def api_list_subject_events():
"""
:rtype: Response
:return the list of subjects in json format
"""
# from sqlalchemy.sql import text
from collections import namedtuple
if 'POST' == request.method:
subject_id = utils.get_safe_int(request.form.get('subject_id'))
else:
subject_id = utils.get_safe_int(request.args.get('subject_id'))
query = """
SELECT
evtID AS id
, evtRedcapArm AS redcap_arm
, evtRedcapEvent AS redcap_event
, evtDayOffset AS day_offset
, COUNT(sfID) AS total_files
, GROUP_CONCAT(sfFileName) AS file_names
FROM
Event
JOIN SubjectFile USING(evtID)
WHERE
sbjID = :subject_id
GROUP BY
evtID
"""
# print subject_id, query
result = db.session.execute(query, {'subject_id': subject_id})
Event = namedtuple('Event', result.keys())
events = [Event(*r) for r in result.fetchall()]
events_ser = [i._asdict() for i in events]
return utils.jsonify_success({'subject_events': events_ser})
def find_subject():
"""
Side effect: This function will synchronize the list of subjects in the
local database with REDCap by sending a REDCap API call
if the local database contains no entries.
:rtype: Response
:return the list of subjects in json format
"""
invalid_id = -1
if 'POST' == request.method:
search_id = utils.get_safe_int(request.form['name'], invalid_id,
invalid_id)
else:
search_id = utils.get_safe_int(request.args.get('name'), invalid_id,
invalid_id)
matching = []
if search_id != invalid_id:
# @TODO: optimize to return one column by default
# http://stackoverflow.com/questions/7533146/how-do-i-select-additional-manual-values-along-with-an-sqlalchemy-query
subject_list = SubjectEntity.query.filter(
SubjectEntity.redcap_id.like("%{}%".format(search_id))).all()
matching = [subject.redcap_id for subject in subject_list]
if len(matching) == 0:
api_import_redcap_subjects()
return utils.jsonify_success({'subjects': matching})
def find_subject():
"""
Side effect: This function will synchronize the list of subjects in the
local database with REDCap by sending a REDCap API call
if the local database contains no entries.
:rtype: Response
:return the list of subjects in json format
"""
invalid_id = -1
if 'POST' == request.method:
search_id = utils.get_safe_int(request.form['name'],
invalid_id, invalid_id)
else:
search_id = utils.get_safe_int(request.args.get('name'),
invalid_id,
invalid_id)
matching = []
if search_id != invalid_id:
# @TODO: optimize to return one column by default
# http://stackoverflow.com/questions/7533146/how-do-i-select-additional-manual-values-along-with-an-sqlalchemy-query
subject_list = SubjectEntity.query.filter(
SubjectEntity.redcap_id.like("%{}%".format(search_id))
).all()
matching = [subject.redcap_id for subject in subject_list]
if len(matching) == 0:
api_import_redcap_subjects()
return utils.jsonify_success({'subjects': matching})
def api_list_subject_events():
"""
:rtype: Response
:return the list of subjects in json format
"""
# from sqlalchemy.sql import text
from collections import namedtuple
if 'POST' == request.method:
subject_id = utils.get_safe_int(request.form.get('subject_id'))
else:
subject_id = utils.get_safe_int(request.args.get('subject_id'))
query = """
SELECT
evtID AS id
, evtRedcapArm AS redcap_arm
, evtRedcapEvent AS redcap_event
, evtDayOffset AS day_offset
, COUNT(sfID) AS total_files
, GROUP_CONCAT(sfFileName) AS file_names
FROM
Event
JOIN SubjectFile USING(evtID)
WHERE
sbjID = :subject_id
GROUP BY
evtID
"""
# print subject_id, query
result = db.session.execute(query, {'subject_id': subject_id})
Event = namedtuple('Event', result.keys())
events = [Event(*r) for r in result.fetchall()]
events_ser = [i._asdict() for i in events]
return utils.jsonify_success({'subject_events': events_ser})
def api_list_logs():
"""
Render the specified page of event logs
@TODO: show user-specific logs for non-admins?
