utils

Utility functions for all routers.

COLLECTIONS: dict[str, AsyncMongoCollection] = {} module-attribute

A lazy-loaded dictionary of asynchronous MongoDB entry-endpoint collections.

aretrieve_queryable_properties(schema, queryable_properties, entry_type=None) async

Asynchronous implementation of retrieve_queryable_properties() from optimade

Reference to the function in the optimade API documentation: retrieve_queryable_properties().

Recursively loops through the schema of a pydantic model and resolves all references, returning a dictionary of all the OPTIMADE-queryable properties of that model.

Parameters:

Name	Type	Description	Default
schema	type[EntryResource]	The schema of the pydantic model.	required
queryable_properties	Iterable[str]	The list of properties to find in the schema.	required
entry_type	str | None	The entry type of the model, if any.	None

Returns:

Type	Description
QueryableProperties	A flat dictionary with properties as keys, containing the field description,
QueryableProperties	unit, sortability, support level, queryability and type, where provided.

Source code in optimade_gateway/routers/utils.py

async def aretrieve_queryable_properties(
    schema: type[EntryResource],
    queryable_properties: Iterable[str],
    entry_type: str | None = None,
) -> QueryableProperties:
    """Asynchronous implementation of `retrieve_queryable_properties()` from `optimade`

    Reference to the function in the `optimade` API documentation:
    [`retrieve_queryable_properties()`](https://www.optimade.org/optimade-python-tools/api_reference/server/schemas/#optimade.server.schemas.retrieve_queryable_properties).

    Recursively loops through the schema of a pydantic model and resolves all
    references, returning a dictionary of all the OPTIMADE-queryable properties of that
    model.

    Parameters:
        schema: The schema of the pydantic model.
        queryable_properties: The list of properties to find in the schema.
        entry_type: The entry type of the model, if any.

    Returns:
        A flat dictionary with properties as keys, containing the field description,
        unit, sortability, support level, queryability and type, where provided.

    """
    return retrieve_queryable_properties(
        schema=schema,
        queryable_properties=queryable_properties,
        entry_type=entry_type,
    )

collection_factory(name) async

Get or initiate an entry-endpoint resource collection.

This factory utilizes the global dictionary COLLECTIONS. It lazily instantiates the collections and then caches them in the dictionary.

Parameters:

Name	Type	Description	Default
name	str	The configured name for the entry-endpoint resource collection.	required

Returns:

Type	Description
AsyncMongoCollection	The OPTIMADE Gateway asynchronous implementation of the
AsyncMongoCollection	MongoCollection.

Raises:

Type	Description
ValueError	If the supplied name is not one of the configured valid collection names.

Source code in optimade_gateway/routers/utils.py

async def collection_factory(name: str) -> AsyncMongoCollection:
    """Get or initiate an entry-endpoint resource collection.

    This factory utilizes the global dictionary
    [`COLLECTIONS`][optimade_gateway.routers.utils.COLLECTIONS].
    It lazily instantiates the collections and then caches them in the dictionary.

    Parameters:
        name: The configured name for the entry-endpoint resource collection.

    Returns:
        The OPTIMADE Gateway asynchronous implementation of the
        [`MongoCollection`](https://www.optimade.org/optimade-python-tools/api_reference/server/entry_collections/mongo/#optimade.server.entry_collections.mongo.MongoCollection).

    Raises:
        ValueError: If the supplied `name` is not one of the configured valid collection
            names.

    """
    if name in COLLECTIONS:
        return COLLECTIONS[name]

    if name == CONFIG.databases_collection:
        from optimade_gateway.mappers.databases import DatabasesMapper as ResourceMapper
    elif name == CONFIG.gateways_collection:
        from optimade_gateway.mappers.gateways import (  # type: ignore[no-redef]
            GatewaysMapper as ResourceMapper,
        )
    elif name == CONFIG.queries_collection:
        from optimade_gateway.mappers.queries import (  # type: ignore[no-redef]
            QueryMapper as ResourceMapper,
        )
    elif name == CONFIG.links_collection:
        from optimade_gateway.mappers.links import (  # type: ignore[no-redef]
            LinksMapper as ResourceMapper,
        )
    else:
        raise ValueError(
            f"{name!r} is not a valid entry-endpoint resource collection name. "
            "Configured valid names: "
            f"{(CONFIG.databases_collection, CONFIG.gateways_collection, CONFIG.queries_collection, CONFIG.links_collection)}"  # noqa: E501
        )

