modos.remote#

Functions related to server storage handling

Classes#

`BearerAuth`	Base class that all auth implementations derive from
`EndpointManager`	Handle modos server endpoints.
`JWT`	Handles storage of JWT tokens for authentication.
`Permissions`	!!! abstract "Usage Documentation"
`S3KeySpec`	!!! abstract "Usage Documentation"
`S3Key`	!!! abstract "Usage Documentation"

Functions#

`get_session`()
`list_remote_items`(url)
`get_metadata_from_remote`(url[, modo_id])	Function to access metadata from one specific or all modos on a remote server
`is_s3_path`(path)	Check if a path is an S3 path
`get_s3_path`(url, query[, exact_match])	Request public S3 path of a specific modo or all modos matching the query string
`get_cache_dir`()

Module Contents#

class modos.remote.BearerAuth[source]#

Bases: requests.auth.AuthBase

Base class that all auth implementations derive from

jwt = None[source]#

__call__(r)[source]#

Parameters:: r (requests.PreparedRequest)
Return type:: requests.PreparedRequest

modos.remote.get_session()[source]#

Return type:: requests.Session

class modos.remote.EndpointManager[source]#

Handle modos server endpoints. If a modos server url is provided, it is used to detect available service urls. Alternatively, service urls can be provided explicitely if no modos server is available.

Parameters:

modos – URL to the modos server.
services – Mapping of services to their urls.

Examples

>>> ex = EndpointManager(modos="http://modos.example.org") 
>>> ex.list() 
{
  's3: 'http://s3.example.org/',
  'htsget': 'http://htsget.example.org/'
}
>>> ex.htsget 
'http://htsget.example.org'
>>> ex = EndpointManager(services={"s3": "http://s3.example.org"})
>>> ex.s3
'http://s3.example.org'

modos: pydantic.HttpUrl | None = None[source]#

services: dict[str, Any][source]#

property session[source]#

list()[source]#

List available endpoints.

Return type:: dict[str, Any]

property auth: dict[str, str | pydantic.HttpUrl] | None[source]#

Return type:: dict[str, str | pydantic.HttpUrl] | None

property kms: pydantic.HttpUrl | None[source]#

Return type:: pydantic.HttpUrl | None

property s3: pydantic.HttpUrl | None[source]#

Return type:: pydantic.HttpUrl | None

property fuzon: pydantic.HttpUrl | None[source]#

Return type:: pydantic.HttpUrl | None

property htsget: pydantic.HttpUrl | None[source]#

Return type:: pydantic.HttpUrl | None

property refget: pydantic.HttpUrl | None[source]#

Return type:: pydantic.HttpUrl | None

modos.remote.list_remote_items(url)[source]#

Parameters:: url (pydantic.HttpUrl)
Return type:: list[pydantic.HttpUrl]

modos.remote.get_metadata_from_remote(url, modo_id=None)[source]#

Function to access metadata from one specific or all modos on a remote server

Parameters:

server_url – Url to the remote modo server
id – id of the modo to retrieve metadata from. Will return all if not specified (default).
url (pydantic.HttpUrl)
modo_id (str | None)

Return type:

dict[str, Any]

modos.remote.is_s3_path(path)[source]#

Check if a path is an S3 path

Parameters:: path (str)

modos.remote.get_s3_path(url, query, exact_match=False)[source]#

Request public S3 path of a specific modo or all modos matching the query string :param remote_url: Url to the remote modo server :param query: query string to specify the modo of interest :param exact_match: if True only modos with exactly that id will be returned, otherwise (default) all matching modos

Parameters:

url (pydantic.HttpUrl)
query (str)
exact_match (bool)

Return type:

dict[str, Any]

modos.remote.get_cache_dir()[source]#

Return type:: pathlib.Path

class modos.remote.JWT[source]#

Handles storage of JWT tokens for authentication.

Examples

>>> token = JWT(access_token="eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJleHAiOjE2MzI5MjU2MDB9.DummySignature")
>>> token.is_expired
True
>>> token.to_cache()
>>> loaded_jwt = JWT.from_cache()
>>> loaded_jwt.access_token == token.access_token
True

access_token: str[source]#

_expires_at: datetime.datetime | None = None[source]#

property expires_at[source]#

static get_cache_path()[source]#

Return type:: pathlib.Path

to_cache()[source]#: Store JWT in cache directory.

classmethod from_cache()[source]#

Load JWT from cache directory if it exists.

Return type:: JWT | None

property is_expired: bool[source]#

Parameters:: skew (int)
Return type:: bool

refresh()[source]#

Return type:: JWT | None

class modos.remote.Permissions(/, **data)[source]#

Bases: pydantic.BaseModel

!!! abstract “Usage Documentation”: [Models](../concepts/models.md)

A base class for creating Pydantic models.

