Changeset 5853

Timestamp:

Mar 6, 2020, 1:44:37 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1230: NullPointerException? in the "Map external data" wizard

Found 2 cases in the export wizard and 2 more cases in the relase exporter plug-in that could be triggered by a sequencer wihtout serial number or a demux without a read-string.

Location:

extensions/net.sf.basedb.reggie/branches/4.25-stable/src/net/sf/basedb/reggie

Files:

• plugins/release/MergedWriter.java (modified) (2 diffs)
• servlet/ExportServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/4.25-stable/src/net/sf/basedb/reggie/plugins/release/MergedWriter.java

@@ -176 +176 @@
     for (SequencingRun sr : sequencingRuns)
     {
-      sequencers.add((String)item.getAnnotationValue(Annotationtype.SERIAL_NUMBER, sr.getItem().getHardware()));
+      String sn = (String)item.getAnnotationValue(Annotationtype.SERIAL_NUMBER, sr.getItem().getHardware());
+      if (sn != null) sequencers.add(sn);
     }
     return sequencers;
@@ -191 +192 @@
     for (DemuxedSequences dx : demuxedSequences)
     {
-      readStrings.add((String)item.getAnnotationValue(Annotationtype.READ_STRING, dx.getItem()));
+      String rs = (String)item.getAnnotationValue(Annotationtype.READ_STRING, dx.getItem());
+      if (rs != null) readStrings.add(rs);
     }
     return readStrings;

extensions/net.sf.basedb.reggie/branches/4.25-stable/src/net/sf/basedb/reggie/servlet/ExportServlet.java

@@ -1872 +1872 @@
         for (Sample s : specimen)
         {
-          allPad.add((String)Annotationtype.PAD.getAnnotationValue(dc, manager, s));
+          String p = (String)Annotationtype.PAD.getAnnotationValue(dc, manager, s);
+          if (p != null) allPad.add(p);
         }
         pad = Values.getString(allPad, ",", true);
@@ -1919 +1920 @@
         for (Sample s : items)
         {
-          allId.add(s.getExternalId());
+          String id = s.getExternalId();
+          if (id != null) allId.add(id);
         }
         idValues = Values.getString(allId, ",", true);