✅ Test filter params, error handling, pagination

tests/conftest.py

@@ -15,6 +15,7 @@
 from dataservice.api.family_relationship.models import FamilyRelationship
 from dataservice.api.biospecimen.models import Biospecimen
 from dataservice.api.sample.models import Sample
+from dataservice.api.sample_relationship.models import SampleRelationship
 from dataservice.api.diagnosis.models import Diagnosis
 from dataservice.api.outcome.models import Outcome
 from dataservice.api.phenotype.models import Phenotype
@@ -57,6 +58,7 @@
     Phenotype: '/phenotypes',
     Outcome: '/outcomes',
     Sample: '/samples',
+    SampleRelationship: '/sample-relationships',
     Biospecimen: '/biospecimens',
     GenomicFile: '/genomic-files',
     BiospecimenGenomicFile: '/biospecimen-genomic-files',
@@ -162,6 +164,7 @@ def make_entities(client):
                          BiospecimenDiagnosis,
                          ReadGroupGenomicFile,
                          SequencingExperimentGenomicFile,
+                         SampleRelationship,
                          Sample}:
                 continue
             for i in range(ENTITY_TOTAL):
@@ -302,6 +305,20 @@ def make_entities(client):
         )
         db.session.add(s)
         _entities[Sample].append(s)
+
+    # Sample relationships
+    for parent, child in iterate_pairwise(_entities[Sample]):
+        r = SampleRelationship(
+            parent=parent,
+            child=child,
+            external_parent_id=parent.external_id,
+            external_child_id=child.external_id,
+        )
+        if model not in _entities:
+            _entities[SampleRelationship] = []
+        _entities[SampleRelationship].append(r)
+        db.session.add(r)
+
     db.session.commit()
 
     return _entities

tests/data.json

@@ -66,6 +66,10 @@
       "preservation_method": "Fresh",
       "visible": true
     },
+    "/sample-relationships": {
+      "external_parent_id": "SA-parent",
+      "external_child_id": "SA-child"
+    },
     "/diagnoses": {
       "external_id": "d0",
       "diagnosis_category": "Structural Birth Defect",
@@ -227,6 +231,13 @@
       },
       "invalid": []
     },
+    "/sample-relationships": {
+      "valid": {
+        "external_parent_id": "sa-001",
+        "external_child_id": "sa-002"
+      },
+      "invalid": []
+    },
     "/diagnoses": {
       "valid": {
         "diagnosis_category": "Cancer",

tests/test_api.py

@@ -80,6 +80,7 @@ def test_status_format(self, client, endpoint, method):
         ('/investigators', []),
         ('/participants', ['study', 'family']),
         ('/family-relationships', ['participant1', 'participant2']),
+        ('/sample-relationships', ['parent', 'child']),
         ('/phenotypes', ['participant']),
         ('/outcomes', ['participant']),
         ('/diagnoses', ['participant', 'biospecimens']),
@@ -353,6 +354,8 @@ def test_bad_visibility_reason(self, client, entities, endpoint):
                                  ('/genomic-files', 'hashes'),
                                  ('/diagnoses', 'participant_id'),
                                  ('/samples', 'participant_id'),
+                                 ('/sample-relationships', 'parent_id'),
+                                 ('/sample-relationships', 'child_id'),
                                  ('/biospecimens', 'analyte_type'),
                                  ('/sequencing-centers', 'name')
                              ])
@@ -392,6 +395,8 @@ def test_missing_required_params(self, client, entities, endpoint,
                               ('/biospecimens', 'participant_id'),
                               ('/biospecimens', 'sample_id'),
                               ('/samples', 'participant_id'),
+                              ('/sample-relationships', 'parent_id'),
+                              ('/sample-relationships', 'child_id'),
                               ('/tasks', 'cavatica_app_id'),
                               ('/task-genomic-files',
                                'task_id'),

tests/test_pagination.py

@@ -171,6 +171,19 @@ def participants(client):
                                    participant1_to_participant2_relation=rel)
             db.session.add(r)
 
+        # Sample relationships
+        for p1, p2 in iterate_pairwise(participants):
+            # Biologically incorrect, but done for testing only
+            parent = p1.samples[0]
+            child = p2.samples[0]
+            r = SampleRelationship(
+                parent=parent,
+                child=child,
+                external_parent_id=parent.external_id,
+                external_child_id=child.external_id,
+            )
+            db.session.add(r)
+
         db.session.commit()
 
     @pytest.mark.parametrize('endpoint, expected_total', [