Merge branch 'bug/JAL-3633_read_proxy_settings_from_jalview_properties_in_getdown...

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 86282c7..b9fe52f 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,6 +20,8 @@
  */
 package jalview.ws.dbsources;
 
+import java.util.Locale;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -40,13 +42,14 @@ 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;
 
 import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
 import javax.xml.bind.JAXBException;
 import javax.xml.stream.FactoryConfigurationError;
 import javax.xml.stream.XMLInputFactory;
@@ -137,7 +140,7 @@ public class Uniprot extends DbSourceProxyImpl
     startQuery();
     try
     {
-      queries = queries.toUpperCase().replaceAll(
+      queries = queries.toUpperCase(Locale.ROOT).replaceAll(
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
@@ -145,21 +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);
@@ -178,16 +187,12 @@ public class Uniprot extends DbSourceProxyImpl
   SequenceI uniprotEntryToSequence(Entry entry)
   {
     String id = getUniprotEntryId(entry);
-    String seqString = entry.getSequence().getValue();
-
     /*
-     * for backwards compatibility with Castor processing,
-     * remove any internal spaces
+     * Sequence should not include any whitespace, but JAXB leaves these in
      */
-    if (seqString.indexOf(' ') > -1)
-    {
-      seqString = seqString.replace(" ", "");
-    }
+    String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+            "");
+
     SequenceI sequence = new Sequence(id,
             seqString);
     sequence.setDescription(getUniprotEntryDescription(entry));
@@ -197,10 +202,12 @@ public class Uniprot extends DbSourceProxyImpl
      */
     final String dbVersion = getDbVersion();
     List<DBRefEntry> dbRefs = new ArrayList<>();
+    boolean canonical=true;
     for (String accessionId : entry.getAccession())
     {
       DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
-              accessionId);
+              accessionId,null,canonical);
+      canonical=false;
       dbRefs.add(dbRef);
     }
 
@@ -505,7 +512,10 @@ public class Uniprot extends DbSourceProxyImpl
       XMLStreamReader streamReader = XMLInputFactory.newInstance()
               .createXMLStreamReader(is);
       javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
-      jalview.xml.binding.uniprot.Uniprot uniprot = (jalview.xml.binding.uniprot.Uniprot) um.unmarshal(streamReader);
+      JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = 
+                 um.unmarshal(streamReader, jalview.xml.binding.uniprot.Uniprot.class);
+      jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement.getValue();
+      
       if (uniprot != null && !uniprot.getEntry().isEmpty())
       {
         entries = uniprot.getEntry();
@@ -513,6 +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;