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  1. Jalview
  2. JAL-1498

Jalview cannot cope with 'inexact CDS records' in ENA

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    • Urgency:
      Urgent

      Description

      Originally: "ENA record parser does not pick up all exons in AC005200"
      This is also a blocker for roundtripping from Uniprot:MYG_SHEEP->ENA

      It should be possible to round trip from ENA AC005200 to Uniprot and back (as with all ENA transcript records with CDS regions annotated). However, retrieve xRefs from EMBL -> Uniprot -> EMBL retrieves a different transcript, and a subsequent view xRefs->Protein opens the original AC005200 entry.

      Exceptions on console output (for ReferenceSeq-2.8.1 branch) were:
      The element type "EMBL_Services" must be terminated by the matching end-tag "</EMBL_Services>".{File: [not available]; line: 2051; column: 7}
      at org.exolab.castor.xml.Unmarshaller.unmarshal(Unmarshaller.java:740)
      at org.exolab.castor.xml.Unmarshaller.unmarshal(Unmarshaller.java:596)
      at jalview.datamodel.xdb.embl.EmblFile.getEmblFile(EmblFile.java:116)
      at jalview.datamodel.xdb.embl.EmblFile.getEmblFile(EmblFile.java:81)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:95)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:69)
      at jalview.ws.dbsources.EmblCdsSouce.getSequenceRecords(EmblCdsSouce.java:63)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:518)
      at java.lang.Thread.run(Thread.java:744)
      Caused by: org.xml.sax.SAXParseException; lineNumber: 2051; columnNumber: 7; The element type "EMBL_Services" must be terminated by the matching end-tag "</EMBL_Services>".
      at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
      at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
      at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
      at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
      at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
      at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
      at org.exolab.castor.xml.Unmarshaller.unmarshal(Unmarshaller.java:726)
      ... 8 more
      Caused by: org.xml.sax.SAXParseException; lineNumber: 2051; columnNumber: 7; The element type "EMBL_Services" must be terminated by the matching end-tag "</EMBL_Services>".
      at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
      at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
      at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
      at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
      at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
      at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
      at org.exolab.castor.xml.Unmarshaller.unmarshal(Unmarshaller.java:726)
      at org.exolab.castor.xml.Unmarshaller.unmarshal(Unmarshaller.java:596)
      at jalview.datamodel.xdb.embl.EmblFile.getEmblFile(EmblFile.java:116)
      at jalview.datamodel.xdb.embl.EmblFile.getEmblFile(EmblFile.java:81)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:95)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:69)
      at jalview.ws.dbsources.EmblCdsSouce.getSequenceRecords(EmblCdsSouce.java:63)
      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:518)
      at java.lang.Thread.run(Thread.java:744)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: