An example script to upload a CSV file to FathomNet

fathomnet_upload_csv.py

#!/usr/bin/env python

import requests
import argparse
import uuid
import json
from io import BytesIO
from typing import Dict
from datetime import datetime, timezone

__author__ = "Brian Schlining"
__copyright__ = "Copyright 2025, Monterey Bay Aquarium Research Institute"

# Exchange API Key for JWT in FathomNet
def exchange_api_key_for_jwt(api_key) -> str:
    headers = {
        'Accept': 'application/json',
        'x-api-key': api_key
    }

    url = 'https://database.fathomnet.org/api/xapikey/auth'
    response = requests.post(url, headers=headers)
    return response.json()['token']
    
def fetch_csv_data(csv_url: str) -> str:
	response = requests.get(csv_url, stream=True)
	return response.text
	
def build_darwincore(collection_code: str) -> Dict[str, str]:
	""" This should be customized with your own institute's metadata """
	return {
		"uuid": str(uuid.uuid4()),
		"recordType": "StillImage",
		"basisOfRecord": "MachineObservation",
		"license": "https://fathomnet.org",
		"modified": datetime.now(timezone.utc).isoformat(),
		"accessRights": "https://database.fathomnet.org/fathomnet/#/license",
		"collectionCode": collection_code,
		"ownerInstitutionCode": "FathomNet",
		"rightsHolder": "FathomNet",
		"institutionCode": "FathomNet",
		"language": "en-US"
	}
	

def upload_file_to_fathomnet(jwt, endpoint, csv_data, darwincore):
    headers = {
        'Authorization': 'Bearer ' + jwt
    }
    files = {
        "file": ("file.csv", csv_data.encode(), "text/csv"),
        "darwincore": ("darwincore.json", json.dumps(darwincore), "application/json")
    }
    response = requests.post(endpoint, headers=headers, files=files)
    print(response.json())


def main(api_key, endpoint, csv_url, collection_code):
    jwt = exchange_api_key_for_jwt(api_key)
    csv_data = fetch_csv_data(csv_url)
    darwincore = build_darwincore(collection_code)
    upload_file_to_fathomnet(jwt, endpoint, csv_data, darwincore)


if __name__ == '__main__':
    """
    Usage: python fathomnet_upload_csv.py <api_key> <endpoint> <csv_url> <collection_code>
    Example: fathomnet_upload_csv.py MyApiKeyFromFathomNet https://database.fathomnet.org/api/boundingboxes/upload/csv https://someserver.com/path/to/somefile.csv "FathomNet Awesome upload 10"
    """
    parser = argparse.ArgumentParser(
        prog="test.py",
        description="Test upload a zip file to FathomNet"
    )
    parser.add_argument("api_key", help="API Key for FathomNet")
    parser.add_argument("endpoint", help="Endpoint to upload file to")
    parser.add_argument("csv_url", help="URL to csv")
    parser.add_argument("collection_code", help="name or code of collection")
    args = parser.parse_args()
    main(args.api_key, args.endpoint, args.csv_url, args.collection_code)

# Upload file to FathomNet