feat(config, website): multi-seg, multi-ref searchUI mockup

integration-tests/tests/pages/search.page.ts

@@ -59,13 +59,16 @@ export class SearchPage {
     }
 
     async selectReference(fieldLabel: string, option: string) {
-        const select = this.page.getByRole('combobox', { name: fieldLabel });
+        const outer = this.page.locator('details', {
+            has: this.page.locator('summary', { hasText: 'Sequence Metadata Filters' }),
+        });
+        const select = outer.getByRole('combobox', { name: fieldLabel });
         await select.focus();
         await this.page.waitForTimeout(500);
         await select.selectOption({ value: option });
         await expect(select).toHaveValue(option);
 
-        const mutations = this.page.getByRole('combobox', { name: 'Mutations' }).first();
+        const mutations = outer.getByRole('combobox', { name: 'Mutations' }).first();
         await expect(mutations).toBeVisible();
         await expect(mutations).toBeEnabled();
     }
@@ -102,6 +105,27 @@ export class SearchPage {
         await this.page.keyboard.press('Escape');
     }
 
+    async enterSegmentedMutation(mutation: string, segment: string) {
+        const outer = this.page.locator('details', {
+            has: this.page.locator('summary', { hasText: 'Sequence Metadata Filters' }),
+        });
+        const innerS = outer.locator('details', {
+            has: this.page.locator('summary', { hasText: new RegExp(`^${segment}$`) }),
+        });
+        await innerS.locator('summary', { hasText: new RegExp(`^${segment}$`) }).click();
+        await expect(innerS).toHaveAttribute('open', '');
+        await expect(innerS.getByText('Mutations', { exact: true })).toBeVisible();
+        const input = innerS.locator('input#mutField');
+        await expect(input).toBeVisible();
+        await expect(input).toBeEditable();
+        await input.click();
+        await input.fill(mutation);
+        const optionRegex = new RegExp(`^${mutation}(\\([0-9,]+\\))?$`);
+        const matchingOption = innerS.getByRole('option', { name: optionRegex }).first();
+        await matchingOption.click({ timeout: 2000 });
+        await this.page.keyboard.press('Escape');
+    }
+
     async enterAccessions(accessions: string) {
         // Target the main accession textbox (avoid header/nav widgets)
         const accessionField = this.page.getByRole('textbox', {

integration-tests/tests/specs/features/search/active-filters.dependent.spec.ts

@@ -39,7 +39,7 @@ test.describe('Search', () => {
     test('multi-segment mutation filter can be added and removed', async ({ page }) => {
         const mutation = 'S:G100A';
         await searchPage.cchf();
-        await searchPage.enterMutation(mutation);
+        await searchPage.enterSegmentedMutation(mutation, 'S');
         await expect(page.getByText(`mutation:${mutation}`)).toBeVisible();
         await page.getByLabel('remove filter').click();
         await expect(page.getByText(`mutation:${mutation}`)).toBeHidden();

kubernetes/loculus/templates/_common-metadata.tpl

@@ -327,6 +327,12 @@ organisms:
     html: {{ .customDisplay.html }}
     {{- end }}
   {{- end }}
+  {{- if .metadataScope }}
+  metadataScope: {{ .metadataScope }}
+  {{- end }}
+  {{- if .sequenceMetadataScope }}
+  sequenceMetadataScope: {{ .sequenceMetadataScope }}
+  {{- end }}
 {{- end }}
 
 {{/* Generate website metadata from passed metadata array */}}
@@ -350,6 +356,9 @@ fields:
   {{- else }}
   header: {{ printf "%s %s" (default "Other" .header) $segment | quote }}
   {{- end }}
+  {{- if eq .metadataScope "sequence" }}
+  sequenceMetadataScope: {{ $segment }}
+  {{- end }}
 {{- end }}
 {{- end }}
 {{- else }}

kubernetes/loculus/values.schema.json

@@ -134,6 +134,17 @@
           "type": "boolean",
           "description": "If true, the field is initially visible in the UI."
         },
+        "metadataScope": {
+          "groups": ["metadata"],
+          "type": "string",
+          "enum": ["sample", "sequence"],
+          "description": "The scope of the metadata field, e.g., sample or sequence. Sample is the default."
+        },
+        "sequenceMetadataScope": {
+          "groups": ["metadata"],
+          "type": "string",
+          "description": "The scope of the sequence metadata field, can be set to any of the segment names defined for the organism."
+        },
         "hideOnSequenceDetailsPage": {
           "groups": ["metadata"],
           "type": "boolean",

