Add LENIENT validation

Author: bbimber

jbrowse/resources/web/jbrowse/window/ModifyJsonConfigWindow.js

@@ -107,6 +107,12 @@ Ext4.define('JBrowse.window.ModifyJsonConfigWindow', {
                         handler: function (gridBtn) {
                             this.addAttribute('infoFieldsForFullTextSearch', null, 'STRING');
                         }
+                    },{
+                        text: 'Allow Lenient Validation for Search Index',
+                        scope: this,
+                        handler: function (gridBtn) {
+                            this.addAttribute('lenientLuceneProcessing', true, 'BOOLEAN');
+                        }
                     },{
                         text: 'Other',
                         scope: this,

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -1004,6 +1004,13 @@ private void prepareLuceneIndex(Logger log) throws PipelineJobException
 
         args.add("--allow-missing-fields");
 
+        JSONObject config = getExtraTrackConfig();
+        if (config != null && !config.isNull("lenientLuceneProcessing") && config.getBoolean("lenientLuceneProcessing"))
+        {
+            args.add("--validation-stringency");
+            args.add("LENIENT");
+        }
+
         runner.execute(args);
     }