diff --git a/WebApp/WebContent/data_file/upload.xhtml b/WebApp/WebContent/data_file/upload.xhtml
index c51ecc28c..e5767dc60 100644
--- a/WebApp/WebContent/data_file/upload.xhtml
+++ b/WebApp/WebContent/data_file/upload.xhtml
@@ -13,21 +13,109 @@
   <ui:define name="pageTitle">#{fileUpload.currentInstrument.name} - Upload Data Files</ui:define>
   <ui:define name="content">
     <h:form id="uploadForm" method="post" charset="utf8">
+      <p:remoteCommand name="processAllFiles"
+        action="#{fileUpload.processAllFiles}"
+        process="@this"
+        update="unrecognisedRunTypeCount missingRunTypes"
+        oncomplete="allFilesProcessed()" />
+
+      <p:remoteCommand name="updateFileList"
+        action="#{fileUpload.noop}"
+        process="@this"
+        update="fileList"/>
+
       <div class="pageBlock">
         <div id="uploadFile">
           <p:messages id="messages" closable="true">
             <p:autoUpdate/>
           </p:messages>
           <div id="messages" class="error listBox hidden"></div>
-          <p:outputLabel value="Select a file to upload" />
-          <p:fileUpload listener="#{fileUpload.handleFileUpload}"
-            mode="advanced" auto="false" oncomplete="extractNext()"
-            multiple="true" update="fileDetails" widgetVar="fileUploadWidget" />
-          <p:outputPanel id="fileDetails"
-            styleClass="#{fileUpload.displayClass}">
-            <p:remoteCommand name="extractNext"
-              action="#{fileUpload.extractNext()}" process="@this"
-              update="fileList storeFileButton" />
+
+          <p:dialog widgetVar="extractProgress" modal="true" closable="false"
+            header="Extracting files" width="50%">
+            <p:progressBar widgetVar="processedProgress"
+              value="#{fileUpload.progress.progress}"
+              ajax="true" interval="1500">
+              <p:ajax event="complete" />
+            </p:progressBar>
+          </p:dialog>
+
+          <h:inputHidden id="unrecognisedRunTypeCount"
+            value="#{fileUpload.unrecognisedRunTypeCount}"/>
+
+          <p:dialog widgetVar="runTypesDialog" modal="true"
+            closable="false"
+            header="Unrecognised Run Types Found">
+            <div id="runTypesDialogContent">
+              <p:fieldset legend="New Run Types">
+                <div class="instructions">
+                  Found unrecognised run types.
+                  Please assign them using the menu options.
+                </div>
+
+                <p:dataTable id="missingRunTypes" var="runType"
+                  value="#{fileUpload.unrecognisedRunTypes}"
+                  rowIndexVar="rowIndex" tableStyle="table-layout: auto;">
+                  <p:column styleClass="label">
+                    <f:facet name="header">Run Type</f:facet>
+                    #{runType.runType().runName}
+                  </p:column>
+                  <p:column>
+                    <f:facet name="header">Category</f:facet>
+                    <p:selectOneMenu
+                    widgetVar="runType_#{rowIndex}"
+                    value="#{runType.runType().categoryCode}"
+                    onchange="runTypeChanged(#{rowIndex})">
+                    <f:selectItems
+                      value="#{fileUpload.runTypeCategories}"
+                      var="category" itemValue="#{category.type}"
+                      itemLabel="#{category.description}" />
+                  </p:selectOneMenu>
+                  </p:column>
+                  <p:column>
+                    <p:selectOneMenu
+                      widgetVar="alias_#{rowIndex}"
+                      value="#{runType.runType().aliasTo}" styleClass="hidden">
+                      <f:selectItems
+                        value="#{fileUpload.getRunTypeValuesWithExclusion(runType.runType().runName)}"
+                        var="runTypeAlias" />
+                    </p:selectOneMenu>
+                  </p:column>
+                </p:dataTable>
+                <h:panelGrid columns="1" styleClass="buttonPanel">
+                  <p:commandButton icon="pi pi-save"
+                    action="#{fileUpload.updateRunTypes}"
+                    process="@this missingRunTypes"
+                    title="Save Run Types" value="Save Run Types"
+                    onclick="PF('runTypesDialog').hide()"
+                    update="fileList" oncomplete="extractFiles()" />
+                </h:panelGrid>
+              </p:fieldset>
