Basespace downloader, obtains urls which you can then wget

bs_download.py

import sys
import requests

# print urls of fastq files to download
# obtain access token by following instructions here:
# https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader

AccessToken=sys.argv[1]

# user
ep='/v1pre3/users/current'
r2 = requests.get('https://api.basespace.illumina.com/'+ep,{'access_token':AccessToken})
r=r2.json()
# projects
ep=r['Response']['HrefProjects']
r2 = requests.get('https://api.basespace.illumina.com/'+ep,{'access_token':AccessToken})
r=r2.json()
for x in r['Response']['Items']:
    pid=x['Id']
    ep='/v1pre3/projects/%s/samples' % pid
    r2 = requests.get('https://api.basespace.illumina.com/'+ep,{'access_token':AccessToken})
    r=r2.json()
    r=r['Response']
    if 'Items' not in r: continue
    for x in r['Items']:
        id=x['Id']
        ep='/v1pre3/samples/%s/files' % id
        r2 = requests.get('https://api.basespace.illumina.com/'+ep,{'access_token':AccessToken})
        r=r2.json()
        r=r['Response']
        if 'Items' not in r: continue
        for x2 in r['Items']:
            ep=x2['HrefContent']
            path=x2['Path']
            print 'wget https://api.basespace.illumina.com/'+ep+'?access_token='+str(AccessToken)+' -O '+str(path)