drs-cli 0.1.0

GA4GH DRS Client

DRS-cli

This repository contains a client for an implementation of the Data Repository Service API schema of the Global Alliance for Genomics and Health, including support for additional endpoints defined in ELIXIR Cloud & AAI's DRS-Filer DRS implementation.

Usage

To use the client import it as follows in your Python code after installation:

Create client instance

from drs_cli.client import DRSClient

client = DRSClient(
    host="https://my-drs.app",
    port=80,
    base_path="ga4gh/drs/v1",
)

It is possible to supply a Bearer token, which will then be added to the Authentication header (prepended by Bearer) for every outbound call:

from drs_cli.client import DRSClient

client = DRSClient(
    host="https://my-drs.app",
    port=80,
    base_path="ga4gh/drs/v1",
    token = "<some_token>",
)

Access endpoints

NOTES:

• All endpoint access methods accept an optional token argument that allows overwriting any token supplied when creating the client instance.
• Responses that do not return the object ID as a single string return Pydantic models instead. If dictionaries are preferred instead, they can be obtained with response.dict(). See the Pydantic export documentation for further details.

GET endpoints

The DRS GET /objects/{object_id} endpoint can then be accessed with, e.g.:

response = client.get_object(
    object_id="A3SF4B",
)

Similarly, the DRS GET /objects/{object_id}/access/{access_id} endpoint can be accessed with, e.g.:

response = client.get_access_url(
    object_id="A3SF4B",
    access_id="B44FG9",
)

POST endpoint

The DRS-Filer POST /objects endpoint can be accessed with, e.g.:

response = client.post_object(
    object_data={
        "created_time": "2019-05-20T00:12:34-07:00",
        "updated_time": "2019-04-24T05:23:43-06:00",
        "version": "1",
        "size": 5,
        "mime_type": "",
        "checksums": [
            {
            "checksum": "18c2f5517e4ddc02cd57f6c7554b8e88",
            "type": "md5"
            }
        ],
        "access_methods": [
            {
            "type": "ftp",
            "access_url": {
                "url": "ftp://my.ftp.server/my_path/my_file_01.txt",
                "headers":  [
                "None"
                ]
            }
            }
        ]
    }
)

DELETE endpoint

The DRS-Filer DELETE /objects/{object_id} endpoint can be accessed with, e.g.:

response = client.delete_object(
    object_id="A3SF4B",
)

API docs

Automatically built API documentation is available.

Installation

You can install DRS-cli in one of two ways:

Installation via package manager

pip install drs_cli

# Or for latest development version:
pip install -e git+https://github.com/elixir-cloud-aai/DRS-cli.git#egg=drs_cli

Manual installation

git clone https://github.com/elixir-cloud-aai/DRS-cli.git
cd DRS-cli
python setup.py install

Contributing

This project is a community effort and lives off your contributions, be it in the form of bug reports, feature requests, discussions, or fixes and other code changes. Please refer to our organization's contributing guidelines if you are interested to contribute. Please mind the code of conduct for all interactions with the community.

Versioning

The project adopts the semantic versioning scheme for versioning. Currently the service is in beta stage, so the API may change without further notice.

License

This project is covered by the Apache License 2.0 also shipped with this repository.

Contact

The project is a collaborative effort under the umbrella of ELIXIR Cloud & AAI. Follow the link to get in touch with us via chat or email. Please mention the name of this service for any inquiry, proposal, question etc.