kubernetes/loculus/values.yaml

@@ -1135,15 +1135,6 @@ defaultOrganismConfig: &defaultOrganismConfig
         displayName: Diagnostic measurement unit
         orderOnDetailsPage: 2600
         header: Diagnostics
-      - name: length
-        type: int
-        header: "Alignment and QC metrics"
-        noInput: true
-        rangeSearch: true
-        initiallyVisible: true
-        perSegment: true
-        displayName: Length
-        orderOnDetailsPage: 2700
       - name: hostNameScientific
         generateIndex: true
         autocomplete: true
@@ -1216,8 +1207,19 @@ defaultOrganismConfig: &defaultOrganismConfig
         header: "INSDC"
         orderOnDetailsPage: 1120
         ingest: ncbiSraAccessions
+      - name: length
+        type: int
+        metadataScope: sequence
+        header: "Alignment and QC metrics"
+        noInput: true
+        rangeSearch: true
+        initiallyVisible: true
+        perSegment: true
+        displayName: Length
+        orderOnDetailsPage: 2700
       - name: totalSnps
         type: int
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         rangeSearch: true
@@ -1228,6 +1230,7 @@ defaultOrganismConfig: &defaultOrganismConfig
           inputs: {input: nextclade.totalSubstitutions}
       - name: totalInsertedNucs
         type: int
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         rangeSearch: true
@@ -1238,6 +1241,7 @@ defaultOrganismConfig: &defaultOrganismConfig
           inputs: {input: nextclade.totalInsertions}
       - name: totalDeletedNucs
         type: int
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         rangeSearch: true
@@ -1248,6 +1252,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         displayName: Total deleted nucs
       - name: totalAmbiguousNucs
         type: int
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         rangeSearch: true
@@ -1259,6 +1264,7 @@ defaultOrganismConfig: &defaultOrganismConfig
       - name: totalUnknownNucs
         orderOnDetailsPage: 2800
         type: int
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         rangeSearch: true
@@ -1267,6 +1273,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         preprocessing:
           inputs: {input: nextclade.totalMissing}
       - name: totalFrameShifts
+        metadataScope: sequence
         type: int
         rangeSearch: true
         header: "Alignment and QC metrics"
@@ -1277,6 +1284,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         preprocessing:
           inputs: {input: nextclade.totalFrameShifts}
       - name: frameShifts
+        metadataScope: sequence
         header: "Alignment and QC metrics"
         noInput: true
         perSegment: true
@@ -1285,6 +1293,7 @@ defaultOrganismConfig: &defaultOrganismConfig
         preprocessing:
           inputs: {input: nextclade.frameShifts}
       - name: totalStopCodons
+        metadataScope: sequence
         perSegment: true
         displayName: Total stop codons
         type: int
@@ -1293,13 +1302,15 @@ defaultOrganismConfig: &defaultOrganismConfig
         preprocessing:
           inputs: {input: nextclade.qc.stopCodons.totalStopCodons}
       - name: stopCodons
+        metadataScope: sequence
         perSegment: true
         displayName: Stop codons
         header: "Alignment and QC metrics"
         noInput: true
         preprocessing:
           inputs: {input: nextclade.qc.stopCodons.stopCodons}
       - name: completeness
+        metadataScope: sequence
         type: float
         header: "Alignment and QC metrics"
         noInput: true
@@ -1416,6 +1427,7 @@ defaultOrganisms:
           url: "https://mapoplexus.genomium.org/?url={{[metadata+accessionVersion,accession,version,geoLocAdmin1,geoLocAdmin2,geoLocCity,geoLocCountry,geoLocSite,hostNameCommon,hostNameScientific,authors,sampleCollectionDate]}}"
       metadataAdd:
         - name: lineage
+          metadataScope: sequence
           header: "Lineage"
           noInput: true
           generateIndex: true
@@ -1533,9 +1545,11 @@ defaultOrganisms:
           autocomplete: true
           header: "Collection Details"
         - name: lineage
+          metadataScope: sequence
           initiallyVisible: false
           notSearchable: true
         - name: pangoLineage
+          metadataScope: sequence
           initiallyVisible: true
           displayName: "Pango lineage"
           autocomplete: true
@@ -1647,6 +1661,7 @@ defaultOrganisms:
             inputs:
               date: date
         - name: lineage
+          metadataScope: sequence
           initiallyVisible: true
           displayName: "Lineage"
           autocomplete: true
@@ -1740,6 +1755,8 @@ defaultOrganisms:
           ingest: ncbiHostName
           initiallyVisible: true
         - name: lineage
+          metadataScope: sequence
+          sequenceMetadataScope: S
           displayName: "Segment S Lineage"
           header: "Lineage"
           noInput: true
@@ -1854,6 +1871,7 @@ defaultOrganisms:
           ingest: ncbiHostName
           initiallyVisible: true
         - name: reference
+          metadataScope: sequence
           displayName: Reference
           noInput: true
           generateIndex: true
@@ -1980,6 +1998,8 @@ defaultOrganisms:
       metadataAdd:
         - &evMetadataAdd
           name: clade_cv_a16
+          metadataScope: sequence
+          sequenceMetadataScope: main
           displayName: Clade CV-A16
           onlyForReference: CV-A16
           header: "Clade"
@@ -1994,6 +2014,8 @@ defaultOrganisms:
             inputs: {input: nextclade.clade}
         - <<: *evMetadataAdd
           name: clade_cv_a10
+          metadataScope: sequence
+          sequenceMetadataScope: main
           displayName: Clade CV-A10
           onlyForReference: CV-A10
           preprocessing:
@@ -2002,6 +2024,8 @@ defaultOrganisms:
             inputs: {input: nextclade.clade}
         - <<: *evMetadataAdd
           name: clade_ev_a71
+          metadataScope: sequence
+          sequenceMetadataScope: main
           displayName: Clade EV-A71
           onlyForReference: EV-A71
           preprocessing:
@@ -2010,13 +2034,16 @@ defaultOrganisms:
             inputs: {input: nextclade.clade}
         - <<: *evMetadataAdd
           name: clade_ev_d68
+          metadataScope: sequence
+          sequenceMetadataScope: main
           displayName: Clade EV-D68
           onlyForReference: EV-D68
           preprocessing:
             args:
               reference: EV-D68
             inputs: {input: nextclade.clade}
         - name: genotype
+          metadataScope: sequence
           displayName: Genotype
           header: "Genotype"
           noInput: true

