feat(jsonschemagen): add --include-null/--no-include-null CLI option

Expose the existing JsonSchemaGenerator.include_null field on the gen-json-schema
CLI. --no-include-null forbids explicit JSON null in optional slots so optionality
is expressed only via absence from required (JSON Schema Validation 6.5.3), keeping
the bare value type (6.1.1) — needed for strict parity with reference schemas that
forbid null. Default unchanged (include_null=True).

Signed-off-by: jdsika <carlo.van-driesten@vdl.digital>

Author: jdsika

packages/linkml/src/linkml/generators/jsonschemagen.py

@@ -1031,6 +1031,17 @@ def serialize(self, **kwargs) -> str:
     show_default=True,
     help="If set, expand subproperty_of constraints to enum constraints.",
 )
+@click.option(
+    "--include-null/--no-include-null",
+    default=True,
+    show_default=True,
+    help="""
+If set (default), optional slots accept an explicit JSON null (type is emitted as
+["<type>", "null"]). Use --no-include-null to forbid explicit null, so optionality
+is expressed solely by absence from "required" — required for strict parity with a
+reference schema that declares a bare type (JSON Schema Validation 6.1.1 / 6.5.3).
+""",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):
     """Generate JSON Schema representation of a LinkML model"""

tests/linkml/test_generators/test_jsonschemagen.py

@@ -1090,3 +1090,39 @@ def test_add_lax_def_missing_required():
     schema["$defs"]["NormalClass"] = {"type": "object", "properties": {"id": {}}, "required": ["id", "name"]}
     schema.add_lax_def("NormalClass", "id")
     assert schema["$defs"]["NormalClass__identifier_optional"]["required"] == ["name"]
+
+
+def test_no_include_null_omits_null_from_optional_slots():
+    """``include_null=False`` must drop ``null`` from optional slot types.
+
+    By default an optional (non-required) slot is rendered as ``["<type>", "null"]``
+    so an explicit JSON ``null`` validates. With ``include_null=False`` optionality is
+    expressed solely by absence from ``required`` (JSON Schema Validation 6.5.3), and
+    the slot keeps its bare type (6.1.1) — required for strict parity with reference
+    schemas that forbid ``null``.
+    """
+    schema = """
+id: https://example.org/test-include-null
+name: test-include-null
+prefixes:
+  linkml: https://w3id.org/linkml/
+default_range: string
+imports:
+  - linkml:types
+classes:
+  C:
+    attributes:
+      opt:
+        range: string
+      req:
+        range: string
+        required: true
+"""
+    with_null = json.loads(JsonSchemaGenerator(schema, include_null=True).serialize())
+    without_null = json.loads(JsonSchemaGenerator(schema, include_null=False).serialize())
+
+    assert with_null["$defs"]["C"]["properties"]["opt"]["type"] == ["string", "null"]
+    assert without_null["$defs"]["C"]["properties"]["opt"]["type"] == "string"
+    # required slots are unaffected either way
+    assert without_null["$defs"]["C"]["properties"]["req"]["type"] == "string"
+    assert with_null["$defs"]["C"]["properties"]["req"]["type"] == "string"