def __init__(self,
ep=PUBONE_EP,
session=CmdLineFtsType(),
logger=None,
debug=0):
self._api = RestApi(ep=ep, session=session, logger=logger, debug=debug)
self._ep = ep
self._session = session
self._logger = logger
self._debug = debug
def test_resource_item():
"""
Test `access to the resource item` functionality.
"""
ep = "http://localhost/api/"
item_x_url = "http://localhost/api/items/x"
item_5_url = "http://localhost/api/items/5"
api = RestApi(ep=ep)
itemres_x = api.items("x")
assert str(itemres_x) == item_x_url # check that the url was normalized.
itemres_5 = api.items(5)
assert str(itemres_5) == item_5_url # check that the url was normalized.
def test_get_item(requests_mock):
ep = "http://localhost/api/"
item_id = 5
item_id_url = ep + f"items/{item_id}"
# prepare response with Mocker
payload = {"result": ["a", "b", "c"]}
requests_mock.get(item_id_url,
json=payload,
headers={"Content-Type": "application/json"})
# use RestApi
api = RestApi(ep=ep)
resp = api.items(item_id).get()
data = resp.data
assert data == payload
def test_create_api_instance():
"""
Test `creation of new instance` functionality.
"""
api_ep = "http://localhost///api/"
api_url = "http://localhost/api/"
api = RestApi(ep=api_ep)
assert api is not None # check that we have got an instance
assert str(api) == api_url # check that the url was normalized.
def test_resource_list():
"""
Test `access to the resource list` functionality.
"""
ep = "http://localhost/api/"
resource_url = "http://localhost/api/items"
api = RestApi(ep=ep)
resource = api.items
assert type(
resource) is RestApi # check creation of the resource of correct type
assert str(resource) == resource_url # check that the url was normalized.
def test_500(requests_mock):
ep = "http://localhost/api/500"
# prepare response with Mocker
requests_mock.get(ep, status_code=500)
# use RestApi
SessionClass = FtsClassFactory(max_tries=3, max_time=2)
api = RestApi(ep=ep, session=SessionClass())
assert str(api._) == ep
with pytest.raises(HttpServerError):
resp = api._.get()
data = resp.data
assert data is None
def test_post_item(requests_mock):
ep = "http://localhost/api/"
items_url = ep + f"items"
# prepare response with Mocker
payload = {"a": 1, "b": 2, "c": 3}
result = {"result": ["a", "b", "c"]}
requests_mock.post(items_url,
json=result,
headers={"Content-Type": "application/json"})
# use RestApi
api = RestApi(ep=ep)
resp = api.items.post(data=payload)
data = resp.data
assert data == result
class PubOneValidator(PubOneBase):
def __init__(self,
ep=PUBONE_EP,
session=CmdLineFtsType(),
logger=None,
debug=0):
self._api = RestApi(ep=ep, session=session, logger=logger, debug=debug)
self._ep = ep
self._session = session
self._logger = logger
self._debug = debug
def _lookup_pubone(self, pmid: int, pmcid: int) -> List[dict]:
params = [
pmid and f"pubmed_{pmid}" or None,
pmcid and f"pmc_{pmcid}" or None,
]
resource_name = ",".join(list(filter(lambda i: i is not None, params)))
try:
response = self._api.lojson(resource_name).get()
except api_ex.HttpServerError as e:
raise ex.PubOneServiceFailed(e)
return response.data
def _validate_item(self, data_item, pmid, pmcid):
if not isinstance(data_item, dict):
raise ex.PubOneServiceFailed(
ValueError(
f"PubOne API returned an unexpected record `{data_item}` "
f"for the following data pmid={pmid} pmcid={pmcid}, "
"contact developer."))
_pmcid_raw = data_item.get("pmcid")
_pmid_raw = data_item.get("id")
_pmcid = self._eval_pmcid(_pmcid_raw)
_pmid = self._eval_pmid(_pmid_raw)
_doi = data_item.get("doi", None)
pmid_exists = pmid if pmid is None else pmid == _pmid
pmcid_exists = pmcid if pmcid is None else pmcid == _pmcid
# print(f"\npmid={pmid} _pmid={_pmid} pmid_exists={pmid_exists}")
# print(f"pmid={pmcid} _pmid={_pmcid} pmcid_exists={pmcid_exists}")
# cases 1, 4, 8
if ((pmid_exists is True and pmcid_exists is True) # 1
or (pmid_exists is True and pmcid_exists is None) # 4
or (pmid_exists is None and pmcid_exists is True) # 8
):
self._pmcid = _pmcid
self._pmid = _pmid
self._doi = _doi
return True
# case 3
if pmid_exists is True and pmcid_exists is False: # 3
raise ex.PmcidAbsent(pmcid)
# case 5
if pmid_exists is False and pmcid_exists is True: # 5
raise ex.PmidAbsent(pmid)
def validate(self, pmid: int = None, pmcid: int = None) -> bool:
"""Validates PubMed Id and PMC Id for presence in PubOne service,
and match to the same article.
Keyword Arguments:
pmid {int} -- PubMed Id (default: {None})
pmcid {int} -- PMC Id (default: {None})
Returns:
bool -- True if result of validation is positive.
Case Outcome pmid pmcid match #Recs - (from PubOne)
0 ValueError None None - -
1 True exists exists yes 1
2 PmidPmcidMismatch exists exists no 2
3 PmcidAbsent exists absent 1
4 True exists None 1
5 PmidAbsent absent exists 1
6 PmidPmcidAbsent absent absent 0
7 PmidAbsent absent None 0
8 True None exists 1
9 PmcidAbsent None absent 0
exists = id is not None and id = _id
where id is one of pmid or pmcid supplied
and _id corresponding identifier received from PubOne.
absent = not(exists)"""
self._pmid = None
self._pmcid = None
self._doi = None
# case 0
if pmid is None and pmcid is None:
raise ValueError("Both `pmid` and `pmcid` are undefined, "
"at least one must be provided.")
pmid = self._validate_id(pmid, "pmid")
pmcid = self._validate_id(pmcid, "pmcid")
data = self._lookup_pubone(pmid, pmcid)
# from devtools import debug as d
# print(f"data={d.format(data)}")
if not isinstance(data, (list)):
raise ex.PubOneServiceFailed(
ValueError(f"A list of records was expected from PubOne, "
f"data={data} was received instead."))
# case 2
if len(data) == 2 and pmid is not None and pmcid is not None:
raise ex.PmidPmcidMismatch(pmid, pmcid)
# cases 1, 4, 8 and 3, 5
elif len(data) == 1:
data_1 = next(iter(data),
{}) # get 1st item of the list `data` or {}
return self._validate_item(data_1, pmid, pmcid)
# cases 6, 7, 9
elif len(data) == 0:
if pmid is not None and pmcid is not None: # 6
raise ex.PmidPmcidAbsent(pmid, pmcid)
if pmid is not None and pmcid is None: # 7
raise ex.PmidAbsent(pmid)
if pmid is None and pmcid is not None: # 9
raise ex.PmcidAbsent(pmcid)
raise RuntimeError(
"PubOne client experienced unexpected outcome, contact developer "
"with following data pmid={pmid} pmcid={pmcid} data={data}.")
@property
def pmid(self):
return self._pmid
@property
def pmcid(self):
return self._pmcid
@property
def doi(self):
return self._doi