def test_post_bundle_condition():
try:
resp1 = requests.post(f"{php}/Bundle",
json=bundle([condition_resc, condition_resc2]))
assert resp1.status_code == 200
resp2 = requests.get(f"{php}/Condition?patient={patient_id}")
assert resp2.status_code == 200
assert resp2.json() == bundle([condition_resc])
finally:
requests.delete(f"{php}/resource")
def get_resource(resource_type, patient_id):
coll = mongo_client[mongo_database][resource_type]
res = coll.find({"subject.reference": f"Patient/{patient_id}"})
records = list(res)
for resc in records:
del resc["_id"]
return bundle(records)
def test_post_observation():
try:
resp1 = requests.post(f"{php}/Observation", json=observation_resc)
assert resp1.status_code == 200
resp2 = requests.get(f"{php}/Observation?patient={patient_id}")
assert resp2.status_code == 200
assert resp2.json() == bundle([observation_resc])
finally:
requests.delete(f"{php}/resource")
def test_post_bundle_patient():
try:
resp1 = requests.post(f"{php}/Bundle",
json=bundle([patient_resc, patient_resc2]))
assert resp1.status_code == 200
resp2 = requests.get(f"{php}/Patient/{patient_id}")
assert resp2.status_code == 200
assert resp2.json() == patient_resc
finally:
requests.delete(f"{php}/resource")
def _get_records(ptids, fhir_plugin_id, timestamp):
pt_records = []
for ptid in ptids:
url_patient = f"{pds_url_base}/{fhir_plugin_id}/Patient/{ptid}"
url_condition = f"{pds_url_base}/{fhir_plugin_id}/Condition?patient={ptid}"
url_observation = f"{pds_url_base}/{fhir_plugin_id}/Observation?patient={ptid}"
val = get(url_patient).bind(lambda patient: get(url_condition).bind(
lambda condition: get(url_observation).
bind(lambda observation: unbundle(condition).bind(
lambda condition_unbundled: unbundle(observation).map(
lambda observation_unbundled: bundle([
patient, *condition_unbundled, *observation_unbundled
]))))))
pt_records.append(val)
return list_traversable_either_applicative.sequence(pt_records)
def handle_requests(requests):
rescs = []
for request in requests:
method = request["method"]
url = request["url"]
result = urlsplit(url)
pcs = result.path.split("/")
qcs = map(lambda x: x.split("="), result.query.split("&"))
if pcs[1] == "Patient":
rescs.append(_get_patient(pcs[2]))
else:
patient_id = None
for qc in qcs:
if qc[0] == "patient":
patient_id = qc[1]
rescs.append(_get_resource(pcs[1], patient_id))
return Right(bundle(rescs, "batch-response"))
def post_resources(resc_types, patient_ids):
patients = []
for patient_id in patient_ids:
requests = []
for resc_type in resc_types:
if resc_type == "Patient":
requests.append({
"url": f"/Patient/{patient_id}",
"method": "GET"
})
else:
requests.append({
"url": f"/{resc_type}?patient={patient_id}",
"method": "GET"
})
batch = bundle(requests, "batch")
patient = _post_batch(batch).value
patients.append(patient)
return patients
def get_patient_resource_entry_array(json_in_dir, pid: str, resource_name):
resource_path = os.path.join(os.path.join(json_in_dir, resource_name))
rescs_filtered = []
if os.path.isdir(resource_path):
for root, _, files in os.walk(resource_path):
for f in files:
pid_fn = os.path.join(root, f)
logger.info(f"looking into {pid_fn}")
with open(pid_fn, encoding='latin-1') as pid_fp:
rescs = unbundle(json.load(pid_fp)).value
logger.info(f"rescs = {rescs}")
if resource_name == "Patient":
rescs_filtered.extend(
filter(lambda x: x["id"] == pid, rescs))
else:
patient_reference = f"Patient/{pid}"
rescs_filtered.extend(
filter(
lambda x: x["subject"]["reference"] ==
patient_reference, rescs))
return bundle(rescs_filtered)
def handle_path(path):
logger = getLogger(f"{__name__}{os.getpid()}", logging.INFO)
logger.info(f"loading {path}")
if not dry_run:
try:
with open(path) as input_stream:
obj = json.load(input_stream)
except:
with open(path, encoding="latin-1") as input_stream:
obj = json.load(input_stream)
rescs = unbundle(obj).value
nrescs = len(rescs)
logger.info(f"{nrescs} resources loaded")
maxlen = 1024
for i in range(0, nrescs, maxlen):
subrescs = rescs[i:min(i + maxlen, nrescs)]
subobj = bundle(subrescs)
logger.info(f"ingesting {path} {i}")
requests.post(f"{base_url}/Bundle", json=subobj)
else:
logger.info(f"post {base_url}/Bundle")
def _get_records(ptid, fhir_plugin_id, timestamp):
url_patient = f"{pds_url_base}/{fhir_plugin_id}/Patient/{ptid}"
url_condition = f"{pds_url_base}/{fhir_plugin_id}/Condition?patient={ptid}"
url_observation = f"{pds_url_base}/{fhir_plugin_id}/Observation?patient={ptid}"
return get(url_patient).bind(lambda patient: get(url_condition).bind(lambda condition: get(url_observation).bind(lambda observation: unbundle(condition).bind(lambda condition_unbundled: unbundle(observation).map(lambda observation_unbundled: bundle([
patient,
*condition_unbundled,
*observation_unbundled
]))))))
