Fix get sequencing groups by analysis IDs (#850)

* Commit failing test * Change inner to left join to fix test --------- Co-authored-by: Michael Franklin <[email protected]>
populationgenomics · Jul 1, 2024 · bcc6392 · bcc6392
1 parent 1162776
commit bcc6392
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diff --git a/db/python/tables/sequencing_group.py b/db/python/tables/sequencing_group.py
@@ -370,7 +370,7 @@ async def get_sequencing_groups_by_analysis_ids(
         FROM analysis_sequencing_group asg
         INNER JOIN sequencing_group sg ON sg.id = asg.sequencing_group_id
         INNER JOIN sample s ON s.id = sg.sample_id
-        INNER JOIN sequencing_group_external_id sgexid ON sg.id = sgexid.sequencing_group_id
+        LEFT JOIN sequencing_group_external_id sgexid ON sg.id = sgexid.sequencing_group_id
         WHERE asg.analysis_id IN :aids
         GROUP BY sg.id, asg.analysis_id
         """

diff --git a/test/test_analysis.py b/test/test_analysis.py
@@ -189,5 +189,71 @@ async def test_get_sample_cram_path_map_for_seqr(self):
             ],
         )
 
-        id_map = await self.al.get_sample_cram_path_map_for_seqr(self.project_id, ['blood'], [part[0].id])
+        id_map = await self.al.get_sample_cram_path_map_for_seqr(
+            self.project_id, ['blood'], [part[0].id]
+        )
         self.assertIsInstance(id_map, list)
+
+    @run_as_sync
+    async def test_get_sgs_by_analysis_id_with_no_eids(self):
+        """
+        Test get_sgs_by_analysis_id()
+        """
+
+        # duplicate here to ensure sgs don't have any external ids
+        assay_meta = {
+            'sequencing_type': 'genome',
+            'sequencing_technology': 'short-read',
+            'sequencing_platform': 'illumina',
+        }
+        sample = await self.sl.upsert_sample(
+            SampleUpsertInternal(
+                external_ids={PRIMARY_EXTERNAL_ORG: 'test_sgs_aid'},
+                type='blood',
+                meta={},
+                active=True,
+                sequencing_groups=[
+                    SequencingGroupUpsertInternal(
+                        type='genome',
+                        technology='short-read',
+                        platform='illumina',
+                        assays=[
+                            AssayUpsertInternal(
+                                type='sequencing',
+                                meta=assay_meta,
+                            )
+                        ],
+                    ),
+                    SequencingGroupUpsertInternal(
+                        type='exome',
+                        technology='short-read',
+                        platform='illumina',
+                        assays=[
+                            AssayUpsertInternal(
+                                type='sequencing',
+                                meta=assay_meta,
+                            )
+                        ],
+                    ),
+                ],
+            )
+        )
+
+        genome_id = sample.sequencing_groups[0].id
+        exome_id = sample.sequencing_groups[1].id
+
+        a_id = await self.al.create_analysis(
+            AnalysisInternal(
+                type='analysis-runner',
+                status=AnalysisStatus.UNKNOWN,
+                sequencing_group_ids=[genome_id, exome_id],
+                meta={},
+            )
+        )
+
+        sgs_by_aid = await self.sgl.get_sequencing_groups_by_analysis_ids([a_id])
+        self.assertIn(a_id, sgs_by_aid)
+        sgs = sorted(sgs_by_aid[a_id], key=lambda sg: sg.id)
+
+        self.assertEqual(sgs[0].id, genome_id)
+        self.assertEqual(sgs[1].id, exome_id)