Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[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 0c707e5..92cb7af 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -57,6 +57,7 @@ import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.api.DBRefEntryI;
 import jalview.api.SiftsClientI;
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
@@ -116,7 +117,7 @@ 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();
 
@@ -188,7 +189,7 @@ public class SiftsClient implements SiftsClientI
     try (InputStream in = new FileInputStream(siftFile);
             GZIPInputStream gzis = new GZIPInputStream(in);)
     {
-      // System.out.println("File : " + siftFile.getAbsolutePath());
+      // jalview.bin.Console.outPrintln("File : " + siftFile.getAbsolutePath());
       JAXBContext jc = JAXBContext.newInstance("jalview.xml.binding.sifts");
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(gzis);
@@ -226,7 +227,7 @@ public class SiftsClient implements SiftsClientI
     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);
+      jalview.bin.Console.outPrintln(">>> SIFTS File already downloaded for " + pdbId);
 
       if (isFileOlderThanThreshold(siftsFile,
               SiftsSettings.getCacheThresholdInDays()))
@@ -281,7 +282,7 @@ public class SiftsClient implements SiftsClientI
       diffInDays = (int) ((new Date().getTime()
               - attr.lastModifiedTime().toMillis())
               / (1000 * 60 * 60 * 24));
-      // System.out.println("Diff in days : " + diffInDays);
+      // jalview.bin.Console.outPrintln("Diff in days : " + diffInDays);
     } catch (IOException e)
     {
       e.printStackTrace();
@@ -305,7 +306,7 @@ 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
@@ -329,7 +330,7 @@ public class SiftsClient implements SiftsClientI
       }
     }
 
-    // System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+    // jalview.bin.Console.outPrintln(">> Download ftp url : " + siftsFileFTPURL);
     // long now = System.currentTimeMillis();
     URL url = new URL(siftsFileFTPURL);
     URLConnection conn = url.openConnection();
@@ -343,11 +344,19 @@ public class SiftsClient implements SiftsClientI
     }
     outputStream.close();
     inputStream.close();
-    // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+    // jalview.bin.Console.outPrintln(">>> File downloaded : " + downloadedSiftsFile
     // + " took " + (System.currentTimeMillis() - now) + "ms");
     return downloadTo;
   }
 
+  public static String getDownloadUrlFor(String siftFile)
+  {
+    String durl = SIFTS_SPLIT_FTP_BASE_URL+siftFile.substring(1, 3)+"/"+siftFile;
+    Console.trace("SIFTS URL for "+siftFile+" is "+durl);
+    return durl;
+    
+  }
+
   /**
    * Delete the SIFTs file for the given PDB Id in the local SIFTs download
    * directory
@@ -450,7 +459,7 @@ public class SiftsClient implements SiftsClientI
       seq = seq.getDatasetSequence();
     }
     structId = (chain == null) ? pdbId : pdbId + "|" + chain;
-    System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+    jalview.bin.Console.outPrintln("Getting SIFTS mapping for " + structId + ": seq "
             + seq.getName());
 
     final StringBuilder mappingDetails = new StringBuilder(128);
@@ -483,7 +492,7 @@ public class SiftsClient implements SiftsClientI
   {
     List<Integer> omitNonObserved = new ArrayList<>();
     int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
-    // System.out.println("Generating mappings for : " + entityId);
+    // jalview.bin.Console.outPrintln("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
     String originalSeq = AlignSeq.extractGaps(
@@ -535,7 +544,7 @@ public class SiftsClient implements SiftsClientI
 
     if (mapping.isEmpty())
     {
-      throw new SiftsException("SIFTS mapping failed");
+      throw new SiftsException("SIFTS mapping failed for "+entityId+" and "+seq.getName());
     }
     // also construct a mapping object between the seq-coord sys and the PDB
     // seq's coord sys
@@ -653,7 +662,7 @@ public class SiftsClient implements SiftsClientI
     int firstPDBResNum = UNASSIGNED;
     for (Segment segment : segments)
     {
-      // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
+      // jalview.bin.Console.outPrintln("Mapping segments : " + segment.getSegId() + "\\"s
       // + segStartEnd);
       List<Residue> residues = segment.getListResidue().getResidue();
       for (Residue residue : residues)
@@ -922,8 +931,8 @@ public class SiftsClient implements SiftsClientI
     // Arrays.sort(keys);
     int firstIndex = keys[0];
     int lastIndex = keys[keys.length - 1];
-    // System.out.println("Min value " + firstIndex);
-    // System.out.println("Max value " + lastIndex);
+    // jalview.bin.Console.outPrintln("Min value " + firstIndex);
+    // jalview.bin.Console.outPrintln("Max value " + lastIndex);
     for (int x = firstIndex; x <= lastIndex; x++)
     {
       if (!resNumMap.containsKey(x) && !omitNonObserved.contains(x))
@@ -956,7 +965,7 @@ public class SiftsClient implements SiftsClientI
    */
   public Entity getEntityByMostOptimalMatchedId(String chainId)
   {
-    // System.out.println("---> advanced greedy entityId matching block
+    // jalview.bin.Console.outPrintln("---> advanced greedy entityId matching block
     // entered..");
     List<Entity> entities = siftsEntry.getEntity();
     SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
@@ -992,8 +1001,8 @@ public class SiftsClient implements SiftsClientI
       ++count;
     }
     Arrays.sort(sPojo, Collections.reverseOrder());
-    // System.out.println("highest matched entity : " + sPojo[0].entityId);
-    // System.out.println("highest matched pid : " + sPojo[0].pid);
+    // jalview.bin.Console.outPrintln("highest matched entity : " + sPojo[0].entityId);
+    // jalview.bin.Console.outPrintln("highest matched pid : " + sPojo[0].pid);
 
     if (sPojo[0].entityId != null)
     {