From 439dcbf32a4e113263d393b2a60e38133668f6f5 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 15 Nov 2024 13:50:52 +0000
Subject: [PATCH] JAL-3914 fix up pdbentry get/setters

---
 src/jalview/datamodel/PDBEntry.java      |   20 +++++++++++++++++---
 test/jalview/datamodel/PDBEntryTest.java |    7 +++++++
 2 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 6385210..08eea3f 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -277,6 +277,12 @@ public class PDBEntry
     {
       this.properties = new Hashtable<String, Object>();
     }
+    if (key!=null && value==null)
+    {
+      properties.remove(key);
+      return;
+    }
+    // null key throws a runtime exception
     properties.put(key, value);
   }
 
@@ -678,7 +684,7 @@ public class PDBEntry
 
   public void setTempFacType(TFType tempfactype)
   {
-    setProperty(TEMPFACTYPE, tempfactype);
+    setProperty(TEMPFACTYPE, tempfactype.name());
   }
 
   /**
@@ -691,7 +697,10 @@ public class PDBEntry
   }
   public TFType getTempFacTypeTFType()
   {
-    return TFType.valueOf((String) getProperty(TEMPFACTYPE));
+    if (_hasProperty(TEMPFACTYPE)) {
+      return TFType.valueOf((String) getProperty(TEMPFACTYPE));
+    }
+    return null;
   }
 
   public boolean hasTempFacType()
@@ -767,6 +776,11 @@ public class PDBEntry
   }
   public DataSourceType getProtocol()
   {
-    return DataSourceType.valueOf((String) getProperty(PROTOCOL));
+    if (_hasProperty(PROTOCOL))
+    {
+      return DataSourceType.valueOf((String) getProperty(PROTOCOL));
+    }
+    // default protocol is
+    return DataSourceType.FILE;
   }
 }
\ No newline at end of file
diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index a006833..e96b968 100644
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -32,6 +32,7 @@ import static org.testng.Assert.fail;
 
 import jalview.datamodel.PDBEntry.Type;
 import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings.TFType;
 
 //import org.testng.Assert;
 import org.testng.annotations.AfterMethod;
@@ -322,4 +323,10 @@ public class PDBEntryTest
     }
   }
 
+  @Test(groups= {"Functional"})
+  public void testMetadataProperties()
+  {
+    PDBEntry pdb = new PDBEntry("af:1xyz","A",null,"a/b/c/File");
+    assertEquals(pdb.getTempFacTypeTFType(),null); 
+  }
 }
-- 
1.7.10.2