Update prod from main

.github/workflows/e2e.yml

@@ -37,14 +37,14 @@ jobs:
       run: echo "branchTag=${TAG##*:}" >> $GITHUB_OUTPUT
 
     - name: Wait for website Docker image
-      uses: lewagon/wait-on-check-action@v1.3.4
+      uses: lewagon/wait-on-check-action@v1.4.0
       with:
         ref: ${{ github.sha }}
         check-name: Build Website Docker Image
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         wait-interval: 10
     - name: Wait for backend Docker image
-      uses: lewagon/wait-on-check-action@v1.3.4
+      uses: lewagon/wait-on-check-action@v1.4.0
       with:
         ref: ${{ github.sha }}
         check-name: Build Backend Docker Image

website/package.json

@@ -50,7 +50,7 @@
         "@testing-library/dom": "^10.4.0",
         "@testing-library/jest-dom": "^6.6.3",
         "@testing-library/react": "^16.3.0",
-        "@types/node": "^22.15.30",
+        "@types/node": "^24.0.3",
         "@types/react": "^18.3.12",
         "@types/react-dom": "^18.3.1",
         "@types/topojson-specification": "^1.0.5",

website/src/components/InfluenzaInformation.astro

@@ -0,0 +1,114 @@
+---
+import Link from './Link.astro';
+
+interface Props {
+    type: string;
+}
+
+const { type } = Astro.props;
+---
+
+<div>
+    <details>
+        <summary class='cursor-pointer font-bold'>How We Process Influenza Data</summary>
+        {
+            type === 'A' && (
+                <p class='mb-4'>
+                    Genspectrum uses all open influenza A data that is available on the INSDC (taxonid: 197911). To
+                    classify influenza segments and subtypes we use nextclade sort (using half of all k-mers for each
+                    subtype defined in{' '}
+                    <Link href='https://github.com/anna-parker/InfluenzaAReferenceDB/blob/main/config/config.yaml'>
+                        https://github.com/anna-parker/InfluenzaAReferenceDB
+                    </Link>
+                    ) to improve classification). Where available we use the assembly information to group segments that
+                    are from the same sample/isolate. For all remaining segments we use a heuristic grouping algorithm
+                    to group all segments from the same sample/isolate using the metadata available from each segment.
+                </p>
+            )
+        }
+        {
+            type === 'B' && (
+                <p class='mb-4'>
+                    Genspectrum uses all open influenza B data that is available on the INSDC (taxonid: 11520). To
+                    classify influenza segments and lineages we use nextclade sort (using half off all k-mers for each
+                    lineage defined in
+                    https://github.com/anna-parker/InfluenzaAReferenceDB/blob/main/influenza-b/config/config.yaml).
+                    Where available we use the assembly information to group segments that are from the same
+                    sample/isolate. For all remaining segments we use a heuristic grouping algorithm to group all
+                    segments from the same sample/isolate using the metadata available from each segment.
+                </p>
+            )
+        }
+    </details>
+    <details>
+        <summary class='cursor-pointer font-bold'>Protein Functions Explained</summary>
+        {
+            type === 'A' && (
+                <div>
+                    <ul class='mb-4 list-inside list-disc'>
+                        <li>Segment 1: PB2 protein (part of the RNA polymerase subunit).</li>
+                        <li>Segment 2: PB1 protein (part of the RNA polymerase subunit).</li>
+                        <li>Segment 3: PA protein (part of the RNA polymerase subunit).</li>
+                        <li>
+                            Segment 4: HA protein (hemagglutinin, part of the envelope, functions as an attachment
+                            factor and membrane fusion protein. It is responsible for binding influenza to sialic acid
+                            on the surface of target cells in the upper respiratory tract.)
+                        </li>
+                        <li>
+                            Segment 5: NP protein (nucleoprotein, at start of infection binds with RNA to enter host
+                            cell nucleus where it is transcribed and replicated).
+                        </li>
+                        <li>
+                            Segment 6: NA protein (Neuraminidase, part of the envelope, is an enzyme that breaks
+                            glycosidic bonds in molecules called neuraminic acids (often found as sialic acids). This
+                            helps the new virus particles leave the infected cell and spread to other cells).
+                        </li>
+                        <li>
+                            Segment 7: M1 and M2 proteins (M1 forms the capsid - a layer between the nucleoprotein and
+                            the envelope, M2 a proton channel protein).
+                        </li>
+                        <li>Segment 8: NS1 and NEP proteins (non-structural protein and nuclear export protein)</li>
+                    </ul>
+                    <p class='mb-4'>
+                        For each individual influenza subtype you can view the CDS of each protein in the genome data
+                        viewer.
+                    </p>
+                </div>
+            )
+        }
+        {
+            type === 'B' && (
+                <div>
+                    <ul class='mb-4 list-inside list-disc'>
+                        <li>Segment 1: PB1 protein (part of the RNA polymerase subunit).</li>
+                        <li>Segment 2: PB2 protein (part of the RNA polymerase subunit).</li>
+                        <li>Segment 3: PA protein (part of the RNA polymerase subunit).</li>
+                        <li>
+                            Segment 4: HA protein (hemagglutinin, functions as an attachment factor and membrane fusion
+                            protein. It is responsible for binding influenza to sialic acid on the surface of target
+                            cells in the upper respiratory tract.)
+                        </li>
+                        <li>
+                            Segment 5: NP protein (nucleoprotein, at start of infection binds with RNA to enter host
+                            cell nucleus where it is transcribed and replicated).
+                        </li>
+                        <li>
+                            Segment 6: NA protein (Neuraminidase is an enzyme that breaks glycosidic bonds in molecules
+                            called neuraminic acids (often found as sialic acids). This helps the new virus particles
+                            leave the infected cell and spread to other cells).
+                        </li>
+                        <li>
+                            Segment 7: M1 and M2 proteins (M1 forms the capsid - a layer between the nucleoprotein and
+                            the envelope, M2 a proton channel protein).
+                        </li>
+                        <li>Segment 8: NS1 and NEP proteins (non-structural protein and nuclear export protein)</li>
+                    </ul>
+                    <p class='mb-4'>
+                        For each individual influenza lineage you can view the CDS of each protein in the genome data
+                        viewer.
+                    </p>
+                </div>
+            )
+        }
+    </details>
+</div>

