swhume

# Copyright 2022 Sam Hume. Licensed under the MIT-0 license https://opensource.org/licenses/MIT-0
import odmlib.define_2_1.model as DEFINE
import datetime

"""
This is the code presented at the PHUSE US Connect 2022 and described in paper PAP_OS01.
The purpose of this code is to demonstrate using odmlib to create and process a very simple Define-XML v2.1 file.
NOTE: In places where paths are referenced, you will need to update them to reflect your system.
"""

swhume

import lxml.etree as ET
import argparse
import os

"""
Example Cmd-line Args:
    example: -x ./data/some.xml -o ./data/some.html -s ./data/transform.xslt
"""

swhume

import sys
import xml.etree.ElementTree as ET
""" Simple program snippet to demonstrate parsing the CXL XML CMAP export format """

ET.register_namespace('', "http://cmap.ihmc.us/xml/cmap/")

# get the CXL file to parse from the command-line
if len(sys.argv) > 1:
    cxl_file = sys.argv[1]
else:

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# scrape XML from a spec grabber generated wiki page
from bs4 import BeautifulSoup
import os
import sys
import getopt

# get the command-line arguments - page id is required
scrape_xml_file = "scrape.xml"
path = ""
page_id = None

swhume

from fhirclient import client
import fhirclient.models.patient as p
settings = {
    'app_id': 'rof_adapter',
    'api_base': 'https://api-v5-stu3.hspconsortium.org/rofphir/open'
}

smart = client.FHIRClient(settings=settings)
patient = p.Patient.read('SMART-1288992', smart.server)

swhume

import requests
import os
import json
import logging
import argparse


class LinkCrawler:
    """ SHARE v2.0 link crawler for testing HATEOAS content in API responses """
    def __init__(self, base_url, start_resource, log_file="link_log.txt", log_path=None, username=None, password=None):

swhume

package json2xml;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.XML;

/**

swhume

import requests
import json

USERNAME = "username"
PWD = "password"
URL = "http://68.183.158.128:5000/odm"

# create ItemDef
itemdef = {
    "_use": "collection",

swhume

from fhirclient import client
import fhirclient.models.observation as ob
settings = {
    'app_id': 'rof_adapter',
    'api_base': 'https://api-v5-stu3.hspconsortium.org/rofphir/open'
}

def get_observations(patient_id, loinc_code):
    smart = client.FHIRClient(settings=settings)
    search_obs = ob.Observation.where(struct=dict(patient=patient_id, code=loinc_code))

swhume

import requests
import json

USERNAME = "username"
PWD = "password"
URL = "http://68.183.158.128:5000/odm"

codelist = {
    "_use": "collection",
    "OID": "CL.Test.02",