JAL-2745 update www.ebi.ac.uk to https

[jalview.git] / src / jalview / ws / ebi / EBIFetchClient.java

diff --git a/src/jalview/ws/ebi/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
index 5531512..50151d9 100644 (file)
--- a/src/jalview/ws/ebi/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -29,6 +29,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.net.HttpURLConnection;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
@@ -91,7 +92,7 @@ public class EBIFetchClient
    * @param format
    *          the format wanted
    * @param extension
-   *          for the temporary file to hold response
+   *          for the temporary file to hold response (without separator)
    * @return the file holding the response
    * @throws OutOfMemoryError
    */
@@ -102,7 +103,7 @@ public class EBIFetchClient
     File outFile = null;
     try
     {
-      outFile = File.createTempFile("jalview", ext);
+      outFile = File.createTempFile("jalview", "." + ext);
       outFile.deleteOnExit();
       fetchData(ids, format, outFile);
       if (outFile.length() == 0)
@@ -139,7 +140,8 @@ public class EBIFetchClient
     }
 
     // note: outFile is currently always specified, so return value is null
-    String[] rslt = fetchBatch(querystring.toString(), database, format, outFile);
+    String[] rslt = fetchBatch(querystring.toString(), database, format,
+            outFile);
 
     return (rslt != null && rslt.length > 0 ? rslt : null);
   }
@@ -204,11 +206,17 @@ public class EBIFetchClient
     {
       URL rcall = new URL(url);
 
-      InputStream is = new BufferedInputStream(rcall.openStream());
+      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)
       {
         FileOutputStream fio = new FileOutputStream(outFile);
-        // fio.write("<?xml version='1.0' encoding='UTF-8'?>\n".getBytes());
         byte[] bb = new byte[32 * 1024];
         int l;
         while ((l = is.read(bb)) > 0)
@@ -242,8 +250,7 @@ public class EBIFetchClient
         return null;
       }
       System.err.println("Unexpected exception when retrieving from "
-              + database
-              + "\nQuery was : '" + ids + "'");
+              + database + "\nQuery was : '" + ids + "'");
       ex.printStackTrace(System.err);
       return null;
     } finally
@@ -268,12 +275,12 @@ public class EBIFetchClient
     if (database.equalsIgnoreCase(DBRefSource.EMBL)
             || database.equalsIgnoreCase(DBRefSource.EMBLCDS))
     {
-      url = "http://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
+      url = "https://www.ebi.ac.uk/ena/data/view/" + ids.toLowerCase()
               + (format != null ? "&" + format : "");
     }
     else
     {
-      url = "http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
+      url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
               + database.toLowerCase() + "/" + ids.toLowerCase()
               + (format != null ? "/" + format : "");
     }