utils

JSONAPIResponse

Bases: JSONResponse

This class simply patches fastapi.responses.JSONResponse to use the JSON:API 'application/vnd.api+json' MIME type.

Source code in optimade/server/routers/utils.py

class JSONAPIResponse(JSONResponse):
    """This class simply patches `fastapi.responses.JSONResponse` to use the
    JSON:API 'application/vnd.api+json' MIME type.

    """

    media_type = "application/vnd.api+json"

get_base_url(parsed_url_request)

Get base URL for current server

Take the base URL from the config file, if it exists, otherwise use the request.

Source code in optimade/server/routers/utils.py

def get_base_url(
    parsed_url_request: Union[
        urllib.parse.ParseResult, urllib.parse.SplitResult, StarletteURL, str
    ],
) -> str:
    """Get base URL for current server

    Take the base URL from the config file, if it exists, otherwise use the request.
    """
    parsed_url_request = (
        urllib.parse.urlparse(parsed_url_request)
        if isinstance(parsed_url_request, str)
        else parsed_url_request
    )
    return (
        CONFIG.base_url.rstrip("/")
        if CONFIG.base_url
        else f"{parsed_url_request.scheme}://{parsed_url_request.netloc}"
    )

get_entries(collection, request, params)

Generalized /{entry} endpoint getter

Source code in optimade/server/routers/utils.py

def get_entries(
    collection: EntryCollection,
    request: Request,
    params: EntryListingQueryParams,
) -> dict[str, Any]:
    """Generalized /{entry} endpoint getter"""
    from optimade.server.routers import ENTRY_COLLECTIONS

    params.check_params(request.query_params)
    (
        results,
        data_returned,
        more_data_available,
        fields,
        include_fields,
    ) = collection.find(params)

    include = []
    if getattr(params, "include", False):
        include.extend(params.include.split(","))

    included = []
    if results is not None:
        included = get_included_relationships(results, ENTRY_COLLECTIONS, include)

    if more_data_available:
        # Deduce the `next` link from the current request
        query = urllib.parse.parse_qs(request.url.query)
        query.update(collection.get_next_query_params(params, results))

        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 results is not None and (fields or include_fields):
        results = handle_response_fields(results, fields, include_fields)  # type: ignore[assignment]

    return {
        "links": links,
        "data": results if results else [],
        "meta": meta_values(
            url=request.url,
            data_returned=data_returned,
            data_available=len(collection),
            more_data_available=more_data_available,
            schema=CONFIG.schema_url
            if not CONFIG.is_index
            else CONFIG.index_schema_url,
        ),
        "included": included,
    }

get_included_relationships(results, ENTRY_COLLECTIONS, include_param)

Filters the included relationships and makes the appropriate compound request to include them in the response.

Parameters:

Name	Type	Description	Default
results	Union[EntryResource, list[EntryResource], dict, list[dict]]	list of returned documents.	required
ENTRY_COLLECTIONS	dict[str, EntryCollection]	dictionary containing collections to query, with key based on endpoint type.	required
include_param	list[str]	list of queried related resources that should be included in included.	required

Returns:

Type	Description
list[Union[EntryResource, dict[str, Any]]]	Dictionary with the same keys as ENTRY_COLLECTIONS, each containing the list of resource objects for that entry type.

Source code in optimade/server/routers/utils.py

def get_included_relationships(
    results: Union[EntryResource, list[EntryResource], dict, list[dict]],
    ENTRY_COLLECTIONS: dict[str, EntryCollection],
    include_param: list[str],
) -> list[Union[EntryResource, dict[str, Any]]]:
    """Filters the included relationships and makes the appropriate compound request
    to include them in the response.

    Parameters:
        results: list of returned documents.
        ENTRY_COLLECTIONS: dictionary containing collections to query, with key
            based on endpoint type.
        include_param: list of queried related resources that should be included in
            `included`.

    Returns:
        Dictionary with the same keys as ENTRY_COLLECTIONS, each containing the list
            of resource objects for that entry type.

