*/
package jalview.ws.dbsources;
+import java.util.Locale;
+
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
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;
startQuery();
try
{
- queries = queries.toUpperCase().replaceAll(
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- String downloadstring = getDomain() + "/uniprot/" + queries
- + ".xml";
+ String downloadstring = getDomain() + "/uniprot/" + queries + ".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);
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(" ", "");
- }
- SequenceI sequence = new Sequence(id,
- seqString);
+ String seqString = entry.getSequence().getValue().replaceAll("\\s*",
+ "");
+
+ SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
/*
*/
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);
}
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();
} 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;