+              <p:fieldset legend="Existing Run Types">
+                <table class="shrink noborder">
+                  <ui:repeat var="runType"
+                    value="#{fileUpload.allRunTypes}">
+                    <tr>
+                      <td class="labels"><h:outputText
+                          value="#{runType.runName}" /></td>
+                      <td style="white-space: nowrap"><h:outputText
+                          value="#{runType.assignmentText}" /></td>
+                    </tr>
+                  </ui:repeat>
+                </table>
+              </p:fieldset>
+            </div>
+          </p:dialog>
+
+          <p:outputPanel id="uploadFiles">
+            <p:outputLabel value="Select files to upload" />
+            <p:fileUpload listener="#{fileUpload.handleFileUpload}"
+              mode="advanced" auto="true" oncomplete="fileUploaded()"
+              sequential="true" multiple="true"
+              widgetVar="fileUploadWidget" />
+          </p:outputPanel>
+
+          <p:outputPanel id="fileDetails" styleClass="hidden">
             <p:dialog id="msgDialog" widgetVar="msgDialog"
               header="Errors and messages" minHeight="40">
               <p:scrollPanel style="height:200px" mode="native">
@@ -42,107 +130,34 @@
                 <h:outputText value="#{uploadedFile.name}" />
               </p:column>
               <p:column headerText="Start date" styleClass="dateTimeCell">
-                <ui:fragment rendered="#{!uploadedFile.processed}">
-                  <div class="tablespinner loading" />
-                </ui:fragment>
-                <h:outputText escape="false" value="#{uploadedFile.startDate}"
-                  rendered="#{uploadedFile.processed}">
+                <h:outputText escape="false" value="#{uploadedFile.startDate}">
                   <f:convertDateTime pattern="#{fileUpload.longDateFormat}" />
                 </h:outputText>
               </p:column>
               <p:column headerText="End date" styleClass="dateTimeCell">
-                <ui:fragment rendered="#{!uploadedFile.processed}">
-                  <div class="tablespinner loading" />
-                </ui:fragment>
-                <h:outputText escape="false" value="#{uploadedFile.endDate}"
-                  rendered="#{uploadedFile.processed}">
+                <h:outputText escape="false" value="#{uploadedFile.endDate}">
                   <f:convertDateTime pattern="#{fileUpload.longDateFormat}" />
                 </h:outputText>
               </p:column>
               <p:column headerText="No. of records" styleClass="rightCell" style="width: 140px">
-                <ui:fragment rendered="#{!uploadedFile.processed}">
-                  <div class="tablespinner loading" />
-                </ui:fragment>
-                <h:outputText value="#{uploadedFile.dataFile.recordCount}"
-                  rendered="#{uploadedFile.processed}" />
+                <h:outputText value="#{uploadedFile.dataFile.recordCount}"/>
                 <h:outputText value=" (Updated file)"
-                  rendered="#{uploadedFile.processed} and #{uploadedFile.replacement}"
+                  rendered="#{uploadedFile.replacement}"
                   styleClass="note"></h:outputText>
               </p:column>
               <p:column headerText="Store file to database"
                 styleClass="centeredCell" style="width: 240px">
-                <ui:fragment rendered="#{!uploadedFile.processed}">
-                  <div class="tablespinner loading" />
-                </ui:fragment>
                 <p:selectBooleanCheckbox id="fileStoreCheckbox"
-                  rendered="#{uploadedFile.processed and !uploadedFile.hasMessages}"
+                  rendered="#{!uploadedFile.hasMessages}"
                   value="#{uploadedFile.store}" />
                 <p:commandButton
-                  rendered="#{uploadedFile.processed and uploadedFile.hasMessages}"
+                  rendered="#{uploadedFile.hasMessages}"
                   icon="pi pi-exclamation-triangle"
                   onclick="renderMessages($(this).data('messages'))"
                   title="Errors" value="Errors">
                   <f:passThroughAttribute name="data-messages"
                     value="#{uploadedFile.messages}" />
                 </p:commandButton>
-                <ui:fragment
-                  rendered="#{uploadedFile.processed and uploadedFile.hasUnrecognisedRunTypes}">
