rxn.utilities.databases.pymongo.PyMongoSettings

class rxn.utilities.databases.pymongo.PyMongoSettings(_case_sensitive=None, _env_prefix=None, _env_file=PosixPath('.'), _env_file_encoding=None, _env_nested_delimiter=None, _secrets_dir=None, **values)

Bases: BaseSettings

Settings for connecting to a MongoDB via pymongo.

Parameters

• _case_sensitive (bool | None, default: None) –

• _env_prefix (str | None, default: None) –

• _env_file (Union[Path, str, List[Union[Path, str]], Tuple[Union[Path, str], ...], None], default: PosixPath('.')) –

• _env_file_encoding (str | None, default: None) –

• _env_nested_delimiter (str | None, default: None) –

• _secrets_dir (str | Path | None, default: None) –

• values (Any) –

• mongo_uri (Optional[str]) –

• tls_ca_certificate_path (Optional[str]) –

__init__(_case_sensitive=None, _env_prefix=None, _env_file=PosixPath('.'), _env_file_encoding=None, _env_nested_delimiter=None, _secrets_dir=None, **values)

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

Parameters

• _case_sensitive (bool | None, default: None) –

• _env_prefix (str | None, default: None) –

• _env_file (Union[Path, str, List[Union[Path, str]], Tuple[Union[Path, str], ...], None], default: PosixPath('.')) –

• _env_file_encoding (str | None, default: None) –

• _env_nested_delimiter (str | None, default: None) –

• _secrets_dir (str | Path | None, default: None) –

• values (Any) –

Return type

None

Methods

__init__([_case_sensitive, _env_prefix, ...])	Create a new model by parsing and validating input data from keyword arguments.
construct([_fields_set])	param cls
copy(*[, include, exclude, update, deep])	Returns a copy of the model.
dict(*[, include, exclude, by_alias, ...])	param include
from_orm(obj)	param cls
get_client([tz_aware])	Instantiate a Mongo client using the provided SSL settings.
instantiate_client(mongo_uri[, ...])	Instantiate a Mongo client using the provided SSL settings.
json(*[, include, exclude, by_alias, ...])	param include
model_construct([_fields_set])	Creates a new instance of the Model class with validated data.
model_copy(*[, update, deep])	Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#model_copy
model_dump(*[, mode, include, exclude, ...])	Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#modelmodel_dump
model_dump_json(*[, indent, include, ...])	Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#modelmodel_dump_json
model_json_schema([by_alias, ref_template, ...])	Generates a JSON schema for a model class.
model_parametrized_name(params)	Compute the class name for parametrizations of generic classes.
model_post_init(_BaseModel__context)	Override this method to perform additional initialization after __init__ and model_construct.
model_rebuild(*[, force, raise_errors, ...])	Try to rebuild the pydantic-core schema for the model.
model_validate(obj, *[, strict, ...])	Validate a pydantic model instance.
model_validate_json(json_data, *[, strict, ...])	Usage docs: https://docs.pydantic.dev/2.6/concepts/json/#json-parsing
model_validate_strings(obj, *[, strict, context])	Validate the given object contains string data against the Pydantic model.
parse_file(path, *[, content_type, ...])	param cls
parse_obj(obj)	param cls
parse_raw(b, *[, content_type, encoding, ...])	param cls
schema([by_alias, ref_template])	param by_alias
schema_json(*[, by_alias, ref_template])	param by_alias
settings_customise_sources(settings_cls, ...)	Define the sources and their order for loading the settings values.
update_forward_refs(**localns)	param localns
validate(value)	param cls

Attributes

model_computed_fields	A dictionary of computed field names and their corresponding ComputedFieldInfo objects.
model_config	Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].
model_extra	Get extra fields set during validation.
model_fields	Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].
model_fields_set	Returns the set of fields that have been explicitly set on this model instance.
mongo_uri
tls_ca_certificate_path

copy(*, include=None, exclude=None, update=None, deep=False)

Returns a copy of the model.

!!! warning “Deprecated”

This method is now deprecated; use model_copy instead.

If you need include or exclude, use:

`py data = self.model_dump(include=include, exclude=exclude, round_trip=True) data = {**data, **(update or {})} copied = self.model_validate(data) `

Parameters

• include (AbstractSetIntStr | MappingIntStrAny | None, default: None) – Optional set or mapping specifying which fields to include in the copied model.

• exclude (AbstractSetIntStr | MappingIntStrAny | None, default: None) – Optional set or mapping specifying which fields to exclude in the copied model.

• update (typing.Dict[str, Any] | None, default: None) – Optional dictionary of field-value pairs to override field values in the copied model.

• deep (bool, default: False) – If True, the values of fields that are Pydantic models will be deep-copied.

• self (Model) –

Return type

Model

Returns

A copy of the model with included, excluded and updated fields as specified.

get_client(tz_aware=False)

Instantiate a Mongo client using the provided SSL settings.

All other options except the tlsCAFile (and tz_aware) are expected to be passed via the mongo_uri. For example for insecure access something like the following could be added to the url: ssl=true&tlsAllowInvalidCertificates=true&tlsAllowInvalidHostnames=true Different mongodb server versions might behave differently!

Parameters

tz_aware (bool, default: False) – flag indicating whether datetime objects returned are timezone aware.

Return type

MongoClient

Returns

a client for MongoDB.

static instantiate_client(mongo_uri, tls_ca_certificate_path=None, tz_aware=False)

Instantiate a Mongo client using the provided SSL settings.

All other options except the tlsCAFile (and tz_aware) are expected to be passed via the mongo_uri. For example for insecure access something like the following could be added to the url: ssl=true&tlsAllowInvalidCertificates=true&tlsAllowInvalidHostnames=true Different mongodb server versions might behave differently!

Parameters

• mongo_uri (str) – connection string for Mongo.

• tls_ca_certificate_path (Optional[str], default: None) – optional path to an SSL CA certificate.

• tz_aware (bool, default: False) – flag indicating whether datetime objects returned are timezone aware.

Return type

MongoClient

Returns

a client for MongoDB.

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}

A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[SettingsConfigDict] = {'arbitrary_types_allowed': True, 'case_sensitive': False, 'env_file': None, 'env_file_encoding': None, 'env_nested_delimiter': None, 'env_prefix': 'RXN_', 'extra': 'ignore', 'protected_namespaces': ('model_', 'settings_'), 'secrets_dir': None, 'validate_default': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod model_construct(_fields_set=None, **values)

Creates a new instance of the Model class with validated data.

Creates a new model setting __dict__ and __pydantic_fields_set__ from trusted or pre-validated data. Default values are respected, but no other validation is performed. Behaves as if Config.extra = ‘allow’ was set since it adds all passed values

Parameters

• _fields_set (set[str] | None, default: None) – The set of field names accepted for the Model instance.

• values (Any) – Trusted or pre-validated data dictionary.

• cls (type[Model]) –

Return type

Model

Returns

A new instance of the Model class with validated data.

model_copy(*, update=None, deep=False)

Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#model_copy

Returns a copy of the model.

Parameters

• update (dict[str, Any] | None, default: None) – Values to change/add in the new model. Note: the data is not validated before creating the new model. You should trust this data.

• deep (bool, default: False) – Set to True to make a deep copy of the model.

• self (Model) –

Return type

Model

Returns

New model instance.

model_dump(*, mode='python', include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True)

Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#modelmodel_dump

Generate a dictionary representation of the model, optionally specifying which fields to include or exclude.

Parameters

• mode (Literal[‘json’, ‘python’] | str, default: 'python') – The mode in which to_python should run. If mode is ‘json’, the output will only contain JSON serializable types. If mode is ‘python’, the output may contain non-JSON-serializable Python objects.

• include (IncEx, default: None) – A list of fields to include in the output.

• exclude (IncEx, default: None) – A list of fields to exclude from the output.

• by_alias (bool, default: False) – Whether to use the field’s alias in the dictionary key if defined.

• exclude_unset (bool, default: False) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool, default: False) – Whether to exclude fields that are set to their default value.

• exclude_none (bool, default: False) – Whether to exclude fields that have a value of None.

• round_trip (bool, default: False) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool, default: True) – Whether to log warnings when invalid fields are encountered.

Return type

dict[str, Any]

Returns

A dictionary representation of the model.

model_dump_json(*, indent=None, include=None, exclude=None, by_alias=False, exclude_unset=False, exclude_defaults=False, exclude_none=False, round_trip=False, warnings=True)

Usage docs: https://docs.pydantic.dev/2.6/concepts/serialization/#modelmodel_dump_json

Generates a JSON representation of the model using Pydantic’s to_json method.

Parameters

• indent (int | None, default: None) – Indentation to use in the JSON output. If None is passed, the output will be compact.

• include (IncEx, default: None) – Field(s) to include in the JSON output.

• exclude (IncEx, default: None) – Field(s) to exclude from the JSON output.

• by_alias (bool, default: False) – Whether to serialize using field aliases.

• exclude_unset (bool, default: False) – Whether to exclude fields that have not been explicitly set.

• exclude_defaults (bool, default: False) – Whether to exclude fields that are set to their default value.

• exclude_none (bool, default: False) – Whether to exclude fields that have a value of None.

• round_trip (bool, default: False) – If True, dumped values should be valid as input for non-idempotent types such as Json[T].

• warnings (bool, default: True) – Whether to log warnings when invalid fields are encountered.

Return type

str

Returns

A JSON string representation of the model.

property model_extra: dict[str, Any] | None

Get extra fields set during validation.

Return type

dict[str, Any] | None

Returns

A dictionary of extra fields, or None if config.extra is not set to “allow”.

model_fields: ClassVar[dict[str, FieldInfo]] = {'mongo_uri': FieldInfo(annotation=Union[str, NoneType], required=False), 'tls_ca_certificate_path': FieldInfo(annotation=Union[str, NoneType], required=False)}

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

property model_fields_set: set[str]

Returns the set of fields that have been explicitly set on this model instance.

