Improve component query

src/npg_irods/ont.py

@@ -31,9 +31,8 @@
 from sqlalchemy.orm import Session
 from structlog import get_logger
 
-from npg_irods.common import update_metadata, update_permissions, infer_zone
+from npg_irods.common import infer_zone, update_metadata, update_permissions
 from npg_irods.db.mlwh import OseqFlowcell, Sample, Study
-from npg_irods.metadata import ont
 from npg_irods.metadata.common import SeqConcept
 from npg_irods.metadata.lims import (
     ensure_consent_withdrawn,
@@ -344,7 +343,7 @@ def find_components_changed(
     if include_tags:
         columns.append(OseqFlowcell.tag_identifier)
 
-    for cols in (
+    query = (
         sess.query(*columns)
         .distinct()
         .join(OseqFlowcell.sample)
@@ -354,9 +353,15 @@ def find_components_changed(
             | (Study.recorded_at >= since)
             | (OseqFlowcell.recorded_at >= since)
         )
-        .group_by(OseqFlowcell.experiment_name, OseqFlowcell.instrument_slot)
-        .order_by(asc(OseqFlowcell.experiment_name), asc(OseqFlowcell.instrument_slot))
-    ):
+        .group_by(*columns)
+    )
+
+    order = [asc(OseqFlowcell.experiment_name), asc(OseqFlowcell.instrument_slot)]
+    if include_tags:
+        order.append(asc(OseqFlowcell.tag_identifier))
+    query = query.order_by(*order)
+
+    for cols in sess.execute(query):
         yield Component(*cols)
 
 

tests/test_ml_warehouse_queries.py

@@ -21,7 +21,7 @@
 
 from pytest import mark as m
 
-from conftest import BEGIN, EARLY, LATE, LATEST
+from conftest import BEGIN, EARLY, LATE, LATEST, ont_tag_identifier
 from npg_irods.metadata import illumina
 from npg_irods.metadata.lims import TrackedSample, TrackedStudy
 from npg_irods.ont import Component, find_components_changed, find_recent_expt
@@ -128,6 +128,37 @@ def test_find_recent_component(self, ont_synthetic_mlwh):
             )
         ] == []
 
+    @m.describe(
+        "Finding updated experiments, positions and tag identifiers by datetime"
+    )
+    @m.context("When a query date is provided")
+    @m.it("Finds the correct experiment, slot, tag identifier tuples")
+    def test_find_recent_component_tag(self, ont_synthetic_mlwh):
+        before_latest = LATEST - timedelta(days=1)
+        odd_positions = []
+
+        # Odd slot multiplexed experiments were done at LATEST time
+        for expt_name in ["multiplexed_experiment_001", "multiplexed_experiment_003"]:
+            for slot in [1, 3, 5]:
+                # Tag identifiers NB01 - NB12
+                for tag_id in [ont_tag_identifier(i + 1) for i in range(12)]:
+                    odd_positions.append(Component(expt_name, slot, tag_id))
+
+        assert [
+            c
+            for c in find_components_changed(
+                ont_synthetic_mlwh, before_latest, include_tags=True
+            )
+        ] == odd_positions
+
+        after_latest = LATEST + timedelta(days=1)
+        assert [
+            c
+            for c in find_components_changed(
+                ont_synthetic_mlwh, after_latest, include_tags=True
+            )
+        ] == []
+
 
 @m.describe("Finding Illumina recently changed information in Illumina tables")
 class TestIlluminaMLWarehouseQueries(object):