website/src/components/genspectrum/GsNumberSequencesOverTime.tsx

@@ -1,13 +1,15 @@
 import '@genspectrum/dashboard-components/components';
 import type { NamedLapisFilter } from '@genspectrum/dashboard-components/util';
 
+import { ComponentWrapper } from '../ComponentWrapper.tsx';
+
 type Views = 'bar' | 'line' | 'table';
 
 type TemporalGranularity = 'day' | 'week' | 'month' | 'year';
 
 export function GsNumberSequencesOverTime({
     lapisDateField,
-    lapisFilter,
+    lapisFilters,
     views,
     width,
     height,
@@ -16,7 +18,7 @@ export function GsNumberSequencesOverTime({
     pageSize,
 }: {
     lapisDateField: string;
-    lapisFilter: NamedLapisFilter[];
+    lapisFilters: NamedLapisFilter[];
     views?: Views[];
     width?: string;
     height?: string;
@@ -25,15 +27,17 @@ export function GsNumberSequencesOverTime({
     pageSize?: boolean | number;
 }) {
     return (
-        <gs-number-sequences-over-time
-            lapisFilter={JSON.stringify(lapisFilter)}
-            lapisDateField={lapisDateField}
-            views={JSON.stringify(views)}
-            width={width}
-            height={height}
-            granularity={granularity}
-            smoothingWindow={smoothingWindow}
-            pageSize={pageSize}
-        ></gs-number-sequences-over-time>
+        <ComponentWrapper title='Number sequences' height={height}>
+            <gs-number-sequences-over-time
+                lapisFilters={JSON.stringify(lapisFilters)}
+                lapisDateField={lapisDateField}
+                views={JSON.stringify(views)}
+                width={width}
+                height={height}
+                granularity={granularity}
+                smoothingWindow={smoothingWindow}
+                pageSize={pageSize}
+            ></gs-number-sequences-over-time>
+        </ComponentWrapper>
     );
 }

