diff options
| -rw-r--r-- | gn3/csvcmp.py | 7 | ||||
| -rw-r--r-- | gn3/db/sample_data.py | 5 | ||||
| -rw-r--r-- | tests/unit/test_csvcmp.py | 8 |
3 files changed, 18 insertions, 2 deletions
diff --git a/gn3/csvcmp.py b/gn3/csvcmp.py index ebd323e..360a101 100644 --- a/gn3/csvcmp.py +++ b/gn3/csvcmp.py @@ -4,6 +4,13 @@ import uuid from gn3.commands import run_cmd +def extract_strain_name(csv_header, data, seek="Strain Name"): + for column, value in zip(csv_header.split(","), data.split(",")): + if seek in column: + return value + return "" + + def create_dirs_if_not_exists(dirs: list): for dir_ in dirs: if not os.path.exists(dir_): diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py index 06b5767..a410978 100644 --- a/gn3/db/sample_data.py +++ b/gn3/db/sample_data.py @@ -1,3 +1,4 @@ +from gn3.csvcmp import extract_strain_name from typing import Any, Tuple, Union import MySQLdb @@ -200,7 +201,7 @@ def delete_sample_data(conn: Any, strain_id, data_id, inbredset_id = get_sample_data_ids( conn=conn, publishxref_id=trait_name, phenotype_id=phenotype_id, - strain_name=strain_name) + strain_name=extract_strain_name(csv_header, data)) none_case_attrs = { "Strain Name": lambda: 0, @@ -273,7 +274,7 @@ def insert_sample_data(conn: Any, # pylint: disable=[R0913] strain_id, data_id, inbredset_id = get_sample_data_ids( conn=conn, publishxref_id=trait_name, phenotype_id=phenotype_id, - strain_name=strain_name) + strain_name=extract_strain_name(csv_header, data)) none_case_attrs = { "Strain Name": lambda _: 0, diff --git a/tests/unit/test_csvcmp.py b/tests/unit/test_csvcmp.py index 4a96f99..fd7aa28 100644 --- a/tests/unit/test_csvcmp.py +++ b/tests/unit/test_csvcmp.py @@ -1,6 +1,7 @@ from gn3.csvcmp import csv_diff from gn3.csvcmp import fill_csv from gn3.csvcmp import remove_insignificant_edits +from gn3.csvcmp import extract_strain_name import pytest @@ -99,3 +100,10 @@ BXD15,14,x,x 'Additions': [], 'Deletions': [], 'Modifications': []}) + + +@pytest.mark.unit_test +def test_extract_strain_name(): + assert(extract_strain_name(csv_header="Strain Name,Value,SE,Count", + data="BXD1,18,x,0") == + "BXD1") |