Add property to indicate a class is top level

[cmungall]

currently jsonschemagen takes a command line arg for the top level class, this is used as the root of the json tree

it would be useful to elevate this to being explicit in the model. It would be semantically silent (except for tree serializations like json) but could help with documentation. The top level class would be the entrypoint for a user rather than throwing them at a big list of classes. It could also be the top level uml diagram in index.md

[jiaola]

@cmungall Can you please show us an example of what the jsonschema output should look like? Harold and I are trying to figure out how it is supposed to work but we don't think the --top-class parameter has worked.

[cmungall]

You can find examples here:

• https://github.com/microbiomedata/nmdc-metadata/
• https://github.com/cmungall/metadata_converter
• https://github.com/cmungall/sssom-py
• https://github.com/cmungall/ontology-change-language

[cmungall]

Try this:

$ gen-json-schema tests/test_issues/input/issue_129.yaml
...
   },
   "properties": {},
   "title": "types",
   "type": "object"
}

compared with

$ gen-json-schema -t c tests/test_issues/input/issue_129.yaml
...
   },
   "properties": {
      "age_in_years": {
         "type": "integer"
      },
      "children": {
         "items": {
            "type": "string"
         },
         "type": "array"
      },
...
      }
   },
   "title": "types",
   "type": "object"
}

[cmungall]

looks like test_issue_129 should explicitly test for this

[jiaola]

@cmungall We added a tree_root in class definition slots. See https://github.com/biolink/biolinkml/pull/195

See https://github.com/biolink/biolinkml/blob/master/tests/test_issues/test_issue_177.py for the test.

It adds the properties to the top level in JSON schema. But it didn't change anything else such as the "title" of the root in JSON.

Please let us know if other things need to be done.

[cmungall]

This is great thanks! Bill, as soon as 1.5.4 comes out we should use this in nmdc-schema

On Mon, Jul 13, 2020 at 7:40 AM Dazhi Jiao notifications@github.com wrote:

@cmungall https://github.com/cmungall We added a tree_root in class definition slots. See #195 https://github.com/biolink/biolinkml/pull/195

See https://github.com/biolink/biolinkml/blob/master/tests/test_issues/test_issue_177.py for the test.

It adds the properties to the top level in JSON schema. But it didn't change anything else such as the "title" of the root in JSON.

Please let us know if other things need to be done.

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