from __future__ import annotations
import datetime
import meds
from femr.transforms import delta_encode, remove_nones
from femr.transforms.stanford import (
move_billing_codes,
move_pre_birth,
move_to_day_end,
move_visit_start_to_first_event_start,
)
def cleanup(patient):
for event in patient["events"]:
for measurement in event["measurements"]:
if "metadata" not in measurement:
measurement["metadata"] = {}
for k in ("numeric_value", "text_value", "datetime_value"):
if k not in measurement:
measurement[k] = None
if "table" not in measurement["metadata"]:
measurement["metadata"]["table"] = None
def test_pre_birth() -> None:
patient = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": meds.birth_code}]},
{"time": datetime.datetime(1999, 7, 11), "measurements": [{"code": 12345}]},
],
}
expected = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": meds.birth_code}]},
{"time": datetime.datetime(1999, 7, 11), "measurements": [{"code": 12345}]},
],
}
cleanup(patient)
cleanup(expected)
assert move_pre_birth(patient) == expected
def test_move_visit_start_ignores_other_visits() -> None:
patient = {
"patient_id": 123,
"events": [
{ # A non-visit event with no explicit start time
"time": datetime.datetime(1999, 7, 2),
"measurements": [{"code": 1234, "metadata": {"visit_id": 9999}}],
},
{ # A visit event with just date specified
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{
"code": 4567,
"metadata": {
"table": "visit",
"visit_id": 9999,
},
}
],
},
{ # A non-visit event from a separate visit ID
"time": datetime.datetime(1999, 7, 2, 11),
"measurements": [{"code": 2345, "metadata": {"visit_id": 8888}}],
},
{ # First recorded non-visit event for visit ID 9999
"time": datetime.datetime(1999, 7, 2, 12),
"measurements": [{"code": 3456, "metadata": {"visit_id": 9999}}],
},
],
}
# Note that events are implicitly sorted first by start time, then by code:
# https://github.com/som-shahlab/femr/blob/main/src/femr/__init__.py#L69
expected = {
"patient_id": 123,
"events": [
{ # A non-visit event with no explicit start time
"time": datetime.datetime(1999, 7, 2),
"measurements": [{"code": 1234, "metadata": {"visit_id": 9999}}],
},
{ # A non-visit event from a separate visit ID
"time": datetime.datetime(1999, 7, 2, 11),
"measurements": [{"code": 2345, "metadata": {"visit_id": 8888}}],
},
{ # Now visit event has date and time specified
"time": datetime.datetime(1999, 7, 2, 12),
"measurements": [
{
"code": 4567,
"metadata": {
"table": "visit",
"visit_id": 9999,
},
}
],
},
{ # First recorded non-visit event for visit ID 9999
"time": datetime.datetime(1999, 7, 2, 12),
"measurements": [{"code": 3456, "metadata": {"visit_id": 9999}}],
},
],
}
cleanup(patient)
cleanup(expected)
assert move_visit_start_to_first_event_start(patient) == expected
def test_move_visit_start_minute_after_midnight() -> None:
patient = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{"code": 3456, "metadata": {"visit_id": 9999, "table": "visit"}},
{"code": 1234, "metadata": {"visit_id": 9999}},
],
},
{
"time": datetime.datetime(1999, 7, 2, 0, 1),
"measurements": [{"code": 2345, "metadata": {"visit_id": 9999}}],
},
{
"time": datetime.datetime(1999, 7, 2, 12),
"measurements": [{"code": 4567, "metadata": {"visit_id": 9999}}],
},
],
}
expected = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [{"code": 1234, "metadata": {"visit_id": 9999}}],
},
{
"time": datetime.datetime(1999, 7, 2, 0, 1),
"measurements": [{"code": 3456, "metadata": {"visit_id": 9999, "table": "visit"}}],
},
{
"time": datetime.datetime(1999, 7, 2, 0, 1),
"measurements": [{"code": 2345, "metadata": {"visit_id": 9999}}],
},
{
"time": datetime.datetime(1999, 7, 2, 12),
"measurements": [{"code": 4567, "metadata": {"visit_id": 9999}}],
},
],
}
cleanup(patient)
cleanup(expected)
assert move_visit_start_to_first_event_start(patient) == expected
def test_move_visit_start_doesnt_move_without_event() -> None:
patient = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{"code": 1234, "metadata": {"visit_id": 9999}},
