From: Jim Procter <j.procter@dundee.ac.uk>
Date: Wed, 29 Sep 2021 14:50:09 +0000 (+0100)
Subject: JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record
X-Git-Tag: Release_2_11_2_0~30^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d80fbc33dfc7ece325c896b33c3296a075e48a30;hp=ab61239b20e51f02341b658a0f74a8c8acd904ec;p=jalview.git

JAL-3884 squish alarming but harmless errors when uniprot doesn’t have a record
---

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index a80a530..b9fe52f 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -34,7 +34,6 @@ import jalview.datamodel.SequenceI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.StringUtils;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
-import jalview.xml.binding.embl.ROOT;
 import jalview.xml.binding.uniprot.DbReferenceType;
 import jalview.xml.binding.uniprot.Entry;
 import jalview.xml.binding.uniprot.FeatureType;
@@ -43,8 +42,8 @@ import jalview.xml.binding.uniprot.PositionType;
 import jalview.xml.binding.uniprot.PropertyType;
 
 import java.io.InputStream;
+import java.net.HttpURLConnection;
 import java.net.URL;
-import java.net.URLConnection;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
@@ -149,21 +148,27 @@ public class Uniprot extends DbSourceProxyImpl
               + ".xml";
 
       URL url = new URL(downloadstring);
-      URLConnection urlconn = url.openConnection();
-      InputStream istr = urlconn.getInputStream();
-      List<Entry> entries = getUniprotEntries(istr);
-      if (entries != null)
+      HttpURLConnection urlconn = (HttpURLConnection)url.openConnection();
+      // anything other than 200 means we don't have data
+      // TODO: JAL-3882 reuse the EnsemblRestClient's fair 
+      // use/backoff logic to retry when the server tells us to go away
+      if (urlconn.getResponseCode() == 200)
       {
-        List<SequenceI> seqs = new ArrayList<>();
-        for (Entry entry : entries)
+        InputStream istr = urlconn.getInputStream();
+        List<Entry> entries = getUniprotEntries(istr);
+        if (entries != null)
         {
-          seqs.add(uniprotEntryToSequence(entry));
+          List<SequenceI> seqs = new ArrayList<>();
+          for (Entry entry : entries)
+          {
+            seqs.add(uniprotEntryToSequence(entry));
+          }
+          al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
         }
-        al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
       }
-
       stopQuery();
       return al;
+      
     } catch (Exception e)
     {
       throw (e);
@@ -518,6 +523,11 @@ public class Uniprot extends DbSourceProxyImpl
     } catch (JAXBException | XMLStreamException
             | FactoryConfigurationError e)
     {
+      if (e instanceof javax.xml.bind.UnmarshalException && e.getCause()!=null && e.getCause() instanceof XMLStreamException && e.getCause().getMessage().contains("[row,col]:[1,1]"))
+      {
+        // trying to parse an empty stream
+        return null;
+      }
       e.printStackTrace();
     }
     return entries;