Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 3c2e703..6c11dd2 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -96,11 +96,9 @@ public class SiftsClient implements SiftsClientI
 
   private static final int PDB_ATOM_POS = 1;
 
-  private static final String NOT_FOUND = "Not_Found";
-
   private static final String NOT_OBSERVED = "Not_Observed";
 
-  private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
+  private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
 
   private final static String NEWLINE = System.lineSeparator();
 
@@ -225,8 +223,9 @@ public class SiftsClient implements SiftsClientI
    */
   public static File getSiftsFile(String pdbId) throws SiftsException
   {
-    File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
-            + pdbId.toLowerCase() + ".xml.gz");
+    String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+            + pdbId.toLowerCase() + ".xml.gz";
+    File siftsFile = new File(siftsFileName);
     if (siftsFile.exists())
     {
       // The line below is required for unit testing... don't comment it out!!!
@@ -235,12 +234,28 @@ public class SiftsClient implements SiftsClientI
       if (isFileOlderThanThreshold(siftsFile,
               SiftsSettings.getCacheThresholdInDays()))
       {
-        // System.out.println("Downloaded file is out of date, hence re-downloading...");
-        siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+        File oldSiftsFile = new File(siftsFileName + "_old");
+        siftsFile.renameTo(oldSiftsFile);
+        try
+        {
+          siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+          oldSiftsFile.delete();
+          return siftsFile;
+        } catch (IOException e)
+        {
+          e.printStackTrace();
+          oldSiftsFile.renameTo(siftsFile);
+          return new File(siftsFileName);
+        }
       }
-      return siftsFile;
     }
-    siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+    try
+    {
+      siftsFile = downloadSiftsFile(pdbId.toLowerCase());
+    } catch (IOException e)
+    {
+      throw new SiftsException(e.getMessage());
+    }
     return siftsFile;
   }
 
@@ -278,8 +293,10 @@ public class SiftsClient implements SiftsClientI
    * @param pdbId
    * @return downloaded SIFTs XML file
    * @throws SiftsException
+   * @throws IOException
    */
-  public static File downloadSiftsFile(String pdbId) throws SiftsException
+  public static File downloadSiftsFile(String pdbId) throws SiftsException,
+          IOException
   {
     if (pdbId.contains(".cif"))
     {
@@ -295,8 +312,6 @@ public class SiftsClient implements SiftsClientI
     {
       siftsDownloadDir.mkdirs();
     }
-    try
-    {
       // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
       URL url = new URL(siftsFileFTPURL);
       URLConnection conn = url.openConnection();
@@ -312,10 +327,6 @@ public class SiftsClient implements SiftsClientI
       outputStream.close();
       inputStream.close();
       // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
-    } catch (IOException ex)
-    {
-      throw new SiftsException(ex.getMessage());
-    }
     return new File(downloadedSiftsFile);
   }