-                  <p:commandButton icon="pi pi-plus"
-                    onclick="PF('runTypesDialog_#{rowIndex}').show()"
-                    title="Unrecognised Run Types Found"
-                    value="Unrecognised Run Types Found" />
-                  <p:dialog widgetVar="runTypesDialog_#{rowIndex}" modal="true">
-                    <p:fieldset legend="Unrecognised Run Types">
-                      <div class="instructions">This file contained
-                        unrecognised Run Types. Please assign them using the
-                        menu options.</div>
-                      <table class="shrink noborder">
-                        <ui:repeat var="runType"
-                          value="#{uploadedFile.dataFile.missingRunTypes}"
-                          varStatus="missingRunTypeStatus">
-                          <tr>
-                            <td class="labelsNoPad"><h:outputText
-                                value="#{runType.runName}" /></td>
-                            <td><p:selectOneMenu
-                                widgetVar="missingRunType_#{rowIndex}_#{missingRunTypeStatus.index}"
-                                value="#{runType.categoryCode}"
-                                onchange="runTypeChanged(#{rowIndex}, #{missingRunTypeStatus.index})">
-                                <f:selectItems
-                                  value="#{fileUpload.runTypeCategories}"
-                                  var="category" itemValue="#{category.type}"
-                                  itemLabel="#{category.description}" />
-                              </p:selectOneMenu></td>
-                            <td><p:selectOneMenu
-                                widgetVar="alias_#{rowIndex}_#{missingRunTypeStatus.index}"
-                                value="#{runType.aliasTo}" styleClass="hidden">
-                                <f:selectItems
-                                  value="#{uploadedFile.dataFile.getRunTypeValuesWithExclusion(runType.runName)}"
-                                  var="runTypeAlias" />
-                              </p:selectOneMenu></td>
-                          </tr>
-                        </ui:repeat>
-                      </table>
-                      <p:commandButton icon="pi pi-save"
-                        actionListener="#{fileUpload.updateRunTypes(uploadedFile.name)}"
-                        title="Save Run Types" value="Save Run Types"
-                        onclick="PF('runTypesDialog_#{rowIndex}').hide()"
-                        update="fileList" oncomplete="reprocessUploadedFiles()" />
-                    </p:fieldset>
-                    <p:fieldset legend="These run types are already defined">
-                      <table class="shrink noborder">
-                        <ui:repeat var="runType"
-                          value="#{uploadedFile.dataFile.fileDefinition.runTypes.values()}">
-                          <tr>
-                            <td class="labels"><h:outputText
-                                value="#{runType.runName}" /></td>
-                            <td><h:outputText
-                                value="#{runType.assignmentText}" /></td>
-                          </tr>
-                        </ui:repeat>
-                      </table>
-                    </p:fieldset>
-                  </p:dialog>
-                </ui:fragment>
               </p:column>
             </p:dataTable>
           </p:outputPanel>
@@ -151,6 +166,7 @@
       <h:panelGrid columns="1" cellpadding="5" class="buttonPanel">
         <p:commandButton id="storeFileButton"
           styleClass="#{fileUpload.storeFileButtonClass}" icon="pi pi-save"
+          process="@this"
           title="Store marked files to database"
           value="Store marked files to database"
           actionListener="#{fileUpload.store()}" ajax="true" update="fileList"
diff --git a/WebApp/WebContent/resources/script/dataFiles.js b/WebApp/WebContent/resources/script/dataFiles.js
index 951a6dfea..3aa128eba 100644
--- a/WebApp/WebContent/resources/script/dataFiles.js
+++ b/WebApp/WebContent/resources/script/dataFiles.js
@@ -1,22 +1,11 @@
-ALIAS_RUN_TYPE = '-2';
-
-// Hide dialog with escape key
-$(document).on('keydown', function(e) {
-  if (e.keyCode === 27) {
-    $.each(PrimeFaces.widgets, function(index, val) {
-      if (index.match(/dialog/i)) {
-        PF(index).hide();
-      }
-    })
-  }
-});
+const ALIAS_RUN_TYPE = '-2';
 
