elasticsearch

ElasticCollection

Bases: EntryCollection

Source code in optimade/server/entry_collections/elasticsearch.py

class ElasticCollection(EntryCollection):
    pagination_mechanism = PaginationMechanism("page_offset")

    def __init__(
        self,
        name: str,
        resource_cls: type[EntryResource],
        resource_mapper: type[BaseResourceMapper],
        client: Optional["Elasticsearch"] = None,
    ):
        """Initialize the ElasticCollection for the given parameters.

        Parameters:
            name: The name of the collection.
            resource_cls: The type of entry resource that is stored by the collection.
            resource_mapper: A resource mapper object that handles aliases and
                format changes between deserialization and response.
            client: A preconfigured Elasticsearch client.

        """
        super().__init__(
            resource_cls=resource_cls,
            resource_mapper=resource_mapper,
            transformer=ElasticTransformer(mapper=resource_mapper),
        )

        self.client = client if client else CLIENT
        self.name = name

        # If we are creating a new collection from scratch, also create the index,
        # otherwise assume it has already been created externally
        if CONFIG.insert_test_data:
            self.create_optimade_index()

    def count(self, *args, **kwargs) -> int:
        raise NotImplementedError

    def create_optimade_index(self) -> None:
        """Load or create an index that can handle aliased OPTIMADE fields and attach it
        to the current client.

        """
        body = self.predefined_index.get(self.name)
        if body is None:
            body = self.create_elastic_index_from_mapper(
                self.resource_mapper, self.all_fields
            )

        properties = {}
        for field in list(body["mappings"]["properties"].keys()):
            properties[self.resource_mapper.get_backend_field(field)] = body[
                "mappings"
            ]["properties"].pop(field)
        properties["id"] = {"type": "keyword"}
        body["mappings"]["properties"] = properties
        self.client.indices.create(index=self.name, ignore=400, **body)

        LOGGER.debug(f"Created Elastic index for {self.name!r} with parameters {body}")

    @property
    def predefined_index(self) -> dict[str, Any]:
        """Loads and returns the default pre-defined index."""
        with open(Path(__file__).parent.joinpath("elastic_indexes.json")) as f:
            index = json.load(f)
        return index

    @staticmethod
    def create_elastic_index_from_mapper(
        resource_mapper: type[BaseResourceMapper], fields: Iterable[str]
    ) -> dict[str, Any]:
        """Create a fallback elastic index based on a resource mapper.

        Arguments:
            resource_mapper: The resource mapper to create the index for.
            fields: The list of fields to use in the index.

        Returns:
            The parameters to pass to `client.indices.create(...)` (previously
                the 'body' parameters).

        """
        properties = {
            resource_mapper.get_optimade_field(field): {"type": "keyword"}
            for field in fields
        }
        properties["id"] = {"type": "keyword"}
        return {"mappings": {"properties": properties}}

    def __len__(self):
        """Returns the total number of entries in the collection."""
        return Search(using=self.client, index=self.name).execute().hits.total.value

    def insert(self, data: list[EntryResource]) -> None:
        """Add the given entries to the underlying database.

        Warning:
            No validation is performed on the incoming data.

        Arguments:
            data: The entry resource objects to add to the database.

        """

        def get_id(item):
            if self.name == "links":
                id_ = f"{item['id']}-{item['type']}"
            elif "id" in item:
                id_ = item["id"]
            elif "_id" in item:
                # use the existing MongoDB ids in the test data
                id_ = str(item["_id"])
            else:
                # ES will generate ids
                id_ = None
            item.pop("_id", None)
            return id_

        bulk(
            self.client,
            (
                {
                    "_index": self.name,
                    "_id": get_id(item),
                    "_source": item,
                }
                for item in data
            ),
        )

    def _run_db_query(
        self, criteria: dict[str, Any], single_entry=False
    ) -> tuple[list[dict[str, Any]], int, bool]:
        """Run the query on the backend and collect the results.

        Arguments:
            criteria: A dictionary representation of the query parameters.
            single_entry: Whether or not the caller is expecting a single entry response.

        Returns:
            The list of entries from the database (without any re-mapping), the total number of
            entries matching the query and a boolean for whether or not there is more data available.

