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).

Tested at the CLI surface via CliRunner over scalar, multivalued, and required
slots; the standards rationale lives in the include_null field docstring.

Signed-off-by: Carlo van Driesten <carlo.van-driesten@bmw.de>

Author: jdsika

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

@@ -423,7 +423,18 @@ class JsonSchemaGenerator(Generator, LifecycleMixin):
     top_level_schema: JsonSchema = None
 
     include_null: bool = True
-    """Whether to include a "null" type in optional slots"""
+    """Whether optional (non-required) slots also accept an explicit JSON ``null``.
+
+    When ``True`` (default) an optional slot is rendered with ``null`` added to its
+    type (e.g. ``["string", "null"]``), so an explicit ``null`` value validates. When
+    ``False`` the slot keeps its bare type and optionality is expressed solely by
+    absence from ``required``.
+
+    JSON Schema treats presence (``required``, Validation 6.5.3) as separate from the
+    value type (``type``, Validation 6.1.1, where ``null`` is one of the value types),
+    and JSON ``null`` is a distinct value, not an absent member (RFC 8259 sec. 3). Set
+    this ``False`` for strict parity with reference schemas that declare a bare type
+    and forbid ``null``."""
 
     preserve_names: bool = False
     """If true, preserve LinkML element names in JSON Schema output (e.g., for $defs, properties, $ref targets)."""
@@ -1064,6 +1075,13 @@ 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 also accept an explicit JSON null. "
+    "Use --no-include-null to forbid explicit null on optional slots.",
+)
 @click.version_option(__version__, "-V", "--version")
 def cli(yamlfile, **kwargs):
     """Generate JSON Schema representation of a LinkML model"""

tests/linkml/test_scripts/test_gen_json_schema.py

@@ -1,3 +1,4 @@
+import json
 import re
 
 import pytest
@@ -70,3 +71,49 @@ def test_include_option(input_path):
     extra_import_path = str(input_path("deprecation.yaml"))
     result = runner.invoke(cli, ["--include", extra_import_path, schema])
     assert "C4" in result.output
+
+
+_INCLUDE_NULL_SCHEMA = """
+id: https://example.org/test-include-null-cli
+name: test-include-null-cli
+prefixes:
+  linkml: https://w3id.org/linkml/
+default_range: string
+imports:
+  - linkml:types
+classes:
+  C:
+    attributes:
+      opt:
+        range: string
+      opt_multi:
+        range: string
+        multivalued: true
+      req:
+        range: string
+        required: true
+"""
+
+
+@pytest.mark.parametrize(
+    "flag,expected_opt,expected_opt_multi",
+    [
+        ([], ["string", "null"], ["array", "null"]),
+        (["--include-null"], ["string", "null"], ["array", "null"]),
+        (["--no-include-null"], "string", "array"),
+    ],
+)
+def test_include_null_cli_option(flag, expected_opt, expected_opt_multi, tmp_path):
+    """The --include-null/--no-include-null CLI option must control whether optional
+    slots accept an explicit JSON null, across scalar and multivalued ranges, while
+    leaving required slots unaffected."""
+    schema = tmp_path / "schema.yaml"
+    schema.write_text(_INCLUDE_NULL_SCHEMA)
+    runner = CliRunner()
+    result = runner.invoke(cli, flag + [str(schema)])
+    assert result.exit_code == 0, result.output
+    props = json.loads(result.output)["$defs"]["C"]["properties"]
+    assert props["opt"]["type"] == expected_opt
+    assert props["opt_multi"]["type"] == expected_opt_multi
+    # required scalar slot is unaffected by the flag
+    assert props["req"]["type"] == "string"