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from pymongo import MongoClient
from datetime import datetime
import pytz
from prefect_utils import trigger_maintenance_request
from prefect import task
import pandas as pd
import os
import asyncio
MONGODB_PASSWORD = os.getenv("MONGODB_PASSWORD")
blinded_connection_string = os.getenv("blinded_connection_string")
connection_string = blinded_connection_string.replace("<db_password>", MONGODB_PASSWORD)
@task
def generate_empty_well():
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["wells"]
rows = ['B', 'C', 'D', 'E', 'F', 'G', 'H']
columns = [str(i) for i in range(1, 13)]
for row in rows:
for col in columns:
well = f"{row}{col}"
metadata = {
"well": well,
"status": "empty",
"project": "OT2"
}
#send_data_to_mongodb(collection="wells", data=metadata)
query = {"well": well}
update_data = {"$set": metadata}
result = collection.update_one(query, update_data, upsert=True)
# close connection
dbclient.close()
@task
def update_used_wells(used_wells):
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["wells"]
for well in used_wells:
metadata = {
"well": well,
"status": "used",
"project": "OT2"
}
#send_data_to_mongodb(collection="wells", data=metadata)
query = {"well": well}
update_data = {"$set": metadata}
result = collection.update_one(query, update_data, upsert=True)
# close connection
dbclient.close()
def find_unused_wells():
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["wells"]
query = {"status": "empty"}
response = list(collection.find(query))
df = pd.DataFrame(response)
# Extract the "well" column as a list
#if "well" not in df.columns:
# raise ValueError("No available wells.")
# Sort obtained list
def well_sort_key(well):
row = well[0] # A, B, C, ...
col = int(well[1:]) # 1, 2, ..., 12
return (row, col)
if "well" in df.columns:
empty_wells = sorted(df["well"].tolist(), key=well_sort_key)
else:
empty_wells = []
if len(empty_wells) == 1:
maintenance_type = "wellplate_maintenance"
if check_maintenance_status(maintenance_type) == 0:
asyncio.run(trigger_maintenance_request(maintenance_type))
set_maintenance_status(maintenance_type,1)
else:
print("[DEBUG] a maintenance request has been sent")
dbclient.close()
# Check if there are any empty wells
#if len(empty_wells) == 0:
# raise ValueError("No empty wells found")
#print(empty_wells)
return empty_wells
@task
def save_result(result_data):
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["result"]
#collection = db["test_result"]
result_data["timestamp"] = datetime.now(pytz.timezone("America/Toronto")) # UTC time
insert_result = collection.insert_one(result_data)
inserted_id = insert_result.inserted_id
# close connection
dbclient.close()
return inserted_id
def get_student_quota(student_id):
with MongoClient(connection_string) as client:
db = client["LCM-OT-2-SLD"]
collection = db["student"]
student = collection.find_one({"student_id": student_id})
if student is None:
raise ValueError(f"Student ID '{student_id}' not found in the database.")
return student.get("quota", 0)
def decrement_student_quota(student_id):
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["student"]
student = collection.find_one({"student_id": student_id})
if not student:
return f"Student ID {student_id} not found."
if student.get("quota", 0) <= 0:
return f"Student ID {student_id} has no remaining quota."
result = collection.update_one(
{"student_id": student_id, "quota": {"$gt": 0}},
{"$inc": {"quota": -1}}
)
if result.modified_count > 0:
return f"Student ID {student_id}'s quota update successfully."
else:
return f"Quota update failed for Student ID {student_id}."
def add_student_quota(student_id, quota):
"""
Adds a new student with a given quota.
:param student_id: The ID of the student.
:param quota: The initial quota for the student.
"""
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["student"]
student_data = {"student_id": student_id, "quota": quota}
collection.update_one({"student_id": student_id}, {"$set": student_data}, upsert=True)
dbclient.close()
def check_maintenance_status(maintenance_type):
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["HITL_status"]
status_doc = collection.find_one({"name": maintenance_type})
dbclient.close()
if status_doc is None:
return 0
return status_doc.get("flag", 0)
def set_maintenance_status(maintenance_type,new_status):
#flag == 1, request sent; flag == 0, no request undergoing
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["HITL_status"]
collection.update_one(
{"name": maintenance_type},
{"$set": {"flag": new_status,
"timestamp": datetime.now(pytz.timezone("America/Toronto"))}
},
upsert=True
)
dbclient.close()
def insert_maintenance_log(maintenance_type, operator="Unknown"):
dbclient = MongoClient(connection_string)
db = dbclient["LCM-OT-2-SLD"]
collection = db["maintenance_logs"]
log_data = {
"maintenance_type": maintenance_type,
"timestamp": datetime.now(pytz.timezone("America/Toronto")),
"operator": operator
}
collection.insert_one(log_data)
dbclient.close()
if __name__ == "__main__":
#generate_empty_well()
find_unused_wells()
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