From 41b0356dc5dd3b7ec6a412bab4f637e317ccd4b7 Mon Sep 17 00:00:00 2001
From: danlu1 <dan.lu@sagebase.org>
Date: Tue, 23 Apr 2024 02:12:35 +0000
Subject: [PATCH] add unit tests
---
tests/test_clinical.py | 59 +++++++++++++++++++++++++++++++++++++++---
1 file changed, 55 insertions(+), 4 deletions(-)
diff --git a/tests/test_clinical.py b/tests/test_clinical.py
index 91815c97..fead33dd 100644
--- a/tests/test_clinical.py
+++ b/tests/test_clinical.py
@@ -1,14 +1,13 @@
-from collections import Counter
import datetime
import json
+from collections import Counter
from unittest import mock
+import genie_registry
import pandas as pd
import pytest
import synapseclient
-
from genie import process_functions, validate
-import genie_registry
from genie_registry.clinical import Clinical
@@ -662,7 +661,6 @@ def test_errors__validate(clin_class):
) as mock_get_onco_map:
error, warning = clin_class._validate(clinicalDf)
mock_get_onco_map.called_once_with(json_oncotreeurl)
-
expectedErrors = (
"Sample Clinical File: SAMPLE_ID must start with GENIE-SAGE\n"
"Patient Clinical File: PATIENT_ID must start with GENIE-SAGE\n"
@@ -700,6 +698,8 @@ def test_errors__validate(clin_class):
"Patient Clinical File: Please double check your YEAR_CONTACT "
"column, it must be an integer in YYYY format <= {year} or "
"'Unknown', 'Not Collected', 'Not Released', '>89', '<18'.\n"
+ "Patient Clinical File: Please double check your YEAR_DEATH "
+ "and YEAR_CONTACT columns. YEAR_DEATH must be >= YEAR_CONTACT.\n"
"Patient Clinical File: Please double check your INT_CONTACT "
"column, it must be an integer, '>32485', '<6570', 'Unknown', "
"'Not Released' or 'Not Collected'.\n"
@@ -1062,6 +1062,57 @@ def test__check_int_dead_consistency_inconsistent(inconsistent_df):
)
+@pytest.mark.parametrize(
+ "df,expected_error",
+ [
+ (
+ pd.DataFrame({"YEAR_DEATH": [420, 555, 390], "YEAR_CONTACT": [50, 40, 22]}),
+ "",
+ ),
+ (
+ pd.DataFrame(
+ {
+ "YEAR_DEATH": [420, float("nan"), 390],
+ "YEAR_CONTACT": [50, 40, float("nan")],
+ }
+ ),
+ "",
+ ),
+ (
+ pd.DataFrame(
+ {
+ "YEAR_DEATH": [float("nan"), float("nan"), 390],
+ "YEAR_CONTACT": [50, 40, float("nan")],
+ }
+ ),
+ "",
+ ),
+ (
+ pd.DataFrame(
+ {"YEAR_DEATH": [420, 666, 390], "YEAR_CONTACT": [50, 40, 555]}
+ ),
+ "Patient Clinical File: Please double check your YEAR_DEATH and YEAR_CONTACT columns. YEAR_DEATH must be >= YEAR_CONTACT.\n",
+ ),
+ (
+ pd.DataFrame(
+ {"YEAR_DEATH": [420, float("nan"), 390], "YEAR_CONTACT": [50, 40, 555]}
+ ),
+ "Patient Clinical File: Please double check your YEAR_DEATH and YEAR_CONTACT columns. YEAR_DEATH must be >= YEAR_CONTACT.\n",
+ ),
+ ],
+ ids=[
+ "valid_dataframe_no_NAs",
+ "valid_dataframe_w_NAs",
+ "valid_dataframe_all_NAs",
+ "invalid_dataframe_no_NAs",
+ "invalid_dataframe_w_NAs",
+ ],
+)
+def test__check_year_death_validity(df, expected_error):
+ error = genie_registry.clinical._check_year_death_validity(clinicaldf=df)
+ assert error == expected_error
+
+
def get_cross_validate_bed_files_test_cases():
return [
{