From 79c9d10d17b3ddf75110ab44a43cf12505baa7dd Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 29 Sep 2017 16:47:48 +0100
Subject: [PATCH] JAL-2745 JAL-2748 direct download of XML from uniprot.org
 patch for 2.10.2b1 branch

---
 src/jalview/ws/dbsources/Uniprot.java |   28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 30808fb..686cd83 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -30,13 +30,13 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 import jalview.datamodel.UniprotFile;
-import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
-import java.io.File;
-import java.io.FileReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.io.Reader;
 import java.net.URL;
+import java.net.URLConnection;
 import java.util.ArrayList;
 import java.util.Vector;
 
@@ -161,17 +161,21 @@ public class Uniprot extends DbSourceProxyImpl
       queries = queries.toUpperCase().replaceAll(
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
-      EBIFetchClient ebi = new EBIFetchClient();
-      // uniprotxml parameter required since december 2007
-      // uniprotkb dbname changed introduced december 2008
-      File file = ebi.fetchDataAsFile("uniprotkb:" + queries, "uniprotxml",
-              "xml");
+
+      String downloadstring = "http://www.uniprot.org/uniprot/" + queries
+              + ".xml";
+      URL url = null;
+      URLConnection urlconn = null;
+
+      url = new URL(downloadstring);
+      urlconn = url.openConnection();
+      InputStream istr = urlconn.getInputStream();
       Vector<UniprotEntry> entries = getUniprotEntries(
-              new FileReader(file));
+              new InputStreamReader(istr, "UTF-8"));
 
       if (entries != null)
       {
-        ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+        ArrayList<SequenceI> seqs = new ArrayList<>();
         for (UniprotEntry entry : entries)
         {
           seqs.add(uniprotEntryToSequenceI(entry));
@@ -183,8 +187,10 @@ public class Uniprot extends DbSourceProxyImpl
       return al;
     } catch (Exception e)
     {
-      stopQuery();
       throw (e);
+    } finally
+    {
+      stopQuery();
     }
   }
 
-- 
1.7.10.2