    COLLECTIONS[name] = AsyncMongoCollection(
        name=name,
        resource_cls=ResourceMapper.ENTRY_RESOURCE_CLASS,
        resource_mapper=ResourceMapper,
    )

    return COLLECTIONS[name]

get_entries(collection, response_cls, request, params) async

Generalized /{entries} endpoint getter

Source code in optimade_gateway/routers/utils.py

async def get_entries(
    collection: AsyncMongoCollection,
    response_cls: EntryResponseMany,
    request: Request,
    params: EntryListingQueryParams,
) -> EntryResponseMany:
    """Generalized `/{entries}` endpoint getter"""
    (
        results,
        data_returned,
        more_data_available,
        fields,
        include_fields,
    ) = await collection.afind(params=params)

    if more_data_available:
        # Deduce the `next` link from the current request
        query = urllib.parse.parse_qs(request.url.query)
        query["page_offset"] = [int(query.get("page_offset", [0])[0]) + len(results)]  # type: ignore[list-item, arg-type]
        urlencoded = urllib.parse.urlencode(query, doseq=True)
        base_url = get_base_url(request.url)

        links = ToplevelLinks(next=f"{base_url}{request.url.path}?{urlencoded}")
    else:
        links = ToplevelLinks(next=None)

    if fields or include_fields:
        results = handle_response_fields(results, fields, include_fields)

    return response_cls(
        links=links,
        data=results,
        meta=meta_values(
            url=request.url,
            data_returned=data_returned,
            data_available=await collection.acount(),
            more_data_available=more_data_available,
            schema=CONFIG.schema_url,
        ),
    )

get_valid_resource(collection, entry_id) async

Validate and retrieve a resource

Source code in optimade_gateway/routers/utils.py

async def get_valid_resource(
    collection: AsyncMongoCollection, entry_id: str
) -> EntryResource:
    """Validate and retrieve a resource"""
    await validate_resource(collection, entry_id)
    return await collection.get_one(filter={"id": entry_id})

resource_factory(create_resource) async

Get or create a resource

Currently supported resources:

• "databases" (DatabaseCreate -> LinksResource)
• "gateways" (GatewayCreate -> GatewayResource)
• "queries" (QueryCreate -> QueryResource)

For each of the resources, "uniqueness" is determined in the following way:

Databases

The base_url field is considered unique across all databases.

If a base_url is provided via a Link model, the base_url.href value is used to query the MongoDB.

Gateways

The collected list of databases.attributes.base_url values is considered unique across all gateways.

In the database, the search is done as a combination of the length/size of the databases' Python list/MongoDB array and a match on all (using the MongoDB $all operator) of the databases.attributes.base_url element values, when compared with the create_resource.

Important

The database_ids attribute must not contain values that are not also included in the databases attribute, in the form of the IDs for the individual databases. If this should be the case an OptimadeGatewayError will be thrown.

Queries

The gateway_id, query_parameters, and endpoint fields are collectively considered to define uniqueness for a QueryResource in the MongoDB collection.

Attention

Only the /structures entry endpoint can be queried with multiple expected responses.

This means the endpoint field defaults to "structures", i.e., the StructureResource resource model.

Parameters:

Name	Type	Description	Default
create_resource	DatabaseCreate | GatewayCreate | QueryCreate	The resource to be retrieved or created anew.	required

Returns:

Type	Description
tuple[LinksResource | GatewayResource | QueryResource, bool]	Two things in a tuple: Either a GatewayResource; a QueryResource; or a LinksResource and whether or not the resource was newly created.

Source code in optimade_gateway/routers/utils.py

async def resource_factory(
    create_resource: DatabaseCreate | GatewayCreate | QueryCreate,
) -> tuple[LinksResource | GatewayResource | QueryResource, bool]:
    """Get or create a resource

    Currently supported resources:

    - `"databases"`
        ([`DatabaseCreate`][optimade_gateway.models.databases.DatabaseCreate]
        ->
        [`LinksResource`](https://www.optimade.org/optimade-python-tools/api_reference/models/links/#optimade.models.links.LinksResource))
    - `"gateways"` ([`GatewayCreate`][optimade_gateway.models.gateways.GatewayCreate] ->
        [`GatewayResource`][optimade_gateway.models.gateways.GatewayResource])
    - `"queries"` ([`QueryCreate`][optimade_gateway.models.queries.QueryCreate] ->
        [`QueryResource`][optimade_gateway.models.queries.QueryResource])

    For each of the resources, "uniqueness" is determined in the following way:

    === "Databases"
        The `base_url` field is considered unique across all databases.

        If a `base_url` is provided via a
        [`Link`](https://www.optimade.org/optimade-python-tools/api_reference/models/jsonapi/#optimade.models.jsonapi.Link)
        model, the `base_url.href` value is used to query the MongoDB.

    === "Gateways"
        The collected list of `databases.attributes.base_url` values is considered
        unique across all gateways.

        In the database, the search is done as a combination of the length/size of the
        `databases`' Python list/MongoDB array and a match on all (using the MongoDB
        `$all` operator) of the
        [`databases.attributes.base_url`](https://www.optimade.org/optimade-python-tools/api_reference/models/links/#optimade.models.links.LinksResourceAttributes.base_url)
        element values, when compared with the `create_resource`.

        !!! important
            The `database_ids` attribute **must not** contain values that are not also
            included in the `databases` attribute, in the form of the IDs for the
            individual databases. If this should be the case an
            [`OptimadeGatewayError`][optimade_gateway.common.exceptions.OptimadeGatewayError]
            will be thrown.

