From 2f9be8aec83686f16c8bbfa7ebd1c2f4d29a08cd Mon Sep 17 00:00:00 2001
From: mgcam <mg8@sanger.ac.uk>
Date: Wed, 12 Jun 2024 16:59:42 +0100
Subject: [PATCH 1/2] Added a check for unlinked data.

---
 lang_qc/db/helper/wells.py         | 27 ++++++++++++++++++---------
 tests/test_pac_bio_qc_data_well.py | 13 +++++++++++++
 2 files changed, 31 insertions(+), 9 deletions(-)

diff --git a/lang_qc/db/helper/wells.py b/lang_qc/db/helper/wells.py
index 69fac7e..57d7b01 100644
--- a/lang_qc/db/helper/wells.py
+++ b/lang_qc/db/helper/wells.py
@@ -85,7 +85,15 @@ def get_metrics_by_well_product_id(
     ) -> QCPoolMetrics | None:
         well = self.get_mlwh_well_by_product_id(id_product)
         if well and well.demultiplex_mode and "Instrument" in well.demultiplex_mode:
+
             product_metrics = well.pac_bio_product_metrics
+            lib_lims_data = [
+                row
+                for row in map(lambda product: product.pac_bio_run, product_metrics)
+                if row is not None
+            ]
+            if len(lib_lims_data) != len(product_metrics):
+                raise Exception("Partially linked LIMS data or no linked LIMS data")
 
             cov: float | None
             if any(p.hifi_num_reads is None for p in product_metrics):
@@ -94,13 +102,13 @@ def get_metrics_by_well_product_id(
                 hifi_reads = [prod.hifi_num_reads for prod in product_metrics]
                 cov = stdev(hifi_reads) / mean(hifi_reads) * 100
 
-            return QCPoolMetrics(
-                pool_coeff_of_variance=cov,
-                products=[
+            sample_stats = []
+            for (i, prod) in enumerate(product_metrics):
+                sample_stats.append(
                     SampleDeplexingStats(
                         id_product=prod.id_pac_bio_product,
-                        tag1_name=prod.pac_bio_run.tag_identifier,
-                        tag2_name=prod.pac_bio_run.tag2_identifier,
+                        tag1_name=lib_lims_data[i].tag_identifier,
+                        tag2_name=lib_lims_data[i].tag2_identifier,
                         deplexing_barcode=prod.barcode4deplexing,
                         hifi_read_bases=prod.hifi_read_bases,
                         hifi_num_reads=prod.hifi_num_reads,
@@ -108,13 +116,14 @@ def get_metrics_by_well_product_id(
                         hifi_bases_percent=prod.hifi_bases_percent,
                         percentage_total_reads=(
                             prod.hifi_num_reads / well.hifi_num_reads * 100
-                            if well.hifi_num_reads
+                            if (well.hifi_num_reads and prod.hifi_num_reads)
                             else None
                         ),
                     )
-                    for prod in product_metrics
-                ],
-            )
+                )
+
+            return QCPoolMetrics(pool_coeff_of_variance=cov, products=sample_stats)
+
         return None
 
     def recent_completed_wells(self) -> List[PacBioRunWellMetrics]:
diff --git a/tests/test_pac_bio_qc_data_well.py b/tests/test_pac_bio_qc_data_well.py
index bd4318a..3be9de9 100644
--- a/tests/test_pac_bio_qc_data_well.py
+++ b/tests/test_pac_bio_qc_data_well.py
@@ -1,3 +1,4 @@
+import pytest
 from npg_id_generation.pac_bio import PacBioEntity
 
 from lang_qc.db.helper.wells import WellWh
@@ -134,3 +135,15 @@ def test_pool_metrics_from_well(mlwhdb_test_session, multiplexed_run):
     assert (
         int(metrics.products[1].percentage_total_reads) == 66
     ), "20 of 30 reads is 66.6%"
+
+
+def test_pool_metrics_from_well(mlwhdb_test_session):
+
+    id = PacBioEntity(
+        run_name="TRACTION-RUN-1140", well_label="C1", plate_number=2
+    ).hash_product_id()
+    helper = WellWh(session=mlwhdb_test_session)
+    with pytest.raises(
+        Exception, match=r"Partially linked LIMS data or no linked LIMS data"
+    ):
+        helper.get_metrics_by_well_product_id(id)

From 372fc567c64a4f70806079291b8e48d0390afa60 Mon Sep 17 00:00:00 2001
From: mgcam <mg8@sanger.ac.uk>
Date: Thu, 13 Jun 2024 12:09:32 +0100
Subject: [PATCH 2/2] Simplified getting linked lims data.

---
 lang_qc/db/helper/wells.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/lang_qc/db/helper/wells.py b/lang_qc/db/helper/wells.py
index 57d7b01..4c8f089 100644
--- a/lang_qc/db/helper/wells.py
+++ b/lang_qc/db/helper/wells.py
@@ -88,9 +88,9 @@ def get_metrics_by_well_product_id(
 
             product_metrics = well.pac_bio_product_metrics
             lib_lims_data = [
-                row
-                for row in map(lambda product: product.pac_bio_run, product_metrics)
-                if row is not None
+                product.pac_bio_run
+                for product in product_metrics
+                if product.pac_bio_run is not None
             ]
             if len(lib_lims_data) != len(product_metrics):
                 raise Exception("Partially linked LIMS data or no linked LIMS data")