Return type

set[str]

Returns

A set of strings representing the fields that have been set,

i.e. that were not filled from defaults.

classmethod model_json_schema(by_alias=True, ref_template='#/$defs/{model}', schema_generator=<class 'pydantic.json_schema.GenerateJsonSchema'>, mode='validation')

Generates a JSON schema for a model class.

Parameters

• by_alias (bool, default: True) – Whether to use attribute aliases or not.

• ref_template (str, default: '#/$defs/{model}') – The reference template.

• schema_generator (type[GenerateJsonSchema], default: <class 'pydantic.json_schema.GenerateJsonSchema'>) – To override the logic used to generate the JSON schema, as a subclass of GenerateJsonSchema with your desired modifications

• mode (Literal[‘validation’, ‘serialization’], default: 'validation') – The mode in which to generate the schema.

Return type

dict[str, Any]

Returns

The JSON schema for the given model class.

classmethod model_parametrized_name(params)

Compute the class name for parametrizations of generic classes.

This method can be overridden to achieve a custom naming scheme for generic BaseModels.

Parameters

params (tuple[type[Any], ...]) – Tuple of types of the class. Given a generic class Model with 2 type variables and a concrete model Model[str, int], the value (str, int) would be passed to params.

Return type

str

Returns

String representing the new class where params are passed to cls as type variables.

Raises

TypeError – Raised when trying to generate concrete names for non-generic models.

model_post_init(_BaseModel__context)

Override this method to perform additional initialization after __init__ and model_construct. This is useful if you want to do some validation that requires the entire model to be initialized.

Parameters

_BaseModel__context (Any) –

Return type

None

classmethod model_rebuild(*, force=False, raise_errors=True, _parent_namespace_depth=2, _types_namespace=None)

Try to rebuild the pydantic-core schema for the model.

This may be necessary when one of the annotations is a ForwardRef which could not be resolved during the initial attempt to build the schema, and automatic rebuilding fails.

Parameters

• force (bool, default: False) – Whether to force the rebuilding of the model schema, defaults to False.

• raise_errors (bool, default: True) – Whether to raise errors, defaults to True.

• _parent_namespace_depth (int, default: 2) – The depth level of the parent namespace, defaults to 2.

• _types_namespace (dict[str, Any] | None, default: None) – The types namespace, defaults to None.

Return type

bool | None

Returns

Returns None if the schema is already “complete” and rebuilding was not required. If rebuilding _was_ required, returns True if rebuilding was successful, otherwise False.

classmethod model_validate(obj, *, strict=None, from_attributes=None, context=None)

Validate a pydantic model instance.

Parameters

• obj (Any) – The object to validate.

• strict (bool | None, default: None) – Whether to enforce types strictly.

• from_attributes (bool | None, default: None) – Whether to extract data from object attributes.

• context (dict[str, Any] | None, default: None) – Additional context to pass to the validator.

• cls (type[Model]) –

Raises

ValidationError – If the object could not be validated.

Return type

Model

Returns

The validated model instance.

classmethod model_validate_json(json_data, *, strict=None, context=None)

Usage docs: https://docs.pydantic.dev/2.6/concepts/json/#json-parsing

Validate the given JSON data against the Pydantic model.

Parameters

• json_data (str | bytes | bytearray) – The JSON data to validate.

• strict (bool | None, default: None) – Whether to enforce types strictly.

• context (dict[str, Any] | None, default: None) – Extra variables to pass to the validator.

• cls (type[Model]) –

Return type

Model

Returns

The validated Pydantic model.

Raises

ValueError – If json_data is not a JSON string.

classmethod model_validate_strings(obj, *, strict=None, context=None)

Validate the given object contains string data against the Pydantic model.

Parameters

• obj (Any) – The object contains string data to validate.

• strict (bool | None, default: None) – Whether to enforce types strictly.

• context (dict[str, Any] | None, default: None) – Extra variables to pass to the validator.

• cls (type[Model]) –

Return type

Model

Returns

The validated Pydantic model.

classmethod settings_customise_sources(settings_cls, init_settings, env_settings, dotenv_settings, file_secret_settings)

Define the sources and their order for loading the settings values.

Parameters

• settings_cls (type[BaseSettings]) – The Settings class.

• init_settings (PydanticBaseSettingsSource) – The InitSettingsSource instance.

• env_settings (PydanticBaseSettingsSource) – The EnvSettingsSource instance.

• dotenv_settings (PydanticBaseSettingsSource) – The DotEnvSettingsSource instance.

• file_secret_settings (PydanticBaseSettingsSource) – The SecretsSettingsSource instance.

Return type

tuple[PydanticBaseSettingsSource, ...]

Returns

A tuple containing the sources and their order for loading the settings values.