LinkML slot attributes for driving validations

[turbomam]

See also #267

This snippet shows how to list all of the attributes that are applicable to LinkML slots:

from linkml_runtime import SchemaView
meta_url = "https://raw.githubusercontent.com/linkml/linkml-model/main/linkml_model/model/schema/meta.yaml"
meta_view = SchemaView(meta_url)
sis = meta_view.class_induced_slots('slot_definition')
for i in sis:
    print(i.name)

Here are some that I think should be used for validations:

slot_attribute	notes
maximum_value	works with the NMDC templates now that @pkalita-lbl  PR'ed a float caster in #299.
minimum_value	works with the NMDC templates now that @pkalita-lbl  PR'ed a float caster in #299.
multivalued	todo, along with min and max cardinality? "|" shouldn't appear in non-multivalued columns?
identifier	I think that this is being acted upon, like for MIxS' source_mat_id, which NMDC entitles XXX. Makes the column required and enforces uniqueness. Can only be applied to one column (i.e. one attribute per class). We need some other way to express that other columns should take unique values.
pattern	works, as composed regular expressions
range	I don't think any action is taken on ranges on their own. NMDC has data and code for matching ranges to (regular expression) patterns within the LinkML schema. Is DataHarmonizer still validating based on xsd types in the linkml-datastructure branch, the way it doe sin the main branch? If so, we should make sure common LinkML classes and types are related to the xsd types.
string_serialization	NMDC has data and code for matching composed string_serializations to (regular expression) patterns, but it's really a misuse of string_serialization, which is meant to generate strings based on a template of attribute names. We should be doing this though structured_patterns instead. Furthermore, structured_patterns should take advantage of pre-composed chunks from LinkML settings. Is there a desire for any of this to happen in real time within DataHarmonizer? We will need to build up a library of settings and expansions, along with some understanding of the MIxS grammar, especially the use of ; and \|
structured_pattern	@sujaypatil96 and others are working the expansion of structured_patterns. See string_serialization above
required	works
id_prefixes	todo? Value in columns with id_prefixes would have to begin with one of the prefixes, then a colon, then some local portion.
maximum_cardinality	todo, along with multivalued?
minimum_cardinality	todo, along with multivalued?
ifabsent	todo? How would this relate to DataHarmonizer's mechanisms for default values?
range_expression	todo for complex cases?

[ddooley]

Latest WIP-validation branch, which will be merged into linkml-datastructure, adds:

• any_of option for multiple ranges. Each range has to be datatype or an enumeration. So far no other range_expression option implemented.

I can see we'll have to carefully go through each of these items!

[ddooley]

Discussed June 21. Will create separate issues for outstanding functionality required.