def test_descriptors():
results = read("MH - Male\nMH - *Humans\nMH - Head/*Sub\n\n")
assert len(results) == 1
assert 'descriptors' in results[0]
assert results[0]['descriptors'] == [{'descriptor': 'Male', 'major': False},
{'descriptor': 'Humans', 'major': True},
{'descriptor': 'Head', 'qualifier': 'Sub', 'major': True}]
def test_ref_dates():
results = read('LR - 20200604\nDEP - 20191231\n\n')
assert len(results) == 1
assert 'last_revision_date' in results[0]
assert results[0]['last_revision_date'] == datetime(2020, 6, 4)
assert 'electronic_publication_date' in results[0]
assert results[0]['electronic_publication_date'] == datetime(2019, 12, 31)
def test_read_authors():
results = read("FAU - Karl J Holub\nAU - KJ Holub\nAD - Nested Knowledge Inc., Minneapolis, MN\nAD - Duluth, MN\nFAU - Other Author\n\n")
assert len(results) == 1
assert 'authors' in results[0]
assert len(results[0]['authors']) == 2
assert {'author': 'Other Author'} in results[0]['authors']
assert {'author': 'Karl J Holub',
'author_abbreviated': 'KJ Holub',
'affiliations': ['Nested Knowledge Inc., Minneapolis, MN',
'Duluth, MN']} in results[0]['authors']
def test_pmid():
results = read("PMID- 12345\n\n")
assert len(results) == 1
assert 'pubmed_id' in results[0]
assert results[0]['pubmed_id'] == 12345
def test_read_multiple_complex_refs():
results = read('PMID- 1\nTI - Nice Title\nFAU - Karl\nAD - Minnesota\n\nPMID- 2\nTI - Another \n Continuation\nPT - Journal Article\nOT - fun\nOT - stuff\n\n')
assert len(results) == 2
assert set(ref['pubmed_id'] for ref in results) == {1, 2}
assert set(ref['title'] for ref in results) == {'Nice Title', 'Another Continuation'}
def test_read_multiple_simple_refs():
results = read('PMID- 1\n\nPMID- 2\n\nPMID- 3\n\n')
assert len(results) == 3
assert all(['pubmed_id' in ref for ref in results])
assert set(ref['pubmed_id'] for ref in results) == {1, 2, 3}
def test_read_full_single_ref():
results = read(single_ref)
assert len(results) == 1
result = results[0]
target_study_attributes = {
'pubmed_id': 28754806,
'citation_owner': 'NLM',
'electronic_issn': '1759-8486',
'linking_issn': '1759-8478',
'journal_volume': '10',
'journal_issue': '4',
'publication_date': '2018 Apr',
'title': 'Impact of balloon guide catheter on technical and clinical outcomes: a systematic review and meta-analysis.',
'pages': '335-339',
'doi': '10.1136/neurintsurg-2017-013179',
'abstract': 'BACKGROUND AND PURPOSE: Flow arrest with balloon guide catheters (BGCs) is becoming increasingly recognized as critical to optimizing patient outcomes for mechanical thrombectomy. And I could go on...',
'copyright': '© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.',
'language': 'eng',
'electronic_publication_date': datetime(2017, 7, 28),
'place_of_publication': 'England',
'journal_abbreviated': 'J Neurointerv Surg',
'journal': 'Journal of neurointerventional surgery',
'nlm_journal_id': '101517079',
'publication_status': 'ppublish',
'entrez_time': datetime(2017, 7, 30, 6),
'medline_time': datetime(2018, 8, 1, 6),
'received_time': datetime(2017, 5, 5)
}
for att, value in target_study_attributes.items():
assert att in result
assert result[att] == value
target_authors = [
{
"author": "Brinjikji, Waleed",
"author_abbreviated": "Brinjikji W",
"affiliations": [
"Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA.",
"Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota, USA.",
"Department of Neuroradiology, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada."
],
'first_name': 'Waleed',
'last_name': 'Brinjikji',
},
{
"author": "Pereira, Vitor M",
"author_abbreviated": "Pereira VM",
"affiliations": [
"Department of Neuroradiology, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada."
],
'first_name': 'Vitor M',
'last_name': 'Pereira',
},
{
"author": "Kallmes, David F",
"author_abbreviated": "Kallmes DF",
"affiliations": [
"Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA.",
"Department of Neurosurgery, Mayo Clinic, Rochester, Minnesota, USA."
],
'first_name': 'David F',
'last_name': 'Kallmes'
}
]
for auth in target_authors:
assert auth in result['authors']
target_keywords = ['mechanical thrombectomy', 'stroke']
for key in target_keywords:
assert key in result['keywords']
target_publication_types = ['Journal Article', 'Meta-Analysis', 'Systematic Review', 'Review']
for pt in target_publication_types:
assert pt in result['publication_types']
target_mesh = [
{'descriptor': 'Aged', 'major': False},
{'descriptor': 'Brain Ischemia', 'qualifier': 'diagnostic imaging', 'major': False},
{'descriptor': 'Brain Ischemia', 'qualifier': 'surgery', 'major': True},
{'descriptor': 'Clinical Trials as Topic', 'qualifier': 'methods', 'major': False},
]
for d in target_mesh:
assert d in result['descriptors']
def test_grants():
results = read('GR - NIH 1234\nGR - NLM RO1\n\n')
assert len(results) == 1
assert 'grants' in results[0]
assert set(results[0]['grants']) == {'NIH 1234', 'NLM RO1'}
def test_read_keywords():
results = read("OT - thing1\nOT - thing2\n\n")
assert len(results) == 1
assert 'keywords' in results[0]
assert set(results[0]['keywords']) == {'thing1', 'thing2'}
def test_publication_type():
results = read("PT - Journal Article\nPT - Meta-Analysis\nPT - Systematic Review\n\n")
assert len(results) == 1
assert 'publication_types' in results[0]
assert set(results[0]['publication_types']) == {'Journal Article', 'Meta-Analysis', 'Systematic Review'}
def test_read_single():
file_results = read_file('tests/resources/single.nbib')
str_results = read(single_ref)
assert file_results == str_results