From 4c1375ccc9943d5cf98cd385c6a848e66099068c Mon Sep 17 00:00:00 2001
From: MattWellie <mattwellie@gmail.com>
Date: Mon, 28 Oct 2024 16:45:37 +1000
Subject: [PATCH] test fixture update - family and individual IDs from Metamist
 Pedigree are always Strings

---
 cpg_workflows/inputs.py | 8 +++-----
 test/test_cohort.py     | 6 +++---
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/cpg_workflows/inputs.py b/cpg_workflows/inputs.py
index f9690b6c9..bcc9066e3 100644
--- 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
index f7a8f13ab..457c20992 100644
--- 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,