    === "Queries"
        The `gateway_id`, `query_parameters`, and `endpoint` fields are collectively
        considered to define uniqueness for a
        [`QueryResource`][optimade_gateway.models.queries.QueryResource] in the MongoDB
        collection.

        !!! attention
            Only the `/structures` entry endpoint can be queried with multiple expected
            responses.

            This means the `endpoint` field defaults to `"structures"`, i.e., the
            [`StructureResource`](https://www.optimade.org/optimade-python-tools/all_models/#optimade.models.structures.StructureResource)
            resource model.

    Parameters:
        create_resource: The resource to be retrieved or created anew.

    Returns:
        Two things in a tuple:

            - Either a
                [`GatewayResource`][optimade_gateway.models.gateways.GatewayResource];
                a [`QueryResource`][optimade_gateway.models.queries.QueryResource]; or a
                [`LinksResource`](https://www.optimade.org/optimade-python-tools/api_reference/models/links/#optimade.models.links.LinksResource)
                and
            - whether or not the resource was newly created.

    """
    created = False

    if isinstance(create_resource, DatabaseCreate):
        collection_name = CONFIG.databases_collection

        base_url = get_resource_attribute(create_resource, "base_url")

        mongo_query: dict[str, Any] = {
            "$or": [
                {"base_url": {"$eq": base_url}},
                {"base_url.href": {"$eq": base_url}},
            ]
        }
    elif isinstance(create_resource, GatewayCreate):
        collection_name = CONFIG.gateways_collection

        # One MUST have taken care of database_ids prior to calling `resource_factory()`
        database_attr_ids = {_.id for _ in create_resource.databases or []}
        unknown_ids = {
            database_id
            for database_id in create_resource.database_ids or []
            if database_id not in database_attr_ids
        }
        if unknown_ids:
            raise OptimadeGatewayError(
                "When using `resource_factory()` for `GatewayCreate`, `database_ids` "
                f"MUST not include unknown IDs. Passed unknown IDs: {unknown_ids}"
            )

        mongo_query = {
            "databases": {"$size": len(create_resource.databases or [])},
            "databases.attributes.base_url": {
                "$all": [_.attributes.base_url for _ in create_resource.databases or []]
            },
        }
    elif isinstance(create_resource, QueryCreate):
        collection_name = CONFIG.queries_collection

        # Currently only /structures entry endpoints can be queried with multiple
        # expected responses.
        create_resource.endpoint = (
            create_resource.endpoint
            if create_resource.endpoint is not None
            else EndpointEntryType("structures")
        )

        mongo_query = {
            "gateway_id": {"$eq": create_resource.gateway_id},
            "query_parameters": {"$eq": create_resource.query_parameters},
            "endpoint": {"$eq": create_resource.endpoint},
        }
    else:
        raise TypeError(
            "create_resource must be either a DatabaseCreate, GatewayCreate, or "
            f"QueryCreate object, not {type(create_resource)!r}"
        )

    collection = await collection_factory(collection_name)
    result, data_returned, more_data_available, _, _ = await collection.afind(
        criteria={"filter": await clean_python_types(mongo_query)}
    )

    if more_data_available:
        raise OptimadeGatewayError(
            "more_data_available MUST be False for a single entry response, however it "
            f"is {more_data_available}"
        )

    if result:
        if data_returned > 1:
            raise OptimadeGatewayError(
                f"More than one {result[0].type} were found. IDs of found "
                f"{result[0].type}: {[_.id for _ in result]}"
            )
        if isinstance(result, list):
            result = result[0]
    else:
        if isinstance(create_resource, DatabaseCreate):
            # Set required `LinksResourceAttributes` values if not set
            if not create_resource.description:
                create_resource.description = (
                    f"{create_resource.name} created by OPTIMADE gateway database "
                    "registration."
                )

            if not create_resource.link_type:
                create_resource.link_type = LinkType.EXTERNAL

            if not create_resource.homepage:
                create_resource.homepage = None

        elif (
            isinstance(create_resource, GatewayCreate)
            and "database_ids" in create_resource.model_fields_set
        ):
            # Do not store `database_ids`
            del create_resource.database_ids
            create_resource.model_fields_set.remove("database_ids")

        elif isinstance(create_resource, QueryCreate):
            create_resource.state = QueryState.CREATED

        result = await collection.create_one(create_resource)
        LOGGER.debug("Created new %s: %r", result.type, result)
        created = True

    return result, created

validate_resource(collection, entry_id) async

Validate whether a resource exists in a collection

Source code in optimade_gateway/routers/utils.py

async def validate_resource(collection: AsyncMongoCollection, entry_id: str) -> None:
    """Validate whether a resource exists in a collection"""
    if not await collection.exists(entry_id):
        raise NotFound(
            detail=f"Resource <id={entry_id}> not found in {collection}.",
        )