def get_username_password(storage_name,
user_input=input,
password_input=getpass,
output=print):
user = keyring.get_password("MosaiqSQL_username", storage_name)
password = keyring.get_password("MosaiqSQL_password", storage_name)
if user is None or user == "":
output("Provide a user that only has `db_datareader` access to the "
"Mosaiq database at `{}`".format(storage_name))
user = user_input()
if user == "":
error_message = "Username should not be blank."
output(error_message)
raise ValueError(error_message)
keyring.set_password("MosaiqSQL_username", storage_name, user)
if password is None:
output("Provide password for '{}' server and '{}' user".format(
storage_name, user))
password = password_input()
keyring.set_password("MosaiqSQL_password", storage_name, password)
return user, password
def mosaiq_input_method(patient_id="", key_namespace="", site=None, **_):
mosaiq_details = _config.get_mosaiq_details()
mosaiq_site = st_misc.site_picker("Mosaiq Site",
default=site,
key=f"{key_namespace}_mosaiq_site")
server = mosaiq_details[mosaiq_site]["server"]
st.write(f"Mosaiq Hostname: `{server}`")
sql_user = keyring.get_password("MosaiqSQL_username", server)
st.write(f"Mosaiq SQL login being used: `{sql_user}`")
patient_id = st.text_input("Patient ID",
patient_id,
key=f"{key_namespace}_patient_id")
st.write(patient_id)
cursor = st_mosaiq.get_mosaiq_cursor(server)
if patient_id == "":
return {}
patient_name = get_patient_name(cursor, patient_id)
st.write(f"Patient Name: `{patient_name}`")
patient_fields = get_patient_fields(cursor, patient_id)
st.write("""
#### Mosaiq patient fields
""")
patient_fields = patient_fields[patient_fields["monitor_units"] != 0]
st.write(patient_fields)
field_ids = patient_fields["field_id"]
field_ids = field_ids.values.tolist()
selected_field_ids = st.multiselect("Select Mosaiq field id(s)",
field_ids,
key=f"{key_namespace}_mosaiq_field_id")
cursor_and_field_ids = [(cursor, field_id)
for field_id in selected_field_ids]
deliveries = _deliveries.cached_deliveries_loading(
cursor_and_field_ids, _deliveries.delivery_from_mosaiq)
identifier = f"{mosaiq_site} Mosaiq ({', '.join([str(field_id) for field_id in selected_field_ids])})"
return {
"site": mosaiq_site,
"patient_id": patient_id,
"patient_name": patient_name,
"data_paths": [],
"identifier": identifier,
"deliveries": deliveries,
}
def mosaiq_input_method(patient_id="", key_namespace="", **_):
mosaiq_details = get_mosaiq_details()
site_options = list(mosaiq_details.keys())
mosaiq_site = st.radio("Mosaiq Site",
site_options,
key=f"{key_namespace}_mosaiq_site")
server = mosaiq_details[mosaiq_site]["server"]
f"Mosaiq Hostname: `{server}`"
sql_user = keyring.get_password("MosaiqSQL_username", server)
f"Mosaiq SQL login being used: `{sql_user}`"
patient_id = st.text_input("Patient ID",
patient_id,
key=f"{key_namespace}_patient_id")
patient_id
cursor = get_mosaiq_cursor(server)
if patient_id == "":
return {}
patient_name = get_patient_name(cursor, patient_id)
f"Patient Name: `{patient_name}`"
patient_fields = get_patient_fields(cursor, patient_id)
"""
#### Mosaiq patient fields
"""
patient_fields = patient_fields[patient_fields["monitor_units"] != 0]
patient_fields
field_ids = patient_fields["field_id"]
field_ids = field_ids.values.tolist()
selected_field_ids = st.multiselect("Select Mosaiq field id(s)",
field_ids,
key=f"{key_namespace}_mosaiq_field_id")
cursor_and_field_ids = [(cursor, field_id)
for field_id in selected_field_ids]
deliveries = cached_deliveries_loading(cursor_and_field_ids,
delivery_from_mosaiq)
identifier = (
f"Mosaiq ({', '.join([str(field_id) for field_id in selected_field_ids])})"
)
return {
"patient_id": patient_id,
"patient_name": patient_name,
"data_paths": selected_field_ids,
"identifier": identifier,
"deliveries": deliveries,
}
def get_zenodo_access_token(hostname):
access_token = keyring.get_password("Zenodo", hostname)
if access_token is None or access_token == "":
print(
"To upload files to Zenodo you need to provide a Zenodo "
"access token. Please go to "
f"<https://{hostname}/account/settings/applications/tokens/new/>, "
"login to Zenodo and create a new access token.\n"
"When creating the access token use the scopes `deposit:actions`, `deposit:write`, "
"and `user:email`. Once you have your token copy it into the prompt below "
"to continue with the upload.")
access_token = getpass.getpass()
set_zenodo_access_token(access_token, hostname)
return access_token