Linking to ontology for file format fields if they exist

Author: MarkRobbo

src/main/java/org/commonwl/view/cwl/CWLElement.java

@@ -33,6 +33,7 @@ public class CWLElement {
     private String label;
     private String doc;
     private String type;
+    private String format;
     private List<String> sourceID;
     private String defaultVal;
 
@@ -64,6 +65,22 @@ public void setType(String type) {
         this.type = type;
     }
 
+    public String getFormat() {
+        return format;
+    }
+
+    public void setFormat(String format) {
+        this.format = format;
+    }
+
+    public List<String> getSourceID() {
+        return sourceID;
+    }
+
+    public void setSourceID(List<String> sourceID) {
+        this.sourceID = sourceID;
+    }
+
     public List<String> getSourceIDs() {
         return sourceID;
     }

src/main/java/org/commonwl/view/cwl/CWLService.java

@@ -268,6 +268,9 @@ public Workflow parseWorkflowWithCwltool(GithubDetails githubInfo,
                 }
             }
 
+            if (input.contains("format")) {
+                wfInput.setFormat(input.get("format").toString());
+            }
             if (input.contains("label")) {
                 wfInput.setLabel(input.get("label").toString());
             }
@@ -326,6 +329,9 @@ public Workflow parseWorkflowWithCwltool(GithubDetails githubInfo,
                 wfOutput.addSourceID(rdfService.stepNameFromURI(url,
                         output.get("src").toString()));
             }
+            if (output.contains("format")) {
+                wfOutput.setFormat(output.get("format").toString());
+            }
             if (output.contains("label")) {
                 wfOutput.setLabel(output.get("label").toString());
             }

src/main/java/org/commonwl/view/cwl/RDFService.java

@@ -105,12 +105,13 @@ public ResultSet getLabelAndDoc(String graphName, String workflowURI) {
     public ResultSet getInputs(String graphName, String workflowURI) {
         ParameterizedSparqlString inputsQuery = new ParameterizedSparqlString();
         inputsQuery.setCommandText(queryCtx +
-                "SELECT ?name ?type ?label ?doc\n" +
+                "SELECT ?name ?type ?format ?label ?doc\n" +
                 "WHERE {\n" +
                 "  GRAPH ?graphName {" +
                 "    ?wf rdf:type cwl:Workflow .\n" +
                 "    ?wf cwl:inputs ?name .\n" +
                 "    OPTIONAL { ?name sld:type ?type }\n" +
+                "    OPTIONAL { ?name cwl:format ?format }\n" +
                 "    OPTIONAL { ?name sld:label|rdfs:label ?label }\n" +
                 "    OPTIONAL { ?name sld:doc|rdfs:comment ?doc }\n" +
                 "  }" +
@@ -129,12 +130,13 @@ public ResultSet getInputs(String graphName, String workflowURI) {
     public ResultSet getOutputs(String graphName, String workflowURI) {
         ParameterizedSparqlString outputsQuery = new ParameterizedSparqlString();
         outputsQuery.setCommandText(queryCtx +
-                "SELECT ?name ?type ?label ?doc\n" +
+                "SELECT ?name ?type ?format ?label ?doc\n" +
                 "WHERE {\n" +
                 "  GRAPH ?graphName {" +
                 "    ?wf rdf:type cwl:Workflow .\n" +
                 "    ?wf cwl:outputs ?name .\n" +
                 "    OPTIONAL { ?name sld:type ?type }\n" +
+                "    OPTIONAL { ?name cwl:format ?format }\n" +
                 "    OPTIONAL { ?name sld:label|rdfs:label ?label }\n" +
                 "    OPTIONAL { ?name sld:doc|rdfs:comment ?doc }\n" +
                 "  }" +

src/main/java/org/commonwl/view/graphviz/ModelDotWriter.java

@@ -144,10 +144,12 @@ private void writeSteps(Workflow workflow) throws IOException {
         // Workaround to force outputs to lowest ranking, see #104
         writeLine("");
         writeLine("  // Invisible links to force outputs to be at lowest rank");
-        for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
-            writeLine("  \"" + step.getKey() + "\" -> \"" +
-                    workflow.getOutputs().keySet().iterator().next() +
-                    "\" [style=invis];");
+        if (workflow.getOutputs().size() > 0) {
+            for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
+                writeLine("  \"" + step.getKey() + "\" -> \"" +
+                        workflow.getOutputs().keySet().iterator().next() +
+                        "\" [style=invis];");
+            }
         }
 
     }

src/main/resources/templates/workflow.html

@@ -198,7 +198,9 @@ <h2>Inputs</h2>
                     <tbody>
                         <tr th:each="input : ${workflow.inputs}">
                             <td th:text="${input.key}">ID</td>
-                            <td th:text="${input.value.type}">Type</td>
+                            <td>
+                                <a th:href="@{${input.value.format}}" th:text="${input.value.type}">Type</a>
+                            </td>
                             <td th:text="${input.value.label}">Label</td>
                             <td>
                                 <p th:if="${input.value.doc != null}" th:utext="${#strings.replace( #strings.escapeXml(input.value.doc),T(java.lang.System).getProperty('line.separator')+T(java.lang.System).getProperty('line.separator'),'&lt;br /&gt;&lt;br /&gt;')}">Description</p>
@@ -255,7 +257,9 @@ <h2>Outputs</h2>
                     <tbody>
                         <tr th:each="output : ${workflow.outputs}">
                             <td th:text="${output.key}">ID</td>
-                            <td th:text="${output.value.type}">Type</td>
+                            <td>
+                                <a th:href="@{${output.value.format}}" th:text="${output.value.type}" target="_blank" rel="noopener">Type</a>
+                            </td>
                             <td th:text="${output.value.label}">Label</td>
                             <td>
                                 <p th:if="${output.value.doc != null}" th:utext="${#strings.replace(#strings.escapeXml(output.value.doc),T(java.lang.System).getProperty('line.separator')+T(java.lang.System).getProperty('line.separator'),'&lt;br /&gt;&lt;br /&gt;')}">Description</p>