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ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
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LIF reader Illegal argument exception #4035

Open jburel opened 1 year ago

jburel commented 1 year ago 
stacktrace=java.lang.IllegalArgumentException
    at java.nio.Buffer.position(Buffer.java:244)
    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:650)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:494)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:482)
    at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:670)

Error using bf 6.3.1 https://www.openmicroscopy.org/qa2/qa/feedback/33438/

Close if no longer relevant

melissalinkert commented 1 year ago

I can't log in to QA - was there more to the stack trace? In particular, we'd need to know the line number in the reader that this skipBytes call is coming from. Also don't see an uploaded file for 33438, so even with more context it may be difficult to say for sure if this was fixed.

jburel commented 1 year ago 
stacktrace=java.lang.IllegalArgumentException
    at java.nio.Buffer.position(Buffer.java:244)
    at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:650)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:494)
    at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:482)
    at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:670)
    at loci.formats.in.LIFReader.openBytes(LIFReader.java:352)
    at loci.formats.ImageReader.openBytes(ImageReader.java:461)
    at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
    at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
    at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
    at ome.services.blitz.repo.ManagedImportRequestI.parseDataByPlane(ManagedImportRequestI.java:872)
    at
jburel commented 1 year ago

no file associated unfortunately

dominikl commented 5 months ago

Another similar one QA 41692.

melissalinkert commented 5 months ago

@dominikl : I can't log in to QA, it looks like as with the previous QA report there is no file. Which version was QA 41692 reported against?