Details
Description
Exceptions like below are raised when invalid IDs or non-existent accessions are received from uniprot. These do not impact function, but they are output to the console log, which can result in slow downs and confusion.
java.io.FileNotFoundException: https://www.uniprot.org/uniprot/A0A2X2CT13;(S)-2-HYDROXY-ACID.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)
at jalview.ws.dbsources.Uniprot.getSequenceRecords(Uniprot.java:149)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:382)
at java.lang.Thread.run(Thread.java:748)
javax.xml.bind.UnmarshalException
- with linked exception:
[javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Premature end of file.]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.handleStreamException(UnmarshallerImpl.java:470)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:402)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:371)
at jalview.ws.dbsources.Uniprot.getUniprotEntries(Uniprot.java:504)
at jalview.ws.dbsources.Uniprot.getSequenceRecords(Uniprot.java:150)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:382)
at java.lang.Thread.run(Thread.java:748)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Premature end of file.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:604)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.StAXStreamConnector.bridge(StAXStreamConnector.java:149)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:400)
... 5 more
java.io.FileNotFoundException: https://www.uniprot.org/uniprot/A0A2X2CT13;(S)-2-HYDROXY-ACID.xml
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:263)
at jalview.ws.dbsources.Uniprot.getSequenceRecords(Uniprot.java:149)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:382)
at java.lang.Thread.run(Thread.java:748)
javax.xml.bind.UnmarshalException
- with linked exception:
[javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Premature end of file.]
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.handleStreamException(UnmarshallerImpl.java:470)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:402)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal(UnmarshallerImpl.java:371)
at jalview.ws.dbsources.Uniprot.getUniprotEntries(Uniprot.java:504)
at jalview.ws.dbsources.Uniprot.getSequenceRecords(Uniprot.java:150)
at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:382)
at java.lang.Thread.run(Thread.java:748)
Caused by: javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,1]
Message: Premature end of file.
at com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:604)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.StAXStreamConnector.bridge(StAXStreamConnector.java:149)
at com.sun.xml.internal.bind.v2.runtime.unmarshaller.UnmarshallerImpl.unmarshal0(UnmarshallerImpl.java:400)
... 5 more