        """

        search = Search(using=self.client, index=self.name)

        if criteria.get("filter", False):
            search = search.query(criteria["filter"])

        page_offset = criteria.get("skip", None)
        page_above = criteria.get("page_above", None)

        limit = criteria.get("limit", CONFIG.page_limit)

        all_aliased_fields = [
            self.resource_mapper.get_backend_field(field) for field in self.all_fields
        ]
        search = search.source(includes=all_aliased_fields)

        elastic_sort = [
            {field: {"order": "desc" if sort_dir == -1 else "asc"}}
            for field, sort_dir in criteria.get("sort", {})
        ]
        if not elastic_sort:
            elastic_sort = [
                {self.resource_mapper.get_backend_field("id"): {"order": "asc"}}
            ]

        search = search.sort(*elastic_sort)

        if page_offset:
            search = search[page_offset : page_offset + limit]

        elif page_above:
            search = search.extra(search_after=page_above, limit=limit)

        else:
            search = search[0:limit]
            page_offset = 0

        search = search.extra(track_total_hits=True)
        response = search.execute()

        results = [hit.to_dict() for hit in response.hits]

        more_data_available = False
        if not single_entry:
            data_returned = response.hits.total.value
            if page_above is not None:
                more_data_available = len(results) == limit and data_returned != limit
            else:
                more_data_available = page_offset + limit < data_returned
        else:
            # SingleEntryQueryParams, e.g., /structures/{entry_id}
            data_returned = len(results)

        return results, data_returned, more_data_available

all_fields: set[str] property

Get the set of all fields handled in this collection, from attribute fields in the schema, provider fields and top-level OPTIMADE fields.

The set of all fields are lazily created and then cached. This means the set is created the first time the property is requested and then cached.

Returns:

Type	Description
set[str]	All fields handled in this collection.

predefined_index: dict[str, Any] property

Loads and returns the default pre-defined index.

__init__(name, resource_cls, resource_mapper, client=None)

Initialize the ElasticCollection for the given parameters.

Parameters:

Name	Type	Description	Default
name	str	The name of the collection.	required
resource_cls	type[EntryResource]	The type of entry resource that is stored by the collection.	required
resource_mapper	type[BaseResourceMapper]	A resource mapper object that handles aliases and format changes between deserialization and response.	required
client	Optional[Elasticsearch]	A preconfigured Elasticsearch client.	None

Source code in optimade/server/entry_collections/elasticsearch.py

def __init__(
    self,
    name: str,
    resource_cls: type[EntryResource],
    resource_mapper: type[BaseResourceMapper],
    client: Optional["Elasticsearch"] = None,
):
    """Initialize the ElasticCollection for the given parameters.

    Parameters:
        name: The name of the collection.
        resource_cls: The type of entry resource that is stored by the collection.
        resource_mapper: A resource mapper object that handles aliases and
            format changes between deserialization and response.
        client: A preconfigured Elasticsearch client.

    """
    super().__init__(
        resource_cls=resource_cls,
        resource_mapper=resource_mapper,
        transformer=ElasticTransformer(mapper=resource_mapper),
    )

    self.client = client if client else CLIENT
    self.name = name

    # If we are creating a new collection from scratch, also create the index,
    # otherwise assume it has already been created externally
    if CONFIG.insert_test_data:
        self.create_optimade_index()

__len__()

Returns the total number of entries in the collection.

Source code in optimade/server/entry_collections/elasticsearch.py

def __len__(self):
    """Returns the total number of entries in the collection."""
    return Search(using=self.client, index=self.name).execute().hits.total.value

create_elastic_index_from_mapper(resource_mapper, fields) staticmethod

Create a fallback elastic index based on a resource mapper.

Parameters:

Name	Type	Description	Default
resource_mapper	type[BaseResourceMapper]	The resource mapper to create the index for.	required
fields	Iterable[str]	The list of fields to use in the index.	required

Returns:

Type	Description
dict[str, Any]	The parameters to pass to client.indices.create(...) (previously the 'body' parameters).

Source code in optimade/server/entry_collections/elasticsearch.py

@staticmethod
def create_elastic_index_from_mapper(
    resource_mapper: type[BaseResourceMapper], fields: Iterable[str]
) -> dict[str, Any]:
    """Create a fallback elastic index based on a resource mapper.

    Arguments:
        resource_mapper: The resource mapper to create the index for.
        fields: The list of fields to use in the index.

    Returns:
        The parameters to pass to `client.indices.create(...)` (previously
            the 'body' parameters).

    """
    properties = {
        resource_mapper.get_optimade_field(field): {"type": "keyword"}
        for field in fields
    }
    properties["id"] = {"type": "keyword"}
    return {"mappings": {"properties": properties}}

create_optimade_index()

Load or create an index that can handle aliased OPTIMADE fields and attach it to the current client.

