Add simple step parsing and storage

Closes #31

Author: Mark Robinson

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

@@ -40,8 +40,11 @@ public class CWLCollection {
     private GitHubService githubService;
     private GithubDetails githubInfo;
 
-    private List<JsonNode> cwlDocs = new ArrayList<>();
-    private int mainWorkflowIndex = -1;
+    // Maps of ID to associated JSON
+    private Map<String, JsonNode> cwlDocs = new HashMap<>();
+
+    // The main workflow
+    private String mainWorkflowKey;
 
     /**
      * Creates a new collection of CWL files from a Github repository
@@ -99,7 +102,7 @@ private void addDocs(List<RepositoryContents> repoContents) throws IOException {
                         JsonNode cwlFile = mapper.valueToTree(reader.load(fileContent));
 
                         // Add document to those being considered
-                        addDoc(cwlFile);
+                        addDoc(cwlFile, repoContent.getName());
                     }
                 }
 
@@ -110,17 +113,18 @@ private void addDocs(List<RepositoryContents> repoContents) throws IOException {
     /**
      * Adds a document to the group of those being parsed
      * @param newDoc The document to be added
+     * @param fileName The name of the file this document has come from
      */
-    private void addDoc(JsonNode newDoc) {
+    private void addDoc(JsonNode newDoc, String fileName) {
         // Make sure that this document is only one object and not multiple under a $graph directive
         if (newDoc.has("$graph")) {
             // Add each of the sub documents
             for (JsonNode jsonNode : newDoc.get("$graph")) {
-                cwlDocs.add(jsonNode);
+                cwlDocs.put(extractID(jsonNode), jsonNode);
             }
         } else {
-            // Otherwise just add the document itself
-            cwlDocs.add(newDoc);
+            // Otherwise just add the document itself with ID of document name
+            cwlDocs.put(fileName, newDoc);
         }
     }
 
@@ -130,9 +134,9 @@ private void addDoc(JsonNode newDoc) {
     private void findMainWorkflow() {
         // Find the first workflow we come across
         // TODO: Consider relationship between run: parameters to better discover this
-        for (int i=0; i < cwlDocs.size(); i++) {
-            if (cwlDocs.get(i).get("class").asText().equals("Workflow")) {
-                mainWorkflowIndex = 0;
+        for (Map.Entry<String, JsonNode> doc : cwlDocs.entrySet()) {
+            if (doc.getValue().get("class").asText().equals("Workflow")) {
+                mainWorkflowKey = doc.getKey();
                 return;
             }
         }
@@ -143,49 +147,83 @@ private void findMainWorkflow() {
      * @return A Workflow object representing the main workflow amongst the files added
      */
     public Workflow getWorkflow() {
-        if (mainWorkflowIndex < 0) {
+        // Get the main workflow
+        if (mainWorkflowKey == null) {
             findMainWorkflow();
 
             // If it is still less than 0 there is no workflow to be found
-            if (mainWorkflowIndex < 0) {
+            if (mainWorkflowKey == null) {
                 return null;
             }
         }
-        JsonNode mainWorkflow = cwlDocs.get(mainWorkflowIndex);
-        return new Workflow(extractLabel(mainWorkflow), extractDoc(mainWorkflow),
-                            getInputs(mainWorkflow), getOutputs(mainWorkflow));
+        JsonNode mainWorkflow = cwlDocs.get(mainWorkflowKey);
+
+        // Use ID/filename for label if there is no defined one
+        String label = extractLabel(mainWorkflow);
+        if (label == null) {
+            label = mainWorkflowKey;
+        }
+
+        return new Workflow(label, extractDoc(mainWorkflow), getInputs(mainWorkflow),
+                            getOutputs(mainWorkflow), getSteps(mainWorkflow));
     }
 
     /**
-     * Get a list of the inputs for a particular document
+     * Get the steps for a particular document
+     * @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) {
+        if (cwlDoc != null && cwlDoc.has("steps")) {
+            Map<String, CWLElement> 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));
+                }
+            } 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()));
+                }
+            }
+
+            return returnMap;
+        }
+        return null;
+    }
+
+    /**
+     * Get a the inputs for a particular document
      * @param cwlDoc The document to get inputs for
      * @return A map of input IDs and details related to them
      */
     private Map<String, CWLElement> getInputs(JsonNode cwlDoc) {
-        if (cwlDoc != null) {
-            if (cwlDoc.has("inputs")) {
-                return getInputsOutputs(cwlDoc.get("inputs"));
-            }
+        if (cwlDoc != null && cwlDoc.has("inputs")) {
+            return getInputsOutputs(cwlDoc.get("inputs"));
         }
         return null;
     }
 
