fallback: get patient id from phenopackets

chord_metadata_service/chord/export_cbio.py

@@ -175,12 +175,21 @@ def sample_export(results, file_handle: TextIO):
 
     samples = []
     for sample in results:
-        # sample.inidividual can be null. Skip the sample in that case.
-        if sample.individual is None:
-            continue
+
+        # sample.inidividual may be null: use Phenopacket model Subject field
+        # instead if available or skip.
+        subject_id = None
+        if sample.individual is not None:
+            subject_id = sample.individual
+        else:
+            phnpkt = pm.Phenopacket.objects.filter(biosamples=sample).first()
+            if phnpkt.subject is not None:
+                subject_id = phnpkt.subject.id
+            else:
+                continue
 
         sample_obj = {
-            'individual_id': sample.individual.id,
+            'individual_id': subject_id,
             'id': sample.id
         }
         if sample.sampled_tissue:

chord_metadata_service/chord/tests/test_export_cbio.py

@@ -58,7 +58,9 @@ def setUp(self) -> None:
 
         self.p = WORKFLOW_INGEST_FUNCTION_MAP[WORKFLOW_PHENOPACKETS_JSON](EXAMPLE_INGEST_OUTPUTS, self.t.identifier)
 
-        # Update the last sample to remove reference to any individual.
+        # Update the last sample to remove direct reference to any individual.
+        # In that case, Sample and Individual are cross referenced through the
+        # Phenopacket model.
         PhModel.Biosample.objects.filter(
                 id=EXAMPLE_INGEST_PHENOPACKET["biosamples"][-1]["id"]
             ).update(individual=None)
@@ -184,7 +186,7 @@ def test_export_cbio_sample_data(self):
                     self.assertIn('SAMPLE_ID', pieces)
                     continue
 
-                # TSV body.
+                # TSV body: 1 row per sample
                 self.assertEqual(field_count, len(pieces))
                 record = dict(zip(field_names, pieces))
 
@@ -198,5 +200,4 @@ def test_export_cbio_sample_data(self):
                 )
                 sample_count += 1
 
-            # samples not attached to an individual are not exported
-            self.assertEqual(sample_count, samples.filter(individual_id__isnull=False).count())
+            self.assertEqual(sample_count, samples.count())