Validation based on hdf tree traversal

[domna]

This is a sketch of a hdf tree traversal by the rough ideas I already had in my head I didn't want to forget during my holidays. With the additional functions I added during the development #323 this easily checks for all the elements in the whole tree dynamically. Mainly it misses the actual checking routines for fields and attributes. Generally, it seems it's much more straightforward than the verification in the dict, because we have much less specialities we need to consider. However, it could be that the performance is not as good, because we traverse the hdf each time. But I tried to build a cached recursive function to balance that off.

This can be used as a proper basis for #133.

Development branches:

1. pynxtools: hdf-based-validation
2. nexus_definition: test_nxdl_hdf5_validator

Needs care on the following points:

• Does not take all required fields in entry level

from pynxtools.dataconverter.template import Template  #

from pynxtools.dataconverter import helpers

nxdl_root = None
# nxdl_name =  "NXtest_extended"
nxdl_name = "NXhdf5_validator_2"
# nxdl_name = "NXspm"
if nxdl_root is None:
    nxdl_root, _ = helpers.get_nxdl_root_and_path(nxdl=nxdl_name)

template = Template()
helpers.generate_template_from_nxdl(nxdl_root, template)

print(template)

generate:

{
"/ENTRY[entry]/experiment_result/hdf5_validator_2_intensity": "None",
"/ENTRY[entry]/hdf5_validator_1_program_name": "None",
"/ENTRY[entry]/hdf5_validator_1_required/required_field": "None",
"/ENTRY[entry]/hdf5_validator_2_users_req/required_field": "None"
}

But expecting field "/ENTRY[entry]/hdf5_validator_2_program_name": "None" as well.

• Add documentation

[coveralls]

Pull Request Test Coverage Report for Build 9517068942

Details

• 1 of 1 (100.0%) changed or added relevant line in 1 file are covered.
• 1 unchanged line in 1 file lost coverage.
• Overall coverage remained the same at 96.916%

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Files with Coverage Reduction	New Missed Lines	%
tests/dataconverter/test_nexus_tree.py	1	87.23%

Totals
Change from base Build 9516791059:	0.0%
Covered Lines:	597
Relevant Lines:	616

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💛 - Coveralls