def _make_index_item(resource_type):
""" """
now_time = datetime.datetime.now()
now_time.replace(tzinfo=pytz.UTC)
tpl = {
"access_scopes": [
"patient/*.*",
f"patient/{resource_type}.*",
f"patient/{resource_type}.read",
f"patient/{resource_type}.write",
"user/*.*",
f"user/{resource_type}.*",
f"user/{resource_type}.read",
f"user/{resource_type}.write",
],
"access_users": ["root"],
}
with open(str(FHIR_EXAMPLE_RESOURCES / (resource_type + ".json")),
"rb") as fp:
data = json_loads(fp.read())
tpl[resource_type] = data
tpl["uid"] = uuid.uuid4().hex
return tpl
async def add_elasticsearch_doc(
es_engine: ElasticsearchEngine,
record: typing.Dict[str, typing.Any],
create: bool = True,
):
""" """
index_name = es_engine.get_index_name()
doc_type = es_engine.get_doc_type()
conn = es_engine.connection.raw_connection
resource_type = record["resource_type"]
if create is False:
await conn.delete(index=index_name, id=record["es_id"], doc_type=doc_type)
body = {
es_engine.calculate_field_index_name(resource_type): json_loads(
record["resource"]
),
"access_scopes": [
"patient/*.*",
f"patient/{resource_type}.*",
f"patient/{resource_type}.read",
f"patient/{resource_type}.write",
"user/*.*",
f"user/{resource_type}.*",
f"user/{resource_type}.read",
f"user/{resource_type}.write",
],
"access_users": ["root"],
}
await conn.create(
index=index_name, id=record["es_id"], body=body, doc_type=doc_type, refresh=True
)
def json_body(request):
try:
data = json_loads(request.get("BODY") or b"{}")
except ValueError:
raise DeserializationError("No JSON object could be decoded")
if not isinstance(data, dict):
raise DeserializationError("Malformed body")
return data
def get_elasticsearch_mapping(resource,
fhir_release="R4",
mapping_dir=None,
cache=True):
"""Elastic search mapping for FHIR resources"""
fhir_release = FHIR_VERSION[fhir_release].name
if mapping_dir is None:
mapping_dir = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"browser",
"static",
"ES_MAPPINGS",
fhir_release,
)
storage = FHIR_ES_MAPPINGS_CACHE.get(fhir_release)
if resource not in storage or cache is False:
file_location = None
expected_filename = "{0}.mapping.json".format(resource)
for root, dirs, files in os.walk(mapping_dir, topdown=True):
for filename in files:
if filename == expected_filename:
file_location = os.path.join(root, filename)
break
if file_location is None:
raise LookupError("Mapping files {0}/{1} doesn't exists.".format(
mapping_dir, expected_filename))
with open(os.path.join(root, file_location), "rb") as f:
content = json_loads(f.read())
assert filename.split(".")[0] == content["resourceType"]
storage[resource] = content
return storage[resource]["mapping"]
def loads(self, s):
try:
return json_loads(s)
except (ValueError, TypeError) as e:
raise SerializationError(s, e)