Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[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 3ec6320..4af4157 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -22,18 +22,24 @@ package jalview.ws.sifts;
 
 import java.io.File;
 import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintStream;
 import java.net.URL;
 import java.net.URLConnection;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
@@ -53,6 +59,7 @@ import jalview.api.SiftsClientI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
@@ -96,6 +103,8 @@ public class SiftsClient implements SiftsClientI
    */
   private jalview.datamodel.Mapping seqFromPdbMapping;
 
+  private static final int BUFFER_SIZE = 4096;
+
   public static final int UNASSIGNED = Integer.MIN_VALUE;
 
   private static final int PDB_RES_POS = 0;
@@ -112,11 +121,9 @@ public class SiftsClient implements SiftsClientI
 
   private static final boolean GET_STREAM = false;
   private static final boolean CACHE_FILE = true;
-
   private String curSourceDBRef;
 
   private HashSet<String> curDBRefAccessionIdsString;
-
   private boolean doCache = false;
 
   private enum CoordinateSys
@@ -242,27 +249,27 @@ public class SiftsClient implements SiftsClientI
     }
 
     String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
-            + pdbId.toLowerCase() + ".xml.gz";
+            + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz";
     File siftsFile = new File(siftsFileName);
     if (siftsFile.exists())
     {
       // The line below is required for unit testing... don't comment it out!!!
       System.out.println(">>> SIFTS File already downloaded for " + pdbId);
 
-      if (Platform.isFileOlderThanThreshold(siftsFile,
+      if (isFileOlderThanThreshold(siftsFile,
               SiftsSettings.getCacheThresholdInDays()))
       {
         File oldSiftsFile = new File(siftsFileName + "_old");
-        siftsFile.renameTo(oldSiftsFile);
+        BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
         try
         {
-          siftsFile = downloadSiftsFile(pdbId);
+          siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
           oldSiftsFile.delete();
           return siftsFile;
         } catch (IOException e)
         {
           e.printStackTrace();
-          oldSiftsFile.renameTo(siftsFile);
+          BackupFiles.moveFileToFile(oldSiftsFile, siftsFile);
           return new File(siftsFileName);
         }
       }
@@ -273,7 +280,7 @@ public class SiftsClient implements SiftsClientI
     }
     try
     {
-      siftsFile = downloadSiftsFile(pdbId);
+      siftsFile = downloadSiftsFile(pdbId.toLowerCase(Locale.ROOT));
     } catch (IOException e)
     {
       throw new SiftsException(e.getMessage());
@@ -305,13 +312,12 @@ public class SiftsClient implements SiftsClientI
    */
   private static Object downloadSifts(String pdbId, boolean asFile) throws IOException
   {
-    pdbId = pdbId.toLowerCase();
+    pdbId = pdbId.toLowerCase(Locale.ROOT);
     if (pdbId.contains(".cif"))
     {
       pdbId = pdbId.replace(".cif", "");
     }
     String siftFile = pdbId + ".xml.gz";
-
     File downloadTo = null;
     if (asFile)
     {
@@ -323,6 +329,7 @@ public class SiftsClient implements SiftsClientI
         siftsDownloadDir.mkdirs();
       }
     }
+
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
     URL url = new URL(siftsFileFTPURL);
     URLConnection conn = url.openConnection();
@@ -345,7 +352,7 @@ public class SiftsClient implements SiftsClientI
   public static boolean deleteSiftsFileByPDBId(String pdbId)
   {
     File siftsFile = new File(SiftsSettings.getSiftDownloadDirectory()
-            + pdbId.toLowerCase() + ".xml.gz");
+            + pdbId.toLowerCase(Locale.ROOT) + ".xml.gz");
     if (siftsFile.exists())
     {
       return siftsFile.delete();
@@ -420,7 +427,7 @@ public class SiftsClient implements SiftsClientI
         for (MapRegion mapRegion : mapRegions)
         {
           accessions
-                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
+                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase(Locale.ROOT));
         }
       }
     }
@@ -490,9 +497,9 @@ public class SiftsClient implements SiftsClientI
     HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
     for (DBRefEntry dbref : seq.getDBRefs())
     {
-      dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
+      dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
     }
-    dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+    dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
 
     curDBRefAccessionIdsString = dbRefAccessionIdsString;
     curSourceDBRef = sourceDBRef.getAccessionId();
@@ -852,14 +859,14 @@ public class SiftsClient implements SiftsClientI
   {
     boolean isStrictMatch = true;
     return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
-            : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+            : curDBRefAccessionIdsString.contains(accession.toLowerCase(Locale.ROOT));
   }
 
   private boolean isFoundInSiftsEntry(String accessionId)
   {
     Set<String> siftsDBRefs = getAllMappingAccession();
     return accessionId != null
-            && siftsDBRefs.contains(accessionId.toLowerCase());
+            && siftsDBRefs.contains(accessionId.toLowerCase(Locale.ROOT));
   }
 
   /**