def test_get_pubmed_item():
# this one exists
qid, _, _ = PublicationHelper("27528457", id_type="pmid", source="europepmc").get_or_create(None)
assert qid == "Q27098545", qid
qid, _, _ = PublicationHelper("4986259", id_type="pmcid", source="europepmc").get_or_create(None)
assert qid == "Q27098545", qid
qid, _, _ = PublicationHelper("10.1186/S12864-016-2855-3", id_type="doi", source="crossref").get_or_create(None)
assert qid == "Q27098545", qid
def create_reference(omim, pmid, login=None):
"""
Reference is:
retrieved: date
stated in: links to pmid items
optional reference URL
"""
#
ref = [
wdi_core.WDItemID(ITEMS['MitoDB'],
PROPS['curator'],
is_reference=True)
]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
ref.append(
wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
pmid_qid, _, success = PublicationHelper(
ext_id=pmid, id_type='pmid',
source="europepmc").get_or_create(login)
if success is True:
ref.append(
wdi_core.WDItemID(pmid_qid,
PROPS['stated in'],
is_reference=True))
ref_url = "http://mitodb.com/symptoms.php?oid={}&symptoms=Show"
ref.append(
wdi_core.WDUrl(ref_url.format(omim),
PROPS['reference URL'],
is_reference=True))
return ref
def test_pubmedstub_bad_pmid():
# invalid pubmed id
qid, _, _ = PublicationHelper("999999999", id_type='pmid', source='europepmc').get_or_create(login='******')
assert qid is None
def test_get_pmc_item():
# only has a pmc id
qid, _, _ = PublicationHelper("3425984", id_type='pmcid', source="europepmc").get_or_create(None)
assert qid == "Q42758027"