     /**
-     * Get a list of the outputs for a particular document
+     * Get the outputs for a particular document
      * @param cwlDoc The document to get outputs for
      * @return A map of output IDs and details related to them
      */
     private Map<String, CWLElement> getOutputs(JsonNode cwlDoc) {
-        if (cwlDoc != null) {
-            if (cwlDoc.has("outputs")) {
-                return getInputsOutputs(cwlDoc.get("outputs"));
-            }
+        if (cwlDoc != null && cwlDoc.has("outputs")) {
+            return getInputsOutputs(cwlDoc.get("outputs"));
         }
         return null;
     }
 
     /**
-     * Get a list of inputs or outputs from an inputs or outputs node
+     * Get inputs or outputs from an inputs or outputs node
      * @param inputsOutputs The inputs or outputs node
      * @return A map of input IDs and details related to them
      */
@@ -203,8 +241,7 @@ private Map<String, CWLElement> getInputsOutputs(JsonNode inputsOutputs) {
             Iterator<Map.Entry<String, JsonNode>> iterator = inputsOutputs.fields();
             while (iterator.hasNext()) {
                 Map.Entry<String, JsonNode> inputOutputNode = iterator.next();
-                String outputID = inputOutputNode.getKey();
-                returnMap.put(outputID, getDetails(inputOutputNode.getValue()));
+                returnMap.put(inputOutputNode.getKey(), getDetails(inputOutputNode.getValue()));
             }
         }
 
@@ -243,16 +280,26 @@ private CWLElement getDetails(JsonNode inputOutput) {
         return null;
     }
 
+    /**
+     * Extract the id from a node
+     * @param node The node to have the id extracted from
+     * @return The string for the id of the node
+     */
+    private String extractID(JsonNode node) {
+        if (node != null && node.has("id")) {
+            return node.get("id").asText();
+        }
+        return null;
+    }
+
     /**
      * Extract the label from a node
      * @param node The node to have the label extracted from
      * @return The string for the label of the node
      */
     private String extractLabel(JsonNode node) {
-        if (node != null) {
-            if (node.has("label")) {
-                return node.get("label").asText();
-            }
+        if (node != null && node.has("label")) {
+            return node.get("label").asText();
         }
         return null;
     }
@@ -330,5 +377,4 @@ private String extractTypes(JsonNode typeNode) {
         }
         return null;
     }
-
 }

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

@@ -60,15 +60,18 @@ public class Workflow {
     private String doc;
     private Map<String, CWLElement> inputs;
     private Map<String, CWLElement> outputs;
+    private Map<String, CWLElement> steps;
 
     // DOT graph of the contents
     private String dotGraph;
 
-    public Workflow(String label, String doc, Map<String, CWLElement> inputs, Map<String, CWLElement> outputs) {
+    public Workflow(String label, String doc, Map<String, CWLElement> inputs,
+                    Map<String, CWLElement> outputs, Map<String, CWLElement> steps) {
         this.label = label;
         this.doc = doc;
         this.inputs = inputs;
         this.outputs = outputs;
+        this.steps = steps;
 
         // Create a DOT graph for this workflow and store it
         StringWriter graphWriter = new StringWriter();
@@ -119,6 +122,14 @@ public void setOutputs(Map<String, CWLElement> outputs) {
         this.outputs = outputs;
     }
 
+    public Map<String, CWLElement> getSteps() {
+        return steps;
+    }
+
+    public void setSteps(Map<String, CWLElement> steps) {
+        this.steps = steps;
+    }
+
     public String getRoBundle() {
         return roBundle;
     }

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

@@ -93,6 +93,9 @@ public void writeGraph(Workflow workflow) throws IOException {
         // Write outputs as a subgraph
         writeOutputs(workflow);
 
+        // Write steps as nodes
+        writeSteps(workflow);
+
         // End graph
         writeLine("}");
     }
@@ -142,6 +145,18 @@ private void writeOutputs(Workflow workflow) throws IOException {
         writeLine("  }");
     }
 
+    /**
+     * Writes a set of steps from a workflow to the Writer
+     * @param workflow The workflow to get the steps from
+     * @throws IOException Any errors in writing which may have occurred
+     */
+    private void writeSteps(Workflow workflow) throws IOException {
+        // Write each of the steps as a node
+        for (Map.Entry<String, CWLElement> step : workflow.getSteps().entrySet()) {
+            writeLine(step.getKey());
+        }
+    }
+
     /**
      * Writes a single input or output to the Writer
      * @param inputOutput The input or output

src/main/java/org/commonwl/viewer/web/WorkflowController.java

@@ -37,7 +37,6 @@
 import javax.servlet.http.HttpServletResponse;
 import javax.validation.Valid;
 import java.io.File;
-import java.io.IOException;
 
 @Controller
 public class WorkflowController {