def poll_deposits(username, password):
for (token, ctn, doi, status) in cursor.execute("select token, ctn, doi, status from ctns where status = ?", [SUBMITTED]):
response = session.get("https://api.crossref.org/deposits/{}".format(token), auth=(username, password))
if response.status_code == 401:
print("Bad username and password")
exit()
new_status = response.json()['message']['status']
print("Update {} in {} status {} -> {}".format(ctn, doi, status, new_status))
cursor.execute("update ctns set status = ? where token = ?", [status, token])
connection.commit()
def send_deposits(username, password):
to_deposit = cursor.execute("select ctn, doi, registry from ctns where status = ?", [NOT_DEPOSITED])
for (ctn, doi, registry) in to_deposit:
print("Deposit {} in {}".format(ctn, doi))
templated = template.format(doi=escape(doi), registry=escape(registry), ctn=escape(ctn))
response = session.post("https://api.crossref.org/deposits", data=templated, auth=(username, password), headers={"Content-Type": "application/vnd.crossref.partial+xml"})
if response.status_code != 200:
print("Error depositing: {}".format(response.status_code))
print(response.text)
else:
token = response.json()['message']['batch-id']
status = response.json()['message']['status']
cursor.execute("update ctns set token = ?, status = ? where ctn = ? and doi = ?", [token, status, ctn, doi])
connection.commit()
print("Status of {} in {}: {}".format(ctn, doi, status))
def print_status():
result = cursor.execute("select status, count(distinct(ctn)) from ctns group by status").fetchall()
print("Number of CTNs per status:")
for (status, count) in result:
print("{}: {}".format(status, count))
response = session.post("https://api.crossref.org/deposits", data=templated, auth=(username, password), headers={"Content-Type": "application/vnd.crossref.partial+xml"})
if response.status_code != 200:
print("Error depositing: {}".format(response.status_code))
print(response.text)
else:
token = response.json()['message']['batch-id']
status = response.json()['message']['status']
cursor.execute("update ctns set token = ?, status = ? where ctn = ? and doi = ?", [token, status, ctn, doi])
connection.commit()
print("Status of {} in {}: {}".format(ctn, doi, status))
try:
curs = connection.execute("select * from ctns limit 0")
except sqlite3.OperationalError:
cursor.execute("create table ctns (ctn text, registry text, doi text, status text, token text);")
parser = argparse.ArgumentParser(description='Collect and deposit Clinical Trial Numbers')
parser.add_argument('action', choices=['import-plos', 'deposit', 'update', 'status'])
parser.add_argument('--username', help='Crossref Username')
parser.add_argument('--password', help='Crossref Password')
args = parser.parse_args()
if args.action == 'import-plos':
plos.fetch_pages()
elif args.action == 'deposit':
send_deposits(args.username, args.password)
