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authorBonfaceKilz2022-04-12 12:07:13 +0300
committerBonfaceKilz2022-04-12 13:26:57 +0300
commitca8a18f00b06a7c6ca4b022223f381ddaebbf930 (patch)
tree1ce666d38009e739e60005c1f8430235f8aaca29 /tests/unit
parent48cc775e5cbcb9cf8e97b966c86527c5344fa6ea (diff)
downloadgenenetwork3-ca8a18f00b06a7c6ca4b022223f381ddaebbf930.tar.gz
Test that a carriage return is removed when generating csv
* tests/unit/db/test_sample_data.py: import "get_trait_csv_sample_data". (test_get_trait_csv_sample_data): New test function.
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/db/test_sample_data.py53
1 files changed, 53 insertions, 0 deletions
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index f631239..0fc20f4 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -7,6 +7,7 @@ from gn3.db.sample_data import delete_sample_data
from gn3.db.sample_data import get_case_attributes
from gn3.db.sample_data import insert_sample_data
from gn3.db.sample_data import update_sample_data
+from gn3.db.sample_data import get_trait_csv_sample_data
@pytest.mark.unit_test
@@ -245,3 +246,55 @@ def test_get_case_attributes(mocker):
"Condition (4)": "Description A",
"Condition (5)": "Description B",
}
+
+
+@pytest.mark.unit_test
+def test_get_trait_csv_sample_data(mocker):
+ """Test fetching trait sample data"""
+ mock_conn = mocker.MagicMock()
+ with mock_conn.cursor() as cursor:
+ cursor.fetchall.return_value = [
+ ["JL00005,896.000000,x,x", "Age", "896"],
+ ["JL00005,896.000000,x,x", "DOB", "4/22/04"],
+ ["JL00005,896.000000,x,x", "Date Geno", "x"],
+ ["JL00005,896.000000,x,x", "Drug/Site", "4OHPBN_J"],
+ ["JL00005,896.000000,x,x", "MOD", "Oct"],
+ ["JL00005,896.000000,x,x", "Platform", "x"],
+ [
+ "JL00005,896.000000,x,x",
+ "SNP",
+ """0
+""",
+ ],
+ ["JL00005,896.000000,x,x", "Sex", "M"],
+ ["JL00005,896.000000,x,x", "Site", "JL"],
+ ["JL00005,896.000000,x,x", "Tx", "1"],
+ ["JL00005,896.000000,x,x", "Year", "2004"],
+ ["JL00058,686.000000,x,x", "Age", "686"],
+ ["JL00058,686.000000,x,x", "DOB", "4/22/04"],
+ ["JL00058,686.000000,x,x", "Date Geno", "2017.06"],
+ ["JL00058,686.000000,x,x", "Drug/Site", "Cont_04_J"],
+ ["JL00058,686.000000,x,x", "MOD", "Mar"],
+ ["JL00058,686.000000,x,x", "Platform", "M"],
+ [
+ "JL00058,686.000000,x,x",
+ "SNP",
+ """2
+""",
+ ],
+ ["JL00058,686.000000,x,x", "Sex", "M"],
+ ["JL00058,686.000000,x,x", "Site", "JL"],
+ ["JL00058,686.000000,x,x", "Tx", "0"],
+ ["JL00058,686.000000,x,x", "Year", "2004"],
+ ]
+ assert get_trait_csv_sample_data(
+ conn=mock_conn, trait_name=10007, phenotype_id=35
+ ) == (
+ "Strain Name,Value,SE,Count,Age,DOB,"
+ "Date Geno,Drug/Site,MOD,"
+ "Platform,SNP,Sex,Site,Tx,Year\n"
+ "JL00005,896.000000,x,x,"
+ "896,4/22/04,x,4OHPBN_J,Oct,x,0,M,JL,1,2004\n"
+ "JL00058,686.000000,x,x,"
+ "686,4/22/04,2017.06,Cont_04_J,Mar,M,2,M,JL,0,2004\n"
+ )