Update pydantic to ~=1.8

openapi/index_openapi.json

@@ -1081,10 +1081,23 @@
             "description": "JSON API links object, pointing to a homepage URL for this implementation"
           },
           "link_type": {
-            "$ref": "#/components/schemas/LinkType"
+            "title": "Link Type",
+            "allOf": [
+              {
+                "$ref": "#/components/schemas/LinkType"
+              }
+            ],
+            "description": "The type of the linked relation.\nMUST be one of these values: 'child', 'root', 'external', 'providers'."
           },
           "aggregate": {
-            "$ref": "#/components/schemas/Aggregate"
+            "title": "Aggregate",
+            "allOf": [
+              {
+                "$ref": "#/components/schemas/Aggregate"
+              }
+            ],
+            "description": "A string indicating whether a client that is following links to aggregate results from different OPTIMADE implementations should follow this link or not.\nThis flag SHOULD NOT be indicated for links where `link_type` is not `child`.\n\nIf not specified, clients MAY assume that the value is `ok`.\nIf specified, and the value is anything different than `ok`, the client MUST assume that the server is suggesting not to follow the link during aggregation by default (also if the value is not among the known ones, in case a future specification adds new accepted values).\n\nSpecific values indicate the reason why the server is providing the suggestion.\nA client MAY follow the link anyway if it has reason to do so (e.g., if the client is looking for all test databases, it MAY follow the links marked with `aggregate`=`test`).\n\nIf specified, it MUST be one of the values listed in section Link Aggregate Options.",
+            "default": "ok"
           },
           "no_aggregate_reason": {
             "title": "No Aggregate Reason",

openapi/openapi.json

@@ -1226,7 +1226,13 @@
             "description": "Defines whether the entry property can be used for sorting with the \"sort\" parameter.\nIf the entry listing endpoint supports sorting, this key MUST be present for sortable properties with value `true`."
           },
           "type": {
-            "$ref": "#/components/schemas/DataType"
+            "title": "Type",
+            "allOf": [
+              {
+                "$ref": "#/components/schemas/DataType"
+              }
+            ],
+            "description": "The type of the property's value.\nThis MUST be any of the types defined in the Data types section.\nFor the purpose of compatibility with future versions of this specification, a client MUST accept values that are not `string` values specifying any of the OPTIMADE Data types, but MUST then also disregard the `type` field.\nNote, if the value is a nested type, only the outermost type should be reported.\nE.g., for the entry resource `structures`, the `species` property is defined as a list of dictionaries, hence its `type` value would be `list`."
           }
         }
       },
@@ -1933,10 +1939,23 @@
             "description": "JSON API links object, pointing to a homepage URL for this implementation"
           },
           "link_type": {
-            "$ref": "#/components/schemas/LinkType"
+            "title": "Link Type",
+            "allOf": [
+              {
+                "$ref": "#/components/schemas/LinkType"
+              }
+            ],
+            "description": "The type of the linked relation.\nMUST be one of these values: 'child', 'root', 'external', 'providers'."
           },
           "aggregate": {
-            "$ref": "#/components/schemas/Aggregate"
+            "title": "Aggregate",
+            "allOf": [
+              {
+                "$ref": "#/components/schemas/Aggregate"
+              }
+            ],
+            "description": "A string indicating whether a client that is following links to aggregate results from different OPTIMADE implementations should follow this link or not.\nThis flag SHOULD NOT be indicated for links where `link_type` is not `child`.\n\nIf not specified, clients MAY assume that the value is `ok`.\nIf specified, and the value is anything different than `ok`, the client MUST assume that the server is suggesting not to follow the link during aggregation by default (also if the value is not among the known ones, in case a future specification adds new accepted values).\n\nSpecific values indicate the reason why the server is providing the suggestion.\nA client MAY follow the link anyway if it has reason to do so (e.g., if the client is looking for all test databases, it MAY follow the links marked with `aggregate`=`test`).\n\nIf specified, it MUST be one of the values listed in section Link Aggregate Options.",
+            "default": "ok"
           },
           "no_aggregate_reason": {
             "title": "No Aggregate Reason",
@@ -2105,7 +2124,7 @@
           1
         ],
         "type": "integer",
-        "description": "An enumeration."
+        "description": "Integer enumeration of dimension_types values"
       },
       "Person": {
         "title": "Person",

optimade/models/entries.py

@@ -167,6 +167,7 @@ class EntryInfoProperty(BaseModel):
 
     type: Optional[DataType] = StrictField(
         None,
+        title="Type",
         description="""The type of the property's value.
 This MUST be any of the types defined in the Data types section.
 For the purpose of compatibility with future versions of this specification, a client MUST accept values that are not `string` values specifying any of the OPTIMADE Data types, but MUST then also disregard the `type` field.

