Fix parameter and cwltool bugs

Author: MarkRobbo

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

@@ -444,7 +444,7 @@ private void setFormat(CWLElement inputOutput, String format) {
                 rdfService.addToOntologies(ontModel);
             }
             String formatLabel = rdfService.getOntLabel(format);
-            inputOutput.setType(inputOutput.getType() + " (" + formatLabel + " format)");
+            inputOutput.setType(inputOutput.getType() + " (" + formatLabel + ")");
         } catch (RiotException ex) {
             inputOutput.setType(inputOutput.getType() + " (format)");
         }

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

@@ -114,6 +114,7 @@ private String runCwltoolOnWorkflow(String argument, String workflowUrl) throws
             // Wait for process to complete
             int exitCode = process.waitFor();
             if (exitCode == 0) {
+                inputGobbler.join();
                 return inputGobbler.getContent();
             } else {
                 throw new CWLValidationException(errorGobbler.getContent());

src/main/java/org/commonwl/view/util/StreamGobbler.java

@@ -43,7 +43,7 @@ public void run() {
             InputStreamReader isr = new InputStreamReader(is);
             BufferedReader br = new BufferedReader(isr);
             String line;
-            while ( (line = br.readLine()) != null) {
+            while ((line = br.readLine()) != null) {
                 content += line + lineSeparator;
             }
         } catch (IOException ex) {

src/main/resources/templates/workflow.html

@@ -260,7 +260,7 @@ <h2>Outputs</h2>
                         <tr th:each="output : ${workflow.outputs}">
                             <td th:text="${output.key}">ID</td>
                             <td>
-                                <a th:if="${output.value.format != null}" th:href="@{${output.value.format}}" th:text="${input.value.type}" target="_blank" rel="noopener">Type</a>
+                                <a th:if="${output.value.format != null}" th:href="@{${output.value.format}}" th:text="${output.value.type}" target="_blank" rel="noopener">Type</a>
                                 <span th:if="${output.value.format == null}" th:text="${output.value.type}"></span>
                             </td>
                             <td th:text="${output.value.label}">Label</td>