Task #12732 (closed)
Bug: bfconvert writes invalid OME-XML containing MetadataOnly
Reported by: | rleigh | Owned by: | mlinkert |
---|---|---|---|
Priority: | major | Milestone: | 5.1.0 |
Component: | Bio-Formats | Version: | 5.0.8 |
Keywords: | OMETiffWriter | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description
Reproducible with 5.0.8:
tools/bfconvert Beta\ Catenin.lif BetaCatenin.ome.tiff ./tools/tiffcomment BetaCatenin.ome.tiff > xml ./tools/xmlvalid xml Parsing schema path http://www.openmicroscopy.org/Schemas/OME/2013-06/ome.xsd Validating xml cvc-complex-type.2.4.a: Invalid content was found starting with element 'MetadataOnly'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData, "http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane, "http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is expected. cvc-complex-type.2.4.a: Invalid content was found starting with element 'MetadataOnly'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData, "http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane, "http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is expected. cvc-complex-type.2.4.a: Invalid content was found starting with element 'MetadataOnly'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData, "http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane, "http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is expected. cvc-complex-type.2.4.a: Invalid content was found starting with element 'MetadataOnly'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData, "http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane, "http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is expected. cvc-complex-type.2.4.a: Invalid content was found starting with element 'MetadataOnly'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2013-06":TiffData, "http://www.openmicroscopy.org/Schemas/OME/2013-06":Plane, "http://www.openmicroscopy.org/Schemas/SA/2013-06":AnnotationRef}' is expected.
Note that the showinf -omexml does validate, but it's validating the OME-XML after we've converted it and mangled it; it's not validating the original OME-XML which it silently accepts without warning.
Change History (5)
comment:1 Changed 9 years ago by mlinkert
- Milestone changed from Unscheduled to 5.1.0
comment:2 Changed 9 years ago by mlinkert
- Resolution set to fixed
- Status changed from new to closed
comment:3 Changed 9 years ago by rleigh
Is this something we want to backport? Should we treat the creation of invalid OME-XML as a serious problem given the interoperability issues it could cause?
comment:4 Changed 9 years ago by mlinkert
Likely not worth backporting unless a 5.0.9 is planned imminently. I don't think this is a particularly serious problem, as actually reading the exported files should be unaffected.
comment:5 Changed 9 years ago by rleigh
It's certainly not an issue with the Java OME-TIFF reader, since it silently ignores the problem when processing the data. But from the POV of an external consumer of OME-XML, we're writing out invalid nonconforming data.
I can reproduce as well with the v5.0.8 tag, but the same test on develop results in valid XML with no MetadataOnly?.