Adjust tests to account for s/external_id/external_ids/g

test_sample.py: Add a test exercising get_sample_id_map_by_external_ids().

test_upsert.py: Update direct SQL queries to use the new tables and
to ensure that their rows are returned in the expected order.

Author: jmarshall

test/test_analysis.py

@@ -9,6 +9,7 @@
 from db.python.utils import GenericFilter
 from models.enums import AnalysisStatus
 from models.models import (
+    PRIMARY_EXTERNAL_ORG,
     AnalysisInternal,
     AssayUpsertInternal,
     SampleUpsertInternal,
@@ -30,7 +31,7 @@ async def setUp(self) -> None:
 
         sample = await self.sl.upsert_sample(
             SampleUpsertInternal(
-                external_id='Test01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'Test01'},
                 type='blood',
                 meta={'meta': 'meta ;)'},
                 active=True,

test/test_assay.py

@@ -7,8 +7,11 @@
 from db.python.layers.sample import SampleLayer
 from db.python.tables.assay import AssayFilter
 from db.python.utils import GenericFilter, NotFoundError
-from models.models.assay import AssayUpsertInternal
-from models.models.sample import SampleUpsertInternal
+from models.models import (
+    PRIMARY_EXTERNAL_ORG,
+    AssayUpsertInternal,
+    SampleUpsertInternal,
+)
 
 default_sequencing_meta = {
     'sequencing_type': 'genome',
@@ -34,7 +37,7 @@ async def setUp(self) -> None:
         self.sample_id_raw = (
             await self.slayer.upsert_sample(
                 SampleUpsertInternal(
-                    external_id=self.external_sample_id,
+                    external_ids={PRIMARY_EXTERNAL_ORG: self.external_sample_id},
                     type='blood',
                     active=True,
                     meta={'Testing': 'test_assay'},
@@ -221,7 +224,7 @@ async def test_query(self):
         """Test query_assays in different combinations"""
         sample = await self.slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='SAM_TEST_QUERY',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'SAM_TEST_QUERY'},
                 type='blood',
                 active=True,
                 meta={'collection-year': '2022'},

test/test_audit_log.py

@@ -1,7 +1,7 @@
 from test.testbase import DbIsolatedTest, run_as_sync
 
 from db.python.layers.sample import SampleLayer
-from models.models.sample import SampleUpsertInternal
+from models.models import PRIMARY_EXTERNAL_ORG, SampleUpsertInternal
 
 
 class TestChangelog(DbIsolatedTest):
@@ -16,7 +16,7 @@ async def test_insert_sample(self):
         slayer = SampleLayer(self.connection)
         sample = await slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='Test01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'Test01'},
                 type='blood',
                 active=True,
                 meta={'meta': 'meta ;)'},

test/test_cohort.py

@@ -6,7 +6,11 @@
 from db.python.layers import CohortLayer, SampleLayer
 from db.python.tables.cohort import CohortFilter
 from db.python.utils import GenericFilter
-from models.models import SampleUpsertInternal, SequencingGroupUpsertInternal
+from models.models import (
+    PRIMARY_EXTERNAL_ORG,
+    SampleUpsertInternal,
+    SequencingGroupUpsertInternal,
+)
 from models.models.cohort import (
     CohortCriteria,
     CohortCriteriaInternal,
@@ -198,7 +202,7 @@ def get_sample_model(
     """Create a minimal sample"""
     return SampleUpsertInternal(
         meta={},
-        external_id=f'EXID{eid}',
+        external_ids={PRIMARY_EXTERNAL_ORG: f'EXID{eid}'},
         type=s_type,
         sequencing_groups=[
             SequencingGroupUpsertInternal(

test/test_get_participants.py

@@ -1,7 +1,7 @@
 from test.testbase import DbIsolatedTest, run_as_sync
 
 from db.python.layers.participant import ParticipantLayer
-from models.models.participant import ParticipantUpsertInternal
+from models.models import PRIMARY_EXTERNAL_ORG, ParticipantUpsertInternal
 
 
 class TestParticipant(DbIsolatedTest):
@@ -11,17 +11,20 @@ class TestParticipant(DbIsolatedTest):
     async def setUp(self) -> None:
         super().setUp()
 
