geni-bioinfo 0.1.0

Python client for the GENI Workflows API

geni-bioinfo

Python client library for the GENI Workflows API — a bioinformatics platform for submitting and managing Nextflow workflow executions on cloud infrastructure.

Installation

pip install geni-bioinfo

Quick start

Authentication

Option 1 — email and password (JWT):

from geni import GeniClient

client = GeniClient()
client.auth_login("[e-mail]", "your-password")

Option 2 — static API token:

from geni import GeniClient

client = GeniClient()
client.auth_token("your-api-token")

The API URL defaults to https://workflows-api.geni-bioinfo.com.br. Override it with the GENI_API_URL environment variable or the api_url constructor argument.

Core workflow

from geni import GeniClient

client = GeniClient()
client.auth_token("your-api-token")

# 1. Upload a workflow
wf = client.workflow_create(
    name="hello-world",
    version="1.0.0",
    file_path="hello.nf",
)
print(wf.name, wf.version)

# 2. Discover available engines and queues
engines = client.engine_list(status="active")
queues  = client.queue_list(status="active")

# 3. Submit the workflow
submission = client.submission_create(
    workflow_name="hello-world",
    engine_id=engines[0].id,
    queue_id=queues[0].id,
    output="s3://my-bucket/runs/hello-001",
    params_path="params.yml",
)
print(submission.submission_id, submission.status)

# 4. Poll status
sub = client.submission_get(submission.submission_id)
print(sub.status)

# 5. Stream logs
print(client.submission_logs(submission.submission_id, text=True))

API reference

GeniClient

Method	Description
auth_login(email, password)	Authenticate with email + password (JWT)
auth_token(token)	Authenticate with a static API key
user_list()	List platform users (admin only)
environment_list(status)	List cloud environments (admin only)
engine_list(status)	List Nextflow engines (admin only)
queue_list(status)	List job queues (admin only)
storage_list(status)	List cloud storage resources (admin only)
workflow_create(name, version, file_path, ...)	Upload and register a workflow version
workflow_list()	List all registered workflow versions
submission_create(workflow_name, engine_id, queue_id, output, params_path, ...)	Submit a workflow for execution
submission_list(status)	List submissions
submission_get(id)	Fetch a single submission by ID
submission_cancel(id)	Cancel a running submission
task_list(submission_id)	List tasks for a submission
task_logs(submission_id, task_id, text)	Fetch task log entries
submission_logs(submission_id, text)	Fetch submission-level Nextflow logs

Exceptions

Exception	Raised when
GeniConfigError	auth_login() or auth_token() was not called before a request
GeniAuthError	Invalid credentials or insufficient permissions (HTTP 401/403)
GeniNotFoundError	A resource ID does not exist (HTTP 404)
GeniAPIError	Any other unexpected HTTP error; exposes .status_code, .method, .url, .response_body

Security

• Never hardcode credentials. Use the GENI_API_URL environment variable for the API URL and load tokens from a secrets manager or .env file.
• All API calls use HTTPS.
• See SECURITY.md for the vulnerability reporting policy.

Tutorial

An interactive Jupyter notebook is available in docs/tutorial.ipynb.

License

MIT — see LICENSE.