USI_submission.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-

"""
USI submission pipeline

Features:
- Creating a new submission
- Adding samples, projects, studies to submission
- check validation status

PreRequest:
    The user MUST get an AAP account at https://explore.aai.ebi.ac.uk/home

Example:
    python3 USI_submission -flags arguments

Note:
    This script doesn't support validation right now. The provided input data
    need to be

Options:
    * Compulsory
    -u Username *
    -sp SampleFile
    TODO -p projectFile
    TODO -r sequencingRunFile
    TODO -d study

"""


import json
import requests
import getpass
import argparse

#username = sys.argv[1]


def cli():
    my_parser = argparse.ArgumentParser(description='Easier USI submission')
    parser = argparse.ArgumentParser(prog=f'\nData submission Portal API tool. \n\nTODO add delete,update actions\n')

    #subparsers = parser.add_subparsers(help='execution modes', dest='exec_mode')
    # ----- Mode 'create' -----
    #sub = subparsers.add_parser('create', help='create a team/submission/sample/proj   ect,etc')

    parser.add_argument('-u','--username', metavar='<Username>', type=str, required=True,
                        help='AAP username, case-sensitive')
    parser.add_argument('-t', '--team', metavar='<Teamname>', type=str, required=True,
                        help='create a unique teamname')
    parser.add_argument('-td', '--team_descirption', type=str,
                        help='enter team description')
    parser.add_argument('-n', '--new-submission', default=True, action="store_true", required=True,
                        help='Create a new submission. Requested for every data submission step')
    parser.add_argument('-p', '--project',
                        help='submit a new project')
    parser.add_argument('-sp', '--sample',
                        help='Submit a new sample')
    parser.add_argument('-seq', '--seqRun',
                        help='Submit a new sequence run')
    parser.add_argument('-a', '--assay',
                        help='Submit a new assay')
    parser.add_argument('-ad', '--assay_data',
                        help='Submit a new assay data')


    args = parser.parse_args()
    # ------- Mode 'delete' ----
    #sub = subparsers.add_parser('delete', help='delete a submission TODO')
    # ----- Mode 'update' -----
    #sub = subparsers.add_parser('update', help=' TODO')
    parser.print_help()
    return args

def authenticate():
    """
    Get token for API submission

    PreRequest: the user must get a valid username from https://explore.api.aai.ebi.ac.uk/auth

    Note:
        1. username is case-sensitive
        2. The token is only valid for one hour
        3. Every time creating a new submission, the token has to be refreshed.

    Output: if credientials correct, return token.
    """
    r = requests.get('https://explore.api.aai.ebi.ac.uk/auth', auth=(username, password))
    if r.status_code == requests.codes.ok:
        return r.text
    else:
        raise r.raise_for_status()

def creat_team(team_name,team_description):
    #TODO new team or check if teamname exist or not

    header = {"Content-Type": "application/json",
              "Authorization": "Bearer " + token,
              "Accept": "application/hal+json"
              }

    team_info = {
        "description":team_description,
        "centreName":team_name
                }
    response = requests.post("https://submission-dev.ebi.ac.uk/api/user/teams",
                             headers = header,json = team_info)
    if response.status_code == requests.codes.created:
        response_json = response.json()
        team = response_json["name"]
        link_submissions_create = response_json['_links']["submissions:create"]['href']
        return team,link_submissions_create
    else:
        raise response.raise_for_status()

def create_submission(link,token):
    header = {"Content-Type": "application/json;charset=UTF-8",
              "Authorization": "Bearer " + token,
              "Accept": "application/hal+json"
              }
    data = {}
    response = requests.post(link,headers = header, json = data)
    if response.status_code == requests.codes.created:
        response_json = response.json()
        return response_json
    else:
        raise response.raise_for_status()

def load_data(filename):
    with open(filename) as f:
        data = json.load(f)
    return data

def update_sample(token, link, data):
    url = link
    header = {
        "Content-Type": "application/json;charset=UTF-8",
        "Accept": "application/hal+json",
        "Authorization": "Bearer " + token
    }
    response = requests.post(url, headers=header, json=data)
    if response.status_code == requests.codes.created:
        pass
    else:
        raise response.raise_for_status()

# Collect links in the content for next submission
def get_content(link,token):
    header = {"Content-Type": "application/json;charset=UTF-8",
              "Authorization": "Bearer " + token,
              "Accept": "application/hal+json"
              }
    data = {}
    response = requests.post(eval("link_contents"),headers = header, json = data)
    # test
    a = response.json()
    return a
    '''
    if response.status_code == requests.codes.created:
        print(response.json())
        response_json = response.json()
        return response_json
    else:
        raise response.raise_for_status()
    '''

def create_domainData(domain,data):
    """
    Create a data in one USI submission. the domains are e.g. samples,sequencingRuns,etc

    :param domain:eg samples, projects,sequencingRuns
    :param data: data in json format, should follow corresponding domain-specific schema requirement
    :return:Data submission response
    """
    header = {"Content-Type": "application/json;charset=UTF-8",
              "Authorization": "Bearer " + token,
              "Accept": "application/hal+json"
              }
    response = requests.post(eval("link_"+domain), headers=header, json=data)
    if response.status_code == requests.codes.created:
        response_json = response.json()
        print(domain+" submit status: ")
        print(response.status_code)
        return response_json
    else:
        raise response.raise_for_status()

def submission_status(link,token):

    header = {
        "Accept": "application/hal+json",
        "Authorization": "Bearer " + token
    }

    response = requests.get(link, headers=header)

    if response.status_code == requests.codes.ok:
        print("submission status")
        print(response.status_code)
        #print(response.json())
    else:
        raise response.raise_for_status()

def validation_status(link,token):
    header = {
        "Accept": "application/hal+json",
        "Authorization": "Bearer " + token
    }

    response = requests.get(link, headers=header)

    if response.status_code == requests.codes.ok:
        print("validation results")
        print(response.status_code)
        responses = response.json()
        #print(responses)
        print(responses['_embedded']['validationResults'][0]['overallValidationOutcomeByAuthor'])
        return responses
    else:
        raise response.raise_for_status()

# Start command line interface
args = cli()

# Getting arguments from command line
username = args.username
team_name = args.team
team_description = args.team_descirption
sample_file = args.sample
project_file = args.project
seq_file = args.seqRun
assay_file = args.assay
assay_data_file = args.assay_data

# Authentification
input("\nPress Enter to continue...\n")

print("Username(case sensitive: )"+username)

if args.username:
    try:
        password = getpass.getpass(prompt="AAP Password:",stream=None)
    except Exception as error:
        print('ERROR', error)

# get original token
token = authenticate()

# creating new team
if args.team:
    teams,link_submission = creat_team(team_name,team_description="new ")
    # Refresh token after created a new team
    token = authenticate()

# creating new submission
if args.new_submission:
    new_submission = create_submission(link_submission,token)

# Create link variable with the links in the submission
for i in list(new_submission['_links'].keys()):
    # If link name includes ":", replace with "_"
    if (":" in i):
        new = i.replace(":","_")
        vars()["link_"+new]= new_submission['_links'][i]['href']
    else:
        vars()["link_"+i]= new_submission['_links'][i]['href']

contents = get_content(eval("link_contents"),token)


# Create variable for link to different types of metadata
for i in list(contents['_links'].keys()):
    # If link name includes ":", replace with "_"
    if (":" in i):
        new = i.replace(":","_")
        vars()["link_"+new]= contents['_links'][i]['href']
    else:
        vars()["link_"+i]= contents['_links'][i]['href']

# TODO: connect args.sample/study/assay to link_samples/assay/study automatically.
if args.sample:
    sample_filename = args.sample
    samples = load_data(sample_filename)
    print(samples)
    domain = "samples"
    create_domainData(domain,eval(domain))
    submission_status(link_submissionStatus,token)
    validation_status(link_validationResults,token)