Hotfix for external IDs on the Project Grid (#824)

* Format external_ids on project grid * Fix external id key * Fix tests * Let linter do it's thang --------- Co-authored-by: Michael Franklin <[email protected]>
populationgenomics · Jun 13, 2024 · 71dddbe · 71dddbe
1 parent c748513
commit 71dddbe
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Showing 3 changed files with 24 additions and 16 deletions.
diff --git a/db/python/layers/web.py b/db/python/layers/web.py
@@ -506,7 +506,7 @@ async def get_project_summary(
         has_reported_gender = any(p.reported_gender for p in pmodels)
         has_karyotype = any(p.karyotype for p in pmodels)
 
-        participant_keys = [('external_id', 'Participant ID')]
+        participant_keys = [('external_ids', 'Participant ID')]
 
         if has_reported_sex:
             participant_keys.append(('reported_sex', 'Reported sex'))
@@ -518,7 +518,7 @@ async def get_project_summary(
         participant_keys.extend(('meta.' + k, k) for k in participant_meta_keys)
         sample_keys: list[tuple[str, str]] = [
             ('id', 'Sample ID'),
-            ('external_id', 'External Sample ID'),
+            ('external_ids', 'External Sample ID'),
             ('created_date', 'Created date'),
         ] + [('meta.' + k, k) for k in sample_meta_keys]
 

diff --git a/test/test_web.py b/test/test_web.py
@@ -165,10 +165,10 @@ def get_test_participant_2():
     },
     batch_sequencing_group_stats={'M001': {'genome': '1'}},
     participants=[],
-    participant_keys=[('external_id', 'Participant ID')],
+    participant_keys=[('external_ids', 'Participant ID')],
     sample_keys=[
         ('id', 'Sample ID'),
-        ('external_id', 'External Sample ID'),
+        ('external_ids', 'External Sample ID'),
         ('created_date', 'Created date'),
     ],
     sequencing_group_keys=[
@@ -349,10 +349,10 @@ async def test_project_summary_multiple_participants(self):
             },
             batch_sequencing_group_stats={'M001': {'genome': '2'}},
             participants=[],  # data_to_class(expected_data_list),
-            participant_keys=[('external_id', 'Participant ID')],
+            participant_keys=[('external_ids', 'Participant ID')],
             sample_keys=[
                 ('id', 'Sample ID'),
-                ('external_id', 'External Sample ID'),
+                ('external_ids', 'External Sample ID'),
                 ('created_date', 'Created date'),
             ],
             sequencing_group_keys=[
@@ -402,10 +402,10 @@ async def test_project_summary_multiple_participants_and_filter(self):
             },
             batch_sequencing_group_stats={'M001': {'genome': '2'}},
             participants=[],  # data_to_class(expected_data_list_filtered),
-            participant_keys=[('external_id', 'Participant ID')],
+            participant_keys=[('external_ids', 'Participant ID')],
             sample_keys=[
                 ('id', 'Sample ID'),
-                ('external_id', 'External Sample ID'),
+                ('external_ids', 'External Sample ID'),
                 ('created_date', 'Created date'),
             ],
             sequencing_group_keys=[
@@ -478,10 +478,10 @@ async def test_field_with_space(self):
             },
             batch_sequencing_group_stats={'M001': {'genome': '2'}},
             participants=[],
-            participant_keys=[('external_id', 'Participant ID')],
+            participant_keys=[('external_ids', 'Participant ID')],
             sample_keys=[
                 ('id', 'Sample ID'),
-                ('external_id', 'External Sample ID'),
+                ('external_ids', 'External Sample ID'),
                 ('created_date', 'Created date'),
             ],
             sequencing_group_keys=[

diff --git a/web/src/pages/project/ProjectGrid.tsx b/web/src/pages/project/ProjectGrid.tsx
@@ -30,6 +30,12 @@ interface ProjectGridProps {
     }) => void
 }
 
+const formatExternalIds = (ids: Record<string, string>) => {
+    return Object.entries(ids)
+        .map(([k, v]) => (k.length === 0 ? sanitiseValue(v) : `${k}: ${v}`))
+        .join(', ')
+}
+
 const ProjectGrid: React.FunctionComponent<ProjectGridProps> = ({
     summary,
     projectName,
@@ -300,9 +306,7 @@ const ProjectGrid: React.FunctionComponent<ProjectGridProps> = ({
                                 // const border = '1px solid'
                                 // debugger
                                 return (
-                                    <SUITable.Row
-                                        key={`${p.external_id}-${s.id}-${sg.id}-${assay.id}`}
-                                    >
+                                    <SUITable.Row key={`${p.id}-${s.id}-${sg.id}-${assay.id}`}>
                                         {isFirstOfGroup && (
                                             <SUITable.Cell
                                                 style={{
@@ -343,7 +347,9 @@ const ProjectGrid: React.FunctionComponent<ProjectGridProps> = ({
                                                     key={`${p.id}participant.${k}`}
                                                     rowSpan={participantRowSpan}
                                                 >
-                                                    {sanitiseValue(_.get(p, k))}
+                                                    {k === 'external_ids'
+                                                        ? formatExternalIds(p.external_ids)
+                                                        : sanitiseValue(_.get(p, k))}
                                                 </SUITable.Cell>
                                             ))}
                                         {sgidx === 0 &&
@@ -364,12 +370,14 @@ const ProjectGrid: React.FunctionComponent<ProjectGridProps> = ({
                                                     key={`${s.id}sample.${k}`}
                                                     rowSpan={samplesRowSpan}
                                                 >
-                                                    {k === 'external_id' || k === 'id' ? (
+                                                    {k === 'external_ids' || k === 'id' ? (
                                                         <SampleLink
                                                             id={s.id}
                                                             projectName={projectName}
                                                         >
-                                                            {sanitiseValue(_.get(s, k))}
+                                                            {k === 'external_ids'
+                                                                ? formatExternalIds(s.external_ids)
+                                                                : sanitiseValue(s.id)}
                                                         </SampleLink>
                                                     ) : (
                                                         sanitiseValue(_.get(s, k))