Python script for interactively resuming an NDA submission.This script allows the user to select local file for each remaining file to be uploaded.This has an advantage over using nda-tools vtcmd command-line client, which will attempt to find the file and can be quite inefficient with multiple directories to scan.

nda-interactive-resume.py

import boto3
from botocore.exceptions import ClientError
import requests
import getpass
import os
import time


username = input('Username:')
password = getpass.getpass()
auth = (username, password)

submission_id = input('Enter submission_id to resume:')
submission_files = requests.get(f'https://nda.nih.gov/api/submission/{submission_id}/files?retrieveFilesToUpload=true', auth=auth).json()

for file in submission_files:
    try:
        credentials = requests.get(file['_links']['multipartUploadCredentials']['href'], auth=auth)
        credentials.raise_for_status()
        credentials = credentials.json()
    except requests.exceptions.HTTPError as err:
        print(credentials.text)
        raise SystemExit(err)
    submission_file_id = file['id']
    file_user_path = file['file_user_path']
    file_remote_path = file['file_remote_path']
    bucket = file_remote_path.split("/", 3)[2]
    key = file_remote_path.split("/", 3)[3]
    full_local_path = input(f'Enter the full path to the local file {file_user_path}:')
    if os.path.isfile(full_local_path):
        local_size = os.path.getsize(full_local_path)
        print(f'Attempting to upload {full_local_path} to s3://{bucket}/{key}')
        try:
            session = boto3.session.Session(aws_access_key_id=credentials['access_key'],
                                            aws_secret_access_key=credentials['secret_key'],
                                            aws_session_token=credentials['session_token'])
            s3_client = session.client(service_name='s3')
            s3_client.upload_file(full_local_path, bucket, key)
            print('Upload completed.')
        except ClientError as e:
            print(f'There was an error uploading the file {e}')
    else:
        print(f'The file {full_local_path} could not be found.')
    requests.put(file['_links']['self']['href'], params={'submissionFileStatus': 'Complete',
                                                         'fileSize': local_size}, auth=auth)
for i in range(5):
    submission_status = requests.get(f'https://nda.nih.gov/api/submission/{submission_id}', auth=auth).json()['submission_status']
    if submission_status in (['Submitted', 'Upload Completed', 'Submitted_Prototype', 'Processing']):
        print('Submission Completed')
        break
    else:
        print(f'Submission is not yet complete, current status is {submission_files}, retrying in 30 seconds ...')
        time.sleep(30)

requirements.txt

botocore
requests
boto3