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Task #12529 (closed)

Opened 10 years ago

Closed 9 years ago

BUG: Bioformats Evotec FLEX File reader (IO exception)

Reported by:	bramalingam	Owned by:	jburel
Priority:	minor	Milestone:	5.1.1
Component:	Bio-Formats	Version:	5.0.3
Keywords:	n.a.	Cc:	kevinchen858@…, mlinkert
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description (last modified by jburel)

Related to issue : http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-August/004660.html

QA : 9456

Stack trace of the error :

java.io.IOException
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:436)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:414)
	at loci.formats.in.FlexReader.parseFlexFile(FlexReader.java:818)
	at loci.formats.in.FlexReader.groupFiles(FlexReader.java:1278)
	at loci.formats.in.FlexReader.initFlexFile(FlexReader.java:507)
	at loci.formats.in.FlexReader.initFile(FlexReader.java:340)
	at loci.formats.FormatReader.setId(FormatReader.java:1317)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:494)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:144)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)
Caused by: org.xml.sax.SAXParseException: Content is not allowed in trailing section.
	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
	at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:174)
	at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:388)
	at com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1476)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDriver.next(XMLDocumentScannerImpl.java:1457)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:647)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:513)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:815)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:744)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:128)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:543)
	at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
	at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
	at loci.common.xml.XMLTools.parseXML(XMLTools.java:428)
	... 16 more

References

Change History (4)

comment:1 Changed 9 years ago by mlinkert

Milestone changed from Unscheduled to 5.1.1

Moving to 5.1.1 for triage.

comment:2 Changed 9 years ago by jburel

Description modified (diff)

comment:3 Changed 9 years ago by jburel

Cc mlinkert added
Owner changed from mlinkert to jburel

comment:4 Changed 9 years ago by jburel

Resolution set to fixed
Status changed from new to closed

https://github.com/openmicroscopy/bioformats/pull/1722

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