    """
    from collections import defaultdict

    if not isinstance(results, list):
        results = [results]

    for entry_type in include_param:
        if entry_type not in ENTRY_COLLECTIONS and entry_type != "":
            raise BadRequest(
                detail=f"'{entry_type}' cannot be identified as a valid relationship type. "
                f"Known relationship types: {sorted(ENTRY_COLLECTIONS.keys())}"
            )

    endpoint_includes: dict[Any, dict] = defaultdict(dict)
    for doc in results:
        # convert list of references into dict by ID to only included unique IDs
        if doc is None:
            continue

        try:
            relationships = doc.relationships  # type: ignore
        except AttributeError:
            relationships = doc.get("relationships", None)

        if relationships is None:
            continue

        if not isinstance(relationships, dict):
            relationships = relationships.model_dump()

        for entry_type in ENTRY_COLLECTIONS:
            # Skip entry type if it is not in `include_param`
            if entry_type not in include_param:
                continue

            entry_relationship = relationships.get(entry_type, {})
            if entry_relationship is not None:
                refs = entry_relationship.get("data", [])
                for ref in refs:
                    if ref["id"] not in endpoint_includes[entry_type]:
                        endpoint_includes[entry_type][ref["id"]] = ref

    included: dict[
        str,
        Union[list[EntryResource], list[dict[str, Any]]],
    ] = {}
    for entry_type in endpoint_includes:
        compound_filter = " OR ".join(
            [f'id="{ref_id}"' for ref_id in endpoint_includes[entry_type]]
        )
        params = EntryListingQueryParams(
            filter=compound_filter,
            response_format="json",
            response_fields="",
            sort="",
            page_limit=0,
            page_offset=0,
        )

        # still need to handle pagination
        ref_results, _, _, _, _ = ENTRY_COLLECTIONS[entry_type].find(params)
        if ref_results is None:
            ref_results = []
        included[entry_type] = ref_results  # type: ignore[assignment]

    # flatten dict by endpoint to list
    return [obj for endp in included.values() for obj in endp]

get_providers(add_mongo_id=False)

Retrieve Materials-Consortia providers (from https://providers.optimade.org/v1/links).

Fallback order if providers.optimade.org is not available:

1. Try Materials-Consortia/providers on GitHub.
2. Try submodule providers' list of providers.
3. Log warning that providers list from Materials-Consortia is not included in the /links-endpoint.

Parameters:

Name	Type	Description	Default
add_mongo_id	bool	Whether to populate the _id field of the provider with MongoDB ObjectID.	False

Returns:

Type	Description
list	List of raw JSON-decoded providers including MongoDB object IDs.

Source code in optimade/utils.py

def get_providers(add_mongo_id: bool = False) -> list:
    """Retrieve Materials-Consortia providers (from https://providers.optimade.org/v1/links).

    Fallback order if providers.optimade.org is not available:

    1. Try Materials-Consortia/providers on GitHub.
    2. Try submodule `providers`' list of providers.
    3. Log warning that providers list from Materials-Consortia is not included in the
       `/links`-endpoint.

    Arguments:
        add_mongo_id: Whether to populate the `_id` field of the provider with MongoDB
            ObjectID.

    Returns:
        List of raw JSON-decoded providers including MongoDB object IDs.

    """
    import json

    import requests

    for provider_list_url in PROVIDER_LIST_URLS:
        try:
            providers = requests.get(provider_list_url, timeout=10).json()
        except (
            requests.exceptions.ConnectionError,
            requests.exceptions.ConnectTimeout,
            json.JSONDecodeError,
        ):
            pass
        else:
            break
    else:
        try:
            from optimade.server.data import providers  # type: ignore
        except ImportError:
            from optimade.server.logger import LOGGER

            LOGGER.warning(
                """Could not retrieve a list of providers!

    Tried the following resources:

{}
    The list of providers will not be included in the `/links`-endpoint.
""".format("".join([f"    * {_}\n" for _ in PROVIDER_LIST_URLS]))
            )
            return []

    providers_list = []
    for provider in providers.get("data", []):
        # Remove/skip "exmpl"
        if provider["id"] == "exmpl":
            continue

        provider.update(provider.pop("attributes", {}))

        # Add MongoDB ObjectId
        if add_mongo_id:
            provider["_id"] = {
                "$oid": mongo_id_for_database(provider["id"], provider["type"])
            }

        providers_list.append(provider)

    return providers_list

handle_response_fields(results, exclude_fields, include_fields)

Handle query parameter response_fields.

