test fixture update - family and individual IDs from Metamist Pedigre…

…e are always Strings
populationgenomics · Oct 28, 2024 · 4c1375c · 4c1375c
1 parent e81db47
commit 4c1375c
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Showing 2 changed files with 6 additions and 8 deletions.
diff --git a/cpg_workflows/inputs.py b/cpg_workflows/inputs.py
@@ -281,7 +281,7 @@ def populate_pedigree(dataset: Dataset) -> None:
     Populate pedigree data for sequencing groups.
     """
 
-    sg_by_participant_id = dict()
+    sg_by_participant_id = {}
     for sg in dataset.get_sequencing_groups():
         sg_by_participant_id[sg.participant_id] = sg
 
@@ -299,13 +299,11 @@ def populate_pedigree(dataset: Dataset) -> None:
             continue
 
         ped_entry = ped_entry_by_participant_id[sequencing_group.participant_id]
-        maternal_sg = sg_by_participant_id.get(ped_entry['maternal_id'])
-        paternal_sg = sg_by_participant_id.get(ped_entry['paternal_id'])
         sequencing_group.pedigree = PedigreeInfo(
             sequencing_group=sequencing_group,
             fam_id=ped_entry['family_id'],
-            mom=maternal_sg,
-            dad=paternal_sg,
+            mom=sg_by_participant_id.get(ped_entry['maternal_id']),
+            dad=sg_by_participant_id.get(ped_entry['paternal_id']),
             sex=Sex.parse(str(ped_entry['sex'])),
             phenotype=ped_entry['affected'] or '0',
         )

diff --git a/test/test_cohort.py b/test/test_cohort.py
@@ -261,15 +261,15 @@ def mock_get_analysis_by_sgs(*args, **kwargs) -> dict:
 def mock_get_pedigree(*args, **kwargs):  # pylint: disable=unused-argument
     return [
         {
-            'family_id': 123,
+            'family_id': '123',
             'individual_id': '8',
-            'paternal_id': 14,
+            'paternal_id': '14',
             'maternal_id': None,
             'sex': 1,
             'affected': 1,
         },
         {
-            'family_id': 124,
+            'family_id': '124',
             'individual_id': '14',
             'paternal_id': None,
             'maternal_id': None,