Sample schema refactor

[sveinugu]

Refactored sample schema to allow for several variants of sample_types, dependent on the biospecimen_class property (renamed from biomaterial_type). Added ontology validation of biospecimen_class terms, and ancestor validation to all new properties.

[sveinugu]

Renamed property:

• biomaterial_type -> biospecimen_class.
  • Now uses ontology terms from NCI Thesaurus, limited to four terms: Cell, Abnormal Cell, Cell Line, Organism Part.
  • Previous "primary cell culture" has been merged with "primary cell", now "Cell".

New properties:

• cell_type
• abnormal_cell_type (typically cancer cells)
• cell_line
• organism_part (typically tissue/organ)
• main_type
  • autogenerated from the other ones, to have a single summary attribute

Validation

• Added in-schema validation of dependency between biospecimen_class and the other types, using the new 'requireIf" attribute in the OPML files (mechanism committed in master, now used here).
• Added "ancestry" attribute (mechanism committed in master, now used here) @jmfernandez This will require implementation in the validator (not hurry!)

[sveinugu]

Fixes: https://github.com/fairtracks/fairtracks_standard/issues/15

[sveinugu]

Referenced in https://github.com/orgs/fairtracks/teams/fairtracks-developers/discussions/20

[jmfernandez]

Hi @sveinugu , some of the functionality you are looking for is already implemented, with the key name of ancestors, as you can read in the documentation:

https://github.com/fairtracks/fairtracks_validator/blob/master/README.md

Could you open issues in FAIRTracks Validator repo describing the new features you are missing, please?

[dzerbino]

Looks good to me.

[sveinugu]

Force pushed a rebased and fixed commit