def result_types(job_id):
url = IPS_URL + '/resulttypes/' + job_id
r = get(url=url, params=None, response_format='xml')
root = ElementTree.fromstring(r.text)
types = root.findall('type')
r = {x.find('identifier').text: {
'Accept': x.find('mediaType').text} for x in types}
return r
def brew_get(package, os, platform, dnld_dir):
url_mac = 'https://formulae.brew.sh/api/formula/{}.json'
url_linux = 'https://formulae.brew.sh/api/formula-linux/{}.json'
if os == 'mac':
if platform == 'Big Sur':
platform = 'big_sur'
elif platform == 'Catalina':
platform = 'catalina'
elif platform == 'Mojave':
platform = 'mojave'
elif platform == 'High Sierra':
platform = 'high_sierra'
elif platform == 'Sierra':
platform = 'sierra'
elif platform == 'El Capitan':
platform = 'el_capitan'
elif platform == 'Yosemite':
platform = 'yosemite'
else:
return None
url = url_mac.format(package)
if os == 'linux':
if platform == 'linux':
platform = 'x86_64_linux'
else:
return None
url = url_linux.format(package)
r = get(url)
try:
r.raise_for_status()
except Exception as e:
print(e)
return None
data = r.json()
version = data['versions']['stable']
dnld_dir = abspath(expanduser(dnld_dir))
file_url = data['bottle']['stable']['files'][platform]['url']
file_name = file_url.split('/')[-1]
dnld_path = opj(dnld_dir, file_name)
download_file(file_url, dnld_path)
return dnld_path, version
def status(job_id):
# Possible response values:
#
# RUNNING: the job is currently being processed.
# FINISHED: job has finished, and the results can then be retrieved.
# ERROR: an error occurred attempting to get the job status.
# FAILURE: the job failed.
# NOT_FOUND: the job cannot be found.
url = IPS_URL + '/status/' + job_id
r = get(url=url, params=None, response_format='text')
job_status = r.text
return job_status
def fasta_by_accession_list(acc_list):
url = PROT_API_URL + '/proteins'
max_recs = 90
pages = int(ceil(len(acc_list) / max_recs))
data = ''
for p in range(pages):
offset = p * max_recs
last = offset + max_recs
acc_param = ','.join(x for x in acc_list[offset:last])
params = {'accession': acc_param}
response = get(url=url, params=params, response_format='fasta')
if response is None:
response = ''
data = data + response.text
return data
def _result(job_id, result_type):
available_result_types = result_types(job_id)
if result_type in available_result_types:
response_format = available_result_types[result_type]
else:
# raise Exception
# ToDo: Just skips if, for some reason, the server
# did not report an error but also did not
# return anything.
# I noticed that in these cases waiting a little and retrying
# sometimes works. Should implement wait and retry in this
# function.
return None
url = IPS_URL + '/result/' + job_id + '/' + result_type
response = get(url=url, params=None, response_format=response_format)
# Returns unparsed response!
return response
def test_get_retry_fail(self):
try:
r = get(url='http://httpbin.org/status/500',
response_format='text')
except RetryError as e:
pass
def test_get_eventual_success(self):
r = get(url='http://httpbin.org/status/200,200,500',
response_format='text')
assert r.status_code == 200