Details
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Type: Bug
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Status: Open
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Priority: Critical
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Resolution: Unresolved
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Affects Version/s: 2.8.2, 2.8.2b1, 2.9, 2.10.0, 2.11.0
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Fix Version/s: None
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Component/s: data retrieval services, file format issue, na
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Labels:
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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)
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)