:rtype: string
:return the json list of logs
"""
if 'POST' == request.method:
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
else:
per_page = get_safe_int(request.args.get('per_page'))
page_num = get_safe_int(request.args.get('page_num'))
"""
pagination = LogEntity.query.paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
app.logger.debug("per_page: {}, page_num: {}".format(per_page, page_num))
return jsonify_success(dict(total_pages=pagination.pages,
list_of_events=items))
"""
logs, total_pages = log_manager.get_logs(per_page, page_num)
# logs_list = [x.to_visible() for x in logs]
return jsonify_success(dict(list_of_events=logs, total_pages=total_pages))
def download_file():
""" Download a file using the database id """
if 'POST' == request.method:
file_id = utils.get_safe_int(request.form['file_id'])
else:
file_id = utils.get_safe_int(request.args.get('file_id'))
subject_file = SubjectFileEntity.get_by_id(file_id)
file_path = subject_file.get_full_path(
app.config['REDIDROPPER_UPLOAD_SAVED_DIR'])
LogEntity.file_downloaded(session['uuid'], file_path)
return send_file(file_path, as_attachment=True)
def download_file():
""" Download a file using the database id """
if 'POST' == request.method:
file_id = utils.get_safe_int(request.form['file_id'])
else:
file_id = utils.get_safe_int(request.args.get('file_id'))
subject_file = SubjectFileEntity.get_by_id(file_id)
file_path = subject_file.get_full_path(
app.config['REDIDROPPER_UPLOAD_SAVED_DIR'])
LogEntity.file_downloaded(session['uuid'], file_path)
return send_file(file_path, as_attachment=True)
def api_list_subjects():
"""
Render the table of subjects and their file counts
:rtype: Response
:return json
"""
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
total_pages, list_of_subjects = \
subject_manager.get_subjects_on_page(per_page, page_num)
return jsonify(total_pages=total_pages, list_of_subjects=list_of_subjects)
def api_list_logs(per_page, page_num):
"""
@app.route('/api/list_logs/<per_page>/<page_num>', methods=['GET', 'POST'])
@app.route('/api/list_logs/<per_page>', defaults={'page_num': 1})
Render the specified page of event logs
@TODO: show user-specific logs for non-admins?
:rtype: string
:return the json list of logs
"""
per_page = get_safe_int(per_page)
page_num = get_safe_int(page_num)
logs, total_pages = log_manager.get_logs(per_page, page_num)
# logs_list = [x.to_visible() for x in logs]
return jsonify(list_of_events=logs, total_pages=total_pages)
def api_send_verification_email():
"""
@TODO: allow POST only
@TODO: Send Verification Email to user_id
:rtype: Response
:return the success or failed in json format
"""
user_id = get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
user = UserEntity.get_by_id(1)
user.email = app.config['MAIL_SENDER_SUPPORT']
try:
emails.send_verification_email(user)
return jsonify_success({"message": "Verification email was sent."})
except Exception as exc:
details = "Connection config: {}/{}:{}".format(
app.config['MAIL_USERNAME'], app.config['MAIL_SERVER'],
app.config['MAIL_PORT'])
app.logger.debug(details)
return jsonify_error({
"message":
"Unable to send email due: {} {}".format(exc, details)
})
def api_list_subject_event_files():
"""
:rtype: Response
:return the list of subjects in json format
"""
if 'POST' == request.method:
subject_id = utils.get_safe_int(request.form.get('subject_id'))
event_id = utils.get_safe_int(request.form.get('event_id'))
else:
subject_id = utils.get_safe_int(request.args.get('subject_id'))
event_id = utils.get_safe_int(request.args.get('event_id'))
files = SubjectFileEntity \
.query.filter_by(subject_id=subject_id,
event_id=event_id).all()
files_ser = [i.serialize() for i in files]
return utils.jsonify_success({'subject_event_files': files_ser})
def api_list_users():
"""
Retrieve the users cached in the local database
:rtype: Response
:return
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
pagination = UserEntity.query.order_by(
db.desc(UserEntity.id)).paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return utils.jsonify_success(
{"total_pages": pagination.pages, "list_of_users": items})
def api_list_users():
"""
Retrieve the users cached in the local database
:rtype: Response
:return
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
pagination = UserEntity.query.order_by(
db.desc(UserEntity.id)).paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return utils.jsonify_success(
{"total_pages": pagination.pages, "list_of_users": items})
def api_list_subject_event_files():
"""
:rtype: Response
:return the list of subjects in json format
"""
if 'POST' == request.method:
subject_id = utils.get_safe_int(request.form.get('subject_id'))
event_id = utils.get_safe_int(request.form.get('event_id'))
else:
subject_id = utils.get_safe_int(request.args.get('subject_id'))
event_id = utils.get_safe_int(request.args.get('event_id'))
files = SubjectFileEntity \
.query.filter_by(subject_id=subject_id,
event_id=event_id).all()
files_ser = [i.serialize() for i in files]
return utils.jsonify_success({'subject_event_files': files_ser})
def api_list_logs():
"""
Render the specified page of event logs
@TODO: show user-specific logs for non-admins?