{"code": 3456, "metadata": {"visit_id": 9999, "table": "visit"}},
{"code": 2345, "metadata": {"visit_id": 9999}},
],
},
],
}
# None of the non-visit events have start time > '00:00:00' so visit event
# start time is unchanged, though order changes based on code under resort.
expected = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{"code": 1234, "metadata": {"visit_id": 9999}},
{"code": 3456, "metadata": {"visit_id": 9999, "table": "visit"}},
{"code": 2345, "metadata": {"visit_id": 9999}},
],
}
],
}
cleanup(patient)
cleanup(expected)
assert move_visit_start_to_first_event_start(patient) == expected
def test_move_to_day_end() -> None:
patient = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 4321}]},
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": meds.birth_code}]},
],
}
expected = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 4321}]},
{"time": datetime.datetime(1999, 7, 2, 23, 59), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 9, 23, 59), "measurements": [{"code": meds.birth_code}]},
],
}
cleanup(patient)
cleanup(expected)
print(move_to_day_end(patient))
print(expected)
assert move_to_day_end(patient) == expected
def test_remove_nones() -> None:
patient = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]}, # No value, to be removed
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 1234, "numeric_value": 3}]},
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": meds.birth_code}]},
],
}
expected = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 1234, "numeric_value": 3}]},
{"time": datetime.datetime(1999, 7, 9), "measurements": [{"code": meds.birth_code}]},
],
}
cleanup(patient)
cleanup(expected)
assert remove_nones(patient) == expected
def test_delta_encode() -> None:
patient = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 1234, "numeric_value": 3}]},
{"time": datetime.datetime(1999, 7, 2, 14), "measurements": [{"code": 1234, "numeric_value": 3}]},
{"time": datetime.datetime(1999, 7, 2, 19), "measurements": [{"code": 1234, "numeric_value": 5}]},
{"time": datetime.datetime(1999, 7, 2, 20), "measurements": [{"code": 1234, "numeric_value": 3}]},
],
}
expected = {
"patient_id": 123,
"events": [
{"time": datetime.datetime(1999, 7, 2), "measurements": [{"code": 1234}]},
{"time": datetime.datetime(1999, 7, 2, 12), "measurements": [{"code": 1234, "numeric_value": 3}]},
{"time": datetime.datetime(1999, 7, 2, 19), "measurements": [{"code": 1234, "numeric_value": 5}]},
{"time": datetime.datetime(1999, 7, 2, 20), "measurements": [{"code": 1234, "numeric_value": 3}]},
],
}
cleanup(patient)
cleanup(expected)
assert delta_encode(patient) == expected
def test_move_billing_codes() -> None:
patient = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{
"code": 1234,
"metadata": {
"end": datetime.datetime(1999, 7, 20),
"visit_id": 10,
"clarity_table": "lpch_pat_enc",
},
}
],
},
{
"time": datetime.datetime(1999, 7, 9),
"measurements": [
{
"code": meds.birth_code,
"metadata": {
"visit_id": 10,
"clarity_table": "lpch_pat_enc_dx",
},
}
],
},
{
"time": datetime.datetime(1999, 7, 10),
"measurements": [
{
"code": 42165,
"metadata": {
"visit_id": 10,
"clarity_table": "shc_pat_enc_dx",
},
}
],
},
{
"time": datetime.datetime(1999, 7, 11),
"measurements": [
{
"code": 12345,
"metadata": {
"visit_id": 10,
},
}
],
},
{
"time": datetime.datetime(1999, 7, 13),
"measurements": [
{
"code": 123,
"metadata": {
"visit_id": 11,
},
}
],
},
],
}
expected = {
"patient_id": 123,
"events": [
{
"time": datetime.datetime(1999, 7, 2),
"measurements": [
{
"code": 1234,
"metadata": {
"end": datetime.datetime(1999, 7, 20),
"visit_id": 10,
"clarity_table": "lpch_pat_enc",
},
}
],
},
{
"time": datetime.datetime(1999, 7, 11),
"measurements": [
{
"code": 12345,
"metadata": {
"visit_id": 10,
},
}
],
},
{
"time": datetime.datetime(1999, 7, 13),
"measurements": [
{
"code": 123,
"metadata": {
"visit_id": 11,
},
}
],
},
{
"time": datetime.datetime(1999, 7, 20),
"measurements": [
{
"code": meds.birth_code,
"metadata": {
"visit_id": 10,
"clarity_table": "lpch_pat_enc_dx",
},
}
],
},
{
"time": datetime.datetime(1999, 7, 20),
"measurements": [
{
"code": 42165,
"metadata": {
"visit_id": 10,
"clarity_table": "shc_pat_enc_dx",
},
}
],
},
],
}
cleanup(patient)
cleanup(expected)
print(move_billing_codes(patient))
print(expected)
assert move_billing_codes(patient) == expected
