def verify_organism_property(organism_id):
token = get_jwt_identity()
user_id = token['user_id']
form = request.get_json()
for row in form:
opid = row['organism_property_id']
q = f"""
INSERT INTO organism_property_log(
organism_property_id
, user_id
, status_id
) VALUES (
{opid}
, {user_id}
, (SELECT status_id FROM status WHERE status_name = 'verified' LIMIT 1)
)
"""
with Mysql() as my:
my.execute(q)
q = _qop + f" AND op.organism_id = {organism_id}"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def metrics_user():
token = get_jwt_identity()
user_id = token['user_id']
with Mysql() as my:
count_organism = my.fetchall("SELECT count(*) AS count FROM organism")
count_organism_property = my.fetchall(
"SELECT count(*) AS count FROM organism_property")
count_verified = my.fetchall(f"""
SELECT count(*) AS count
FROM organism_property_log
WHERE status_id = (SELECT status_id FROM status WHERE status_name = 'verified' limit 1)
AND user_id = {user_id}
""")
count_other = my.fetchall(f"""
SELECT count(*) AS count
FROM organism_property_log
WHERE status_id = (SELECT status_id FROM status WHERE status_name != 'verified' limit 1)
AND user_id = {user_id}
""")
records = {
'count_organism': count_organism,
'count_organism_property': count_organism_property,
'count_verified': count_verified,
'count_other': count_other
}
return utils.generate_success_response([records])
def login():
form = request.get_json()
q = "SELECT * FROM user where email = %s"
params = [form['email']]
with Mysql() as my:
record = my.fetchone(q, params)
if not bcrypt.check_password_hash(record['password'], form['password']):
return jsonify({"error": "Invalid username and password"})
access_token = create_access_token(
identity={
'user_id': record['user_id'],
'name': record['name'],
'email': record['email']
})
result = {
'success': True,
'records': {
'user_id': record['user_id'],
'name': record['name'],
'email': record['email']
}
}
# resp = jsonify({'success': True})
resp = jsonify(result)
# Set the JWT cookies in the response
set_access_cookies(resp, access_token)
return resp, 200
def organism_property(organism_id):
q = _qop + f" AND op.organism_id = {organism_id}"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def get_organism(organism_id):
q = f"SELECT * FROM organism WHERE organism_id = {organism_id} LIMIT 1"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def all_organism():
q = "SELECT * FROM organism"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def metrics():
with Mysql() as my:
count_organism = my.fetchall("SELECT count(*) AS count FROM organism")
count_organism_property = my.fetchall(
"SELECT count(*) AS count FROM organism_property")
records = {
'count_organism': count_organism,
'count_organism_property': count_organism_property,
}
return utils.generate_success_response([records])
def search_reference():
args = request.args.to_dict()
if 'search' not in args:
return utils.generate_success_response()
name = f"%{args['search']}%"
q = "SELECT * FROM reference WHERE value LIKE %s"
p = [name]
with Mysql() as my:
records = my.fetchall(q, p)
return utils.generate_success_response(records)
def all_property():
q = """
SELECT
p.*
, pc.property_category_name
, pt.property_type_name
FROM property p
JOIN property_category pc on p.property_category_id = pc.property_category_id
JOIN property_type pt on p.property_type_id = pt.property_type_id
"""
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def set_organism():
form = request.get_json()
q1 = f"INSERT INTO organism (organism_name) VALUES (%s);"
p1 = [form["title"]]
qp1 = [q1, p1]
qp2 = ['select * from organism where organism_id = LAST_INSERT_ID()']
qps = [qp1, qp2]
with Mysql() as my:
records = my.execute_statements(qps)
return utils.generate_success_response(records)
def register():
form = request.get_json()
sql = """
INSERT INTO user ( email, password , name)
VALUES ( %s , %s , %s)
"""
passenc = bcrypt.generate_password_hash(form["password"]).decode("utf-8")
params = [form["email"], passenc, form["name"]]
sql2 = "SELECT * from user where user_id = LAST_INSERT_ID()"
sps = [[sql, params], [sql2]]
with Mysql() as my:
result = my.execute_statements(sps)
return utils.generate_success_response(result)
def all_category():
q = "SELECT * FROM property_category ORDER BY property_category_order"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)
def set_organism_property(organism_id):
token = get_jwt_identity()
user_id = token['user_id']
form = request.get_json()
reference = form['reference']
data = form['data']
if (isinstance(reference, dict)):
rid = reference['reference_id']
elif (isinstance(reference, str)):
q1 = "INSERT INTO reference(value) VALUES (%s)"
q2 = "SELECT LAST_INSERT_ID() AS reference_id"
with Mysql() as my:
record = my.execute_statements([[q1, [reference]], q2])
rid = record[0]['reference_id']
for k in data:
v = data[k]
sps = []
if ('organism_property_id' in v):
opid = v['organism_property_id']
q1 = "UPDATE organism_property SET value = %s WHERE organism_property_id = %s"
p1 = [v["value"], opid]
q2 = f"""
INSERT INTO organism_property_log(
organism_property_id
, user_id
, status_id
) VALUES (
{opid}
, {user_id}
, (SELECT status_id FROM status WHERE status_name = 'updated' LIMIT 1)
)
"""
else:
q1 = """
INSERT INTO organism_property (
organism_id
, property_id
, value
) VALUES (%s, %s, %s)
"""
p1 = [v["organism_id"], v["property_id"], v["value"]]
q2 = f"""
INSERT INTO organism_property_log(
organism_property_id
, user_id
, status_id
) VALUES (
LAST_INSERT_ID()
, {user_id}
, (SELECT status_id FROM status WHERE status_name = 'input' LIMIT 1)
)
"""
q3 = f"""
INSERT INTO organism_property_reference(
organism_property_id
, reference_id
, user_id
) VALUES (
(SELECT organism_property_id FROM organism_property_log WHERE organism_property_log_id = LAST_INSERT_ID())
, {rid}
, {user_id}
)
"""
sps.append([q1, p1])
sps.append(q2)
sps.append(q3)
with Mysql() as my:
my.execute_statements(sps)
q = _qop + f" AND op.organism_id = {organism_id}"
with Mysql() as my:
records = my.fetchall(q)
return utils.generate_success_response(records)