Added root validator that warns on missing expected fields, plus asso…

…ciated tests

optimade/models/structures.py

@@ -1,5 +1,6 @@
 # pylint: disable=no-self-argument,line-too-long,no-name-in-module
 import re
+import warnings
 from enum import IntEnum, Enum
 from sys import float_info
 from typing import List, Optional, Union
@@ -16,6 +17,7 @@
     ANONYMOUS_ELEMENTS,
     CHEMICAL_FORMULA_REGEXP,
 )
+from optimade.server.warnings import MissingExpectedField
 
 EXTENDED_CHEMICAL_SYMBOLS = CHEMICAL_SYMBOLS + EXTRA_SYMBOLS
 
@@ -242,6 +244,14 @@ def check_self_consistency(cls, v, values):
         return v
 
 
+CORRELATED_STRUCTURE_FIELDS = (
+    {"dimension_types", "nperiodic_dimensions"},
+    {"cartesian_site_positions", "species_at_sites"},
+    {"nsites", "cartesian_site_positions"},
+    {"species_at_sites", "species"},
+)
+
+
 class StructureResourceAttributes(EntryResourceAttributes):
     """This class contains the Field for the attributes used to represent a structure, e.g. unit cell, atoms, positions."""
 
@@ -790,6 +800,24 @@ def schema_extra(schema, model):
             for prop in nullable_props:
                 schema["properties"][prop]["nullable"] = True
 
+    @root_validator(pre=True)
+    def warn_on_missing_correlated_fields(cls, values):
+        """Emit warnings if a field takes a null value when a value
+        was expected based on the value/nullity of another field.
+        """
+        accumulated_warnings = []
+        for field_set in CORRELATED_STRUCTURE_FIELDS:
+            missing_fields = {f for f in field_set if values.get(f) is None}
+            if missing_fields and len(missing_fields) != len(field_set):
+                accumulated_warnings += [
+                    f"Structure with values {values} is missing fields {missing_fields} which are required if {field_set - missing_fields} are present."
+                ]
+
+        for warn in accumulated_warnings:
+            warnings.warn(warn, MissingExpectedField)
+
+        return values
+
     @validator("chemical_formula_reduced", "chemical_formula_hill")
     def check_ordered_formula(cls, v, field):
         if v is None:

optimade/server/warnings.py

@@ -37,3 +37,8 @@ class TooManyValues(OptimadeWarning):
 
 class QueryParamNotUsed(OptimadeWarning):
     """A query parameter is not used in this request."""
+
+
+class MissingExpectedField(OptimadeWarning):
+    """A field was provided with a null value when a related field was provided
+    with a value."""

tests/models/test_structures.py

@@ -4,7 +4,8 @@
 
 from pydantic import ValidationError
 
-from optimade.models.structures import StructureResource
+from optimade.models.structures import StructureResource, CORRELATED_STRUCTURE_FIELDS
+from optimade.server.warnings import MissingExpectedField
 
 
 MAPPER = "StructureMapper"
@@ -20,6 +21,7 @@ def test_good_structures(mapper):
         StructureResource(**mapper(MAPPER).map_back(structure))
 
 
+@pytest.mark.filterwarnings("ignore", category=MissingExpectedField)
 def test_good_structure_with_missing_data(mapper, good_structure):
     """Check deserialization of well-formed structure used
     as example data with all combinations of null values
@@ -168,7 +170,7 @@ def test_bad_structures(bad_structures, mapper):
 
 
 @pytest.mark.parametrize("deformity", deformities)
-def test_structure_deformities(good_structure, deformity):
+def test_structure_fatal_deformities(good_structure, deformity):
     """Make specific checks upon performing single invalidating deformations
     of the data of a good structure.
 
@@ -182,3 +184,21 @@ def test_structure_deformities(good_structure, deformity):
     good_structure["attributes"].update(deformity)
     with pytest.raises(ValidationError, match=fr".*{re.escape(message)}.*"):
         StructureResource(**good_structure)
+
+
+minor_deformities = (
+    {f: None} for f in set(f for _ in CORRELATED_STRUCTURE_FIELDS for f in _)
+)
+
+
+@pytest.mark.parametrize("deformity", minor_deformities)
+def test_structure_minor_deformities(good_structure, deformity):
+    """Make specific checks upon performing single minor invalidations
+    of the data of a good structure that should emit warnings.
+    """
+    if deformity is None:
+        StructureResource(**good_structure)
+    else:
+        good_structure["attributes"].update(deformity)
+        with pytest.warns(MissingExpectedField):
+            StructureResource(**good_structure)