*/
package jalview.ws.dbsources;
-import java.io.InputStream;
-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;
-import javax.xml.stream.XMLStreamException;
-import javax.xml.stream.XMLStreamReader;
-
-import com.stevesoft.pat.Regex;
-
+import java.util.Locale;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
-import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import jalview.xml.binding.uniprot.DbReferenceType;
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.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;
+import javax.xml.stream.XMLStreamException;
+import javax.xml.stream.XMLStreamReader;
+
+import com.stevesoft.pat.Regex;
+
/**
* This class queries the Uniprot database for sequence data, unmarshals the
* returned XML, and converts it to Jalview Sequence records (including attached
private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
private static final String BAR_DELIMITER = "|";
-
private static Regex ACCESSION_REGEX;
/**
startQuery();
try
{
- queries = queries.toUpperCase().replaceAll(
+ queries = queries.toUpperCase(Locale.ROOT).replaceAll(
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
+ ".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)
stopQuery();
return al;
+
} catch (Exception e)
{
throw (e);
*/
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);
}
} 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;