def test_get_pubmed_item():
# this one exists
qid = PubmedItem(27528457).get_or_create()
assert qid == "Q27098545"
qid = PubmedItem("4986259", id_type="PMC").get_or_create()
assert qid == "Q27098545"
qid = PubmedItem("10.1186/S12864-016-2855-3", id_type="DOI").get_or_create()
assert qid == "Q27098545"
def run(ext_id, id_type='MED'):
try:
p = PubmedItem(ext_id, id_type)
qid = p.get_or_create(login)
except Exception as e:
traceback.print_exc()
return flask.jsonify({'success': False, 'message': str(e)})
if qid:
return flask.jsonify({
'success': True,
'result': qid,
'errors': p.errors,
'warnings': p.warnings
})
else:
return flask.jsonify({
'success': False,
'errors': p.errors,
'warnings': p.warnings
})
def test_pubmedstub_bad_pmid():
# invalid pubmed id
wdid = PubmedItem(999999999).get_or_create(login='******')
assert wdid is None
def test_get_pubmed_item_cache():
# this one exists
wdid = PubmedItem(1234).get_or_create()
assert ('1234', 'MED') in PubmedItem._cache
assert PubmedItem._cache[('1234', 'MED')] == "Q27442302"
def test_get_pmc_item():
# only has a pmc id
qid = PubmedItem("PMC3425984", id_type='PMC').get_or_create()
assert qid == "Q42758027"
def test_get_pubmed_item():
# this one exists
wdid = PubmedItem(1234).get_or_create()
assert wdid == "Q27442302"