Source code in optimade/server/entry_collections/elasticsearch.py

def create_optimade_index(self) -> None:
    """Load or create an index that can handle aliased OPTIMADE fields and attach it
    to the current client.

    """
    body = self.predefined_index.get(self.name)
    if body is None:
        body = self.create_elastic_index_from_mapper(
            self.resource_mapper, self.all_fields
        )

    properties = {}
    for field in list(body["mappings"]["properties"].keys()):
        properties[self.resource_mapper.get_backend_field(field)] = body[
            "mappings"
        ]["properties"].pop(field)
    properties["id"] = {"type": "keyword"}
    body["mappings"]["properties"] = properties
    self.client.indices.create(index=self.name, ignore=400, **body)

    LOGGER.debug(f"Created Elastic index for {self.name!r} with parameters {body}")

find(params)

Fetches results and indicates if more data is available.

Also gives the total number of data available in the absence of page_limit. See EntryListingQueryParams for more information.

Returns a list of the mapped database reponse.

If no results match the query, then results is set to None.

Parameters:

Name	Type	Description	Default
params	Union[EntryListingQueryParams, SingleEntryQueryParams]	Entry listing URL query params.	required

Returns:

Type	Description
Optional[Union[dict[str, Any], list[dict[str, Any]]]]	A tuple of various relevant values:
Optional[int]	(results, data_returned, more_data_available, exclude_fields, include_fields).

Source code in optimade/server/entry_collections/entry_collections.py

def find(
    self, params: Union[EntryListingQueryParams, SingleEntryQueryParams]
) -> tuple[
    Optional[Union[dict[str, Any], list[dict[str, Any]]]],
    Optional[int],
    bool,
    set[str],
    set[str],
]:
    """
    Fetches results and indicates if more data is available.

    Also gives the total number of data available in the absence of `page_limit`.
    See [`EntryListingQueryParams`][optimade.server.query_params.EntryListingQueryParams]
    for more information.

    Returns a list of the mapped database reponse.

    If no results match the query, then `results` is set to `None`.

    Parameters:
        params: Entry listing URL query params.

    Returns:
        A tuple of various relevant values:
        (`results`, `data_returned`, `more_data_available`, `exclude_fields`, `include_fields`).

    """
    criteria = self.handle_query_params(params)
    single_entry = isinstance(params, SingleEntryQueryParams)
    response_fields: set[str] = criteria.pop("fields")

    raw_results, data_returned, more_data_available = self._run_db_query(
        criteria, single_entry
    )

    exclude_fields = self.all_fields - response_fields
    include_fields = (
        response_fields - self.resource_mapper.TOP_LEVEL_NON_ATTRIBUTES_FIELDS
    )

    bad_optimade_fields: set[str] = set()
    bad_provider_fields: set[str] = set()
    supported_prefixes = self.resource_mapper.SUPPORTED_PREFIXES
    all_attributes: set[str] = self.resource_mapper.ALL_ATTRIBUTES
    for field in include_fields:
        if field not in all_attributes:
            if field.startswith("_"):
                if any(
                    field.startswith(f"_{prefix}_") for prefix in supported_prefixes
                ):
                    bad_provider_fields.add(field)
            else:
                bad_optimade_fields.add(field)

    if bad_provider_fields:
        warnings.warn(
            message=f"Unrecognised field(s) for this provider requested in `response_fields`: {bad_provider_fields}.",
            category=UnknownProviderProperty,
        )

    if bad_optimade_fields:
        raise BadRequest(
            detail=f"Unrecognised OPTIMADE field(s) in requested `response_fields`: {bad_optimade_fields}."
        )

    results: Optional[Union[list[dict[str, Any]], dict[str, Any]]] = None

    if raw_results:
        results = [self.resource_mapper.map_back(doc) for doc in raw_results]

        if single_entry:
            results = results[0]

            if (
                CONFIG.validate_api_response
                and data_returned is not None
                and data_returned > 1
            ):
                raise NotFound(
                    detail=f"Instead of a single entry, {data_returned} entries were found",
                )
            else:
                data_returned = 1

    return (
        results,
        data_returned,
        more_data_available,
        exclude_fields,
        include_fields,
    )

get_attribute_fields()

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.

Returns:

Type	Description
set[str]	Property names.

Source code in optimade/server/entry_collections/entry_collections.py

def get_attribute_fields(self) -> set[str]:
    """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.

    """
    annotation = _get_origin_type(
        self.resource_cls.model_fields["attributes"].annotation
    )

    if annotation in (None, NoneType) or not issubclass(annotation, Attributes):
        raise TypeError(
            "resource class 'attributes' field must be a subclass of 'EntryResourceAttributes'"
        )

    return set(annotation.model_fields)  # type: ignore[attr-defined]

get_next_query_params(params, results)

Provides url query pagination parameters that will be used in the next link.

