Merge pull request #236 from nerdstrike/sample_in_poolstats

Add sample name to the pool stats table.

frontend/src/components/PoolStats.vue

@@ -18,6 +18,7 @@ const active = ref([])
       </el-tooltip>
       <table>
         <tr>
+          <th>Sample</th>
           <th>Tag 1</th>
           <th>Tag 2</th>
           <th>Deplexing barcode ID</th>
@@ -28,6 +29,7 @@ const active = ref([])
           <th>Percentage of total reads</th>
         </tr>
         <tr :key="library.id_product" v-for="library in props.pool.products">
+          <td>{{ library.sample_name }}</td>
           <td>{{ library.tag1_name }}</td>
           <td>{{ library.tag2_name }}</td>
           <td>{{ library.deplexing_barcode }}</td>

frontend/src/components/__tests__/PoolStats.spec.js

@@ -13,6 +13,7 @@ const wrapper = mount(PoolStats, {
             pool_coeff_of_variance: 47.2,
             products: [{
                 id_product: 'A'.repeat(64),
+                sample_name: 'allthets',
                 tag1_name: 'TTTTTTTT',
                 tag2_name: null,
                 deplexing_barcode: 'bc10--bc10',
@@ -23,6 +24,7 @@ const wrapper = mount(PoolStats, {
                 percentage_total_reads: 66.6
             },{
                 id_product: 'B'.repeat(64),
+                sample_name: null,
                 tag1_name: 'GGGGGGGG',
                 tag2_name: null,
                 deplexing_barcode: 'bc11--bc11',
@@ -54,7 +56,11 @@ describe('Create poolstats table with good data', () => {
         expect(rows.length).toEqual(3)
 
         // Check tag 1 has been set
-        expect(rows[1].find('td').text()).toEqual('TTTTTTTT')
-        expect(rows[2].find('td').text()).toEqual('GGGGGGGG')
+        expect(rows[1].findAll('td')[1].text()).toEqual('TTTTTTTT')
+        expect(rows[2].findAll('td')[1].text()).toEqual('GGGGGGGG')
+
+        // Sample name column set appropriately
+        expect(rows[1].find('td').text()).toEqual('allthets')
+        expect(rows[2].find('td').text()).toEqual('')
     })
 })

lang_qc/models/pacbio/qc_data.py

@@ -170,6 +170,7 @@ class SampleDeplexingStats(BaseModel):
     """
 
     id_product: PacBioProductSHA256
+    sample_name: str | None
     tag1_name: str | None
     tag2_name: str | None
     deplexing_barcode: str | None
@@ -235,6 +236,7 @@ def pre_root(cls, values: dict[str, Any]) -> dict[str, Any]:
                 sample_stats.append(
                     SampleDeplexingStats(
                         id_product=prod.id_pac_bio_product,
+                        sample_name=lib_lims_data[i].sample.name,
                         tag1_name=lib_lims_data[i].tag_identifier,
                         tag2_name=lib_lims_data[i].tag2_identifier,
                         deplexing_barcode=prod.barcode4deplexing,

tests/fixtures/sample_data.py

@@ -162,10 +162,7 @@ def multiplexed_run(mlwhdb_test_session):
         well_label=well_label,
         plate_number=plate_number,
         id_pac_bio_run_lims=1,
-        sample=Sample(
-            id_lims="pooled_id_1",
-            id_sample_lims="2",
-        ),
+        sample=Sample(id_lims="pooled_id_1", id_sample_lims="2", name="It's a test"),
         study=study,
         plate_barcode="ABCD",
         pac_bio_product_metrics=[product_1],

tests/test_pac_bio_qc_data_well.py

@@ -104,7 +104,11 @@ def test_creating_qc_data_well(mlwhdb_test_session, mlwhdb_load_runs):
 
 
 def test_pool_metrics_from_single_sample_well(mlwhdb_test_session, simplex_run):
-
+    """
+    Applies to samples where deplexing was left as an exercise for the user.
+    Other single-sample wells with requested deplexing will have a single entry
+    in the products
+    """
     id = PacBioEntity(
         run_name=simplex_run.pac_bio_run_name,
         well_label=simplex_run.well_label,
@@ -146,6 +150,13 @@ def test_pool_metrics_from_well(mlwhdb_test_session, multiplexed_run):
             metrics.products[1].percentage_total_reads == 66.67
         ), "20Mb of 30Mb reads is 66.67% (2 d.p.)"
 
+    assert (
+        metrics.products[0].sample_name is None
+    ), "Sample without name returned successfully"
+    assert (
+        metrics.products[1].sample_name == "It's a test"
+    ), "Sample name added to products when present"
+
 
 def test_errors_instantiating_pool_metrics(mlwhdb_test_session):