drs_cli package

Submodules

drs_cli.client module

Class implementing DRS client.

class drs_cli.client.DRSClient(uri: str, port: Optional[int] = None, base_path: Optional[str] = 'ga4gh/drs/v1', use_http: bool = False, token: Optional[str] = None)

Bases: object

Client to communicate with a GA4GH DRS instance. Supports additional endpoints defined in DRS-filer (https://github.com/elixir-cloud-aai/drs-filer).

Parameters:

• uri – Either the base URI of the DRS instance to connect to in either ‘https’ or ‘http’ schema (note that fully compliant DRS instances will use ‘https’ exclusively), e.g., https://my-drs.app, OR a hostname-based DRS URI, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• port – Override default port at which the DRS instance can be accessed. Only required for DRS instances that are not fully spec-compliant, as the default port is defined in the DRS documentation, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• base-path – Override default path at which the DRS API is accessible at the given DRS instance. Only required for DRS instances that are not fully spec-compliant, as the default port is defined in the DRS documentation, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• use_http – Set the URI schema of the DRS instance to http instead of https`when a DRS URI was provided to `uri.
• token – Bearer token to send along with DRS API requests. Set if required by DRS implementation. Alternatively, specify in API endpoint access methods.

uri

URI to DRS endpoints, built from uri, port and base_path, e.g.,”https://my-drs.app:443/ga4gh/drs/v1”.

token

Bearer token for gaining access to DRS endpoints.

headers

Dictionary of request headers.

delete_object(object_id: str, token: Optional[str] = None) → Union[str, drs_cli.models.Error]

Delete DRS object.

Parameters:

• object_id – Implementation-specific DRS identifier OR hostname-based DRS URI pointing to a given object, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• token – Bearer token for authentication. Set if required by DRS implementation and if not provided when instatiating client or if expired.

Returns:

ID of previously registered DRS object in case of a 200 response, or an instance of Error for all other responses.

Raises:

• requests.exceptions.ConnectionError – A connection to the provided DRS instance could not be established.
• drs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.

get_access_url(object_id: str, access_id: str, token: Optional[str] = None) → Union[drs_cli.models.AccessURL, drs_cli.models.Error]

Retrieve access URL of DRS object.

Parameters:

• object_id – Implementation-specific DRS identifier OR hostname-based DRS URI pointing to a given object, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• access_id – Identifier of one of a DRS object’s access methods.
• token – Bearer token for authentication. Set if required by DRS implementation and if not provided when instatiating client or if expired.

Returns:

Unmarshalled DRS response as either an instance of AccessURL in case of a 200 response, or an instance of Error for all other reponses.

Raises:

• requests.exceptions.ConnectionError – A connection to the provided DRS instance could not be established.
• drs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.

get_object(object_id: str, token: Optional[str] = None) → Union[drs_cli.models.Error, drs_cli.models.DrsObject]

Retrieve DRS object.

Parameters:

• object_id – Implementation-specific DRS identifier OR hostname-based DRS URI pointing to a given object, cf. https://ga4gh.github.io/data-repository-service-schemas/preview/develop/docs/#_hostname_based_drs_uris.
• token – Bearer token for authentication. Set if required by DRS implementation and if not provided when instatiating client or if expired.

Returns:

Unmarshalled DRS response as either an instance of DRSObject in case of a 200 response, or an instance of Error for all other JSON reponses.

Raises:

• requests.exceptions.ConnectionError – A connection to the provided DRS instance could not be established.
• drs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.

post_object(object_data: Dict[KT, VT], token: Optional[str] = None) → Union[str, drs_cli.models.Error]

Register DRS object.

Parameters:

• object_data – DRS object data.
• token – Bearer token for authentication. Set if required by DRS implementation and if not provided when instatiating client or if expired.

Returns:

ID of registered DRS object in case of a 200 response, or an instance of Error for all other responses.

Raises:

• requests.exceptions.ConnectionError – A connection to the provided DRS instance could not be established.
• drs_cli.errors.InvalidObjectData – The object data payload could not be validated against the API schema.
• drs_cli.errors.InvalidResponseError – The response could not be validated against the API schema.

drs_cli.errors module

exception drs_cli.errors.InvalidObjectData

Bases: Exception

Exception raised when object data cannot be validated against the API schema.

exception drs_cli.errors.InvalidResponseError

Bases: Exception

Exception raised when an invalid API response is encountered.

exception drs_cli.errors.InvalidURI

Bases: Exception

Exception raised for invalid URIs.

drs_cli.errors.exception_handler(_type: type, value: BaseException, traceback: traceback) → None

Error handler for all exceptions.

drs_cli.models module

API models; autogenerated by https://github.com/koxudaxi/datamodel-code-generator/.

class drs_cli.models.AccessMethod

Bases: pydantic.main.BaseModel

class drs_cli.models.AccessPostMethod

Bases: pydantic.main.BaseModel

class drs_cli.models.AccessURL

Bases: pydantic.main.BaseModel

class drs_cli.models.Checksum

Bases: pydantic.main.BaseModel

class drs_cli.models.DrsObject

Bases: pydantic.main.BaseModel

class drs_cli.models.Error

Bases: pydantic.main.BaseModel

class drs_cli.models.PostDrsObject

Bases: pydantic.main.BaseModel

class drs_cli.models.Type

Bases: enum.Enum

An enumeration.

file = 'file'

ftp = 'ftp'

globus = 'globus'

gs = 'gs'

gsiftp = 'gsiftp'

htsget = 'htsget'

https = 'https'

s3 = 's3'