multi ffqs fix (#581)

* addresses #579

* lint and update tests

* update source id for vioscreen test

* update exp

* test

* update vioscreen test

* test2

* test3

* test4

* fix vioscreen test

* update per_sample based on feedback

* use vio_id instead of source, update query

Author: ayobi

microsetta_private_api/admin/sample_summary.py

@@ -49,10 +49,24 @@ def per_sample(project, barcodes, strip_sampleid):
             barcode_project = '; '.join(sorted(all_projects))
 
             if source is not None and source_type == Source.SOURCE_TYPE_HUMAN:
-
                 vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
                                                                   source.id,
                                                                   sample.id)
+                # fall back on matching with source id
+                if not vio_id:
+                    vio_id = \
+                        template_repo.get_vioscreen_id_if_exists(account.id,
+                                                                 source.id,
+                                                                 None)
+                if vio_id:
+                    ffq_complete, ffq_taken, _ = \
+                        vs_repo.get_ffq_status_by_vio_id(vio_id)
+                else:
+                    ffq_complete = False
+                    ffq_taken = False
+            else:
+                ffq_complete = False
+                ffq_taken = False
 
             # at least one sample has been observed that "is_microsetta",
             # described in the barcodes.project_barcode table, but which is
@@ -80,10 +94,6 @@ def per_sample(project, barcodes, strip_sampleid):
                     sample_date = None
                     sample_time = None
 
-                ffq_complete, ffq_taken, _ = vs_repo.get_ffq_status_by_sample(
-                    sample.id
-                )
-
             summary = {
                 "sampleid": None if strip_sampleid else barcode,
                 "project": barcode_project,

microsetta_private_api/repo/tests/test_vioscreen_sessions.py

@@ -18,6 +18,9 @@ def _to_dt(mon, day, year):
 # in ag_test db, this uuid corresponds to VIOSCREEN_USERNAME1
 BARCODE_UUID_FOR_VIOSESSION = '66ec7d9a-400d-4d71-bce8-fdf79d2be554'
 BARCODE_UUID_NOTIN_REGISTRY = 'edee4af9-65b2-4ed1-ba66-5bf58383005e'
+SOURCE_ID_FOR_VIOSESSION = '6d343527-ab68-4e01-9ef7-16943dc5cee0'
+SOURCE_ID_NOTIN_REGISTRY = 'aaaaaaaa-aaaa-aaaa-aaaa-aaaaaaaaaaaa'
+
 
 today = date.today()
 VIOSCREEN_SESSION = VioscreenSession(sessionId='a session',
@@ -265,33 +268,33 @@ def test_get_ffq_status_by_sample(self):
             r.upsert_session(session_copy)
             session = r.get_sessions_by_username(VIOSCREEN_USERNAME1)[0]
 
-            obs = r.get_ffq_status_by_sample(BARCODE_UUID_NOTIN_REGISTRY)
-            self.assertEqual(obs, (False, False, None))
+            obs = r.get_ffq_status_by_vio_id(VIOSCREEN_USERNAME1)
+            self.assertEqual(obs, (False, False, 'something'))
 
             session.status = 'Finished'
             session.endDate = _to_dt(2, 1, 1970)
             r.upsert_session(session)
 
             # enumerate the empirically observed states from vioscreen
             # (is_complete, has_taken, exact_status)
-            obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
+            obs = r.get_ffq_status_by_vio_id(VIOSCREEN_USERNAME1)
             self.assertEqual(obs, (True, True, 'Finished'))
 
             session.status = 'Started'
             session.endDate = None
             r.upsert_session(session)
 
-            obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
+            obs = r.get_ffq_status_by_vio_id(VIOSCREEN_USERNAME1)
             self.assertEqual(obs, (False, True, 'Started'))
 
             session.status = 'New'
             r.upsert_session(session)
-            obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
+            obs = r.get_ffq_status_by_vio_id(VIOSCREEN_USERNAME1)
             self.assertEqual(obs, (False, False, 'New'))
 
             session.status = 'Review'
             r.upsert_session(session)
-            obs = r.get_ffq_status_by_sample(BARCODE_UUID_FOR_VIOSESSION)
+            obs = r.get_ffq_status_by_vio_id(VIOSCREEN_USERNAME1)
             self.assertEqual(obs, (False, True, 'Review'))
 
 

microsetta_private_api/repo/vioscreen_repo.py

@@ -168,12 +168,12 @@ def get_unfinished_sessions(self):
 
             return not_in_vioscreen_sessions + incomplete_sessions
 
-    def get_ffq_status_by_sample(self, sample_uuid):
-        """Obtain the FFQ status for a given sample
+    def get_ffq_status_by_vio_id(self, vio_id):
+        """Obtain the FFQ status for a given source
 
         Parameters
         ----------
-        sample_uuid : UUID4
+        source_uuid : UUID4
             The UUID to check the status of
 
         Returns
@@ -186,21 +186,38 @@ def get_ffq_status_by_sample(self, sample_uuid):
                 if there is no FFQ associated with the sample.
         """
         with self._transaction.cursor() as cur:
-            cur.execute("""SELECT status
+            cur.execute("""SELECT source_id
+                           FROM ag.vioscreen_registry
+                           WHERE vio_id = %s""", (vio_id, ))
+
+            source_res = cur.fetchone()
+
+            if source_res is None:
+                return (False, False, None)
+
+            source_id = source_res[0]
+
+            cur.execute("""SELECT vs.status, akb.sample_date,
+                           akb.sample_time, vs.startdate
                            FROM ag.vioscreen_sessions AS vs
                            JOIN ag.vioscreen_registry AS vr
-                               ON vs.username=vr.vio_id
-                           WHERE sample_id=%s""", (sample_uuid, ))
-            res = cur.fetchall()
-            if len(res) == 0:
+                                ON vs.username = vr.vio_id
+                           LEFT JOIN ag.ag_kit_barcodes AS akb
+                                ON vr.source_id = akb.source_id
+                           WHERE vr.source_id = %s
+                           ORDER BY ABS(EXTRACT(EPOCH FROM
+                                (akb.sample_date - vs.startdate)))
+                           LIMIT 1""", (source_id, ))
+
+            res = cur.fetchone()
+
+            if res is None:
                 return (False, False, None)
-            elif len(res) == 1:
-                status = res[0][0]
+            else:
+                status = res[0]
                 is_complete = status == 'Finished'
                 is_taken = status in ('Started', 'Review', 'Finished')
-                return (is_complete, is_taken, status)
-            else:
-                raise ValueError("A sample should not have multiple FFQs")
+                return is_complete, is_taken, status
 
     def get_missing_ffqs(self):
         """The set of valid sessions which lack FFQ data