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Task #11245 (closed)

Opened 11 years ago

Closed 11 years ago

BUG: Import fail if XML Comment

Reported by: ajpatterson Owned by: mlinkert
Priority: blocker Milestone: n.a.
Component: Bio-Formats Version: 4.4.8
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

If there is an XML comment inside an XMLAnnotation in an OME-TIFF file the import fails.

If I try an showinf -debug FLIM-modulo-sample7.tiff it is ok

If I try an showinf -debug FLIM-modulo-sample6.tiff it crashes

loci.formats.in.OMETiffReader.initFile(/Users/andrew/Work/bioformats/components/specification/samples/2013-06/FLIM-modulo-sample6.tiff)
Expecting node name of Annotation got XMLAnnotation
Expecting node name of TextAnnotation got XMLAnnotation
Exception in thread "main" java.lang.ClassCastException: com.sun.org.apache.xerces.internal.dom.DeferredCommentImpl cannot be cast to org.w3c.dom.Element
	at loci.formats.services.OMEXMLServiceImpl.getOriginalMetadata(OMEXMLServiceImpl.java:547)
	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:376)
	at loci.formats.FormatReader.setId(FormatReader.java:1333)
	at loci.formats.ImageReader.setId(ImageReader.java:762)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:564)
	at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1017)
	at loci.formats.tools.ImageInfo.main(ImageInfo.java:1062)

Only difference is the comment in the XML Annotation

Attachments (2)

FLIM-modulo-sample6.tiff​ (449.4 KB) - added by ajpatterson 11 years ago.
FLIM-modulo-sample7.tiff​ (449.4 KB) - added by ajpatterson 11 years ago.

Download all attachments as: .zip

Change History (3)

Changed 11 years ago by ajpatterson

Changed 11 years ago by ajpatterson

comment:1 Changed 11 years ago by mlinkert

  • Resolution set to fixed
  • Status changed from new to closed

This should have been fixed with ​https://github.com/openmicroscopy/bioformats/pull/643

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