johngrimes

{
  "resourceType": "ViewDefinition",
  "id": "UsCoreBloodPressures",
  "language": "en",
  "name": "us_core_blood_pressures",
  "_name": {
    "extension": [
      {
        "extension": [
          {

johngrimes

#!/usr/bin/env python3
"""
Read a CycloneDX 1.4 *JSON* BOM from stdin and print one line per component:

    <name>@<version> – <license1>, <license2>, …

Usage:
    python3 cyclonedx-deps-json.py < bom.json
"""

johngrimes

#!/usr/bin/env python3
"""
ECL Formatter - Formats SNOMED CT Expression Constraint Language queries
with consistent indentation and spacing.
Usage: cat ecl.txt | ./ecl_formatter.py > formatted_ecl.txt
"""

import re
import sys

johngrimes

#!/usr/bin/env python3

"""
Consumer module for processing FHIR resources from Kafka with ETL pipeline.

This module defines constants for the base directory and Spark checkpoint
directory, and implements functions to create Spark sessions, define FHIR
resource views, and start a Kafka consumer to process and persist FHIR data in
PostgreSQL.
"""

johngrimes

{
  "resourceType": "Condition",
  "id": "1",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "active"
      }
    ]

johngrimes

import requests


def get_oauth2_token(client_id, client_secret, token_url):
    """
    Obtain an OAuth2 token using client credentials grant.

    :param client_id: OAuth2 Client ID
    :param client_secret: OAuth2 Client Secret
    :param token_url: OAuth2 Token Endpoint URL

johngrimes

johngrimes

Dependencies

• jq
• Pathling Python library

Step 1

bash get-codings.sh fhir/*.json >codings.ndjson

johngrimes

import json
import multiprocessing as mp
import sys
from math import floor
from time import time

import requests


def update_resource(file):

johngrimes

import multiprocessing as mp
import sys
from time import time

import requests


def upload_bundle(file):
    with open(file) as bundle:
        data = bundle.read()