Ticket #383 (closed defect: fixed)
Opened 2009-04-23T15:16:25-05:00
Last modified 2010-07-13T17:02:33-05:00
Generated OME-TIFF files have elements in the wrong order
| Reported by: | curtis | Owned by: | curtis |
|---|---|---|---|
| Priority: | major | Milestone: |
|
| Component: | bio-formats | Severity: | serious |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: |
Description
There are many cases, but for example, according to the OME-XML schema, Instrument elements must precede Image elements:
$ bfconvert data/al3d/franz/Iron\ Plate.al3d Iron\ Plate.ome.tif
data/al3d/franz/Iron Plate.al3d [Alicona AL3D] -> Iron Plate.ome.tif [OME-TIFF] ... [done]
1.339s elapsed (734.0+166.0ms per image, 438ms overhead)
$ showinf -nopix -omexml Iron\ Plate.ome.tif
Checking file format [OME-TIFF]
...
Generating OME-XML (schema version 2008-09)
...
<Image DefaultPixels="Pixels:0" ID="Image:0" Name="">
...
<Instrument ID="Instrument:0">
...
Validating OME-XML
...
error: cvc-complex-type.2.4.a: Invalid content was found starting with element 'Instrument'. One of '{"http://www.openmicroscopy.org/Schemas/OME/2008-09":Image, "http://www.openmicroscopy.org/Schemas/STD/2008-09":SemanticTypeDefinitions, "http://www.openmicroscopy.org/Schemas/AnalysisModule/2008-09":AnalysisModuleLibrary, "http://www.openmicroscopy.org/Schemas/CA/2008-09":CustomAttributes, "http://www.openmicroscopy.org/Schemas/SA/2008-09":StructuredAnnotations}' is expected.
Change History
comment:1 Changed 2009-04-23T15:19:00-05:00 by curtis
comment:2 Changed 2009-12-17T12:00:52-06:00 by curtis
- Status changed from new to closed
- Resolution set to fixed
This problem was fixed a while ago in r5467. It uses a stylesheet (thanks to Andrew Patterson) to reorder the elements into their correct order. Eventually, the OME-XML Java library will generate output XML in the correct order by default, as described above, but for now the stylesheet does the trick.
comment:3 Changed 2010-07-09T12:55:02-05:00 by melissa
- Milestone bio-formats-4.2 deleted
Milestone bio-formats-4.2 deleted
The solution will be to alter the xsd-fu class template to generate OME-XML Java library classes that do not rely on the org.w3c.dom implementation. That way, no matter what order elements are registered in the model, the generated XML will be output in the proper order.