8000 model extension: unique keys by cmungall · Pull Request #16 · linkml/linkml-model · GitHub
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model extension: unique keys #16

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Merged
merged 4 commits into from
Jun 30, 2021
Merged

model extension: unique keys #16

merged 4 commits into from
Jun 30, 2021

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cmungall
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@cmungall cmungall commented Apr 2, 2021 •
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This introduces compound keys

need to add tests

this example should illustrate concept:

classes:
  isotope:
    slots:
      - id
      - atomic number
      - neutron number
      - symbol
   compound_keys:
     proton_neutron_key:
       unique_for: isotope
       primary: false
       compound_key_slots:
         - atomic number
         - neutron number
    symbol uniqueness:
      unique_for: isotope
       primary: false
      compound_key_slots:
         - symbol

slots:
   id:
    identifier: true

See linkml/linkml#42

@cmungall cmungall requested a review from hsolbrig April 2, 2021 00:37
@cmungall cmungall marked this pull request as draft April 2, 2021 00:38
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hsolbrig commented Apr 6, 2021

We should draft a prototype of what compound keys looks like in each of the emitted idioms:

  • markdown - how to document
  • python - what does a compound key look like in generated python and what contract(s) does it enforce
  • owl -
  • rdf -
  • json schema -
  • others?

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cmungall commented Apr 7, 2021

good Qs, rough sketch of answers:

markdown

should pretty much follow the yaml. Each compound key on one line. E.g.


### Compound Keys

1. proton_neutron_key: an isotope is uniquely identified by the combination of (atomic number, neutron number)
2. symbol_key: an isotype is uniquely identified by the symbol field

python

this may not be easy to validate at the python level

rdf/owl

trivial mapping to hasKey

jsonschema

no equivalent?

@cmungall cmungall mentioned this pull request May 7, 2021
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this is also necessary for sqlalchemy bindings - each class must have a primary key (which may be compound)

@cmungall cmungall marked this pull request as ready for review June 29, 2021 21:06
@cmungall cmungall changed the title model extension: compound keys model extension: unique keys Jun 29, 2021
hsolbrig
hsolbrig reviewed Jun 30, 2021
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I wonder whether we should use this as an opportunity to create a new mixin that has the set of slots and mixins that you've enumerated below. I think we ended up with a similar set in the enumerations and I'd prefer to minimize repetition and fragmentation.

If you agree, will be happy to make the proposal

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regarding nul//none values in the key:

We could have slot to indicate whether nulls are to be treated as unknown vs a special None value. If the former, then it's not valid to translate the unique_key to SQL unique constraint (since Nulls represent unknowns)

@cmungall cmungall merged commit 2b930be into main Jun 30, 2021
@cmungall cmungall deleted the compound-key branch June 30, 2021 16:49
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