Bugfix situation when importing an alignment not in the top-level file root

Author: bbimber

SequenceAnalysis/resources/web/SequenceAnalysis/panel/AlignmentImportPanel.js

@@ -723,13 +723,19 @@ Ext4.define('SequenceAnalysis.panel.AlignmentImportPanel', {
             if (rec.get('error'))
                 totalErrors++;
             else {
-                if (!rec.get('fileId'))
-                    fields.inputFiles.push({
-                        fileName: rec.get('fileName'),
-                        relPath: rec.get('relPath')
-                    });
-                else
+                if (!rec.get('fileId')) {
+                    var recIdx = this.fileNameStore.find('fileName', rec.get('fileName'));
+                    if (recIdx > -1) {
+                        var r = this.fileNameStore.getAt(recIdx);
+                        fields.inputFiles.push({
+                            fileName: r.get('fileName'),
+                            relPath: r.get('relPath')
+                        });
+                    }
+                }
+                else {
                     fields.inputFiles.push({dataId: rec.get('fileId')});
+                }
             }
         }, this);
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -2148,7 +2148,7 @@ else if (o.containsKey("relPath") || o.containsKey("fileName"))
 
                     if (f == null || !f.exists())
                     {
-                        throw new PipelineValidationException("Unknown file: " + o.getString("relPath"));
+                        throw new PipelineValidationException("Unknown file: " + o.getString("relPath") + " / " + o.getString("fileName"));
                     }
 
                     ret.add(f);