+        self.ex01 = {PRIMARY_EXTERNAL_ORG: 'EX01', 'other': 'OTHER1'}
+        self.ex02 = {PRIMARY_EXTERNAL_ORG: 'EX02'}
+
         pl = ParticipantLayer(self.connection)
         await pl.upsert_participants(
             [
                 ParticipantUpsertInternal(
-                    external_id='EX01',
+                    external_ids=self.ex01,
                     reported_sex=2,
                     karyotype='XX',
                     meta={'field': 1},
                 ),
                 ParticipantUpsertInternal(
-                    external_id='EX02',
+                    external_ids=self.ex02,
                     reported_sex=1,
                     karyotype='XY',
                     meta={'field': 2},
@@ -37,11 +40,11 @@ async def test_get_all_participants(self):
 
         self.assertEqual(2, len(ps))
 
-        self.assertEqual('EX01', ps[0].external_id)
+        self.assertEqual(self.ex01, ps[0].external_ids)
         self.assertEqual(1, ps[0].meta['field'])
         self.assertEqual('XX', ps[0].karyotype)
 
-        self.assertEqual('EX02', ps[1].external_id)
+        self.assertEqual(self.ex02, ps[1].external_ids)
 
     @run_as_sync
     async def test_get_participant_by_eid(self):
@@ -51,6 +54,6 @@ async def test_get_participant_by_eid(self):
 
         self.assertEqual(1, len(ps))
 
-        self.assertEqual('EX02', ps[0].external_id)
+        self.assertEqual(self.ex02, ps[0].external_ids)
         self.assertEqual(2, ps[0].meta['field'])
         self.assertEqual('XY', ps[0].karyotype)

test/test_pedigree.py

@@ -2,7 +2,7 @@
 
 from db.python.layers.family import FamilyLayer
 from db.python.layers.participant import ParticipantLayer
-from models.models.participant import ParticipantUpsertInternal
+from models.models import PRIMARY_EXTERNAL_ORG, ParticipantUpsertInternal
 
 
 class TestPedigree(DbIsolatedTest):
@@ -51,12 +51,12 @@ async def test_pedigree_without_family(self):
 
         await pl.upsert_participant(
             ParticipantUpsertInternal(
-                external_id='EX01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'EX01'},
                 reported_sex=1,
             )
         )
         await pl.upsert_participant(
-            ParticipantUpsertInternal(external_id='EX02', reported_sex=None)
+            ParticipantUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'EX02'}, reported_sex=None)
         )
 
         rows = await fl.get_pedigree(

test/test_sample.py

@@ -1,7 +1,7 @@
 from test.testbase import DbIsolatedTest, run_as_sync
 
 from db.python.layers.sample import SampleLayer
-from models.models.sample import SampleUpsertInternal
+from models.models import PRIMARY_EXTERNAL_ORG, SampleUpsertInternal
 
 
 class TestSample(DbIsolatedTest):
@@ -19,7 +19,7 @@ async def test_add_sample(self):
         """Test inserting a sample"""
         sample = await self.slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='Test01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'Test01'},
                 type='blood',
                 active=True,
                 meta={'meta': 'meta ;)'},
@@ -32,13 +32,16 @@ async def test_add_sample(self):
         self.assertEqual(1, len(samples))
         self.assertEqual(sample.id, samples[0]['id'])
 
+        mapping = await self.slayer.get_sample_id_map_by_external_ids(['Test01'])
+        self.assertDictEqual({'Test01': sample.id}, mapping)
+
     @run_as_sync
     async def test_get_sample(self):
         """Test getting formed sample"""
         meta_dict = {'meta': 'meta ;)'}
         s = await self.slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='Test01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'Test01'},
                 type='blood',
                 active=True,
                 meta=meta_dict,
@@ -56,21 +59,21 @@ async def test_update_sample(self):
         meta_dict = {'meta': 'meta ;)'}
         s = await self.slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='Test01',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'Test01'},
                 type='blood',
                 active=True,
                 meta=meta_dict,
             )
         )
 
