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Task #13322 (new)

Opened 3 years ago

Last modified 2 years ago

Bug: ND2 Bfconvert issues

Reported by: bramalingam Owned by:
Priority: minor Milestone: Unscheduled
Component: Bio-Formats Version: Bio-Formats-5.1.8
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

ref: https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8217

Testing summary:
Tested with Bio-Formats 5.3.3 command line tools and the error was reproducible.

Command:

ls29010:bftools533 bramalingam$ ./bfconvert /Users/bramalingam/Desktop/17541/supernd2.nd2 -debug -series 0 /Users/bramalingam/Desktop/17541/test/testseries_new.tiff

Stack trace:

Exception in thread "main" java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 72; Character reference "&#55663" is an invalid XML character.
	at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:265)
	at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:234)
	at ome.xml.model.StructuredAnnotations.asXMLElement(StructuredAnnotations.java:679)
	at ome.xml.model.StructuredAnnotations.asXMLElement(StructuredAnnotations.java:660)
	at ome.xml.model.OME.asXMLElement(OME.java:896)
	at ome.xml.model.OME.asXMLElement(OME.java:773)
	at ome.xml.meta.AbstractOMEXMLMetadata.dumpXML(AbstractOMEXMLMetadata.java:110)
	at ome.xml.meta.OMEXMLMetadataImpl.dumpXML(OMEXMLMetadataImpl.java:105)
	at loci.formats.services.OMEXMLServiceImpl.getOMEXML(OMEXMLServiceImpl.java:465)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:414)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:880)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 72; Character reference "&#55663" is an invalid XML character.
	at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at ome.xml.model.XMLAnnotation.asXMLElement(XMLAnnotation.java:261)
	... 10 more

Change History (2)

comment:1 Changed 3 years ago by dgault

An update from forum thread https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=8217

As of Bio-Formats 5.4.0 the error is now occurring every time regardless of the use of flags. 5.1.10 still works correctly though in all cases tested by the user.

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