Merge pull request #3489 from broadinstitute/write-pedigree-family-guid

add family guid to write pedigree
broadinstitute · Jul 14, 2023 · 8a7d768 · 8a7d768
2 parents 3430f1d + 57f50ce
commit 8a7d768
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/seqr/views/apis/data_manager_api.py b/seqr/views/apis/data_manager_api.py
@@ -400,7 +400,7 @@ def write_pedigree(request, project_guid):
         )
 
     annotations = OrderedDict({
-        'Project_GUID': Value(project.guid), 'Family_ID': F('family__family_id'), 'Individual_ID': F('individual_id'),
+        'Project_GUID': Value(project.guid), 'Family_GUID': F('family__guid'), 'Family_ID': F('family__family_id'), 'Individual_ID': F('individual_id'),
         'Paternal_ID': F('father__individual_id'), 'Maternal_ID': F('mother__individual_id'), 'Sex': F('sex'),
     })
     data = Individual.objects.filter(family__project=project).order_by('family_id', 'individual_id').values(**dict(annotations))

diff --git a/seqr/views/apis/data_manager_api_tests.py b/seqr/views/apis/data_manager_api_tests.py
@@ -1175,11 +1175,11 @@ def test_write_pedigree(self, mock_subprocess, mock_temp_dir, mock_open):
         file = [row.split('\t') for row in write_call.split('\n')]
         self.assertEqual(len(file), 15)
         self.assertListEqual(file[:5], [
-            ['Project_GUID', 'Family_ID', 'Individual_ID', 'Paternal_ID', 'Maternal_ID', 'Sex'],
-            ['R0001_1kg', '1', 'NA19675_1', 'NA19678', 'NA19679', 'M'],
-            ['R0001_1kg', '1', 'NA19678', '', '', 'M'],
-            ['R0001_1kg', '1', 'NA19679', '', '', 'F'],
-            ['R0001_1kg', '2', 'HG00731', 'HG00732', 'HG00733', 'F'],
+            ['Project_GUID', 'Family_GUID', 'Family_ID', 'Individual_ID', 'Paternal_ID', 'Maternal_ID', 'Sex'],
+            ['R0001_1kg', 'F000001_1', '1', 'NA19675_1', 'NA19678', 'NA19679', 'M'],
+            ['R0001_1kg', 'F000001_1', '1', 'NA19678', '', '', 'M'],
+            ['R0001_1kg', 'F000001_1', '1', 'NA19679', '', '', 'F'],
+            ['R0001_1kg', 'F000002_2', '2', 'HG00731', 'HG00732', 'HG00733', 'F'],
          ])
 
         mock_subprocess.assert_has_calls(