Parameters:

Name	Type	Description	Default
results	Optional[Union[dict[str, Any], list[dict[str, Any]]]]	The results produced by find.	required
params	EntryListingQueryParams	The parsed request params produced by handle_query_params.	required

Returns:

Type	Description
dict[str, list[str]]	A dictionary with the necessary query parameters.

Source code in optimade/server/entry_collections/entry_collections.py

def get_next_query_params(
    self,
    params: EntryListingQueryParams,
    results: Optional[Union[dict[str, Any], list[dict[str, Any]]]],
) -> dict[str, list[str]]:
    """Provides url query pagination parameters that will be used in the next
    link.

    Arguments:
        results: The results produced by find.
        params: The parsed request params produced by handle_query_params.

    Returns:
        A dictionary with the necessary query parameters.

    """
    query: dict[str, list[str]] = dict()
    if isinstance(results, list) and results:
        # If a user passed a particular pagination mechanism, keep using it
        # Otherwise, use the default pagination mechanism of the collection
        pagination_mechanism = PaginationMechanism.OFFSET
        for pagination_key in (
            "page_offset",
            "page_number",
            "page_above",
        ):
            if getattr(params, pagination_key, None) is not None:
                pagination_mechanism = PaginationMechanism(pagination_key)
                break

        if pagination_mechanism == PaginationMechanism.OFFSET:
            query["page_offset"] = [
                str(params.page_offset + len(results))  # type: ignore[list-item]
            ]

    return query

handle_query_params(params)

Parse and interpret the backend-agnostic query parameter models into a dictionary that can be used by the specific backend.

Note

Currently this method returns the pymongo interpretation of the parameters, which will need modification for modified for other backends.

Parameters:

Name	Type	Description	Default
params	Union[EntryListingQueryParams, SingleEntryQueryParams]	The initialized query parameter model from the server.	required

Raises:

Type	Description
Forbidden	If too large of a page limit is provided.
BadRequest	If an invalid request is made, e.g., with incorrect fields or response format.

Returns:

Type	Description
dict[str, Any]	A dictionary representation of the query parameters.

Source code in optimade/server/entry_collections/entry_collections.py

def handle_query_params(
    self, params: Union[EntryListingQueryParams, SingleEntryQueryParams]
) -> dict[str, Any]:
    """Parse and interpret the backend-agnostic query parameter models into a dictionary
    that can be used by the specific backend.

    Note:
        Currently this method returns the pymongo interpretation of the parameters,
        which will need modification for modified for other backends.

    Parameters:
        params: The initialized query parameter model from the server.

    Raises:
        Forbidden: If too large of a page limit is provided.
        BadRequest: If an invalid request is made, e.g., with incorrect fields
            or response format.

    Returns:
        A dictionary representation of the query parameters.

    """
    cursor_kwargs = {}

    # filter
    if getattr(params, "filter", False):
        cursor_kwargs["filter"] = self.transformer.transform(
            self.parser.parse(params.filter)  # type: ignore[union-attr]
        )
    else:
        cursor_kwargs["filter"] = {}

    # response_format
    if (
        getattr(params, "response_format", False)
        and params.response_format != "json"
    ):
        raise BadRequest(
            detail=f"Response format {params.response_format} is not supported, please use response_format='json'"
        )

    # page_limit
    if getattr(params, "page_limit", False):
        limit = params.page_limit  # type: ignore[union-attr]
        if limit > CONFIG.page_limit_max:
            raise Forbidden(
                detail=f"Max allowed page_limit is {CONFIG.page_limit_max}, you requested {limit}",
            )
        cursor_kwargs["limit"] = limit
    else:
        cursor_kwargs["limit"] = CONFIG.page_limit

    # response_fields
    cursor_kwargs["projection"] = {
        f"{self.resource_mapper.get_backend_field(f)}": True
        for f in self.all_fields
    }

    if getattr(params, "response_fields", False):
        response_fields = set(params.response_fields.split(","))
        response_fields |= self.resource_mapper.get_required_fields()
    else:
        response_fields = self.all_fields.copy()

    cursor_kwargs["fields"] = response_fields

    # sort
    if getattr(params, "sort", False):
        cursor_kwargs["sort"] = self.parse_sort_params(params.sort)  # type: ignore[union-attr]

