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base

The base for all adapters.

An entry resource adapter is a tool to wrap OPTIMADE JSON-deserialized Python dictionaries in the relevant pydantic model for the particular resource.

This means data resources in an OPTIMADE REST API response can be converted to valid Python types written specifically for them. One can then use the standard pydantic functionality on the wrapped objects, reasoning about the embedded hierarchical types as well as retrieve default values for properties not supplied by the raw API response resource.

Furthermore, the entry resource adapter allows conversion between the entry resource and any implemented equivalent data structure.

See Reference and Structure to find out what the entry resources can be converted to for ReferenceResources and StructureResources, respectively.

EntryAdapter

Base class for lazy resource entry adapters.

Attributes:

Name Type Description
ENTRY_RESOURCE type[EntryResource]

Entry resource to store entry as.
_type_converters dict[str, Callable]

Dictionary of valid conversion types for entry.
_type_ingesters dict[str, Callable]

Dictionary of valid ingestion types mapped to ingestion functions.
_type_ingesters_by_type dict[str, type]

Dictionary mapping the keys of _type_ingesters to data types that can be ingested.
as_<_type_converters> dict[str, type]

Convert entry to a type listed in _type_converters.
from_<_type_converters> dict[str, type]

Convert an external type to the corresponding OPTIMADE model.
Source code in optimade/adapters/base.py 
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class EntryAdapter:
    """
    Base class for lazy resource entry adapters.

    Attributes:
        ENTRY_RESOURCE: Entry resource to store entry as.
        _type_converters: Dictionary of valid conversion types for entry.
        _type_ingesters: Dictionary of valid ingestion types mapped to ingestion functions.
        _type_ingesters_by_type: Dictionary mapping the keys of `_type_ingesters` to data
            types that can be ingested.
        as_<_type_converters>: Convert entry to a type listed in `_type_converters`.
        from_<_type_converters>: Convert an external type to the corresponding OPTIMADE model.

    """

    ENTRY_RESOURCE: type[EntryResource] = EntryResource
    _type_converters: dict[str, Callable] = {}
    _type_ingesters: dict[str, Callable] = {}
    _type_ingesters_by_type: dict[str, type] = {}

    def __init__(self, entry: dict[str, Any]) -> None:
        """
        Parameters:
            entry (dict): A JSON OPTIMADE single resource entry.
        """
        self._converted: dict[str, Any] = {}

        self._entry = self.ENTRY_RESOURCE(**entry)

        # Note that these return also the default values for otherwise non-provided properties.
        self._common_converters = {
            # Return JSON serialized string, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeljson
            "json": self.entry.model_dump_json,
            # Return Python dict, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeldict
            "dict": self.entry.model_dump,
        }

    @property
    def entry(self) -> EntryResource:
        """Get OPTIMADE entry.

        Returns:
            The entry resource.

        """
        return self._entry

    def convert(self, format: str) -> Any:
        """Convert OPTIMADE entry to desired format.

        Parameters:
            format (str): Type or format to which the entry should be converted.

        Raises:
            AttributeError: If `format` can not be found in `_type_converters` or `_common_converters`.

        Returns:
            The converted entry according to the desired format or type.

        """
        if (
            format not in self._type_converters
            and format not in self._common_converters
        ):
            raise AttributeError(
                f"Non-valid entry type to convert to: {format}\nValid entry types: "
                f"{tuple(self._type_converters.keys()) + tuple(self._common_converters.keys())}"
            )

        if self._converted.get(format, None) is None:
            if format in self._type_converters:
                self._converted[format] = self._type_converters[format](self.entry)
            else:
                self._converted[format] = self._common_converters[format]()

        return self._converted[format]

    @classmethod
    def ingest_from(cls, data: Any, format: Optional[str] = None) -> Any:
        """Convert desired format to OPTIMADE format.

        Parameters:
            data (Any): The data to convert.
            format (str): Type or format to which the entry should be converted.

        Raises:
            AttributeError: If `format` can not be found in `_type_ingesters`.

        Returns:
            The ingested Structure.