It is assumed that all fields are under attributes. This is due to all other top-level fields are REQUIRED in the response.

Parameters:

Name	Type	Description	Default
exclude_fields	set[str]	Fields under attributes to be excluded from the response.	required
include_fields	set[str]	Fields under attributes that were requested that should be set to null if missing in the entry.	required

Returns:

Type	Description
list[dict[str, Any]]	List of resulting resources as dictionaries after pruning according to
list[dict[str, Any]]	the response_fields OPTIMADE URL query parameter.

Source code in optimade/server/routers/utils.py

def handle_response_fields(
    results: Union[list[EntryResource], EntryResource, list[dict], dict],
    exclude_fields: set[str],
    include_fields: set[str],
) -> list[dict[str, Any]]:
    """Handle query parameter `response_fields`.

    It is assumed that all fields are under `attributes`.
    This is due to all other top-level fields are REQUIRED in the response.

    Parameters:
        exclude_fields: Fields under `attributes` to be excluded from the response.
        include_fields: Fields under `attributes` that were requested that should be
            set to null if missing in the entry.

    Returns:
        List of resulting resources as dictionaries after pruning according to
        the `response_fields` OPTIMADE URL query parameter.

    """
    if not isinstance(results, list):
        results = [results]

    new_results = []
    while results:
        new_entry = results.pop(0)
        try:
            new_entry = new_entry.model_dump(exclude_unset=True, by_alias=True)  # type: ignore[union-attr]
        except AttributeError:
            pass

        # Remove fields excluded by their omission in `response_fields`
        for field in exclude_fields:
            if field in new_entry["attributes"]:
                del new_entry["attributes"][field]

        # Include missing fields that were requested in `response_fields`
        for field in include_fields:
            if field not in new_entry["attributes"]:
                new_entry["attributes"][field] = None

        new_results.append(new_entry)

    return new_results

meta_values(url, data_returned, data_available, more_data_available, schema=None, **kwargs)

Helper to initialize the meta values

Source code in optimade/server/routers/utils.py

def meta_values(
    url: Union[urllib.parse.ParseResult, urllib.parse.SplitResult, StarletteURL, str],
    data_returned: Optional[int],
    data_available: int,
    more_data_available: bool,
    schema: Optional[str] = None,
    **kwargs,
) -> ResponseMeta:
    """Helper to initialize the meta values"""
    from optimade.models import ResponseMetaQuery

    if isinstance(url, str):
        url = urllib.parse.urlparse(url)

    # To catch all (valid) variations of the version part of the URL, a regex is used
    if re.match(r"/v[0-9]+(\.[0-9]+){,2}/.*", url.path) is not None:
        url_path = re.sub(r"/v[0-9]+(\.[0-9]+){,2}/", "/", url.path)
    else:
        url_path = url.path

    if schema is None:
        schema = CONFIG.schema_url if not CONFIG.is_index else CONFIG.index_schema_url

    return ResponseMeta(
        query=ResponseMetaQuery(representation=f"{url_path}?{url.query}"),
        api_version=__api_version__,
        time_stamp=datetime.now(),
        data_returned=data_returned,
        more_data_available=more_data_available,
        provider=CONFIG.provider,
        data_available=data_available,
        implementation=CONFIG.implementation,
        schema=schema,
        **kwargs,
    )

mongo_id_for_database(database_id, database_type)

Produce a MongoDB ObjectId for a database

Source code in optimade/utils.py

def mongo_id_for_database(database_id: str, database_type: str) -> str:
    """Produce a MongoDB ObjectId for a database"""
    from bson.objectid import ObjectId

    oid = f"{database_id}{database_type}"
    if len(oid) > 12:
        oid = oid[:12]
    elif len(oid) < 12:
        oid = f"{oid}{'0' * (12 - len(oid))}"

    return str(ObjectId(oid.encode("UTF-8")))