add lxml as parser in from_xml calls

[colobas]

Description

Add parser="lxml" to ome_types.from_xml calls.
This silences a FutureWarning, which lets us know that ome_types's default parser will be changing from xmlschema to lxml. This way we're adopting the incoming change explicitly, and since we're already depending on lxml we're not requiring any additional libs and we can stop requiring xmlschema.

I wanted to add a test to make sure the right error is raised here but not quite sure how to produce a corrupted ome.tiff

Pull request recommendations:

• Name your pull request your-development-type/short-description. Ex: feature/read-tiff-files
• Link to any relevant issue in the PR description. Ex: Resolves [gh-], adds tiff file format support
• Provide relevant tests for your feature or bug fix.
• Provide or update documentation for any feature added by your pull request.

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[codecov-commenter]

Codecov Report

Base: 93.90% // Head: 68.79% // Decreases project coverage by -25.11% ⚠️

Coverage data is based on head (65a7981) compared to base (8099b70).
Patch coverage: 66.66% of modified lines in pull request are covered.

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #442       +/-   ##
===========================================
- Coverage   93.90%   68.79%   -25.12%     
===========================================
  Files          46       46               
  Lines        4001     4002        +1     
===========================================
- Hits         3757     2753     -1004     
- Misses        244     1249     +1005     

Impacted Files	Coverage Δ
aicsimageio/writers/ome_tiff_writer.py	66.23% <50.00%> (-26.07%)	⬇️
aicsimageio/readers/ome_tiff_reader.py	84.54% <75.00%> (-13.62%)	⬇️
aicsimageio/tests/test_aics_image.py	0.00% <0.00%> (-100.00%)	⬇️
aicsimageio/tests/test_dimensions.py	0.00% <0.00%> (-100.00%)	⬇️
aicsimageio/tests/utils/test_io_utils.py	0.00% <0.00%> (-100.00%)	⬇️
aicsimageio/tests/readers/test_glob_reader.py	0.00% <0.00%> (-100.00%)	⬇️
aicsimageio/tests/writers/test_ome_tiff_writer.py	0.00% <0.00%> (-100.00%)	⬇️
...icsimageio/tests/readers/test_array_like_reader.py	0.00% <0.00%> (-100.00%)	⬇️
aicsimageio/tests/readers/test_tiff_reader.py	0.00% <0.00%> (-99.04%)	⬇️
aicsimageio/tests/test_transforms.py	0.00% <0.00%> (-99.00%)	⬇️
... and 13 more

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[evamaxfield]

Would approve but it seems like you just need to update the tests which handle / check exceptions that are returned from bad parsing.

[colobas]

So I updated the errors we're checking for related to XML parsing here which solved part of the problem with the tests.

However, there are three test cases which should be failing but aren't:

• variance-cfe.ome.tiff and pre-variance-cfe.ome.tiff used to fail with a XMLSchemaChildrenValidationError saying

  failed validating <Element '{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels' at 0x7f1acc837830> with  XsdGroup(model='sequence', occurs=[1, 1]):
  E
  E                   Reason: Unexpected child with tag 'OME:Plane' at position 5. Tag ('OME:BinData' | 'OME:TiffData' |  'OME:MetadataOnly') expected.
  

• 3d-cell-viewer.ome.tiff used to fail with a XMLSchemaChildrenValidationError saying

  failed validating <Element '{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels' at 0x7f1acc8f41d0> with XsdGroup(model='sequence', occurs=[1, 1]):
  E
  E                   Reason: Unexpected child with tag 'OME:Channel' at position 302.
  

Any ideas why these wouldn't get thrown with parser="lxml" but do get thrown by parser="xmlschema"? Or tips on where to look for answers?

[SeanLeRoy]

Duplicate of #478 now?

[toloudis]

oops, I totally forgot about this. I suppose it is a duplicate yes

[SeanLeRoy]

Closing as duplicate of #478