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upload_json.py
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upload_json.py
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import os
import json
from database import Database
def upload_json(path, db: Database):
with open(os.path.join(path, "patients.json"), "r") as f:
patients_data = json.load(f)
for tuple in patients_data["patients"]:
db.insert_patient_pseudo(tuple["patient_ID"], tuple["patient_pseudo_ID"])
with open(os.path.join(path, "predictive.json"), "r") as f:
predictive_data = json.load(f)
for tuple in predictive_data["predictive"]:
db.insert_predictive_pseudo(tuple["predictive_number"], tuple["pseudo_number"])
with open(os.path.join(path, "samples.json"), "r") as f:
samples_data = json.load(f)
for tuple in samples_data["samples"]:
db.insert_samples_pseudo(tuple["sample_ID"], tuple["pseudo_sample_ID"])
if __name__=="__main__":
db = Database(
os.environ["PSQL_NAME"],
os.environ["PSQL_HOST"],
os.environ["PSQL_PORT"],
os.environ["PSQL_USER"],
os.environ["PSQL_PSSWD"]
)
path = os.environ["PSEUDO_TABLE_JSON"]
upload_json(path, db)