basic_example.py

#!/usr/bin/env python3

"""
    A basic example for parsing an XML file, fetching some attribute values,
    and converting them to an OMOP concept_id.
    Uses some support for keeping the OMOP concept table in Spark.
"""

import xml.etree.ElementTree as ET
from util import vocab_spark
from util.xml_ns import ns
from util import spark_util

INPUT_FILENAME = 'resources/CCDA_CCD_b1_InPatient_v2.xml'

# INIT SPARK
spark_util_object = spark_util.SparkUtil()

# PARSE/LOAD
tree = ET.parse(INPUT_FILENAME)

# FIND DATA
observations = tree.findall(
    "./component/structuredBody/component/section/entry/organizer/component/observation", ns)

for observation in observations:
    observation_code = observation.find("code", ns)
    vocabulary_id = observation_code.attrib['codeSystem']
    concept_code = observation_code.attrib['code']

    # CONVERT TO OMOP
    observation_concept_id = vocab_spark.map_hl7_to_omop(
        vocabulary_id,
        concept_code)

    # OUTPUT
    print((f"vocaublary_id {vocabulary_id} concept_code {concept_code} "
           f"maps to {observation_concept_id}"))