Merge branch 'develop' into features/JAL-2068groovyAnnotationWorker

[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 e04bbb7..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-        // System.out.println("Downloaded file is out of date, hence re-downloading...");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);
   }
 
@@ -360,7 +371,8 @@ public class SiftsClient implements SiftsClientI
       DBRefEntry[] dbRefs = seq.getDBRefs();
       if (dbRefs == null || dbRefs.length < 1)
       {
-        throw new SiftsException("Could not get source DB Ref");
+        throw new SiftsException(
+                "Source DBRef could not be determined. DBRefs might not have been retrieved.");
       }
 
       for (DBRefEntryI dbRef : dbRefs)
@@ -374,6 +386,7 @@ public class SiftsClient implements SiftsClientI
                 && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
                         .getSource().equalsIgnoreCase(DBRefSource.PDB)))
         {
+          seq.setSourceDBRef(dbRef);
           return dbRef;
         }
       }
@@ -413,7 +426,8 @@ public class SiftsClient implements SiftsClientI
                 .getMapRegion();
         for (MapRegion mapRegion : mapRegions)
         {
-          accessions.add(mapRegion.getDb().getDbAccessionId());
+          accessions
+                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
         }
       }
     }
@@ -464,12 +478,9 @@ public class SiftsClient implements SiftsClientI
             jalview.util.Comparison.GapChars, seq.getSequenceAsString());
     HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
     DBRefEntryI sourceDBRef = seq.getSourceDBRef();
-    if (sourceDBRef == null)
-    {
-      sourceDBRef = getValidSourceDBRef(seq);
-      // TODO ensure sequence start/end is in the same coordinate system and
-      // consistent with the choosen sourceDBRef
-    }
+    sourceDBRef = getValidSourceDBRef(seq);
+    // TODO ensure sequence start/end is in the same coordinate system and
+    // consistent with the choosen sourceDBRef
 
     // set sequence coordinate system - default value is UniProt
     if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
@@ -752,8 +763,9 @@ public class SiftsClient implements SiftsClientI
 
   private boolean isFoundInSiftsEntry(String accessionId)
   {
+    HashSet<String> siftsDBRefs = getAllMappingAccession();
     return accessionId != null
-            && getAllMappingAccession().contains(accessionId);
+            && siftsDBRefs.contains(accessionId.toLowerCase());
   }
 
   /**