Module omnipy.modules.fairtracks.functions

Overview

View Source

import requests

ENCODE_HEADERS = {'accept': 'application/json'}

ENCODE_BASE_URL = 'https://www.encodeproject.org/'

GDC_BASE_URL = 'https://api.gdc.cancer.gov/'

# ['experiments', 'biosample']

def encode_api(endpoint='experiments', id=None, limit=None, format='json', frame='object'):

    api_url = ENCODE_BASE_URL + endpoint + '/' + (id if id else '@@listing') + '?' + '&'.join(

        (['limit=' + limit] if limit else []) + (['format=' + format] if format else [])

        + (['frame=' + frame] if frame else []))

    print(api_url)

    response = requests.get(api_url, headers=ENCODE_HEADERS)

    if response.status_code == 200:

        results = response.json()

        if results['notification'] == 'Success':

            graph = results['@graph']

            return graph

    else:

        print('No result found')

# ['projects', 'cases', 'files', 'annotations'], starting_point='0', size='25'

def gdc_api(object_type='projects', starting_point=None, size=None):

    api_url = GDC_BASE_URL + object_type + '/' + '?' + '&'.join(

        (['from=' + starting_point] if starting_point else []) + (['size=' + size] if size else [])

        + ([+ 'project'] if object_type == 'cases' else []))

    print(api_url)

    response = requests.get(api_url)

    if response.status_code != 200:

        print('No result found')

        return None

    results = response.json()

    if len(results['warnings']) > 0:

        print('The following warnings have been encountered:')

        print(results['warnings'])

        return None

    hits = (results['data']['hits'])

    return hits

Variables

ENCODE_BASE_URL

ENCODE_HEADERS

GDC_BASE_URL

Functions

encode_api

def encode_api(
    endpoint='experiments',
    id=None,
    limit=None,
    format='json',
    frame='object'
)

Parameters:

Name	Type	Description	Default
endpoint			experiments
id
limit
format			json
frame			object

View Source

def encode_api(endpoint='experiments', id=None, limit=None, format='json', frame='object'):

    api_url = ENCODE_BASE_URL + endpoint + '/' + (id if id else '@@listing') + '?' + '&'.join(

        (['limit=' + limit] if limit else []) + (['format=' + format] if format else [])

        + (['frame=' + frame] if frame else []))

    print(api_url)

    response = requests.get(api_url, headers=ENCODE_HEADERS)

    if response.status_code == 200:

        results = response.json()

        if results['notification'] == 'Success':

            graph = results['@graph']

            return graph

    else:

        print('No result found')

gdc_api

def gdc_api(
    object_type='projects',
    starting_point=None,
    size=None
)

Parameters:

Name	Type	Description	Default
object_type			projects
starting_point
size

View Source

def gdc_api(object_type='projects', starting_point=None, size=None):

    api_url = GDC_BASE_URL + object_type + '/' + '?' + '&'.join(

        (['from=' + starting_point] if starting_point else []) + (['size=' + size] if size else [])

        + ([+ 'project'] if object_type == 'cases' else []))

    print(api_url)

    response = requests.get(api_url)

    if response.status_code != 200:

        print('No result found')

        return None

    results = response.json()

    if len(results['warnings']) > 0:

        print('The following warnings have been encountered:')

        print(results['warnings'])

        return None

    hits = (results['data']['hits'])

    return hits