def test_post_resources():
try:
resp1 = requests.post(f"{php}/Patient", json=patient_resc)
resp1 = requests.post(f"{php}/Patient", json=patient_resc2)
resp1 = requests.post(f"{php}/Observation", json=observation_resc)
resp1 = requests.post(f"{php}/Observation", json=observation_resc2)
resp1 = requests.post(f"{php}/Condition", json=condition_resc)
resp1 = requests.post(f"{php}/Condition", json=condition_resc2)
resp1 = requests.post(f"{php}/MedicationRequest",
json=medication_request_resc)
resp1 = requests.post(f"{php}/MedicationRequest",
json=medication_request_resc2)
resp1 = requests.post(
f"{php}/resource",
json={
"resourceTypes":
["Patient", "Observation", "Condition", "MedicationRequest"],
"patientIds": [patient_id, patient_id2]
})
assert resp1.status_code == 200
patients = resp1.json()
assert len(patients) == 2
for patient in patients:
assert patient["resourceType"] == "Bundle"
assert patient["type"] == "batch-response"
assert set(
map(lambda x: x["resourceType"],
unbundle(patient).value)) == {"Patient", "Bundle"}
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 update_resource(resc_type, patient_id, bundle):
coll = mongo_client[mongo_database][resc_type]
res = coll.delete_many({"subject.reference": f"Patient/{patient_id}"})
logger.debug(
f"bundle={bundle}, copy.deepcopy(bundle)={copy.deepcopy(bundle)}")
records = unbundle(copy.deepcopy(bundle)).value
if len(records) > 0:
coll.insert_many(records)
def post_bundle(bundle):
rescs = unbundle(bundle).value
x = {}
for resc in rescs:
resc_type = resc["resourceType"]
if resc_type in x:
x[resc_type].append(resc)
else:
x[resc_type] = [resc]
for coll, rescs in x.items():
post_resources(coll, rescs)
def get_condition_icd_code(patient_id, fhir):
records = unbundle(fhir[patient_id]['Condition']).value
icd_codes = []
icd_10_url = 'http://hl7.org/fhir/sid/icd-10-cm'
icd_9_url = 'http://hl7.org/fhir/sid/icd-9-cm'
for rec in records:
codes = rec.get('code', {}).get('coding', [])
for code in codes:
icd_system = code.get('system', '')
if icd_system == icd_10_url or icd_system == icd_9_url:
icd_codes.append({
'system': icd_system,
'code': code.get('code', '')
})
return icd_codes
def test_post_resources_output_to_file():
try:
resp1 = requests.post(f"{php}/Patient", json=patient_resc)
resp1 = requests.post(f"{php}/Patient", json=patient_resc2)
resp1 = requests.post(f"{php}/Observation", json=observation_resc)
resp1 = requests.post(f"{php}/Observation", json=observation_resc2)
resp1 = requests.post(f"{php}/Condition", json=condition_resc)
resp1 = requests.post(f"{php}/Condition", json=condition_resc2)
resp1 = requests.post(f"{php}/MedicationRequest",
json=medication_request_resc)
resp1 = requests.post(f"{php}/MedicationRequest",
json=medication_request_resc2)
files = [patient_id, patient_id2]
resp = requests.post(
f"{php}/resource",
json={
"resourceTypes":
["Patient", "Observation", "Condition", "MedicationRequest"],
"patientIds":
files,
"outputFile":
"outputname"
})
assert resp.status_code == 200
assert "$ref" in resp.json()
name = resp.json()["$ref"]
patients = []
for f in files:
with open(
os.path.join(os.environ.get("OUTPUT_DIR"), name,
f + ".json")) as out:
patients.append(json.load(out))
assert len(patients) == 2
for patient in patients:
assert patient["resourceType"] == "Bundle"
assert patient["type"] == "batch-response"
assert set(
map(lambda x: x["resourceType"],
unbundle(patient).value)) == {"Patient", "Bundle"}
finally:
requests.delete(f"{php}/resource")
def _post_batch(batch):
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"))
return unbundle(batch).bind(handle_requests)
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_patient(patient_id, fhir):
return unbundle(fhir[patient_id]["Patient"]).bind(one)
def get_medication_request(patient_id, fhir):
return unbundle(fhir[patient_id]["MedicationRequest"])
def get_condition(patient_id, fhir):
return unbundle(fhir[patient_id]["Condition"])
def get_observation(patient_id, fhir):
return unbundle(fhir[patient_id]["Observation"])
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
]))))))
def get_patient(patient_id, fhir):
records = unbundle(fhir)
return records.bind(lambda xs: one(
list(filter(lambda x: x["resourceType"] == "Patient", xs))))
def get_condition(patient_id, fhir):
records = unbundle(fhir)
return records.map(lambda xs: list(
filter(lambda x: x["resourceType"] == "Condition", xs)))
