(quince-science#2962) Correctly process missing run types

When an instrument has multiple file definitions, and at least one has no run type column, uploading new files with missing run types would fail.

WebApp/src/uk/ac/exeter/QuinCe/data/Instrument/FileDefinition.java

@@ -658,9 +658,11 @@ public RunTypeAssignments getRunTypes() {
    * @return The run type values
    */
   public List<String> getRunTypeValues() {
-    List<String> values = null;
+    List<String> values;
 
-    if (null != runTypes) {
+    if (null == runTypes) {
+      values = new ArrayList<String>(0);
+    } else {
       values = new ArrayList<String>(runTypes.size());
       values.addAll(runTypes.keySet());
     }

WebApp/src/uk/ac/exeter/QuinCe/web/files/MissingRunType.java

@@ -1,15 +1,21 @@
 package uk.ac.exeter.QuinCe.web.files;
 
-import java.util.List;
+import java.util.Set;
 
 import uk.ac.exeter.QuinCe.data.Instrument.FileDefinition;
 import uk.ac.exeter.QuinCe.data.Instrument.RunTypes.RunTypeAssignment;
 
 public record MissingRunType(FileDefinition fileDefinition,
-  RunTypeAssignment runType) {
-  protected static boolean contains(List<MissingRunType> list,
+  RunTypeAssignment runType) implements Comparable<MissingRunType> {
+
+  protected static boolean contains(Set<MissingRunType> list,
     FileDefinition fileDefinition, String runName) {
     return list.stream().anyMatch(r -> r.fileDefinition.equals(fileDefinition)
       && r.runType.getRunName().equals(runName));
   }
+
+  @Override
+  public int compareTo(MissingRunType o) {
+    return runType.getRunName().compareTo(o.runType.getRunName());
+  }
 }

WebApp/src/uk/ac/exeter/QuinCe/web/files/MultipleFileUploadBean.java

@@ -1,6 +1,5 @@
 package uk.ac.exeter.QuinCe.web.files;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.TreeSet;
@@ -29,7 +28,7 @@ public class MultipleFileUploadBean extends FileUploadBean {
    */
   private TreeSet<UploadedDataFile> dataFiles = new TreeSet<UploadedDataFile>();
 
-  private List<MissingRunType> unrecognisedRunTypes;
+  private TreeSet<MissingRunType> unrecognisedRunTypes;
 
   @Override
   public void processUploadedFile() {
@@ -131,7 +130,7 @@ private void unsetDataFiles() {
   }
 
   private void buildUnrecognisedRunTypes() {
-    unrecognisedRunTypes = new ArrayList<MissingRunType>();
+    unrecognisedRunTypes = new TreeSet<MissingRunType>();
 
     for (UploadedDataFile file : dataFiles) {
       for (RunTypeAssignment runType : file.getMissingRunTypes()) {
@@ -144,7 +143,7 @@ private void buildUnrecognisedRunTypes() {
     }
   }
 
-  public List<MissingRunType> getUnrecognisedRunTypes() {
+  public TreeSet<MissingRunType> getUnrecognisedRunTypes() {
 
     if (null == unrecognisedRunTypes) {
       buildUnrecognisedRunTypes();