website/src/components/SearchPage/DownloadDialog/DownloadDialog.spec.tsx

@@ -371,7 +371,7 @@ describe('DownloadDialog', () => {
                 referenceIdentifierField: 'genotype',
             });
 
-            expect(screen.getByText('select a genotype display name', { exact: false })).toBeVisible();
+            expect(screen.getByText('select genotype display name', { exact: false })).toBeVisible();
             expect(screen.queryByLabelText(alignedNucleotideSequencesLabel)).not.toBeInTheDocument();
             expect(screen.queryByLabelText(alignedAminoAcidSequencesLabel)).not.toBeInTheDocument();
         });
@@ -452,6 +452,7 @@ describe('DownloadDialog', () => {
                 header: 'Group 1',
                 includeInDownloadsByDefault: true,
                 onlyForReference: 'ref1',
+                sequenceMetadataScope: 'main',
             },
             {
                 name: 'field2',
@@ -460,6 +461,7 @@ describe('DownloadDialog', () => {
                 header: 'Group 1',
                 includeInDownloadsByDefault: true,
                 onlyForReference: 'ref2',
+                sequenceMetadataScope: 'main',
             },
             {
                 name: ACCESSION_VERSION_FIELD,

website/src/components/SearchPage/DownloadDialog/DownloadDialog.tsx

@@ -69,7 +69,11 @@ export const DownloadDialog: FC<DownloadDialogProps> = ({
         return new Map(
             schema.metadata.map((field) => [
                 field.name,
-                new MetadataVisibility(selectedFields.has(field.name), field.onlyForReference),
+                new MetadataVisibility(
+                    selectedFields.has(field.name),
+                    field.onlyForReference,
+                    field.sequenceMetadataScope,
+                ),
             ]),
         );
     }, [selectedFields, schema]);