add env mock

Author: bpblanken

v03_pipeline/lib/tasks/write_remapped_and_subsetted_callset_test.py

@@ -1,4 +1,5 @@
 import shutil
+from unittest.mock import Mock, patch
 
 import hail as hl
 import luigi.worker
@@ -83,7 +84,6 @@ def test_write_remapped_and_subsetted_callset_task(
             project_remap_path=TEST_REMAP,
             project_pedigree_path=TEST_PEDIGREE_3,
             skip_validation=True,
-            skip_check_sex_and_relatedness=False,
         )
         worker.add(wrsc_task)
         worker.run()
@@ -104,9 +104,12 @@ def test_write_remapped_and_subsetted_callset_task(
             ],
         )
 
+    @patch('v03_pipeline.lib.tasks.write_remapped_and_subsetted_callset.Env')
     def test_write_remapped_and_subsetted_callset_task_failed_sex_check_family(
         self,
+        mock_env: Mock,
     ) -> None:
+        mock_env.CHECK_SEX_AND_RELATEDNESS = True
         worker = luigi.worker.Worker()
         wrsc_task = WriteRemappedAndSubsettedCallsetTask(
             reference_genome=ReferenceGenome.GRCh38,
@@ -117,7 +120,6 @@ def test_write_remapped_and_subsetted_callset_task_failed_sex_check_family(
             project_remap_path=TEST_REMAP,
             project_pedigree_path=TEST_PEDIGREE_4,
             skip_validation=True,
-            skip_check_sex_and_relatedness=False,
         )
         worker.add(wrsc_task)
         worker.run()