        """

        if format is None:
            for key, instance_type in cls._type_ingesters_by_type.items():
                if isinstance(data, instance_type):
                    format = key
                    break

            else:
                raise AttributeError(
                    f"Non entry type to data of type {type(data)} from.\n"
                    f"Valid entry types: {tuple(cls._type_ingesters.keys())}"
                )

        if format not in cls._type_ingesters:
            raise AttributeError(
                f"Non-valid entry type to ingest from: {format}\n"
                f"Valid entry types: {tuple(cls._type_ingesters.keys())}"
            )

        return cls(
            {
                "attributes": cls._type_ingesters[format](data).model_dump(),
                "id": "",
                "type": "structures",
            }
        )

    @staticmethod
    def _get_model_attributes(
        starting_instances: Union[tuple[BaseModel, ...], list[BaseModel]], name: str
    ) -> Any:
        """Helper method for retrieving the OPTIMADE model's attribute, supporting "."-nested attributes"""
        for res in starting_instances:
            nested_attributes = name.split(".")
            for nested_attribute in nested_attributes:
                if nested_attribute in getattr(res, "model_fields", {}):
                    res = getattr(res, nested_attribute)
                else:
                    res = None
                    break
            if res is not None:
                return res
        raise AttributeError

    def __getattr__(self, name: str) -> Any:
        """Get converted entry or attribute from OPTIMADE entry.

        Support any level of "."-nested OPTIMADE `ENTRY_RESOURCE` attributes, e.g.,
        `attributes.species` for [`StuctureResource`][optimade.models.structures.StructureResource].

        Note:
            All nested attributes must individually be subclasses of `pydantic.BaseModel`,
            i.e., one can not access nested attributes in lists by passing a "."-nested `name` to this method,
            e.g., `attributes.species.name` or `attributes.species[0].name` will not work for variable `name`.

        Order:

        - Try to return converted entry if using `as_<_type_converters key>`.
        - Try to return OPTIMADE `ENTRY_RESOURCE` (nested) attribute.
        - Try to return OPTIMADE `ENTRY_RESOURCE.attributes` (nested) attribute.
        - Raise `AttributeError`.

        Parameters:
            name (str): Requested attribute.

        Raises:
            AttributeError: If the requested attribute is not recognized.
                See above for the description of the order in which an attribute is tested for validity.

        """
        # as_<entry_type>
        if name.startswith("as_"):
            entry_type = "_".join(name.split("_")[1:])
            return self.convert(entry_type)

        # Try returning ENTRY_RESOURCE attribute
        try:
            res = self._get_model_attributes((self.entry, self.entry.attributes), name)
        except AttributeError:
            pass
        else:
            return res

        # Non-valid attribute
        _entry_resource_name = re.match(
            r"(<class ')([a-zA-Z_]+\.)*([a-zA-Z_]+)('>)", str(self.ENTRY_RESOURCE)
        )
        entry_resource_name = (
            _entry_resource_name.group(3)
            if _entry_resource_name is not None
            else "UNKNOWN RESOURCE"
        )
        raise AttributeError(
            f"Unknown attribute: {name}\n"
            "If you want to get a converted entry as <entry_type> use `as_<entry_type>`, "
            f"where `<entry_type>` is one of {tuple(self._type_converters.keys()) + tuple(self._common_converters.keys())}\n"
            f"Otherwise, you can try to retrieve an OPTIMADE {entry_resource_name} attribute or property."
        )

entry: EntryResource property

Get OPTIMADE entry.

Returns:

Type Description
EntryResource

The entry resource.

__getattr__(name)

Get converted entry or attribute from OPTIMADE entry.

Support any level of "."-nested OPTIMADE ENTRY_RESOURCE attributes, e.g., attributes.species for StuctureResource.

Note

All nested attributes must individually be subclasses of pydantic.BaseModel, i.e., one can not access nested attributes in lists by passing a "."-nested name to this method, e.g., attributes.species.name or attributes.species[0].name will not work for variable name.

Order:

  • Try to return converted entry if using as_<_type_converters key>.
  • Try to return OPTIMADE ENTRY_RESOURCE (nested) attribute.
  • Try to return OPTIMADE ENTRY_RESOURCE.attributes (nested) attribute.
  • Raise AttributeError.

