NGS machine analysis associated w file output (Observations w DocumentReference as focus)

[teslajoy]

Incorporate file extension vs update for Observations. ex:

import os
import orjson
from fhir.resources import get_fhir_model_class

def is_valid_fhir_resource_type(resource_type):
    try:
        model_class = get_fhir_model_class(resource_type)
        return model_class is not None
    except KeyError:
        return False

def create_or_extend(new_items, folder_path='META', resource_type='Observation', update_existing=False):
    assert is_valid_fhir_resource_type(resource_type), f"Invalid resource type: {resource_type}"

    file_name = "".join([resource_type, ".ndjson"])
    file_path = os.path.join(folder_path, file_name)

    file_existed = os.path.exists(file_path)

    existing_data = {}

    if file_existed:
        with open(file_path, 'r') as file:
            for line in file:
                try:
                    item = orjson.loads(line)
                    existing_data[item.get("id")] = item
                except orjson.JSONDecodeError:
                    continue

    for new_item in new_items:
        new_item_id = new_item["id"]
        if new_item_id not in existing_data or update_existing:
            existing_data[new_item_id] = new_item

    with open(file_path, 'w') as file:
        for item in existing_data.values():
            file.write(orjson.dumps(item).decode('utf-8') + '\n')

    if file_existed:
        if update_existing:
            print(f"{file_name} has new updates to existing data.")
        else:
            print(f"{file_name} has been extended, without updating existing data.")
    else:
        print(f"{file_name} has been created.")