    # warn if multiple pagination keys are present, and only use the first from this list
    received_pagination_option = False
    warn_multiple_keys = False

    if getattr(params, "page_offset", False):
        received_pagination_option = True
        cursor_kwargs["skip"] = params.page_offset  # type: ignore[union-attr]

    if isinstance(getattr(params, "page_number", None), int):
        if received_pagination_option:
            warn_multiple_keys = True
        else:
            received_pagination_option = True
            if params.page_number < 1:  # type: ignore[union-attr]
                warnings.warn(
                    message=f"'page_number' is 1-based, using 'page_number=1' instead of {params.page_number}",  # type: ignore[union-attr]
                    category=QueryParamNotUsed,
                )
                page_number = 1
            else:
                page_number = params.page_number  # type: ignore[union-attr]
            cursor_kwargs["skip"] = (page_number - 1) * cursor_kwargs["limit"]

    if isinstance(getattr(params, "page_above", None), str):
        if received_pagination_option:
            warn_multiple_keys = True
        else:
            received_pagination_option = True
            cursor_kwargs["page_above"] = params.page_above  # type: ignore[union-attr]

    if warn_multiple_keys:
        warnings.warn(
            message="Multiple pagination keys were provided, only using the first one of 'page_offset', 'page_number' or 'page_above'",
            category=QueryParamNotUsed,
        )

    return cursor_kwargs

insert(data)

Add the given entries to the underlying database.

Warning

No validation is performed on the incoming data.

Parameters:

Name	Type	Description	Default
data	list[EntryResource]	The entry resource objects to add to the database.	required

Source code in optimade/server/entry_collections/elasticsearch.py

def insert(self, data: list[EntryResource]) -> None:
    """Add the given entries to the underlying database.

    Warning:
        No validation is performed on the incoming data.

    Arguments:
        data: The entry resource objects to add to the database.

    """

    def get_id(item):
        if self.name == "links":
            id_ = f"{item['id']}-{item['type']}"
        elif "id" in item:
            id_ = item["id"]
        elif "_id" in item:
            # use the existing MongoDB ids in the test data
            id_ = str(item["_id"])
        else:
            # ES will generate ids
            id_ = None
        item.pop("_id", None)
        return id_

    bulk(
        self.client,
        (
            {
                "_index": self.name,
                "_id": get_id(item),
                "_source": item,
            }
            for item in data
        ),
    )

parse_sort_params(sort_params)

Handles any sort parameters passed to the collection, resolving aliases and dealing with any invalid fields.

Raises:

Type	Description
BadRequest	if an invalid sort is requested.

Returns:

Type	Description
Iterable[tuple[str, int]]	A list of tuples containing the aliased field name and
Iterable[tuple[str, int]]	sort direction encoded as 1 (ascending) or -1 (descending).

Source code in optimade/server/entry_collections/entry_collections.py

def parse_sort_params(self, sort_params: str) -> Iterable[tuple[str, int]]:
    """Handles any sort parameters passed to the collection,
    resolving aliases and dealing with any invalid fields.

    Raises:
        BadRequest: if an invalid sort is requested.

    Returns:
        A list of tuples containing the aliased field name and
        sort direction encoded as 1 (ascending) or -1 (descending).

    """
    sort_spec: list[tuple[str, int]] = []
    for field in sort_params.split(","):
        sort_dir = 1
        if field.startswith("-"):
            field = field[1:]
            sort_dir = -1
        aliased_field = self.resource_mapper.get_backend_field(field)
        sort_spec.append((aliased_field, sort_dir))

    unknown_fields = [
        field
        for field, _ in sort_spec
        if self.resource_mapper.get_optimade_field(field) not in self.all_fields
    ]

    if unknown_fields:
        error_detail = "Unable to sort on unknown field{} '{}'".format(
            "s" if len(unknown_fields) > 1 else "",
            "', '".join(unknown_fields),
        )

        # If all unknown fields are "other" provider-specific, then only provide a warning
        if all(
            (
                re.match(r"_[a-z_0-9]+_[a-z_0-9]*", field)
                and not field.startswith(f"_{self.provider_prefix}_")
            )
            for field in unknown_fields
        ):
            warnings.warn(error_detail, FieldValueNotRecognized)

        # Otherwise, if all fields are unknown, or some fields are unknown and do not
        # have other provider prefixes, then return 400: Bad Request
        else:
            raise BadRequest(detail=error_detail)

    # If at least one valid field has been provided for sorting, then use that
    sort_spec = [
        (field, sort_dir)
        for field, sort_dir in sort_spec
        if field not in unknown_fields
    ]

    return sort_spec