def test_get_annotations():
time.sleep(0.5)
pmid = '30971'
tree = pubmed_client.get_full_xml(pmid)
results = pubmed_client.get_metadata_from_xml_tree(tree,
mesh_annotations=True)
assert len(results) == 1, len(results)
assert 'mesh_annotations' in results[pmid], results[pmid]
me_ans = results[pmid]['mesh_annotations']
assert len(me_ans) == 9, len(me_ans)
assert all(d['mesh'].startswith('D') for d in me_ans)
assert any(d['major_topic'] for d in me_ans)
def test_get_annotations():
pmid = '30971'
tree = pubmed_client.send_request(
pubmed_client.pubmed_fetch, dict(db='pubmed', retmode='xml', id=pmid))
results = pubmed_client.get_metadata_from_xml_tree(tree,
mesh_annotations=True)
assert len(results) == 1, len(results)
assert 'mesh_annotations' in results[pmid].keys(), results[pmid].keys()
me_ans = results[pmid]['mesh_annotations']
assert len(me_ans) == 9, len(me_ans)
assert all(d['mesh'].startswith('D') for d in me_ans)
assert any(d['major_topic'] for d in me_ans)
def get_article_info(self, xml_file, q=None):
tree = self.ftp.get_xml_file(xml_file)
article_info = pubmed_client.get_metadata_from_xml_tree(
tree,
get_abstracts=True,
prepend_title=False
)
if q is not None:
q.put((xml_file, article_info))
return
else:
return article_info
def test_get_annotations():
pmid = '30971'
tree = pubmed_client.send_request(pubmed_client.pubmed_fetch,
dict(db='pubmed', retmode='xml',
id=pmid))
results = pubmed_client.get_metadata_from_xml_tree(tree,
mesh_annotations=True)
assert len(results) == 1, len(results)
assert 'mesh_annotations' in results[pmid].keys(), results[pmid].keys()
me_ans = results[pmid]['mesh_annotations']
assert len(me_ans) == 9, len(me_ans)
assert all(d['mesh'].startswith('D') for d in me_ans)
assert any(d['major_topic'] for d in me_ans)