 function renderMessages(messages) {
-  var html = $('<ul/>');
-  for (var i = 0; i < messages.length; i++) {
-    var row = $('<li/>');
+  let html = $('<ul/>');
+  for (let i = 0; i < messages.length; i++) {
+    let row = $('<li/>');
     row.addClass(messages[i].severity);
-    var summary = $('<span>');
+    let summary = $('<span>');
     if (messages[i].type == "file") {
       summary = $('<h3/>');
     }
@@ -29,17 +18,36 @@ function renderMessages(messages) {
   $('.ui-scrollpanel')[0].scrollTop = 0;
 }
 
-function reprocessUploadedFiles() {
-  $('#uploadForm\\:fileList_data>tr').each(function() {
-    extractNext();
-  });
+function runTypeChanged(rowIndex) {
+  let runType = PF('runType_' + rowIndex).getSelectedValue();
+  if (runType == ALIAS_RUN_TYPE) {
+    PF('alias_' + rowIndex).jq.show()
+  } else {
+    PF('alias_' + rowIndex).jq.hide()
+  }
 }
 
-function runTypeChanged(rowIndex, runTypeIndex) {
-  var runType = PF('missingRunType_' + rowIndex + '_' + runTypeIndex).getSelectedValue();
-  if (runType == ALIAS_RUN_TYPE) {
-    PF('alias_' + rowIndex + '_' + runTypeIndex).jq.show()
+function fileUploaded() {
+  if (PF('fileUploadWidget').files.length == 0) {
+    extractFiles();
+  }
+}
+
+function extractFiles() {
+  $('#uploadForm\\:uploadFiles').hide();
+  processAllFiles(); // PF RemoteCommand
+  PF('extractProgress').show();
+  PF('processedProgress').start();
+}
+
+function allFilesProcessed() {
+  PF('processedProgress').cancel();
+  PF('extractProgress').hide();
+  if ($('#uploadForm\\:unrecognisedRunTypeCount').val() > 0) {
+    PF('runTypesDialog').show();
   } else {
-    PF('alias_' + rowIndex + '_' + runTypeIndex).jq.hide()
+    $('#uploadForm\\:fileDetails').show();
+    $('#uploadForm\\:storeFileButton').show();
+    updateFileList(); // PF remoteCommand
   }
 }
diff --git a/WebApp/WebContent/resources/style/dataFiles.css b/WebApp/WebContent/resources/style/dataFiles.css
index ad1d3d3c3..b8180a933 100644
--- a/WebApp/WebContent/resources/style/dataFiles.css
+++ b/WebApp/WebContent/resources/style/dataFiles.css
@@ -53,3 +53,8 @@
 .runTypeFile >.ui-fieldset {
   margin:  0 0 20px 0;
 }
+
+#runTypesDialogContent {
+  display: flex;
+  flex-wrap: nowrap;
+}
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/data/Instrument/InstrumentDB.java b/WebApp/src/uk/ac/exeter/QuinCe/data/Instrument/InstrumentDB.java
index a8f507109..7a18b36d7 100644
--- a/WebApp/src/uk/ac/exeter/QuinCe/data/Instrument/InstrumentDB.java
+++ b/WebApp/src/uk/ac/exeter/QuinCe/data/Instrument/InstrumentDB.java
@@ -8,6 +8,7 @@
 import java.sql.Statement;
 import java.sql.Types;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
@@ -48,6 +49,7 @@
 import uk.ac.exeter.QuinCe.utils.MissingParam;
 import uk.ac.exeter.QuinCe.utils.MissingParamException;
 import uk.ac.exeter.QuinCe.utils.RecordNotFoundException;
+import uk.ac.exeter.QuinCe.web.files.MissingRunType;
 import uk.ac.exeter.QuinCe.web.system.ResourceManager;
 
 /**
@@ -1330,24 +1332,24 @@ public static PreparedStatement storeFileRunType(Connection conn, long fileId,
    * @throws MissingParamException
    *           If any required parameters are missing
    */
-  public static void storeFileRunTypes(DataSource dataSource, long fileId,
-    List<RunTypeAssignment> assignments)
+  public static void storeFileRunTypes(DataSource dataSource,
+    Collection<MissingRunType> runTypes)
     throws MissingParamException, DatabaseException {
 
     MissingParam.checkMissing(dataSource, "dataSource");
-    MissingParam.checkPositive(fileId, "fileDefinitionId");
-    MissingParam.checkMissing(assignments, "runTypes", true);
+    MissingParam.checkMissing(runTypes, "runTypes", true);
 