-        new_external_id = 'Test02'
+        new_external_id_dict = {PRIMARY_EXTERNAL_ORG: 'Test02'}
         await self.slayer.upsert_sample(
-            SampleUpsertInternal(id=s.id, external_id=new_external_id)
+            SampleUpsertInternal(id=s.id, external_ids=new_external_id_dict)
         )
 
         sample = await self.slayer.get_by_id(s.id, check_project_id=False)
 
-        self.assertEqual(new_external_id, sample.external_id)
+        self.assertDictEqual(new_external_id_dict, sample.external_ids)
 
     # @run_as_sync
     # async def test_update_sample(self):

test/test_search.py

@@ -8,6 +8,7 @@
 from db.python.tables.family_participant import FamilyParticipantTable
 from models.enums import SearchResponseType
 from models.models import (
+    PRIMARY_EXTERNAL_ORG,
     AssayUpsertInternal,
     FamilySearchResponseData,
     ParticipantSearchResponseData,
@@ -52,7 +53,7 @@ async def test_search_unavailable_sample_by_internal_id(self):
         Mock this in testing by limiting scope to non-existent project IDs
         """
         sample = await self.slayer.upsert_sample(
-            SampleUpsertInternal(external_id='EX001', type='blood')
+            SampleUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'EX001'}, type='blood')
         )
         cpg_id = sample_id_format(sample.id)
 
@@ -67,7 +68,7 @@ async def test_search_isolated_sample_by_id(self):
         Search by valid CPG sample ID (special case)
         """
         sample = await self.slayer.upsert_sample(
-            SampleUpsertInternal(external_id='EX001', type='blood')
+            SampleUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'EX001'}, type='blood')
         )
         cpg_id = sample_id_format(sample.id)
         results = await self.schlay.search(query=cpg_id, project_ids=[self.project_id])
@@ -87,7 +88,7 @@ async def test_search_isolated_sequencing_group_by_id(self):
         Search by valid CPG sequencing group ID (special case)
         """
         sample = await self.slayer.upsert_sample(
-            SampleUpsertInternal(external_id='EXS001', type='blood')
+            SampleUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'EXS001'}, type='blood')
         )
         sg = await self.sglayer.upsert_sequencing_groups(
             [
@@ -134,7 +135,7 @@ async def test_search_isolated_sample_by_external_id(self):
         should only return one result
         """
         sample = await self.slayer.upsert_sample(
-            SampleUpsertInternal(external_id='EX001', type='blood')
+            SampleUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'EX001'}, type='blood')
         )
         results = await self.schlay.search(query='EX001', project_ids=[self.project_id])
 
@@ -159,7 +160,7 @@ async def test_search_participant_isolated(self):
         should only return one result
         """
         p = await self.player.upsert_participant(
-            ParticipantUpsertInternal(external_id='PART01')
+            ParticipantUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'PART01'})
         )
         results = await self.schlay.search(
             query='PART01', project_ids=[self.project_id]
@@ -197,7 +198,7 @@ async def test_search_mixed(self):
         fptable = FamilyParticipantTable(self.connection)
 
         p = await self.player.upsert_participant(
-            ParticipantUpsertInternal(external_id='X:PART01')
+            ParticipantUpsertInternal(external_ids={PRIMARY_EXTERNAL_ORG: 'X:PART01'})
         )
         f_id = await self.flayer.create_family(external_id='X:FAM01')
         await fptable.create_rows(
@@ -216,7 +217,7 @@ async def test_search_mixed(self):
 
         sample = await self.slayer.upsert_sample(
             SampleUpsertInternal(
-                external_id='X:SAM001',
+                external_ids={PRIMARY_EXTERNAL_ORG: 'X:SAM001'},
                 type='blood',
                 participant_id=p.id,
             )

test/test_sequencing_groups.py

@@ -6,6 +6,7 @@
 from db.python.utils import GenericFilter
 from models.enums.analysis import AnalysisStatus
 from models.models import (
+    PRIMARY_EXTERNAL_ORG,
     AnalysisInternal,
     AssayUpsertInternal,
     SampleUpsertInternal,
@@ -20,7 +21,7 @@ def get_sample_model():
     """
     return SampleUpsertInternal(
         meta={},
-        external_id='EX_ID',
+        external_ids={PRIMARY_EXTERNAL_ORG: 'EX_ID'},
         sequencing_groups=[
             SequencingGroupUpsertInternal(
                 type='genome',