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  1. Jalview
  2. JAL-2254

Fetch DBRefs from EMBL gives Illegal Text data found as child of: ROOT

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      Load http://www.jalview.org/tutorial/alignment.fa and go to Web Service | Fetch DB References | From EMBL … UNIPROT, then choose EMBL. This runs and completes with no effect, console output shows:

      Verifying against EMBL
      INFO : org.exolab.castor.mapping.Mapping - Loading mapping descriptors from file:/Users/kmourao/jalview/jalview/classes/embl_mapping.xml
      INFO - Loading mapping descriptors from file:/Users/kmourao/jalview/jalview/classes/embl_mapping.xml
      Illegal Text data found as child of: ROOT
        value: "Entry: fer1_sollc display type is either not supported or entry is not found."{File: [not available]; line: 4; column: 8}
      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:134)
      at jalview.datamodel.xdb.embl.EmblFile.getEmblFile(EmblFile.java:97)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:101)
      at jalview.ws.dbsources.EmblXmlSource.getEmblSequenceRecords(EmblXmlSource.java:75)
      at jalview.ws.dbsources.EmblSource.getSequenceRecords(EmblSource.java:94)
      at jalview.ws.DBRefFetcher.run(DBRefFetcher.java:418)
      at java.lang.Thread.run(Thread.java:745)
      Caused by: org.xml.sax.SAXException: Illegal Text data found as child of: ROOT
        value: "Entry: fer1_sollc display type is either not supported or entry is not found."
      at org.exolab.castor.xml.UnmarshalHandler.endElement(UnmarshalHandler.java:874)
      at org.exolab.castor.xml.UnmarshalHandler.endElement(UnmarshalHandler.java:1108)
      at org.apache.xerces.parsers.AbstractSAXParser.endElement(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

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              kmourao Kira Mourão
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                Created:
                Updated:
                Resolved: