Changeset 6216

Timestamp:

Apr 16, 2021, 2:03:41 PM (13 months ago)

Author:

Nicklas Nordborg

Message:

References #1295: Registration of specimen handled by external lab

The SCAN-B report failed if the library doesn't have a protocol.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/ScanBReportWorker.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/pdf/ScanBReportWorker.java

@@ -26 +26 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
+import net.sf.basedb.core.Protocol;
 import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.Sample;
@@ -219 +220 @@
     Map<Subtype, BioMaterial> parents = raw.findParentBioMaterial(dc, Subtype.PATIENT, Subtype.CASE, Subtype.SPECIMEN, Subtype.LYSATE, Subtype.RNA, Subtype.LIBRARY);
     Extract lib = (Extract)parents.get(Subtype.LIBRARY);
+    Protocol libProtocol = lib == null ? null : lib.getProtocol();
     Extract rna = (Extract)parents.get(Subtype.RNA);
     Extract lysate = (Extract)parents.get(Subtype.LYSATE);
@@ -334 +336 @@
       header[1] = translations.get(Annotationtype.LATERALITY.getAnnotationValue(dc, specimen));
       header[2] = lib == null ? null : DATE_FORMAT.convert(lib.getCreationEvent().getEventDate());
-      header[3] = lib == null ? null : translations.get(lib.getProtocol().getName());
+      header[3] = libProtocol == null ? null : translations.get(libProtocol.getName());
       header[4] = count.format(dc, Annotationtype.FRAGMENT_SIZE_AVG, aligned) + "/" + count.format(dc, Annotationtype.FRAGMENT_SIZE_STDEV, aligned);
       header[5] = translations.get(Annotationtype.PIPELINE.getAnnotationValue(dc, rba));