def test_get_id_count():
time.sleep(0.5)
id_count = pubmed_client.get_id_count('SDLFKJSLDKJH')
assert id_count == 0
id_count = pubmed_client.get_id_count('KRAS')
assert id_count > 0
def test_get_id_count():
id_count = pubmed_client.get_id_count('SDLFKJSLDKJH')
assert id_count == 0
id_count = pubmed_client.get_id_count('KRAS')
assert id_count > 0
import csv
from time import sleep
from indra.literature.pubmed_client import get_id_count
def save(citation_counts, filename):
with open(filename, 'wt') as f:
csvwriter = csv.writer(f, delimiter=',')
csvwriter.writerows(citation_counts)
if __name__ == '__main__':
corrs = []
with open('test_dir_path_all_correlations.csv', 'rt') as f:
csvreader = csv.reader(f, delimiter=',')
for row in csvreader:
corrs.append(row)
citation_counts = []
for g1, g2, corr in corrs[18000:]:
search_query = '%s AND %s' % (g1, g2)
cite_count = get_id_count(search_query)
citation_counts.append((g1, g2, corr, str(cite_count)))
print("%d. %s: %d" % (len(citation_counts), search_query, cite_count))
if len(citation_counts) % 1000 == 0:
save(citation_counts,
'citation_counts_%d.csv' % len(citation_counts))
sleep(0.5)
save(citation_counts, 'citation_counts_%d.csv' % len(citation_counts))
def test_get_id_count():
time.sleep(0.3)
id_count = pubmed_client.get_id_count('SDLFKJSLDKJH')
assert id_count == 0
id_count = pubmed_client.get_id_count('KRAS')
assert id_count > 0