info/scripts/organize/organize_genetics_data.py

"""Pipeline to organize raw data."""

import yaml
import logging

from almirah import Specification

# Get inputs
modality = input("Enter modality to organize: ")
position = input("Enter index position of modality in rules: ")

logging.basicConfig(
    filename=f"logs/organize_{modality}_detailed.log",
    format="%(asctime)s %(levelname)s: %(message)s",
    level=logging.DEBUG,
)


logging.getLogger().addHandler(logging.StreamHandler())

# Read rules yaml
with open("configs/rules/rules.yaml") as f:
    rules = yaml.load_all(f, yaml.SafeLoader)
    spec = Specification.create_from_file("configs/specifications/gids.yaml")

    for pos, rule in enumerate(rules):
        if pos == int(position):
            logging.info(f"Organizing by rule: \n {rule}")
            spec.organize(rule)