Parameters:

Name Type Description Default
name str

Requested attribute.

 required

Raises:

Type Description
AttributeError

If the requested attribute is not recognized. See above for the description of the order in which an attribute is tested for validity.
Source code in optimade/adapters/base.py 
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def __getattr__(self, name: str) -> Any:
    """Get converted entry or attribute from OPTIMADE entry.

    Support any level of "."-nested OPTIMADE `ENTRY_RESOURCE` attributes, e.g.,
    `attributes.species` for [`StuctureResource`][optimade.models.structures.StructureResource].

    Note:
        All nested attributes must individually be subclasses of `pydantic.BaseModel`,
        i.e., one can not access nested attributes in lists by passing a "."-nested `name` to this method,
        e.g., `attributes.species.name` or `attributes.species[0].name` will not work for variable `name`.

    Order:

    - Try to return converted entry if using `as_<_type_converters key>`.
    - Try to return OPTIMADE `ENTRY_RESOURCE` (nested) attribute.
    - Try to return OPTIMADE `ENTRY_RESOURCE.attributes` (nested) attribute.
    - Raise `AttributeError`.

    Parameters:
        name (str): Requested attribute.

    Raises:
        AttributeError: If the requested attribute is not recognized.
            See above for the description of the order in which an attribute is tested for validity.

    """
    # as_<entry_type>
    if name.startswith("as_"):
        entry_type = "_".join(name.split("_")[1:])
        return self.convert(entry_type)

    # Try returning ENTRY_RESOURCE attribute
    try:
        res = self._get_model_attributes((self.entry, self.entry.attributes), name)
    except AttributeError:
        pass
    else:
        return res

    # Non-valid attribute
    _entry_resource_name = re.match(
        r"(<class ')([a-zA-Z_]+\.)*([a-zA-Z_]+)('>)", str(self.ENTRY_RESOURCE)
    )
    entry_resource_name = (
        _entry_resource_name.group(3)
        if _entry_resource_name is not None
        else "UNKNOWN RESOURCE"
    )
    raise AttributeError(
        f"Unknown attribute: {name}\n"
        "If you want to get a converted entry as <entry_type> use `as_<entry_type>`, "
        f"where `<entry_type>` is one of {tuple(self._type_converters.keys()) + tuple(self._common_converters.keys())}\n"
        f"Otherwise, you can try to retrieve an OPTIMADE {entry_resource_name} attribute or property."
    )

__init__(entry)

Parameters:

Name Type Description Default
entry dict

A JSON OPTIMADE single resource entry.

 required
Source code in optimade/adapters/base.py 
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def __init__(self, entry: dict[str, Any]) -> None:
    """
    Parameters:
        entry (dict): A JSON OPTIMADE single resource entry.
    """
    self._converted: dict[str, Any] = {}

    self._entry = self.ENTRY_RESOURCE(**entry)

    # Note that these return also the default values for otherwise non-provided properties.
    self._common_converters = {
        # Return JSON serialized string, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeljson
        "json": self.entry.model_dump_json,
        # Return Python dict, see https://pydantic-docs.helpmanual.io/usage/exporting_models/#modeldict
        "dict": self.entry.model_dump,
    }

convert(format)

Convert OPTIMADE entry to desired format.

Parameters:

Name Type Description Default
format str

Type or format to which the entry should be converted.

 required

Raises:

Type Description
AttributeError

If format can not be found in _type_converters or _common_converters.

Returns:

Type Description
Any

The converted entry according to the desired format or type.
Source code in optimade/adapters/base.py 
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def convert(self, format: str) -> Any:
    """Convert OPTIMADE entry to desired format.

    Parameters:
        format (str): Type or format to which the entry should be converted.

    Raises:
        AttributeError: If `format` can not be found in `_type_converters` or `_common_converters`.

    Returns:
        The converted entry according to the desired format or type.

