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  1. Jalview
  2. JAL-3884

Suppress XMLParsing Error exceptions when retrieving Uniprot database refs for sequences

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.11.0, 2.11.1
    • Fix Version/s: 2.11.2, 2.11.2.0
    • Component/s: None
    • Labels:
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      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

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated:
              Resolved: