check_picsure_status

check_picsure_status.py

import PicSureClient, PicSureHpdsLib


# Based on: https://github.com/hms-dbmi/pic-sure-python-client
#      and: https://terra.biodatacatalyst.nhlbi.nih.gov/#workspaces/biodata-catalyst/BioData%20Catalyst%20PIC-SURE%20API%20Python%20examples/notebooks
#
# +--------------------------------------+------------------------------------------------------+
# |  Resource UUID                       |  Resource Name                                       |
# +--------------------------------------+------------------------------------------------------+
# | 02e23f52-f354-4e8b-992c-d37c8b9ba140 |                                                      |
# | 70c837be-5ffc-11eb-ae93-0242ac130002 |                                                      |
# +--------------------------------------+------------------------------------------------------+

def picsure_health_check():
    token = 'somethingsomething'
    domain = 'https://picsure.biodatacatalyst.nhlbi.nih.gov/info/resources'
    resource_id = '02e23f52-f354-4e8b-992c-d37c8b9ba140'
    
    try:
        client = PicSureClient.Client()
        connection = client.connect(domain, token)
        adapter = PicSureHpdsLib.Adapter(connection)
        resource = adapter.useResource(resource_id)
        # TODO: Check contents of this and only return True if something is there:
        copdgene_data = resource.dictionary().find("Genetic Epidemiology of COPD (COPDGene)").DataFrame()
        header_seen = 'Genetic Epidemiology of COPD (COPDGene)' in str(copdgene_data)
        # last line looks like: "[353 rows x 7 columns]"; parse this to determine a non-zero # of rows
        rows_are_non_zero = int(str(copdgene_data).split('\n')[-1].split(' ')[0][1:]) > 0
        return header_seen and rows_are_non_zero
    except Exception:  # if not authorized, this returns a KeyError
        return False