WIP: ShEx validation method

[stain]

Work in progress that adds ShEx validation of Workflow Run crates.

runcrate validate tests/data/profile-examples/process-ex1/
/home/stain/miniconda3/envs/validate/lib/python3.11/site-packages/rdflib_jsonld/__init__.py:9: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.0.  Please remove rdflib-jsonld from your project's dependencies.
  warnings.warn(
Validating RO-Crate tests/data/profile-examples/process-ex1
   OK File existence
   OK File size
   OK Metadata file existence
   OK Json check
   OK Json-ld check
   OK File descriptor check
ERROR Direct property check:
      Semantic Error: datePublished of Direct Property ./ is not in ISO 8601 date format or not Provided
   OK Referencing check
   OK Encoding check
   OK Web-based data entity check
   OK Person entity check
   OK Organization entity check
   OK Contact information check
   OK Citation property check
   OK Publisher property check
   OK Funder property check
   OK Licensing property check
   OK Places property check
   OK Time property check
ERROR Scripts and workflow check:
      Semantic Error: Scripts and Workflow is Wrong
Validating against Process Run profile
CONFORMS

The initial checks on the RO-Crate are from https://github.com/ResearchObject/ro-crate-validator-py but may not be always appropriate. E.g. above it should skip the Scripts-check when it is a process crate profile being tested.

Note that so far only process run profile is complete. I've taken the stand that SHOULDs are required by the validation, as breaking a should is something done knowingly. However this may not be appropriate for checking the inherted profiles.

The remaining workflow/provenance profiles are not finished, as I think I need to add a second ComputationalWorkflow bioschemas profile that is currently just implied.

[simleo]

See workflowhub-eu/about#46 re: ComputationalWorkflow