Allow non-ontology formats to be linked for inputs and outputs

Author: MarkRobbo

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

@@ -33,6 +33,7 @@
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Statement;
 import org.apache.jena.rdf.model.StmtIterator;
+import org.apache.jena.riot.RiotException;
 import org.commonwl.view.docker.DockerService;
 import org.commonwl.view.github.GitHubService;
 import org.commonwl.view.github.GithubDetails;
@@ -268,15 +269,7 @@ public Workflow parseWorkflowWithCwltool(GithubDetails githubInfo,
 
             if (input.contains("format")) {
                 String format = input.get("format").toString();
-                wfInput.setFormat(format);
-
-                if (!rdfService.ontPropertyExists(format)) {
-                    Model ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
-                    ontModel.read(format, null, "RDF/XML");
-                    rdfService.addToOntologies(ontModel);
-                }
-                String formatLabel = rdfService.getOntLabel(format);
-                wfInput.setType(wfInput.getType() + " (" + formatLabel + " format)");
+                setFormat(wfInput, format);
             }
             if (input.contains("label")) {
                 wfInput.setLabel(input.get("label").toString());
@@ -338,15 +331,7 @@ public Workflow parseWorkflowWithCwltool(GithubDetails githubInfo,
             }
             if (output.contains("format")) {
                 String format = output.get("format").toString();
-                wfOutput.setFormat(format);
-
-                if (!rdfService.ontPropertyExists(format)) {
-                    Model ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
-                    ontModel.read(format, null, "RDF/XML");
-                    rdfService.addToOntologies(ontModel);
-                }
-                String formatLabel = rdfService.getOntLabel(format);
-                wfOutput.setType(wfOutput.getType() + " (" + formatLabel + " format)");
+                setFormat(wfOutput, format);
             }
             if (output.contains("label")) {
                 wfOutput.setLabel(output.get("label").toString());
@@ -492,6 +477,26 @@ public WorkflowOverview getWorkflowOverview(GithubDetails githubInfo) throws IOE
 
     }
 
+    /**
+     * Set the format for an input or output, handling ontologies
+     * @param inputOutput The input or output CWL Element
+     * @param format The format URI
+     */
+    private void setFormat(CWLElement inputOutput, String format) {
+        inputOutput.setFormat(format);
+        try {
+            if (!rdfService.ontPropertyExists(format)) {
+                Model ontModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+                ontModel.read(format, null, "RDF/XML");
+                rdfService.addToOntologies(ontModel);
+            }
+            String formatLabel = rdfService.getOntLabel(format);
+            inputOutput.setType(inputOutput.getType() + " (" + formatLabel + " format)");
+        } catch (RiotException ex) {
+            inputOutput.setType(inputOutput.getType() + " (format)");
+        }
+    }
+
     /**
      * Convert RDF URI for a type to a name
      * @param uri The URI for the type

src/main/resources/templates/workflow.html

@@ -199,7 +199,7 @@ <h2>Inputs</h2>
                         <tr th:each="input : ${workflow.inputs}">
                             <td th:text="${input.key}">ID</td>
                             <td>
-                                <a th:href="@{${input.value.format}}" th:text="${input.value.type}">Type</a>
+                                <a th:href="@{${input.value.format}}" th:text="${input.value.type}" target="_blank" rel="noopener">Type</a>
                             </td>
                             <td th:text="${input.value.label}">Label</td>
                             <td>