X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Febi%2FEBIFetchClient.java;h=1d04351f06a9f057a9b6d1e5e58dab20ae245998;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=50151d962f92fa0c1810d19485712c373985c5a9;hpb=2467c106c4be8b70f244a160739be63efc6b58ea;p=jalview.git

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 50151d9..1d04351 100644
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -20,13 +20,15 @@
  */
 package jalview.ws.ebi;
 
+import java.util.Locale;
+
 import jalview.datamodel.DBRefSource;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
-import java.io.BufferedInputStream;
 import java.io.BufferedReader;
 import java.io.File;
-import java.io.FileOutputStream;
+import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.HttpURLConnection;
@@ -91,7 +93,7 @@ public class EBIFetchClient
    *          the query formatted as db:query1;query2;query3
    * @param format
    *          the format wanted
-   * @param extension
+   * @param ext
    *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
@@ -193,50 +195,40 @@ public class EBIFetchClient
    * @param database
    * @param format
    * @param outFile
-   * @return
+   * @return array of lines from EBI only if outFile is null (which it will not
+   *         be)
    * @throws OutOfMemoryError
    */
   String[] fetchBatch(String ids, String database, String format,
           File outFile) throws OutOfMemoryError
   {
-    // long time = System.currentTimeMillis();
     String url = buildUrl(ids, database, format);
-
+    InputStream is = null;
+    BufferedReader br = null;
     try
     {
       URL rcall = new URL(url);
-
       HttpURLConnection conn = (HttpURLConnection) rcall.openConnection();
       int responseCode = conn.getResponseCode();
-      if (responseCode != 200)
-      {
-        System.out.println("Warning: response code " + responseCode
-                + " for " + url);
-      }
-      InputStream is = new BufferedInputStream(conn.getInputStream());
-      if (outFile != null)
+      if (responseCode == 200)
       {
-        FileOutputStream fio = new FileOutputStream(outFile);
-        byte[] bb = new byte[32 * 1024];
-        int l;
-        while ((l = is.read(bb)) > 0)
+        is = conn.getInputStream();
+        if (outFile != null)
         {
-          fio.write(bb, 0, l);
+          Platform.streamToFile(is, outFile);
+          return null;
         }
-        fio.close();
-        is.close();
-      }
-      else
-      {
-        BufferedReader br = new BufferedReader(new InputStreamReader(is));
+        br = new BufferedReader(new InputStreamReader(is));
         String rtn;
-        List<String> arl = new ArrayList<String>();
+        List<String> arl = new ArrayList<>();
         while ((rtn = br.readLine()) != null)
         {
           arl.add(rtn);
         }
-        return arl.toArray(new String[arl.size()]);
+        return (String[]) arl.toArray();
       }
+      System.err.println(
+              "Warning: response code " + responseCode + " for " + url);
     } catch (OutOfMemoryError er)
     {
       System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + database
@@ -244,19 +236,33 @@ public class EBIFetchClient
       throw er;
     } catch (Exception ex)
     {
-      if (ex.getMessage().startsWith(
+      if (!ex.getMessage().startsWith(
               "uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
       {
-        return null;
+        System.err.println("Unexpected exception when retrieving from "
+                + database + "\nQuery was : '" + ids + "'");
+        ex.printStackTrace(System.err);
       }
-      System.err.println("Unexpected exception when retrieving from "
-              + database + "\nQuery was : '" + ids + "'");
-      ex.printStackTrace(System.err);
-      return null;
     } finally
     {
-      // System.err.println("EBIFetch took " + (System.currentTimeMillis() -
-      // time) + " ms");
+      if (is != null)
+      {
+        try
+        {
+          is.close();
+        } catch (IOException e)
+        {
+        }
+      }
+      if (br != null)
+      {
+        try
+        {
+          br.close();
+        } catch (IOException e)
+        {
+        }
+      }
     }
     return null;
   }
@@ -275,13 +281,13 @@ public class EBIFetchClient
     if (database.equalsIgnoreCase(DBRefSource.EMBL)
             || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
     {
-      url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
-              + (format != null ? "&" + format : "");
+      url = "https://www.ebi.ac.uk/ena/browser/api/embl/"
+              + ids.toLowerCase(Locale.ROOT) + "?download=true&gzip=true";
     }
     else
     {
       url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
-              + database.toLowerCase() + "/" + ids.toLowerCase()
+              + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
               + (format != null ? "/" + format : "");
     }
     return url;