Displaying steps in workflows on output page

Currently only draft versions of CWL supported

Author: Mark Robinson

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

@@ -181,18 +181,17 @@ private Map<String, CWLStep> getSteps(JsonNode cwlDoc) {
             if (steps.getClass() == ArrayNode.class) {
                 // Explicit ID and other fields within each input list
                 for (JsonNode step : steps) {
-                    String id = step.get("id").asText();
-                    CWLStep stepObject = new CWLStep(extractID(step), extractDoc(step),
+                    CWLStep stepObject = new CWLStep(extractLabel(step), extractDoc(step),
                             extractTypes(step), getInputs(step), getOutputs(step));
-                    returnMap.put(id, stepObject);
+                    returnMap.put(extractID(step), 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();
                     JsonNode stepJson = stepNode.getValue();
-                    CWLStep stepObject = new CWLStep(extractID(stepJson), extractDoc(stepJson),
+                    CWLStep stepObject = new CWLStep(extractLabel(stepJson), extractDoc(stepJson),
                             extractTypes(stepJson), getInputs(stepJson), getOutputs(stepJson));
                     returnMap.put(stepNode.getKey(), stepObject);
                 }

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

@@ -166,15 +166,19 @@ 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()) {
-            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() + "\";");
+            if (step.getValue().getInputs() != null) {
+                for (Map.Entry<String, CWLElement> input : step.getValue().getInputs().entrySet()) {
+                    String sourceID = input.getValue().getSourceID();
+                    String defaultVal = input.getValue().getDefaultVal();
+                    if (sourceID != null) {
+                        // Regular link from source step to destination step
+                        writeLine("  \"" + sourceID + "\" -> \"" + step.getKey() + "\";");
+                    } else if (defaultVal != null) {
+                        // New node for a default value to be used as the source
+                        defaultCount++;
+                        writeLine("  \"default" + defaultCount + "\" [label=\"" + defaultVal + "\", fillcolor=\"#D5AEFC\"]");
+                        writeLine("  \"default" + defaultCount + "\" -> \"" + step.getKey() + "\";");
+                    }
                 }
             }
         }

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

@@ -27,7 +27,6 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import java.io.IOException;
 import java.util.Date;
 
 @Service
@@ -37,15 +36,12 @@ public class WorkflowFactory {
 
     private final GitHubService githubService;
     private final ROBundleFactory ROBundleFactory;
-    private final WorkflowRepository workflowRepository;
 
     @Autowired
     public WorkflowFactory(GitHubService githubService,
-                           ROBundleFactory ROBundleFactory,
-                           WorkflowRepository workflowRepository) {
+                           ROBundleFactory ROBundleFactory) {
         this.githubService = githubService;
         this.ROBundleFactory = ROBundleFactory;
-        this.workflowRepository = workflowRepository;
     }
 
     /**
@@ -77,7 +73,7 @@ public Workflow workflowFromGithub(GithubDetails githubInfo) {
                 logger.error("No workflow could be found");
             }
         } catch (Exception ex) {
-            logger.error(ex.getMessage());
+            logger.error("Error creating workflow: " + ex.getMessage());
         }
 
         return null;

src/main/resources/static/bower_components/graphviz-d3-renderer/.bower.json

@@ -1,6 +1,6 @@
 {
   "name": "graphviz-d3-renderer",
-  "version": "0.9.20",
+  "version": "0.9.21",
   "dependencies": {
     "requirejs": "2.1.15",
     "d3": "3.5.3",
@@ -46,11 +46,11 @@
     "karma.conf.js"
   ],
   "homepage": "https://github.com/mstefaniuk/graph-viz-d3-js",
-  "_release": "0.9.20",
+  "_release": "0.9.21",
   "_resolution": {
     "type": "version",
-    "tag": "0.9.20",
-    "commit": "077cadb3005a37e6c69a9873520dd3f8cde72206"
+    "tag": "0.9.21",
+    "commit": "9cba7e58b832f59e51271f8f98367ab676ef206f"
   },
   "_source": "https://github.com/mstefaniuk/graph-viz-d3-js.git",
   "_target": "^0.9.18",

src/main/resources/templates/workflow.html

@@ -167,6 +167,23 @@ <h2>Outputs</h2>
                     </tr>
                 </tbody>
             </table>
+            <h2>Steps</h2>
+            <table class="table table-striped">
+                <thead>
+                <th>ID</th>
+                <th>Type</th>
+                <th>Label</th>
+                <th>Doc</th>
+                </thead>
+                <tbody>
+                <tr th:each="step : ${workflow.steps}">
+                    <td th:text="${step.key}">ID</td>
+                    <td th:text="${step.value.type}">Type</td>
+                    <td th:text="${step.value.label}">Label</td>
+                    <td th:text="${step.value.doc}">Description</td>
+                </tr>
+                </tbody>
+            </table>
         </div>
     </div>
 </div>