:rtype: string
:return the json list of logs
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
logs, total_pages = LogEntity.get_logs(per_page, page_num)
return utils.jsonify_success(
dict(list_of_events=logs, total_pages=total_pages))
def api_list_users():
"""
@TODo: use the page_num in the query
:rtype: Response
:return
"""
if 'POST' == request.method:
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
else:
per_page = get_safe_int(request.args.get('per_page'))
page_num = get_safe_int(request.args.get('page_num'))
# users = UserEntity.query.filter(UserEntity.id >= 14).all()
pagination = UserEntity.query.order_by(
db.desc(UserEntity.id)).paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return jsonify_success({"total_pages": pagination.pages,
"list_of_users": items})
def api_list_logs():
"""
Render the specified page of event logs
@TODO: show user-specific logs for non-admins?
:rtype: string
:return the json list of logs
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
logs, total_pages = LogEntity.get_logs(per_page, page_num)
return utils.jsonify_success(
dict(list_of_events=logs, total_pages=total_pages))
def api_list_users():
"""
@TODo: use the page_num in the query
:rtype: Response
:return
"""
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
app.logger.debug("Show page {} of users".format(page_num))
users = UserEntity.query.all()
# users = UserEntity.query.filter(UserEntity.id >= 14).all()
if users is None:
return make_response(pack_error("no users found"))
list_of_users = [i.serialize() for i in users]
total_pages = math.ceil(len(list_of_users)/float(per_page))
data = {"total_pages": total_pages, "list_of_users": list_of_users}
return make_response(pack_success_result(data))
def api_list_users():
"""
@TODo: use the page_num in the query
:rtype: Response
:return
"""
if 'POST' == request.method:
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
else:
per_page = get_safe_int(request.args.get('per_page'))
page_num = get_safe_int(request.args.get('page_num'))
# users = UserEntity.query.filter(UserEntity.id >= 14).all()
pagination = UserEntity.query.order_by(db.desc(UserEntity.id)).paginate(
page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return jsonify_success({
"total_pages": pagination.pages,
"list_of_users": items
})
def api_deactivate_account():
"""
De-activate an user.
@TODO: should change expiration date too?
:rtype: Response
:return the success or failed in json format
"""
user_id = get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
user = UserEntity.update(user, active=False)
return jsonify_success({"message": "User deactivated."})
def api_deactivate_account():
"""
De-activate an user.
@TODO: should change expiration date too?
:rtype: Response
:return the success or failed in json format
"""
user_id = get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
user = UserEntity.update(user, active=False)
return jsonify_success({"message": "User deactivated."})
def api_list_local_subjects():
"""
Render the table of subjects and their file counts
@see http://pythonhosted.org/Flask-SQLAlchemy/api.html
#flask.ext.sqlalchemy.BaseQuery.paginate
paginate(page, per_page=20, error_out=True)
:rtype: Response
:return json
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
pagination = SubjectEntity.query.paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return utils.jsonify_success(
dict(total_pages=pagination.pages, list_of_subjects=items))
def api_list_local_subjects():
"""
Render the table of subjects and their file counts
@see http://pythonhosted.org/Flask-SQLAlchemy/api.html
#flask.ext.sqlalchemy.BaseQuery.paginate
paginate(page, per_page=20, error_out=True)
:rtype: Response
:return json
"""
if 'POST' == request.method:
per_page = utils.get_safe_int(request.form.get('per_page'))
page_num = utils.get_safe_int(request.form.get('page_num'))
else:
per_page = utils.get_safe_int(request.args.get('per_page'))
page_num = utils.get_safe_int(request.args.get('page_num'))
pagination = SubjectEntity.query.paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
return utils.jsonify_success(
dict(total_pages=pagination.pages, list_of_subjects=items))
def api_activate_account():
"""
Activate an user.