     List<PreparedStatement> stmts = new ArrayList<PreparedStatement>(
-      assignments.size());
+      runTypes.size());
     Connection conn = null;
 
     try {
       conn = dataSource.getConnection();
       conn.setAutoCommit(false);
 
-      for (RunTypeAssignment assignment : assignments) {
-        stmts.add(storeFileRunType(conn, fileId, assignment));
+      for (MissingRunType runType : runTypes) {
+        stmts.add(storeFileRunType(conn,
+          runType.fileDefinition().getDatabaseId(), runType.runType()));
       }
 
       conn.commit();
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/BaseManagedBean.java b/WebApp/src/uk/ac/exeter/QuinCe/web/BaseManagedBean.java
index c73ae018d..aab423e4e 100644
--- a/WebApp/src/uk/ac/exeter/QuinCe/web/BaseManagedBean.java
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/BaseManagedBean.java
@@ -86,6 +86,11 @@ public abstract class BaseManagedBean {
    */
   private boolean forceInstrumentReload = false;
 
+  /**
+   * Information for a progress bar.
+   */
+  protected Progress progress = new Progress();
+
   /**
    * Set a message that can be displayed to the user on a form
    *
@@ -582,4 +587,13 @@ public LocalDateTime getLastDate() {
     }
     return result;
   }
+
+  /**
+   * Get the progress bar information.
+   *
+   * @return The progress bar information.
+   */
+  public Progress getProgress() {
+    return progress;
+  }
 }
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/Progress.java b/WebApp/src/uk/ac/exeter/QuinCe/web/Progress.java
new file mode 100644
index 000000000..74c9ea707
--- /dev/null
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/Progress.java
@@ -0,0 +1,84 @@
+package uk.ac.exeter.QuinCe.web;
+
+/**
+ * Information holder for a progress bar.
+ *
+ * <p>
+ * The maximum value defaults to 100, in which case the progress value is
+ * assumed to be a percentage. Otherwise the value will be calculated as a
+ * percentage of the maximum.
+ * </p>
+ */
+public class Progress {
+
+  /**
+   * The label for the progress bar.
+   */
+  private String name = "Progress";
+
+  /**
+   * The maximum (target) value of the progress bar.
+   *
+   * <p>
+   * Defaults to 100 so it acts as a percentage.
+   * </p>
+   */
+  private float max = 100F;
+
+  /**
+   * The current value. Starts at zero.
+   */
+  private float value = 0F;
+
+  /**
+   * Set the name/label for the progress bar.
+   *
+   * @param name
+   *          The name.
+   */
+  public void setName(String name) {
+    this.name = name;
+  }
+
+  /**
+   * Set the maximum value for the progress bar.
+   *
+   * @param max
+   *          The maximum value.
+   */
+  public void setMax(float max) {
+    this.max = max;
+  }
+
+  /**
+   * Set the value for the progress bar.
+   *
+   * @param value
+   *          The value.
+   */
+  public void setValue(float value) {
+    this.value = value;
+  }
+
+  public void increment() {
+    this.value += 1;
+  }
+
+  /**
+   * Get the name/label for the progress bar.
+   *
+   * @return The name.
+   */
+  public String getName() {
+    return name;
+  }
+
+  /**
+   * Get the current progress as a percentage.
+   *
+   * @return The progress percentage.
+   */
+  public float getProgress() {
+    return max == 100F ? value : (value / max) * 100;
+  }
+}
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/files/DataFilesBean.java b/WebApp/src/uk/ac/exeter/QuinCe/web/files/DataFilesBean.java
index 37094e1cf..2dd5cec8e 100644
--- a/WebApp/src/uk/ac/exeter/QuinCe/web/files/DataFilesBean.java
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/files/DataFilesBean.java
@@ -23,7 +23,7 @@
 public class DataFilesBean extends FileUploadBean {
 
   /**
-   * Navigation to the file upload page
+   * Navigation to the file list page
    */
   public static final String NAV_FILE_LIST = "file_list";
 
