pangea_metasub_download_example.py

import sys
from pangea_api import (
    Knex,
    User,
    Organization,
)

username, password = sys.argv[1], sys.argv[2]

knex = Knex('https://pangea.gimmebio.com')
User(knex, username, password).login()
org = Organization(knex, 'MetaSUB Consortium').get()
grp = org.sample_group('MetaSUB').get()

for sample in grp.get_samples():
    try:
        ar = sample.analysis_result('cap1::krakenhll_taxonomy_profiling').get()
        report = ar.field('report').get()
        report.download_file()
        read_assignments = ar.field('read_assignments').get()
        read_assignments.download_file()
    except:
        pass