optimade/models/index_metadb.py

@@ -57,6 +57,7 @@ class IndexInfoResource(BaseInfoResource):
         None, Dict[DefaultRelationship, IndexRelationship]
     ] = StrictField(
         ...,
+        title="Relationships",
         description="""Reference to the Links identifier object under the `links` endpoint that the provider has chosen as their 'default' OPTIMADE API database.
 A client SHOULD present this database as the first choice when an end-user chooses this provider.""",
     )

optimade/models/links.py

@@ -59,12 +59,14 @@ class LinksResourceAttributes(Attributes):
 
     link_type: LinkType = StrictField(
         ...,
+        title="Link Type",
         description="""The type of the linked relation.
 MUST be one of these values: 'child', 'root', 'external', 'providers'.""",
     )
 
     aggregate: Optional[Aggregate] = StrictField(
         Aggregate.OK,
+        title="Aggregate",
         description="""A string indicating whether a client that is following links to aggregate results from different OPTIMADE implementations should follow this link or not.
 This flag SHOULD NOT be indicated for links where `link_type` is not `child`.
 

optimade/models/structures.py

@@ -41,6 +41,8 @@
 
 
 class Periodicity(IntEnum):
+    """Integer enumeration of dimension_types values"""
+
     APERIODIC = 0
     PERIODIC = 1
 
@@ -442,6 +444,7 @@ class StructureResourceAttributes(EntryResourceAttributes):
         conlist(Periodicity, min_items=3, max_items=3)
     ] = OptimadeField(
         None,
+        title="Dimension Types",
         description="""List of three integers.
 For 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`).
 Note: 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.
@@ -757,6 +760,7 @@ class StructureResourceAttributes(EntryResourceAttributes):
 
     structure_features: List[StructureFeatures] = OptimadeField(
         ...,
+        title="Structure Features",
         description="""A list of strings that flag which special features are used by the structure.
 
 - **Type**: list of strings

optimade/models/utils.py

@@ -19,6 +19,8 @@
 
 
 class SupportLevel(Enum):
+    """OPTIMADE property/field support levels"""
+
     MUST = "must"
     SHOULD = "should"
     OPTIONAL = "optional"

optimade/server/entry_collections/entry_collections.py

@@ -101,8 +101,15 @@ def all_fields(self) -> set:
         return fields
 
     def get_attribute_fields(self) -> set:
-        """Get the set of attribute fields from the schema of the
-        resource class, resolving references along the way.
+        """Get the set of attribute fields
+
+        Return only the _first-level_ attribute fields from the schema of the resource class,
+        resolving references along the way if needed.
+
+        Note:
+            It is not needed to take care of other special OpenAPI schema keys than `allOf`,
+            since only `allOf` will be found in this context.
+            Other special keys can be found in [the Swagger documentation](https://swagger.io/docs/specification/data-models/oneof-anyof-allof-not/).
 
         Returns:
             Property names.

requirements.txt

@@ -1,6 +1,6 @@
 fastapi==0.63.0
 lark-parser==0.11.2
-pydantic==1.6.1
+pydantic==1.8.1
 email_validator==1.1.2
 requests==2.25.1
 uvicorn==0.13.4

setup.py

@@ -93,7 +93,7 @@
     install_requires=[
         "lark-parser~=0.11.2",
         "fastapi~=0.63.0",
-        "pydantic~=1.6.1",
+        "pydantic~=1.8",
         "email_validator~=1.1",
         "requests~=2.25",
         "typing-extensions~=3.7;python_version<'3.8'",

tests/server/entry_collections/test_entry_collections.py

@@ -0,0 +1,26 @@
+"""Test the EntryCollection abstract base class"""
+
+
+def test_get_attribute_fields():
+    """Test get_attribute_fields() method"""
+    from optimade.models import (
+        LinksResourceAttributes,
+        ReferenceResourceAttributes,
+        StructureResourceAttributes,
+    )
+    from optimade.server.routers import ENTRY_COLLECTIONS
+
+    entry_name_attributes = {
+        "links": LinksResourceAttributes,
+        "references": ReferenceResourceAttributes,
+        "structures": StructureResourceAttributes,
+    }
+
+    # Make sure we're hitting all collections
+    assert set(entry_name_attributes.keys()) == set(ENTRY_COLLECTIONS.keys())
+
+    for entry_name, attributes_model in entry_name_attributes.items():
+        assert (
+            set(attributes_model.__fields__.keys())
+            == ENTRY_COLLECTIONS[entry_name].get_attribute_fields()
+        )