Merge branch 'patch/JAL-4119_sifts_ftp_split' into develop

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index f384b1e..3b1757b 100755 (executable)
--- 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/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 0c707e5..037854b 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -116,7 +116,7 @@ public class SiftsClient implements SiftsClientI
 
   private static final String NOT_OBSERVED = "Not_Observed";
 
-  private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+  private static final String SIFTS_SPLIT_FTP_BASE_URL = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/";
 
   private final static String NEWLINE = System.lineSeparator();
 
@@ -305,7 +305,7 @@ public class SiftsClient implements SiftsClientI
       pdbId = pdbId.replace(".cif", "");
     }
     String siftFile = pdbId + ".xml.gz";
-    String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
+    String siftsFileFTPURL = getDownloadUrlFor(siftFile);
 
     /*
      * Download the file from URL to either
@@ -348,6 +348,11 @@ public class SiftsClient implements SiftsClientI
     return downloadTo;
   }
 
+  public static String getDownloadUrlFor(String siftFile)
+  {
+    return SIFTS_SPLIT_FTP_BASE_URL +siftFile.substring(1, 3)+"/"+siftFile;
+  }
+
   /**
    * Delete the SIFTs file for the given PDB Id in the local SIFTs download
    * directory

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 44a6a02..0f5bd4d 100644 (file)
--- 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);
   }
 
@@ -205,6 +207,12 @@ public class SiftsClientTest
   {
     siftsClient = null;
   }
+  
+  @Test(groups= {"Functional"})
+  public void testSIFTsDownloadURL() {
+    String expectedUrl = "https://ftp.ebi.ac.uk/pub/databases/msd/sifts/split_xml/xy/1xyz.sifts.xml.gz";
+    Assert.assertEquals(SiftsClient.getDownloadUrlFor("1xyz.sifts.xml.gz"), expectedUrl);
+  }
 
   @Test(groups = { "Network" })
   public void getSIFTsFileTest() throws SiftsException, IOException
@@ -215,7 +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);
@@ -368,7 +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);
   }