Details
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Type: Bug
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Status: Closed
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Priority: Minor
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Resolution: Fixed
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Affects Version/s: 2.10.0
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Fix Version/s: 2.10.0b1
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Component/s: web service bug
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Labels:
Description
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
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
Attachments
Issue Links
- related with
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JAL-2246 Create suite of "Network" tests that verify fetched data is in an expected format
- In Progress