swhume

package definevalidate;

import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import javax.xml.XMLConstants;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.dom.DOMSource;

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"""
freq_dist.py prints frequency distributions for 3 variables H1DA2, H1FS11, H1FS15

@author: swhume
last_updated 2020-03-18
"""
import pandas
import os

# set path and filename for the data file and load the dataset

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import odmlib.odm_1_3_2.model as ODM
import datetime

ODM_XML_FILE = "./data/simple_create.xml"
ODM_JSON_FILE = "./data/simple_create.json"

current_datetime = datetime.datetime.utcnow().replace(tzinfo=datetime.timezone.utc).isoformat()
root = ODM.ODM(FileOID="ODM.DEMO.001", Granularity="Metadata", AsOfDateTime=current_datetime,
               CreationDateTime=current_datetime, ODMVersion="1.3.2", FileType="Snapshot",
               Originator="swhume", SourceSystem="odmlib", SourceSystemVersion="0.1")

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import requests
import json

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

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

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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))

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import requests
import json

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

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

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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;

/**

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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):

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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)

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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