this.doc = doc;
+        this.type = type;
+        this.inputs = inputs;
+        this.outputs = outputs;
+    }
+
+    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;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public void setType(String type) {
+        this.type = type;
+    }
+
+    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;
+    }
+
+}

src/main/java/org/commonwl/viewer/domain/Workflow.java

@@ -60,13 +60,13 @@ public class Workflow {
     private String doc;
     private Map<String, CWLElement> inputs;
     private Map<String, CWLElement> outputs;
-    private Map<String, CWLElement> steps;
+    private Map<String, CWLStep> steps;
 
     // DOT graph of the contents
     private String dotGraph;
 
     public Workflow(String label, String doc, Map<String, CWLElement> inputs,
-                    Map<String, CWLElement> outputs, Map<String, CWLElement> steps) {
+                    Map<String, CWLElement> outputs, Map<String, CWLStep> steps) {
         this.label = label;
         this.doc = doc;
         this.inputs = inputs;
@@ -122,11 +122,11 @@ public void setOutputs(Map<String, CWLElement> outputs) {
         this.outputs = outputs;
     }
 
-    public Map<String, CWLElement> getSteps() {
+    public Map<String, CWLStep> getSteps() {
         return steps;
     }
 
-    public void setSteps(Map<String, CWLElement> steps) {
+    public void setSteps(Map<String, CWLStep> steps) {
         this.steps = steps;
     }
 

src/main/java/org/commonwl/viewer/services/DotWriter.java

@@ -20,6 +20,7 @@
 package org.commonwl.viewer.services;
 
 import org.commonwl.viewer.domain.CWLElement;
+import org.commonwl.viewer.domain.CWLStep;
 import org.commonwl.viewer.domain.Workflow;
 
 import java.io.IOException;
@@ -152,14 +153,30 @@ private void writeOutputs(Workflow workflow) throws IOException {
      */
     private void writeSteps(Workflow workflow) throws IOException {
         // Write each of the steps as a node
-        for (Map.Entry<String, CWLElement> step : workflow.getSteps().entrySet()) {
+        for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
             writeLine("  \"" + step.getKey() + "\"");
         }
 
         // Write the links between nodes
         // Write links between outputs and penultimate steps
         for (Map.Entry<String, CWLElement> output : workflow.getOutputs().entrySet()) {
-            writeLine("  \"" + output.getValue().getSourceID() + "\" -> \"" + output.getKey() + "\"");
+            writeLine("  \"" + output.getValue().getSourceID() + "\" -> \"" + output.getKey() + "\";");
+        }
+
+        // Write links between the remaining steps
+        int defaultCount = 0;
+        for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
+            for (Map.Entry<String, CWLElement> input : step.getValue().getInputs().entrySet()) {
+                String sourceID = input.getValue().getSourceID();
+                String defaultVal = input.getValue().getDefaultVal();
+                if (sourceID != null) {
+                    writeLine("  \"" + sourceID + "\" -> \"" + step.getKey() + "\";");
+                } else if (defaultVal != null) {
+                    defaultCount++;
+                    writeLine("  \"default" + defaultCount + "\" [label=\"" + defaultVal + "\", fillcolor=\"#D5AEFC\"]");
+                    writeLine("  \"default" + defaultCount + "\" -> \"" + step.getKey() + "\";");
+                }
+            }
         }
     }