Backport: Timeout for querying for Uniprot features (#933)

Author: labkey-jeckels

protein/api-src/org/labkey/api/protein/fasta/FastaProtein.java

@@ -84,7 +84,7 @@ public FastaProtein(String header, byte[] bytes)
         if (header.startsWith("gi|"))
         {
             firstAliasIndex = header.indexOf(" gi|", 2) + 1;
-            if (firstAliasIndex < 0 || firstAliasIndex > 30)
+            if (firstAliasIndex > 30)
                 firstAliasIndex = 0;
         }
 

protein/src/org/labkey/protein/ProteinServiceImpl.java

@@ -300,6 +300,8 @@ public List<ProteinFeature> load(@NotNull String accession, @Nullable Object arg
                 HttpURLConnection con = (HttpURLConnection) obj.openConnection();
                 con.setRequestProperty("Accept", "application/xml");
                 con.setRequestMethod("GET");
+                con.setConnectTimeout(20_000);
+                con.setReadTimeout(20_000);
                 int responseCode = con.getResponseCode();
                 if (responseCode == HttpURLConnection.HTTP_OK)
                 { // success
@@ -370,7 +372,7 @@ else if (location.getChildNodes().getLength() == 2)
                 {
                     if (responseCode != 404)
                     {
-                        LOG.error("HTTP GET failed to " + url + " with error code " + responseCode);
+                        LOG.warn("HTTP GET failed to " + url + " with error code " + responseCode);
                     }
                     else
                     {