broken overlays crashed migration script

CHANGELOG

@@ -13,6 +13,7 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
     are supported (#1452, #1450, #1420)
   * Bug fix: removing plugin that does not exist anymore does not raise an error
     (#1289)
+  * Bug fix: broken overlays crashed minerva upgrade (#1453)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2020 08:00:00 +0200
 

persist/src/main/java/lcsb/mapviewer/persist/migration/V16_0_0_20200930_2__generic_data_overlay_entry_data.java

@@ -95,7 +95,8 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
     return DEFAULT_GENOME_VERSION;
   }
 
-  private void addEntries(Integer overlayId, Set<? extends DataOverlayEntry> entries, Context context) throws SQLException {
+  private void addEntries(Integer overlayId, Set<? extends DataOverlayEntry> entries, Context context)
+      throws SQLException {
     for (DataOverlayEntry dataOverlayEntry : entries) {
       String distinguisher = "GENERIC_DATA_OVERLAY";
       if (dataOverlayEntry instanceof GeneVariantDataOverlayEntry) {
@@ -340,7 +341,11 @@ public abstract class V16_0_0_20200930_2__generic_data_overlay_entry_data extend
 
     for (int i = 0; i < columns.length; i++) {
       String column = columns[i].trim().toLowerCase();
-      String value = data[i];
+      String value = null;
+      //there might be some broken entries
+      if (data.length > i) {
+        value = data[i];
+      }
 
       if (value != null && !value.trim().isEmpty()) {