From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 2 Feb 2023 16:51:41 +0000 (+0000)
Subject: JAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null version field - never candidate... 
X-Git-Tag: Release_2_11_4_0~243^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=faaea5e75f32c615b8f7d5adbd8468118cfb8c3a;p=jalview.git

JAL-4119 JAL-2144 ‘invalid’ DBRefEntry has a null version field - never candidate for a primary sequence accession
---

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index f384b1e..3b1757b 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -154,6 +154,11 @@ public class DBRefSource
 
   public static boolean isPrimaryCandidate(String ucversion)
   {
+    if (ucversion==null)
+    {
+      // Null/empty version is not a real reference ?
+      return false;
+    }
     // tricky - this test really needs to search the sequence's set of dbrefs to
     // see if there is a primary reference that derived this reference.
     for (int i = allSources.length; --i >= 0;)
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index b003cb5..0f5bd4d 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -195,8 +195,10 @@ public class SiftsClientTest
     SiftsSettings.setCacheThresholdInDays("2");
     SiftsSettings.setFailSafePIDThreshold("70");
     PDBfile pdbFile;
+    
     pdbFile = new PDBfile(false, false, false,
             "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
+    // TODO: this uses a network connection - we should mock the sifts testPDBId.xml.gz
     siftsClient = new SiftsClient(pdbFile);
   }
 
@@ -221,7 +223,7 @@ public class SiftsClientTest
     long t1 = siftsFile.lastModified();
 
     // re-read file should be returned from cache
-    siftsFile = SiftsClient.downloadSiftsFile(testPDBId);
+    siftsFile = SiftsClient.getSiftsFile(testPDBId);
     FileAssert.assertFile(siftsFile);
     long t2 = siftsFile.lastModified();
     assertEquals(t1, t2);
@@ -374,7 +376,7 @@ public class SiftsClientTest
   {
     SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
     DBRefEntry invalidDBRef = new DBRefEntry();
-    invalidDBRef.setAccessionId("BLAR");
+    invalidDBRef.setAccessionId("BLAR"); // note no version is set, so also invalid
     invalidTestSeq.addDBRef(invalidDBRef);
     siftsClient.getValidSourceDBRef(invalidTestSeq);
   }