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Authentication

The SeqDB API uses JWT (JSON Web Token) Bearer authentication. Read-only endpoints are public; write operations require a token.

Register

curl -X POST http://localhost:8000/api/v1/auth/register \
  -H "Content-Type: application/json" \
  -d '{
    "email": "researcher@university.edu",
    "password": "secure-password-123",
    "full_name": "Ahmed Ali",
    "role": "researcher"
  }'

Response (201): 

{
  "id": 1,
  "email": "researcher@university.edu",
  "full_name": "Ahmed Ali",
  "role": "researcher"
}

Login

curl -X POST http://localhost:8000/api/v1/auth/login \
  -H "Content-Type: application/json" \
  -d '{"email": "researcher@university.edu", "password": "secure-password-123"}'

Response: 

{
  "access_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9...",
  "refresh_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9...",
  "expires_in": 3600
}

Using the token

Include the access_token in the Authorization header:

curl -H "Authorization: Bearer eyJhbG..." \
  http://localhost:8000/api/v1/projects/

Token expiration

Tokens expire after 1 hour (3600 seconds). When a token expires, login again to get a new one.

Scripting

TOKEN=$(curl -s -X POST http://localhost:8000/api/v1/auth/login \
  -H "Content-Type: application/json" \
  -d '{"email": "user@example.com", "password": "pass123"}' \
  | python3 -c "import sys,json; print(json.load(sys.stdin)['access_token'])")

# Use in subsequent requests
curl -H "Authorization: Bearer $TOKEN" http://localhost:8000/api/v1/staging/files

import requests

BASE = "http://localhost:8000/api/v1"

# Login
resp = requests.post(f"{BASE}/auth/login", json={
    "email": "user@example.com",
    "password": "pass123"
})
token = resp.json()["access_token"]

# Use in subsequent requests
headers = {"Authorization": f"Bearer {token}"}
projects = requests.get(f"{BASE}/projects/", headers=headers).json()

Public endpoints

These endpoints work without authentication:

  • GET /projects/, GET /projects/{accession}
  • GET /samples/, GET /samples/{accession}
  • GET /experiments/, GET /experiments/{accession}
  • GET /runs/, GET /runs/{accession}, GET /runs/{accession}/download
  • GET /filereport
  • GET /search/
  • GET /checklists/
  • GET /bulk-submit/template/{checklist_id}
  • GET /health