Get document xmls from ENA

[ESapenaVentura]

Wrote a script:

import argparse

import requests

from os.path import join, isfile, isdir
from typing import List
from argparse import ArgumentParser

def str_or_file_path(value: str) -> List:
    if isfile(value):
        with open(value, 'r') as f:
            values = f.readlines()
    else:
        values = value.split(',')
    return values

def directory_exists(value):
    if isdir(value):
        return value
    raise FileNotFoundError(f"folder '{value}' does not exist. Please create and re-try.")

def parse_arguments() -> argparse.Namespace:
    parser = ArgumentParser()
    parser.add_argument('-a', '--accessions', type=str_or_file_path, required=True, help='ENA sample accession. A file '
                                                                                         'path or a commma-separated '
                                                                                         'list of values can be '
                                                                                         'provided')
    parser.add_argument('-o', '--out_dir', type=directory_exists, required=True, help='Output directory. Please note, documents will'
                                                                         'be saved as {accession}.xml')
    arguments = parser.parse_args()
    return arguments

def get_document(accession):
    url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}"
    response = requests.get(url)
    response.raise_for_status()
    return response.text

def write_document(output_path, content):
    with open(output_path, 'w') as f:
        f.write(content)

def main(accessions, output_path):
    documents = {}
    for accession in accessions:
        documents[accession] = get_document(accession)

    for accession, content in documents.items():
        output_file_path = join(output_path, f"{accession}.xml")
        write_document(output_file_path, content)

if __name__ == '__main__':
    args = parse_arguments()
    main(args.accessions, args.out_dir)

Takes a single accession, a comma-separated list of accessions or a file path with newline-separated accessions, and an output directory, and creates xml documents named after the accession

[ESapenaVentura]

I am still unsure about where to upload the script, though - here? https://github.com/ebi-ait/checklist

[ESapenaVentura]

Script is here