Handling nulls in descriptions

josemduarte · josemduarte · commit a8a96ec12213 · 2023-05-11T14:11:58.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java
@@ -100,11 +100,11 @@ protected CifFile getInternal(Structure structure, List<WrappedAtom> wrappedAtom
                 EntityInfo e = entityInfos.get(i);
                 entityIds[i] = Integer.toString(e.getMolId());
                 entityTypes[i] = e.getType().getEntityType();
-                entityDescriptions[i] = e.getDescription();
+                entityDescriptions[i] = e.getDescription() == null? "?" : e.getDescription();
             }
 
             String[] polyEntityIds = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> Integer.toString(e.getMolId())).collect(Collectors.toList()).toArray(new String[]{});
-            String[] entitySeqs = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> e.getChains().get(0).getSeqResSequence()).collect(Collectors.toList()).toArray(new String[]{});
+            String[] polyEntitySeqs = entityInfos.stream().filter(e -> e.getType() == EntityType.POLYMER).map(e -> e.getChains().get(0).getSeqResSequence()).collect(Collectors.toList()).toArray(new String[]{});
 
             blockBuilder.enterEntity()
                     .enterId()
@@ -127,7 +127,7 @@ protected CifFile getInternal(Structure structure, List<WrappedAtom> wrappedAtom
                     .leaveColumn()
 
                     .enterPdbxSeqOneLetterCodeCan()
-                    .add(entitySeqs)
+                    .add(polyEntitySeqs)
                     .leaveColumn()
 
                     .leaveCategory();
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/cif/CifFileSupplierImplTest.java
@@ -10,8 +10,7 @@
 import java.io.InputStream;
 import java.util.zip.GZIPInputStream;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 public class CifFileSupplierImplTest {
 
@@ -29,6 +28,7 @@ public void shouldReadRawPdbOutputtingCifWithEntity() throws IOException {
         String cifText = CifStructureConverter.toText(s);
         assertTrue(cifText.contains("_entity.type"));
         assertTrue(cifText.contains("_entity_poly.pdbx_seq_one_letter_code_can"));
+        assertFalse(cifText.contains("null"));
 
         InputStream inputStream = new ByteArrayInputStream(cifText.getBytes());
         Structure readStruct = CifStructureConverter.fromInputStream(inputStream);
