submit_microreact.py

#!/usr/bin/env python

import argparse
import json
from typing import TextIO
import urllib3


def submit_project(project_name: str, csv_file: TextIO, newick_file: TextIO,
                   access_token: str = None):
    http = urllib3.PoolManager()

    csv_data = csv_file.read()
    tree_data = newick_file.read()
    data = {
        'name': project_name,
        'data': csv_data,
        'tree': tree_data,
    }
    encoded_data = json.dumps(data).encode('utf-8')
    headers = {
        'Content-Type': 'application/json',
    }
    if access_token is not None:
        headers['access-token'] = access_token
    response = http.request('POST', 'https://microreact.org/api/project/',
                            body=encoded_data,
                            headers=headers)
    if response.status == 400 or response.status == 200:
        response_data = json.loads(response.data.decode('utf-8'))
        if response.status == 200:
            print(response_data['shortId'])
            print(response_data['url'])
        elif response.status == 400:
            print('ERROR:', response_data['error'])


if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        description='Upload data and create Microreact project')
    parser.add_argument('--access_token',
                        help='Microreact access token, get it from the API access tab of https://microreact.org/myaccount')
    parser.add_argument('project_name')
    parser.add_argument('csv_file', type=argparse.FileType(),
                        help='Sample metadata as described here: https://microreact.org/instructions')
    parser.add_argument('newick_file', type=argparse.FileType(),
                        help='Newick format tree file (tip labels must match IDs in CSV file)')
    args = parser.parse_args()

    submit_project(args.project_name, args.csv_file, args.newick_file, args.access_token)