Context Navigation

Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #9066 (closed)

Opened 7 years ago

Closed 7 years ago

Last modified 7 years ago

Bug: Import li-flim

Reported by:	jburel	Owned by:	mlinkert
Priority:	critical	Milestone:	OMERO-4.4
Component:	Bio-Formats	Version:	n.a.
Keywords:	n.a.	Cc:	ux@…
Resources:	n.a.	Referenced By:	n.a.
References:	n.a.	Remaining Time:	n.a.
Sprint:	n.a.

Description

The following file li-flim/jean-marie/Flimdata/D Reference fluorescein4ns-CFPbpFILTER-multifreq.fli failed to import

Error below

java.io.EOFException: Unexpected end of ZLIB input stream
	at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:216)
	at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:134)
	at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:87)
	at java.io.DataInputStream.readFully(DataInputStream.java:176)
	at java.io.DataInputStream.readFully(DataInputStream.java:152)
	at loci.formats.in.LiFlimReader.openBytes(LiFlimReader.java:173)
	at loci.formats.ImageReader.openBytes(ImageReader.java:401)
	at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:184)
	at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:213)
	at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:304)
	at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
	at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:872)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:797)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:573)
	at

References

Change History (4)

comment:1 Changed 7 years ago by mlinkert

Resolution set to fixed
Status changed from new to closed

Fixed with this commit: https://github.com/melissalinkert/bioformats/commit/dbbef64c91444a817ee25c6a6f4be24f6e7ef814

comment:2 Changed 7 years ago by jburel

Resolution fixed deleted
Status changed from closed to reopened

Imported with this morning build. same error.

comment:3 Changed 7 years ago by mlinkert

Resolution set to fixed
Status changed from reopened to closed

That's because the submodule pointer wasn't updated, so the fixes never made it into the build. The submodule will be updated before tomorrow's build.

comment:4 Changed 7 years ago by jburel

Retested and imported correctly.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

Download in other formats: