Remove nullable field from properties

This is no longer part of the OpenAPI spec as of v3.1.

Fixes #1814

openapi/openapi.json

@@ -4125,7 +4125,6 @@
             ],
             "title": "Last Modified",
             "description": "Date and time representing when the entry was last modified.\n\n- **Type**: timestamp.\n\n- **Requirements/Conventions**:\n    - **Support**: SHOULD be supported by all implementations, i.e., SHOULD NOT be `null`.\n    - **Query**: MUST be a queryable property with support for all mandatory filter features.\n    - **Response**: REQUIRED in the response unless the query parameter `response_fields` is present and does not include this property.\n\n- **Example**:\n    - As part of JSON response format: `\"2007-04-05T14:30:20Z\"` (i.e., encoded as an [RFC 3339 Internet Date/Time Format](https://tools.ietf.org/html/rfc3339#section-5.6) string.)",
-            "nullable": true,
             "x-optimade-queryable": "must",
             "x-optimade-support": "should"
           },
@@ -4255,7 +4254,6 @@
             ],
             "title": "Dimension Types",
             "description": "List of three integers.\nFor each of the three directions indicated by the three lattice vectors (see property `lattice_vectors`), this list indicates if the direction is periodic (value `1`) or non-periodic (value `0`).\nNote: the elements in this list each refer to the direction of the corresponding entry in `lattice_vectors` and *not* the Cartesian x, y, z directions.\n\n- **Type**: list of integers.\n\n- **Requirements/Conventions**:\n    - **Support**: SHOULD be supported by all implementations, i.e., SHOULD NOT be `null`.\n    - **Query**: Support for queries on this property is OPTIONAL.\n    - MUST be a list of length 3.\n    - Each integer element MUST assume only the value 0 or 1.\n\n- **Examples**:\n    - For a molecule: `[0, 0, 0]`\n    - For a wire along the direction specified by the third lattice vector: `[0, 0, 1]`\n    - For a 2D surface/slab, periodic on the plane defined by the first and third lattice vectors: `[1, 0, 1]`\n    - For a bulk 3D system: `[1, 1, 1]`",
-            "nullable": true,
             "x-optimade-queryable": "optional",
             "x-optimade-support": "should"
           },
@@ -4301,7 +4299,6 @@
             ],
             "title": "Lattice Vectors",
             "description": "The three lattice vectors in Cartesian coordinates, in \u00e5ngstr\u00f6m (\u00c5).\n\n- **Type**: list of list of floats or unknown values.\n\n- **Requirements/Conventions**:\n    - **Support**: SHOULD be supported by all implementations, i.e., SHOULD NOT be `null`.\n    - **Query**: Support for queries on this property is OPTIONAL.\n      If supported, filters MAY support only a subset of comparison operators.\n    - MUST be a list of three vectors *a*, *b*, and *c*, where each of the vectors MUST BE a list of the vector's coordinates along the x, y, and z Cartesian coordinates.\n      (Therefore, the first index runs over the three lattice vectors and the second index runs over the x, y, z Cartesian coordinates).\n    - For databases that do not define an absolute Cartesian system (e.g., only defining the length and angles between vectors), the first lattice vector SHOULD be set along *x* and the second on the *xy*-plane.\n    - MUST always contain three vectors of three coordinates each, independently of the elements of property `dimension_types`.\n      The vectors SHOULD by convention be chosen so the determinant of the `lattice_vectors` matrix is different from zero.\n      The vectors in the non-periodic directions have no significance beyond fulfilling these requirements.\n    - The coordinates of the lattice vectors of non-periodic dimensions (i.e., those dimensions for which `dimension_types` is `0`) MAY be given as a list of all `null` values.\n        If a lattice vector contains the value `null`, all coordinates of that lattice vector MUST be `null`.\n\n- **Examples**:\n    - `[[4.0,0.0,0.0],[0.0,4.0,0.0],[0.0,1.0,4.0]]` represents a cell, where the first vector is `(4, 0, 0)`, i.e., a vector aligned along the `x` axis of length 4 \u00c5; the second vector is `(0, 4, 0)`; and the third vector is `(0, 1, 4)`.",
-            "nullable": true,
             "x-optimade-queryable": "optional",
             "x-optimade-support": "should",
             "x-optimade-unit": "\u00c5"
@@ -4409,9 +4406,7 @@
         "type": "object",
         "required": [
           "last_modified",
-          "structure_features",
-          "dimension_types",
-          "lattice_vectors"
+          "structure_features"
         ],
         "title": "StructureResourceAttributes",
         "description": "This class contains the Field for the attributes used to represent a structure, e.g. unit cell, atoms, positions."

optimade/models/structures.py

@@ -2,12 +2,11 @@
 import re
 import warnings
 from enum import Enum, IntEnum
-from typing import Annotated, Any, Dict, List, Optional, Set, Type, Union
+from typing import Annotated, List, Optional, Set, Union
 
 from pydantic import (
     BaseModel,
     BeforeValidator,
-    ConfigDict,
     Field,
     ValidationInfo,
     field_validator,
@@ -272,38 +271,9 @@ def check_self_consistency(
 )
 
 
-def structure_json_schema_extra(
-    schema: Dict[str, Any], model: Type["StructureResourceAttributes"]
-) -> None:
-    """Two things need to be added to the schema:
-
-    1. Constrained types in pydantic do not currently play nicely with
-    "Required Optional" fields, i.e. fields must be specified but can be null.
-    The two constrained list fields, `dimension_types` and `lattice_vectors`,
-    are OPTIMADE 'SHOULD' fields, which means that they are allowed to be null.
-
-    2. All OPTIMADE 'SHOULD' fields are allowed to be null, so we manually set them
-    to be `nullable` according to the OpenAPI definition.
-
-    """
-    schema["required"].insert(7, "dimension_types")
-    schema["required"].insert(9, "lattice_vectors")
-
-    nullable_props = (
-        prop
-        for prop in schema["required"]
-        if schema["properties"][prop].get("x-optimade-support")
-        == SupportLevel.SHOULD.value
-    )
-    for prop in nullable_props:
-        schema["properties"][prop]["nullable"] = True
-
-
 class StructureResourceAttributes(EntryResourceAttributes):
     """This class contains the Field for the attributes used to represent a structure, e.g. unit cell, atoms, positions."""
 
-    model_config = ConfigDict(json_schema_extra=structure_json_schema_extra)
-
     elements: Optional[List[str]] = OptimadeField(
         None,
         description="""The chemical symbols of the different elements present in the structure.

optimade/models/utils.py

@@ -69,7 +69,6 @@ def StrictField(
     allowed_keys = [
         "pattern",
         "uniqueItems",
-        "nullable",
     ] + OPTIMADE_SCHEMA_EXTENSION_KEYS
     _banned = [k for k in kwargs if k not in set(_PYDANTIC_FIELD_KWARGS + allowed_keys)]