Parameters:: data (Any)

__class_vars__[source]#: The names of the class variables defined on the model.

__private_attributes__[source]#: Metadata about the private attributes of the model.

__signature__[source]#: The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__[source]#: Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__[source]#: The core schema of the model.

__pydantic_custom_init__[source]#: Whether the model has a custom __init__ function.

__pydantic_decorators__[source]#: Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__[source]#: Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__[source]#: Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__[source]#: The name of the post-init method for the model, if defined.

__pydantic_root_model__[source]#: Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__[source]#: The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__[source]#: The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_fields__[source]#: A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects.

__pydantic_computed_fields__[source]#: A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.

__pydantic_extra__[source]#: A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__[source]#: The names of fields explicitly set during instantiation.

__pydantic_private__[source]#: Values of private attributes set on the model instance.

read: bool[source]#

write: bool[source]#

owner: bool[source]#

classmethod default()[source]#

Return type:: Self

__str__()[source]#

class modos.remote.S3KeySpec(/, **data)[source]#

Bases: pydantic.BaseModel

!!! abstract “Usage Documentation”: [Models](../concepts/models.md)

A base class for creating Pydantic models.

Parameters:: data (Any)

__class_vars__[source]#: The names of the class variables defined on the model.

__private_attributes__[source]#: Metadata about the private attributes of the model.

__signature__[source]#: The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__[source]#: Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__[source]#: The core schema of the model.

__pydantic_custom_init__[source]#: Whether the model has a custom __init__ function.

__pydantic_decorators__[source]#: Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__[source]#: Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__[source]#: Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__[source]#: The name of the post-init method for the model, if defined.

__pydantic_root_model__[source]#: Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__[source]#: The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__[source]#: The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_fields__[source]#: A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects.

__pydantic_computed_fields__[source]#: A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.

__pydantic_extra__[source]#: A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__[source]#: The names of fields explicitly set during instantiation.

__pydantic_private__[source]#: Values of private attributes set on the model instance.

bucket: str[source]#

expiration: datetime.datetime[source]#

prefixes: list[str] | None[source]#

permissions: Permissions[source]#

name: str | None = None[source]#

class modos.remote.S3Key(/, **data)[source]#

Bases: pydantic.BaseModel

!!! abstract “Usage Documentation”: [Models](../concepts/models.md)

A base class for creating Pydantic models.

Parameters:: data (Any)

__class_vars__[source]#: The names of the class variables defined on the model.

__private_attributes__[source]#: Metadata about the private attributes of the model.

__signature__[source]#: The synthesized __init__ [Signature][inspect.Signature] of the model.

__pydantic_complete__[source]#: Whether model building is completed, or if there are still undefined fields.

__pydantic_core_schema__[source]#: The core schema of the model.

__pydantic_custom_init__[source]#: Whether the model has a custom __init__ function.

__pydantic_decorators__[source]#: Metadata containing the decorators defined on the model. This replaces Model.__validators__ and Model.__root_validators__ from Pydantic V1.

__pydantic_generic_metadata__[source]#: Metadata for generic models; contains data used for a similar purpose to __args__, __origin__, __parameters__ in typing-module generics. May eventually be replaced by these.

__pydantic_parent_namespace__[source]#: Parent namespace of the model, used for automatic rebuilding of models.

__pydantic_post_init__[source]#: The name of the post-init method for the model, if defined.

__pydantic_root_model__[source]#: Whether the model is a [RootModel][pydantic.root_model.RootModel].

__pydantic_serializer__[source]#: The pydantic-core SchemaSerializer used to dump instances of the model.

__pydantic_validator__[source]#: The pydantic-core SchemaValidator used to validate instances of the model.

__pydantic_fields__[source]#: A dictionary of field names and their corresponding [FieldInfo][pydantic.fields.FieldInfo] objects.

__pydantic_computed_fields__[source]#: A dictionary of computed field names and their corresponding [ComputedFieldInfo][pydantic.fields.ComputedFieldInfo] objects.

__pydantic_extra__[source]#: A dictionary containing extra values, if [extra][pydantic.config.ConfigDict.extra] is set to ‘allow’.

__pydantic_fields_set__[source]#: The names of fields explicitly set during instantiation.

__pydantic_private__[source]#: Values of private attributes set on the model instance.

spec: S3KeySpec[source]#

access_key_id: str[source]#

secret_access_key: str | None[source]#

valid_paths()[source]#

Prints the valid S3 paths for this key.

Return type:: str

modos.remote#

Classes#

Functions#

Module Contents#

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