fix test

Author: bpblanken

v03_pipeline/lib/misc/family_loading_failures.py

@@ -31,10 +31,11 @@ def passes_relatedness_check(
     return True, None
 
 
-def passes_all_relatedness_checks(  # noqa: C901
+def all_relatedness_checks(  # noqa: C901
     relatedness_check_lookup: dict[tuple[str, str], list],
     sample: Sample,
-) -> tuple[bool, str | None]:
+) -> list[str]:
+    failure_reasons = []
     for parent_id in [sample.mother, sample.father]:
         success, reason = passes_relatedness_check(
             relatedness_check_lookup,
@@ -43,7 +44,7 @@ def passes_all_relatedness_checks(  # noqa: C901
             Relation.PARENT,
         )
         if not success:
-            return False, reason
+            failure_reasons.append(reason)
 
     for grandparent_id in [
         sample.maternal_grandmother,
@@ -58,7 +59,7 @@ def passes_all_relatedness_checks(  # noqa: C901
             Relation.GRANDPARENT,
         )
         if not success:
-            return False, reason
+            failure_reasons.append(reason)
 
     for sibling_id in sample.siblings:
         success, reason = passes_relatedness_check(
@@ -68,7 +69,7 @@ def passes_all_relatedness_checks(  # noqa: C901
             Relation.SIBLING,
         )
         if not success:
-            return False, reason
+            failure_reasons.append(reason)
 
     for half_sibling_id in sample.half_siblings:
         # NB: A "half sibling" parsed from the pedigree may actually be a sibling, so we allow those
@@ -86,7 +87,7 @@ def passes_all_relatedness_checks(  # noqa: C901
             Relation.HALF_SIBLING,
         )
         if not success1 and not success2:
-            return False, reason
+            failure_reasons.append(reason)
 
     for aunt_nephew_id in sample.aunt_nephews:
         success, reason = passes_relatedness_check(
@@ -96,8 +97,8 @@ def passes_all_relatedness_checks(  # noqa: C901
             Relation.AUNT_NEPHEW,
         )
         if not success:
-            return False, reason
-    return True, None
+            failure_reasons.append(reason)
+    return failure_reasons
 
 
 def build_relatedness_check_lookup(
@@ -156,12 +157,12 @@ def get_families_failed_relatedness_check(
     failed_families = defaultdict(list)
     for family in families:
         for sample in family.samples.values():
-            success, reason = passes_all_relatedness_checks(
+            failure_reasons = all_relatedness_checks(
                 relatedness_check_lookup,
                 sample,
             )
-            if not success:
-                failed_families[family].append(reason)
+            if failure_reasons:
+                failed_families[family].extend(failure_reasons)
     return dict(failed_families)
 
 

v03_pipeline/lib/misc/family_loading_failures_test.py

@@ -6,7 +6,7 @@
     build_relatedness_check_lookup,
     build_sex_check_lookup,
     get_families_failed_sex_check,
-    passes_all_relatedness_checks,
+    all_relatedness_checks,
 )
 from v03_pipeline.lib.misc.io import import_pedigree
 from v03_pipeline.lib.misc.pedigree import Sample, parse_pedigree_ht_to_families
@@ -81,7 +81,7 @@ def test_build_sex_check_lookup(self):
             },
         )
 
-    def test_passes_all_relatedness_checks(self):
+    def test_all_relatedness_checks(self):
         relatedness_check_lookup = {
             # Parent
             ('sample_1', 'sample_2'): [
@@ -102,8 +102,8 @@ def test_passes_all_relatedness_checks(self):
             paternal_grandfather='sample_3',
             half_siblings=['sample_4'],
         )
-        success, _ = passes_all_relatedness_checks(relatedness_check_lookup, sample)
-        self.assertTrue(success)
+        failure_reasons = all_relatedness_checks(relatedness_check_lookup, sample)
+        self.assertListEqual(failure_reasons, [])
 
         # Defined grandparent missing in relatedness table
         sample = Sample(
@@ -113,14 +113,13 @@ def test_passes_all_relatedness_checks(self):
             paternal_grandfather='sample_3',
             paternal_grandmother='sample_5',
         )
-        success, reason = passes_all_relatedness_checks(
+        failure_reasons = all_relatedness_checks(
             relatedness_check_lookup,
             sample,
         )
-        self.assertFalse(success)
-        self.assertEqual(
-            reason,
-            'Sample sample_1 has expected relation "grandparent" to sample_5 but has coefficients []',
+        self.assertListEqual(
+            failure_reasons,
+            ['Sample sample_1 has expected relation "grandparent" to sample_5 but has coefficients []'],
         )
 
         # Sibling is actually a half sibling.
@@ -135,17 +134,15 @@ def test_passes_all_relatedness_checks(self):
             paternal_grandfather='sample_3',
             siblings=['sample_4'],
         )
-        success, reason = passes_all_relatedness_checks(
+        failure_reasons = all_relatedness_checks(
             relatedness_check_lookup,
             sample,
         )
-        self.assertFalse(success)
-        self.assertEqual(
-            reason,
-            'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]',
+        self.assertListEqual(
+            failure_reasons,
+            ['Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]'],
         )
 
-        # Sibling is actually a half sibling.
         relatedness_check_lookup = {
             **relatedness_check_lookup,
             ('sample_1', 'sample_2'): [
@@ -162,14 +159,17 @@ def test_passes_all_relatedness_checks(self):
             paternal_grandfather='sample_3',
             siblings=['sample_4'],
         )
-        success, reason = passes_all_relatedness_checks(
+        failure_reasons = all_relatedness_checks(
             relatedness_check_lookup,
             sample,
         )
-        self.assertFalse(success)
-        self.assertEqual(
-            reason,
-            'Sample sample_1 has expected relation "parent" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]',
+        print('ben', failure_reasons)
+        self.assertListEqual(
+            failure_reasons,
+            [
+                'Sample sample_1 has expected relation "parent" to sample_2 but has coefficients [0.5, 0.5, 0.5, 0.5]', 
+                'Sample sample_1 has expected relation "sibling" to sample_4 but has coefficients [0.5, 0.5, 0, 0.25]'
+            ],
         )
 
     def test_get_families_failed_sex_check(self):