From 72cbe293bdfc802039f5be51d53351e97b89d28a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 21 Mar 2016 14:46:40 +0000
Subject: [PATCH] JAL-1855 dbfetch from /ena_sequence/, /ena_coding/

---
 src/jalview/ws/ebi/EBIFetchClient.java |   45 ++++++++++++++++++++------------
 1 file changed, 29 insertions(+), 16 deletions(-)

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index c33871d..b09cbaa 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.ebi;
 
+import jalview.datamodel.DBRefSource;
 import jalview.util.MessageManager;
 
 import java.io.BufferedInputStream;
@@ -90,14 +91,14 @@ public class EBIFetchClient
    * 
    * @param ids
    *          the query formatted as db:query1;query2;query3
-   * @param f
+   * @param format
    *          the format wanted
    * @param s
    *          - unused parameter
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
-  public File fetchDataAsFile(String ids, String f, String s)
+  public File fetchDataAsFile(String ids, String format, String s)
           throws OutOfMemoryError
   {
     File outFile = null;
@@ -105,7 +106,7 @@ public class EBIFetchClient
     {
       outFile = File.createTempFile("jalview", ".xml");
       outFile.deleteOnExit();
-      fetchData(ids, f, s, outFile);
+      fetchData(ids, format, s, outFile);
       if (outFile.length() == 0)
       {
         outFile.delete();
@@ -122,20 +123,20 @@ public class EBIFetchClient
    * 
    * @param ids
    *          db:query1;query2;query3
-   * @param f
+   * @param format
    *          raw/xml
    * @param s
    *          not used - remove?
    * 
    * @return Raw string array result of query set
    */
-  public String[] fetchData(String ids, String f, String s)
+  public String[] fetchData(String ids, String format, String s)
           throws OutOfMemoryError
   {
-    return fetchData(ids, f, s, null);
+    return fetchData(ids, format, s, null);
   }
 
-  public String[] fetchData(String ids, String f, String s, File outFile)
+  String[] fetchData(String ids, String f, String s, File outFile)
           throws OutOfMemoryError
   {
     // Need to split
@@ -183,16 +184,27 @@ public class EBIFetchClient
     return (rslts.length == 0 ? null : rslts);
   }
 
-  public String[] fetchBatch(String ids, String db, String f, String s,
+  public String[] fetchBatch(String ids, String dbPath, String format, String s,
           File outFile) throws OutOfMemoryError
   {
-    long time = System.currentTimeMillis();
-    // max 200 ids can be added at one time
+    // long time = System.currentTimeMillis();
+    /*
+     * JAL-1855 dbfetch from ena_sequence, ena_coding
+     */
+    if (dbPath.equalsIgnoreCase(DBRefSource.EMBL))
+    {
+      dbPath = "ena_sequence";
+    }
+    else if (dbPath.equalsIgnoreCase(DBRefSource.EMBLCDS))
+    {
+      dbPath = "ena_coding";
+    }
+
     try
     {
       URL rcall = new URL("http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-              + db.toLowerCase() + "/" + ids.toLowerCase()
-              + (f != null ? "/" + f : ""));
+              + dbPath.toLowerCase() + "/" + ids.toLowerCase()
+              + (format != null ? "/" + format : ""));
 
       InputStream is = new BufferedInputStream(rcall.openStream());
       if (outFile != null)
@@ -221,7 +233,7 @@ public class EBIFetchClient
     } catch (OutOfMemoryError er)
     {
 
-      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db
+      System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + dbPath
               + ":\n" + ids);
       throw er;
     } catch (Exception ex)
@@ -231,14 +243,15 @@ public class EBIFetchClient
       {
         return null;
       }
-      System.err.println("Unexpected exception when retrieving from " + db
+      System.err.println("Unexpected exception when retrieving from "
+              + dbPath
               + "\nQuery was : '" + ids + "'");
       ex.printStackTrace(System.err);
       return null;
     } finally
     {
-      // System.err.println("Took " + (System.currentTimeMillis() - time)
-      // / 1000 + " secs for one call.");
+      // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
+      // time) + " ms");
     }
     return null;
   }
-- 
1.7.10.2