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fhir_parse_resources.py
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fhir_parse_resources.py
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# -*- coding: utf-8 -*-
# @Date : 2018-05-28 18:30:52
# @Author : Md Nazrul Islam (email2nazrul@gmail.com)
# @Link : http://nazrul.me/
# @Version : $Id$
# All imports here
import asyncio
import datetime
import hashlib
import io
import json
import os
import pathlib
import shutil
import sys
import tempfile
import zipfile
import aiohttp
import tqdm
from aiohttp.client_exceptions import ClientOSError
from aiohttp.client_exceptions import ClientResponseError
from aiohttp.client_exceptions import ServerDisconnectedError
from helpers import cmd
__author__ = "Md Nazrul Islam (email2nazrul@gmail.com)"
BASE_URL = "http://hl7.org/fhir"
VERSION = "STU3"
EXT = ".zip"
FHIR_DEFINITION = "definitions.json" + EXT
FHIR_EXAMPLE = "examples-json" + EXT
FHIR_SCHEMAS = "fhir.schema.json" + EXT
OUTPUT_DIR = (
pathlib.Path(__file__).parent.parent
/ "src"
/ "plone"
/ "app"
/ "fhirfield"
/ "browser"
/ "static"
/ "FHIR"
/ "HL7"
)
RESOURCES_DIR = OUTPUT_DIR / "ResourceList"
CACHE_DIR = pathlib.Path(__file__).parent / ".cache"
async def write_stream(filename, response):
""" """
# Progress Bar added
with tqdm.tqdm(total=int(response.content_length)) as pbar:
try:
with open(filename, "wb") as f:
while True:
chunk = await response.content.read(io.DEFAULT_BUFFER_SIZE)
if not chunk:
break
pbar.update(len(chunk))
f.write(chunk)
except (
ServerDisconnectedError,
ClientResponseError,
ClientOSError,
asyncio.TimeoutError,
) as exc:
print(str(exc))
sys.stderr.write(str(exc))
os.unlink(filename)
async def download_archieves(uris, session, offline):
""" """
global CACHE_DIR
files = list()
for uri in uris:
cache_id = hashlib.md5(uri.encode("utf-8")).hexdigest()
cached_file = CACHE_DIR / cache_id
if offline:
if not cached_file.exists():
sys.stdout.write(
"No offline file found! at {0!s}, "
"going to dowanload fresh".format(cached_file)
)
else:
files.append((uri, cached_file))
continue
try:
async with await session.get(uri, allow_redirects=True) as response:
if response.status == 200:
sys.stdout.write("Start downloading file from {0}\n".format(uri))
await write_stream(str(cached_file), response)
files.append((uri, cached_file))
except (
ServerDisconnectedError,
ClientResponseError,
ClientOSError,
asyncio.TimeoutError,
) as exc:
print(str(exc))
sys.stderr.write(str(exc))
return files
async def make_save_resources_list(archive_file, container):
""" """
tmp_dir = tempfile.mkdtemp()
with zipfile.ZipFile(archive_file, "r") as zip_ref:
zip_ref.extractall(tmp_dir)
for root, dirs, files in os.walk(tmp_dir):
for filename in files:
if not filename.endswith(".schema.json"):
continue
with open(os.path.join(root, filename), "r") as f:
content = json.load(f)
if content.get("id", None) is None:
continue
resource_name = content["id"].split("/")[-1]
assert filename.split(".")[0] == resource_name
container["resources"][resource_name.lower()] = {
"name": resource_name,
"url": content["id"] + ".schema.json",
}
container["meta"]["lastUpdated"] = datetime.datetime.now().isoformat("T")
# write to disk
global RESOURCES_DIR
global VERSION
if not RESOURCES_DIR.exists():
RESOURCES_DIR.mkdir()
target = RESOURCES_DIR / "{0}.json".format(VERSION)
with open(str(target), "w") as f:
json.dump(container, f, indent=4, sort_keys=True)
sys.stdout.write("==> file {0} has been created\n".format(target))
shutil.rmtree(tmp_dir)
@cmd
async def main(destination_dir, output_stream, offline, verbosity_level):
""" """
# try:
# response = requests.get(RESOURCE_URL)
# except requests.RequestException as e:
# raise e
global BASE_URL
global VERSION
global FHIR_DEFINITION
global FHIR_EXAMPLE
global FHIR_SCHEMAS
archived_files = (
"/".join([BASE_URL, VERSION, FHIR_DEFINITION]),
"/".join([BASE_URL, VERSION, FHIR_EXAMPLE]),
"/".join([BASE_URL, VERSION, FHIR_SCHEMAS]),
)
async with aiohttp.ClientSession() as session:
results = await download_archieves(archived_files, session, offline)
for url, location in results:
if FHIR_SCHEMAS in url:
container = dict(
meta=dict(profile=url, versionId=VERSION), resources=dict()
)
await make_save_resources_list(location, container)