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/files/MissingRunType.java b/WebApp/src/uk/ac/exeter/QuinCe/web/files/MissingRunType.java
new file mode 100644
index 000000000..5bb302a67
--- /dev/null
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/files/MissingRunType.java
@@ -0,0 +1,15 @@
+package uk.ac.exeter.QuinCe.web.files;
+
+import java.util.List;
+
+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,
+    FileDefinition fileDefinition, String runName) {
+    return list.stream().anyMatch(r -> r.fileDefinition.equals(fileDefinition)
+      && r.runType.getRunName().equals(runName));
+  }
+}
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/files/MultipleFileUploadBean.java b/WebApp/src/uk/ac/exeter/QuinCe/web/files/MultipleFileUploadBean.java
index f4981268f..fda669df2 100644
--- a/WebApp/src/uk/ac/exeter/QuinCe/web/files/MultipleFileUploadBean.java
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/files/MultipleFileUploadBean.java
@@ -1,16 +1,20 @@
 package uk.ac.exeter.QuinCe.web.files;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 import java.util.TreeSet;
+import java.util.stream.Collectors;
 
 import javax.faces.bean.ManagedBean;
 import javax.faces.bean.ViewScoped;
 
 import org.primefaces.model.file.UploadedFile;
 
-import uk.ac.exeter.QuinCe.data.Files.DataFile;
 import uk.ac.exeter.QuinCe.data.Files.DataFileDB;
 import uk.ac.exeter.QuinCe.data.Files.FileExistsException;
 import uk.ac.exeter.QuinCe.data.Instrument.InstrumentDB;
+import uk.ac.exeter.QuinCe.data.Instrument.RunTypes.RunTypeAssignment;
 import uk.ac.exeter.QuinCe.utils.DatabaseException;
 import uk.ac.exeter.QuinCe.utils.ExceptionUtils;
 import uk.ac.exeter.QuinCe.utils.MissingParamException;
@@ -24,34 +28,49 @@ public class MultipleFileUploadBean extends FileUploadBean {
    * The data file object
    */
   private TreeSet<UploadedDataFile> dataFiles = new TreeSet<UploadedDataFile>();
-  private String displayClass = "hidden";
+
+  private List<MissingRunType> unrecognisedRunTypes;
 
   @Override
   public void processUploadedFile() {
     processUploadedFile(getFile());
   }
 
-  public void processUploadedFile(UploadedFile uploadedFile) {
+  public synchronized void processUploadedFile(UploadedFile uploadedFile) {
     UploadedDataFile uploadedDataFile = new PrimeFacesUploadedDataFile(
       uploadedFile);
     dataFiles.add(uploadedDataFile);
-    setDisplayClass("");
   }
 
   public TreeSet<UploadedDataFile> getUploadedFiles() {
     return dataFiles;
   }
 
+  public List<RunTypeAssignment> getAllRunTypes() {
+    return getCurrentInstrument().getFileDefinitions().stream()
+      .map(df -> df.getRunTypes().values()).flatMap(Collection::stream)
+      .distinct().collect(Collectors.toList());
+  }
+
+  public List<RunTypeAssignment> getAllRunTypesWithExclusion(String exclusion) {
+    return getCurrentInstrument().getFileDefinitions().stream()
+      .map(df -> df.getRunTypes().values()).flatMap(Collection::stream)
+      .distinct().collect(Collectors.toList());
+  }
+
   /**
-   * Extract files in file list that are not yet extracted
+   * (Re-)extract all files in the file list.
    */
-  public void extractNext() {
+  public void processAllFiles() {
+    progress.setMax(dataFiles.size());
+    progress.setValue(0);
+    dataFiles.forEach(f -> f.setProcessed(false));
     for (UploadedDataFile file : dataFiles) {
-      if (file.getDataFile() == null && file.isStore()) {
-        file.extractFile(getCurrentInstrument(), getAppConfig(), false, false);
-        break;
-      }
+      file.extractFile(getCurrentInstrument(), getAppConfig(), false, false);
+      progress.increment();
     }
+
+    buildUnrecognisedRunTypes();
   }
 
   /**
@@ -77,21 +96,6 @@ public void store() throws MissingParamException, FileExistsException,
     }
   }
 
