Commit 559134cb authored by Piotr Gawron's avatar Piotr Gawron
Browse files

broken overlays crashed migration script

parent 1c3e1264
Pipeline #37388 passed with stage
in 22 minutes and 29 seconds
......@@ -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
......
......@@ -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()) {
......
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