@TODO: should change expiration date too?
:rtype: Response
:return the success or failed in json format
"""
user_id = utils.get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
user = UserEntity.update(user, active=True)
LogEntity.account_modified(session['uuid'],
"User activated: {}".format(user))
return utils.jsonify_success({"message": "User activated."})
def api_expire_account():
"""
Change the `User.usrAccessExpiresAt` to today's date and 00:00:00 time
effectively blocking the user access.
:rtype: Response
:return the success or failed in json format
"""
user_id = get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
today = datetime.today()
today_start = datetime(today.year, today.month, today.day)
user = UserEntity.update(user, access_expires_at=today_start)
return jsonify_success({"message": "User access was expired."})
def api_expire_account():
"""
Change the `User.usrAccessExpiresAt` to today's date and 00:00:00 time
effectively blocking the user access.
:rtype: Response
:return the success or failed in json format
"""
user_id = get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
today = datetime.today()
today_start = datetime(today.year, today.month, today.day)
user = UserEntity.update(user, access_expires_at=today_start)
return jsonify_success({"message": "User access was expired."})
def api_activate_account():
"""
Activate an user.
@TODO: should change expiration date too?
:rtype: Response
:return the success or failed in json format
"""
user_id = utils.get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
user = UserEntity.update(user, active=True)
LogEntity.account_modified(session['uuid'],
"User activated: {}".format(user))
return utils.jsonify_success({"message": "User activated."})
def api_list_logs():
"""
Render the specified page of event logs
@TODO: show user-specific logs for non-admins?
:rtype: string
:return the json list of logs
"""
if 'POST' == request.method:
per_page = get_safe_int(request.form.get('per_page'))
page_num = get_safe_int(request.form.get('page_num'))
else:
per_page = get_safe_int(request.args.get('per_page'))
page_num = get_safe_int(request.args.get('page_num'))
"""
pagination = LogEntity.query.paginate(page_num, per_page, False)
items = [i.serialize() for i in pagination.items]
app.logger.debug("per_page: {}, page_num: {}".format(per_page, page_num))
return jsonify_success(dict(total_pages=pagination.pages,
list_of_events=items))
"""
logs, total_pages = log_manager.get_logs(per_page, page_num)
# logs_list = [x.to_visible() for x in logs]
return jsonify_success(dict(list_of_events=logs, total_pages=total_pages))
def api_expire_account():
"""
Change the `User.usrAccessExpiresAt` to today's date and 00:00:00 time
effectively blocking the user access.
:rtype: Response
:return the success or failed in json format
"""
user_id = utils.get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
today = datetime.today()
today_start = datetime(today.year, today.month, today.day)
user = UserEntity.update(user, access_expires_at=today_start)
# @TODO: add dedicated log type
LogEntity.account_modified(
session['uuid'], "User access was expired. {}".format(user.email))
return utils.jsonify_success({"message": "User access was expired."})
def api_expire_account():
"""
Change the `User.usrAccessExpiresAt` to today's date and 00:00:00 time
effectively blocking the user access.
:rtype: Response
:return the success or failed in json format
"""
user_id = utils.get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
today = datetime.today()
today_start = datetime(today.year, today.month, today.day)
user = UserEntity.update(user, access_expires_at=today_start)
# @TODO: add dedicated log type
LogEntity.account_modified(session['uuid'],
"User access was expired. {}".format(user.email))
return utils.jsonify_success({"message": "User access was expired."})
def api_send_verification_email():
"""
@TODO: Send Verification Email to user_id
:rtype: Response
:return the success or failed in json format
"""
user_id = utils.get_safe_int(request.form.get('user_id'))
user = UserEntity.get_by_id(user_id)
try:
emails.send_verification_email(user)
return utils.jsonify_success(
{"message": "Verification email was sent."})
except Exception as exc:
details = "Connection config: {}/{}:{}".format(
app.config['MAIL_USERNAME'],
app.config['MAIL_SERVER'],
app.config['MAIL_PORT'])
app.logger.debug(details)
return utils.jsonify_error(
{"message": "Unable to send email due: {} {}".format(exc, details)})