website/src/components/genspectrum/GsSequencesByLocation.tsx

@@ -0,0 +1,55 @@
+import { type LapisFilter } from '@genspectrum/dashboard-components/util';
+import type { FC } from 'react';
+
+import { getSequencesByLocationMapData } from '../../util/getSequencesByLocationMapData';
+import { defaultTablePageSize } from '../../views/View';
+import { ComponentWrapper } from '../ComponentWrapper.tsx';
+
+export type GsSequencesByLocationProps = {
+    title: string;
+    lapisLocationField: string;
+    lapisFilter: LapisFilter;
+    height?: string;
+    mapName?: string;
+    pageSize?: number;
+};
+
+export const GsSequencesByLocation: FC<GsSequencesByLocationProps> = ({
+    title,
+    height,
+    lapisLocationField,
+    lapisFilter,
+    mapName,
+    pageSize,
+}) => {
+    const mapData = getSequencesByLocationMapData(mapName, window.location.href);
+
+    return (
+        <ComponentWrapper title={title} height={height}>
+            {mapData === undefined ? (
+                <gs-sequences-by-location
+                    lapisLocationField={lapisLocationField}
+                    lapisFilter={JSON.stringify(lapisFilter)}
+                    pageSize={pageSize ?? defaultTablePageSize}
+                    views={JSON.stringify(['table'])}
+                    width='100%'
+                    height={height ? '100%' : undefined}
+                />
+            ) : (
+                <gs-sequences-by-location
+                    lapisLocationField={lapisLocationField}
+                    lapisFilter={JSON.stringify(lapisFilter)}
+                    pageSize={pageSize ?? defaultTablePageSize}
+                    views={JSON.stringify(['map', 'table'])}
+                    mapSource={JSON.stringify(mapData.mapSource)}
+                    width='100%'
+                    height={height ? '100%' : undefined}
+                    zoom={mapData.zoom}
+                    offsetX={mapData.offsetX}
+                    offsetY={mapData.offsetY}
+                    enableMapNavigation
+                />
+            )}
+        </ComponentWrapper>
+    );
+};

website/src/components/pageStateSelectors/BaselineSelector.tsx

@@ -100,14 +100,18 @@ export function BaselineSelector({
                                             },
                                         });
                                     }}
-                                    lapisFilter={lapisFilter}
+                                    lapisFilter={{ ...lapisFilter, [config.lapisField]: undefined }}
                                 />
                             </label>
                         );
                     }
                     case 'location': {
                         const filterIdentifier = locationFieldsToFilterIdentifier(config.locationFields);
 
+                        const lapisFilerWithoutLocationFields = Object.fromEntries(
+                            Object.entries(lapisFilter).filter(([key]) => !config.locationFields.includes(key)),
+                        );
+
                         return (
                             <label className='form-control' key={`label${filterIdentifier}`}>
                                 <div className='label'>
@@ -126,7 +130,7 @@ export function BaselineSelector({
                                     }}
                                     value={datasetFilter.locationFilters[filterIdentifier]}
                                     placeholderText={config.placeholderText}
-                                    lapisFilter={lapisFilter}
+                                    lapisFilter={lapisFilerWithoutLocationFields}
                                 ></GsLocationFilter>
                             </label>
                         );

website/src/components/pageStateSelectors/VariantSelector.tsx

@@ -91,7 +91,7 @@ export function VariantSelector({
                                 });
                             }}
                             key={lineageFilterConfig.lapisField}
-                            lapisFilter={lapisFilter}
+                            lapisFilter={{ ...lapisFilter, [lineageFilterConfig.lapisField]: undefined }}
                             value={variantFilter.lineages?.[lineageFilterConfig.lapisField]}
                         />
                     ))}

website/src/components/subscriptions/create/FilterDisplay.tsx

@@ -38,7 +38,7 @@ export function FilterDisplay({
                         <h2 className='component-title'>Count over time</h2>
                         <div className='h-[400px]'>
                             <GsNumberSequencesOverTime
-                                lapisFilter={[
+                                lapisFilters={[
                                     {
                                         displayName: 'Your variant',
                                         lapisFilter: addDateWindowToFilter(