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Ticket #298 (closed defect: fixed)

Opened 2008-05-24T08:45:06-05:00

Last modified 2008-05-29T15:54:18-05:00

SPW changes break Flex reader

Reported by:	melissa	Owned by:	curtis
Priority:	major	Milestone:
Component:	bio-formats	Severity:	serious
Keywords:		Cc:
Blocked By:		Blocking:

Description

Attempting to read a Flex file with r4065 produces the following exception:

melissa@zu:~$ inf -omexml /data/flex/karsten/BioFormats_FLEX181_PKI/SomeBasicFiles/003001000.flex
Checking file format [Evotec Flex]
Initializing reader
        Reading IFDs
        Populating metadata
Exception in thread "main" java.lang.ClassCastException: ome.xml.CustomNode cannot be cast to ome.xml.r200802.spw.PlateNode
           at loci.formats.ome.OMEXML200802Metadata.getPlateNode(OMEXML200802Metadata.java:2693)
           at loci.formats.ome.OMEXML200802Metadata.setPlateName(OMEXML200802Metadata.java:1971)
           at loci.formats.meta.FilterMetadata.setPlateName(FilterMetadata.java:682)
           at loci.formats.in.FlexReader$FlexHandler.characters(FlexReader.java:230)
           at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.characters(AbstractSAXParser.java:538)
           at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:461)
           at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807)
           at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
           at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107)
           at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
           at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)
           at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)
           at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)
           at loci.formats.in.FlexReader.initStandardMetadata(FlexReader.java:145)
           at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:189)
           at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:763)
           at loci.formats.FormatReader.setId(FormatReader.java:216)
           at loci.formats.ImageReader.setId(ImageReader.java:564)
           at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:227)
           at loci.formats.tools.ImageInfo.main(ImageInfo.java:622)

The same file is read properly using r4064.

Change History

comment:1 Changed 2008-05-29T15:54:18-05:00 by curtis

Status changed from new to closed
Resolution set to fixed

Fixed in r4075.