slot_usage induces new sub-slots, these should be hidden in many exports

[cmungall]

blml allows the usage of a slot to be refined (or even defined) on a per-class basis.

E.g The label slot may be generic for any kind of name. For a person class we may add documentation that states this should be a string that is typically first and last concatenated (OK, this would not be a very good rule for many names but you get the idea).

Originally I had conceived of information about a slot always being retrieved via a compound key of (class,slot). If there is a slot usage for a class, use that. Otherwise a superclass. Otherwise generic slot.

In the current implementation rather than compound key, a primary key is synthesized by concatenating class and slot. This is fine as an underlying implementation, but this should be hidden in many cases, as it causes confusion (e.g biolink/biolinkml#228).

here is a test example:

id: https://github.com/biolink/biolinkml/issues/228
name: test228
title: induced slots

types:
  string:
    base: str
    uri: xsd:string

  

classes:

  r1: {}
  r2:
    is_a: r1
  r3:
    is_a: r2
  
  c1:
    slots:
      - s
    slot_usage:
      s:
        description: s in c1
        range: r1
  c2:
    is_a: c1
    slots:
      - s
    slot_usage:
      s:
        description: s in c2
        range: r2
  c3:
    is_a: c2
    slots:
      - s
    slot_usage:
      s:
        description: s in c3
        range: r3
  d:
    slots:
      - s
    slot_usage:
      s:
        required: true

slots:
  s:
    description: >-
      generic s description     

markdown changes required:

currently this generates pages for c{1,2,3}_s, as well as s. Only pages for s should be generated. c1,2,3 specific usage can be included in the markdown file for s

All usages of the arrow notation in the generated markdown docs should be removed

owlgen changes required:

currently uris are made for c{1,2,3}_s. We should only have a uri for s.

class-specific ranges can be expressed using an owl subclass axiom

python changes:

reported separately by @wdduncan here: biolink/biolinkml#228 -- but I think current behavior may be ok, if a little confusing

json schema changes:

the current json schema generation is almost correct. There are no induced slots created - only s.

Currently gen-json-schema on the above makes:

{
   "$id": "https://github.com/biolink/biolinkml/issues/228",
   "$schema": "http://json-schema.org/draft-07/schema#",
   "definitions": {
      "C1": {
         "additionalProperties": false,
         "description": "",
         "properties": {
            "s": {
               "$ref": "#/definitions/R1",
               "description": "s in c1"
            }
         },
         "required": [],
         "title": "C1",
         "type": "object"
      },
      "C2": {
         "additionalProperties": false,
         "description": "",
         "properties": {
            "s": {
               "description": "generic s description",
               "type": "string"
            }
         },
         "required": [],
         "title": "C2",
         "type": "object"
      },
      "C3": {
         "additionalProperties": false,
         "description": "",
         "properties": {
            "s": {
               "$ref": "#/definitions/R3",
               "description": "s in c3"
            }
         },
         "required": [],
         "title": "C3",
         "type": "object"
      },
      "R1": {
         "additionalProperties": false,
         "description": "",
         "properties": {},
         "required": [],
         "title": "R1",
         "type": "object"
      },
      "R2": {
         "additionalProperties": false,
         "description": "",
         "properties": {},
         "required": [],
         "title": "R2",
         "type": "object"
      },
      "R3": {
         "additionalProperties": false,
         "description": "",
         "properties": {},
         "required": [],
         "title": "R3",
         "type": "object"
      }
   },
   "properties": {},
   "title": "test228",
   "type": "object"
}

this is pretty good. C1 and C3 are perfect. the localized use of s is correct. However, C2 is deferring to the generic slot, which is bizaarre

[cmungall]

See also https://github.com/biolink/biolinkml/discussions/347

[cmungall]

When running gen-markdown on the above

I get D.md as:

# Type: d




URI: [https://github.com/biolink/biolinkml/issues/228/D](https://github.com/biolink/biolinkml/issues/228/D)


![img](http://yuml.me/diagram/nofunky;dir:TB/class/[D|s:string])

## Referenced by class


## Attributes


### Own

 * [d➞s](d_s.md)  <sub>REQ</sub>
    * range: [String](types/String.md)

this is not good. The description has not been overridden, so the generic description should be used.

[nlharris]

is this fixed?

[vincentvialard]

owlgen changes required:

currently uris are made for c{1,2,3}_s. We should only have a uri for s.

class-specific ranges can be expressed using an owl subclass axiom

True for range (because the class specific range must be included in the inherited one), but you can not use an axiom for description, required, multivalued, etc.

So the class_slot uris are necessary.

[cmungall]

Fixed