def test_smartfetch_ok(self):
"""[summary]
"""
with patch('requests.post') as mock_requests:
mock_requests.return_value.status_code = 200
smart_fetch = SmartFetch('')
smart_fetch.post(code=200)
self.assertIsInstance(smart_fetch, SmartFetch)
def test_smartfetch_fails():
"""[summary]
"""
with patch('requests.post') as mock_requests:
mock_requests.return_value.status_code = 200
smart_fetch = SmartFetch('')
value = smart_fetch.post(code=200)
assert value.status_code == 200
def test_smartfetch_fails(self):
"""
Test that errors are properly raised on a failed request.
"""
with patch('requests.post') as mock_requests:
mock_requests.return_value.status_code = 200
with self.assertRaises(RuntimeError):
smart_fetch = SmartFetch('')
smart_fetch.post(code=300)
from cidc_utils.requests import SmartFetch
from constants import EVE_URL
EVE_FETCHER = SmartFetch(EVE_URL)
def fetch_assays(jwt: str) -> dict:
"""
Fetch all available assays in the system.
Arguments:
jwt {str} -- Requestor's JWT
Returns:
dict -- Assay records.
"""
users_response = EVE_FETCHER.get(token=jwt, endpoint="assays")
user_list = users_response.json()["_items"]
return user_list
import logging
import json
from ftplib import FTP
import gzip
from io import BytesIO
from typing import List
from cidc_utils.requests import SmartFetch
from framework.celery.celery import APP
from framework.tasks.authorized_task import AuthorizedTask
from framework.tasks.variables import EVE_URL
from framework.tasks.parallelize_tasks import execute_in_parallel
HUGO_URL = "ftp.ncbi.nlm.nih.gov"
HUGO_DIRECTORY = "gene/DATA/GENE_INFO/Mammalia"
HUGO_FILE_NAME = "Homo_sapiens.gene_info.gz"
EVE = SmartFetch(EVE_URL)
IDENTIFIER_FIELDS = [
{
"key": 2,
"is_array": False
}, # Symbol
{
"key": 4,
"is_array": True
}, # Synonyms
{
"key": 10,
"is_array": False
}, # Symbol_from_nomenclature_authority
]
def test_smartfetch_instatiate():
"""
Test the creation of a new SmartFetch object.
"""
smart_fetch = SmartFetch('')
assert smart_fetch.base_url == ''