    """
    if (
        format not in self._type_converters
        and format not in self._common_converters
    ):
        raise AttributeError(
            f"Non-valid entry type to convert to: {format}\nValid entry types: "
            f"{tuple(self._type_converters.keys()) + tuple(self._common_converters.keys())}"
        )

    if self._converted.get(format, None) is None:
        if format in self._type_converters:
            self._converted[format] = self._type_converters[format](self.entry)
        else:
            self._converted[format] = self._common_converters[format]()

    return self._converted[format]

ingest_from(data, format=None) classmethod

Convert desired format to OPTIMADE format.

Parameters:

Name Type Description Default
data Any

The data to convert.

 required
format str

Type or format to which the entry should be converted.

 None

Raises:

Type Description
AttributeError

If format can not be found in _type_ingesters.

Returns:

Type Description
Any

The ingested Structure.
Source code in optimade/adapters/base.py 
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@classmethod
def ingest_from(cls, data: Any, format: Optional[str] = None) -> Any:
    """Convert desired format to OPTIMADE format.

    Parameters:
        data (Any): The data to convert.
        format (str): Type or format to which the entry should be converted.

    Raises:
        AttributeError: If `format` can not be found in `_type_ingesters`.

    Returns:
        The ingested Structure.

    """

    if format is None:
        for key, instance_type in cls._type_ingesters_by_type.items():
            if isinstance(data, instance_type):
                format = key
                break

        else:
            raise AttributeError(
                f"Non entry type to data of type {type(data)} from.\n"
                f"Valid entry types: {tuple(cls._type_ingesters.keys())}"
            )

    if format not in cls._type_ingesters:
        raise AttributeError(
            f"Non-valid entry type to ingest from: {format}\n"
            f"Valid entry types: {tuple(cls._type_ingesters.keys())}"
        )

    return cls(
        {
            "attributes": cls._type_ingesters[format](data).model_dump(),
            "id": "",
            "type": "structures",
        }
    )

EntryResource

Bases: Resource

The base model for an entry resource.

Source code in optimade/models/entries.py 
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class EntryResource(Resource):
    """The base model for an entry resource."""

    id: Annotated[
        str,
        OptimadeField(
            description="""An entry's ID as defined in section Definition of Terms.

- **Type**: string.

- **Requirements/Conventions**:
    - **Support**: MUST be supported by all implementations, MUST NOT be `null`.
    - **Query**: MUST be a queryable property with support for all mandatory filter features.
    - **Response**: REQUIRED in the response.

- **Examples**:
    - `"db/1234567"`
    - `"cod/2000000"`
    - `"cod/2000000@1234567"`
    - `"nomad/L1234567890"`
    - `"42"`""",
            support=SupportLevel.MUST,
            queryable=SupportLevel.MUST,
        ),
    ]

    type: Annotated[
        str,
        OptimadeField(
            description="""The name of the type of an entry.

- **Type**: string.

- **Requirements/Conventions**:
    - **Support**: MUST be supported by all implementations, MUST NOT be `null`.
    - **Query**: MUST be a queryable property with support for all mandatory filter features.
    - **Response**: REQUIRED in the response.
    - MUST be an existing entry type.
    - The entry of type `<type>` and ID `<id>` MUST be returned in response to a request for `/<type>/<id>` under the versioned base URL.

- **Example**: `"structures"`""",
            support=SupportLevel.MUST,
            queryable=SupportLevel.MUST,
        ),
    ]

    attributes: Annotated[
        EntryResourceAttributes,
        StrictField(
            description="""A dictionary, containing key-value pairs representing the entry's properties, except for `type` and `id`.
Database-provider-specific properties need to include the database-provider-specific prefix (see section on Database-Provider-Specific Namespace Prefixes).""",
        ),
    ]

    relationships: Annotated[
        Optional[EntryRelationships],
        StrictField(
            description="""A dictionary containing references to other entries according to the description in section Relationships encoded as [JSON API Relationships](https://jsonapi.org/format/1.0/#document-resource-object-relationships).
The OPTIONAL human-readable description of the relationship MAY be provided in the `description` field inside the `meta` dictionary of the JSON API resource identifier object.""",
        ),
    ] = None