-  /**
-   * @return the displayClass
-   */
-  public String getDisplayClass() {
-    return displayClass;
-  }
-
-  /**
-   * @param displayClass
-   *          the displayClass to set
-   */
-  public void setDisplayClass(String displayClass) {
-    this.displayClass = displayClass;
-  }
-
   /**
    * @return the class "hidden" if there are no datafiles yet. Otherwise returns
    *         an empty string.
@@ -104,25 +108,12 @@ public String getStoreFileButtonClass() {
    * Called when run types have been updated. This will initiate re-processing
    * of the uploaded files.
    */
-  public void updateRunTypes(String fileName) {
-    DataFile dataFile = null;
-
-    for (UploadedDataFile file : dataFiles) {
-      if (file.getName().equals(fileName)) {
-        dataFile = file.getDataFile();
-      }
+  public void updateRunTypes() {
+    try {
+      InstrumentDB.storeFileRunTypes(getDataSource(), unrecognisedRunTypes);
+    } catch (Exception e) {
+      ExceptionUtils.printStackTrace(e);
     }
-
-    if (null != dataFile) {
-      try {
-        InstrumentDB.storeFileRunTypes(getDataSource(),
-          dataFile.getFileDefinition().getDatabaseId(),
-          dataFile.getMissingRunTypes());
-      } catch (Exception e) {
-        ExceptionUtils.printStackTrace(e);
-      }
-    }
-
     unsetDataFiles();
   }
 
@@ -137,4 +128,37 @@ private void unsetDataFiles() {
         ((PrimeFacesUploadedDataFile) file).getUploadedFile());
     }
   }
+
+  private void buildUnrecognisedRunTypes() {
+    unrecognisedRunTypes = new ArrayList<MissingRunType>();
+
+    for (UploadedDataFile file : dataFiles) {
+      for (RunTypeAssignment runType : file.getMissingRunTypes()) {
+        if (!MissingRunType.contains(unrecognisedRunTypes,
+          file.getDataFile().getFileDefinition(), runType.getRunName())) {
+          unrecognisedRunTypes.add(new MissingRunType(
+            file.getDataFile().getFileDefinition(), runType));
+        }
+      }
+    }
+  }
+
+  public List<MissingRunType> getUnrecognisedRunTypes() {
+
+    if (null == unrecognisedRunTypes) {
+      buildUnrecognisedRunTypes();
+    }
+
+    return unrecognisedRunTypes;
+  }
+
+  public int getUnrecognisedRunTypeCount() {
+    return null == unrecognisedRunTypes ? 0 : unrecognisedRunTypes.size();
+  }
+
+  public List<String> getRunTypeValuesWithExclusion(String exclusion) {
+    return getCurrentInstrument().getFileDefinitions().stream()
+      .map(fd -> fd.getRunTypeValues()).flatMap(Collection::stream).distinct()
+      .filter(r -> !r.equals(exclusion)).toList();
+  }
 }
diff --git a/WebApp/src/uk/ac/exeter/QuinCe/web/files/UploadedDataFile.java b/WebApp/src/uk/ac/exeter/QuinCe/web/files/UploadedDataFile.java
index 6e0ea1aee..869e7b644 100644
--- a/WebApp/src/uk/ac/exeter/QuinCe/web/files/UploadedDataFile.java
+++ b/WebApp/src/uk/ac/exeter/QuinCe/web/files/UploadedDataFile.java
@@ -24,6 +24,7 @@
 import uk.ac.exeter.QuinCe.data.Instrument.FileDefinition;
 import uk.ac.exeter.QuinCe.data.Instrument.Instrument;
 import uk.ac.exeter.QuinCe.data.Instrument.InstrumentFileSet;
+import uk.ac.exeter.QuinCe.data.Instrument.RunTypes.RunTypeAssignment;
 import uk.ac.exeter.QuinCe.utils.ExceptionUtils;
 import uk.ac.exeter.QuinCe.web.system.ResourceManager;
 
@@ -263,6 +264,11 @@ public boolean getHasUnrecognisedRunTypes() {
     return null != dataFile && dataFile.getMissingRunTypes().size() > 0;
   }
 
+  public List<RunTypeAssignment> getMissingRunTypes() {
+    return null == dataFile ? new ArrayList<RunTypeAssignment>()
+      : dataFile.getMissingRunTypes();
+  }
+
   /**
    * Determine whether or not this file will replace an existing file
    *