feat(website): add CCHF dashboard

resolves #528

backend/src/main/resources/application-dashboards-prod.yaml

@@ -176,6 +176,29 @@ dashboards:
         - url: "https://pathoplexus.org/ebola-zaire"
           label: "Browse data"
           menuIcon: "database"
+    cchf:
+      lapis:
+        url: "https://lapis.pathoplexus.org/cchf"
+        mainDateField: "sampleCollectionDateRangeLower"
+        locationFields:
+          - "geoLocCountry"
+          - "geoLocAdmin1"
+        hostField: "hostNameScientific"
+        authorAffiliationsField: "authorAffiliations"
+        authorsField: "authors"
+        additionalFilters:
+          versionStatus: "LATEST_VERSION"
+          isRevocation: "false"
+        accessionDownloadFields:
+          - "insdcAccessionFull"
+          - "accessionVersion"
+          - "dataUseTerms"
+          - "dataUseTermsUrl"
+          - "dataUseTermsRestrictedUntil"
+      externalNavigationLinks:
+        - url: "https://pathoplexus.org/cchf"
+          label: "Browse data"
+          menuIcon: "database"
   auth:
     github:
       clientId: "Iv23liLcTmoYOEje50sW"

backend/src/main/resources/application-dashboards-staging.yaml

@@ -176,6 +176,29 @@ dashboards:
         - url: "https://pathoplexus.org/ebola-zaire"
           label: "Browse data"
           menuIcon: "database"
+    cchf:
+      lapis:
+        url: "https://lapis.pathoplexus.org/cchf"
+        mainDateField: "sampleCollectionDateRangeLower"
+        locationFields:
+          - "geoLocCountry"
+          - "geoLocAdmin1"
+        hostField: "hostNameScientific"
+        authorAffiliationsField: "authorAffiliations"
+        authorsField: "authors"
+        additionalFilters:
+          versionStatus: "LATEST_VERSION"
+          isRevocation: "false"
+        accessionDownloadFields:
+          - "insdcAccessionFull"
+          - "accessionVersion"
+          - "dataUseTerms"
+          - "dataUseTermsUrl"
+          - "dataUseTermsRestrictedUntil"
+      externalNavigationLinks:
+        - url: "https://pathoplexus.org/cchf"
+          label: "Browse data"
+          menuIcon: "database"
   auth:
     github:
       clientId: "Iv23li4tJm7xQ3VkM3OC"

website/src/pages/cchf/compare-side-by-side.astro

@@ -0,0 +1,6 @@
+---
+import GenericCompareSideBySidePage from '../../components/views/compareSideBySide/GenericCompareSideBySidePage.astro';
+import { Organisms } from '../../types/Organism';
+---
+
+<GenericCompareSideBySidePage organism={Organisms.cchf} />

website/src/pages/cchf/compare-to-baseline.astro

@@ -0,0 +1,6 @@
+---
+import GenericCompareToBaselinePage from '../../components/views/compareToBaseline/GenericCompareToBaselinePage.astro';
+import { Organisms } from '../../types/Organism';
+---
+
+<GenericCompareToBaselinePage organism={Organisms.cchf} />

website/src/pages/cchf/compare-variants.astro

@@ -0,0 +1,6 @@
+---
+import GenericCompareVariantsPage from '../../components/views/compareVariants/GenericCompareVariantsPage.astro';
+import { Organisms } from '../../types/Organism';
+---
+
+<GenericCompareVariantsPage organism={Organisms.cchf} />

website/src/pages/cchf/index.astro

@@ -0,0 +1,11 @@
+---
+import { Organisms } from '../../types/Organism';
+import { ServerSide } from '../../views/serverSideRouting';
+import { singleVariantViewKey } from '../../views/viewKeys';
+
+return Astro.redirect(
+    ServerSide.routing
+        .getOrganismView(`${Organisms.cchf}.${singleVariantViewKey}`)
+        .pageStateHandler.getDefaultPageUrl(),
+);
+---

website/src/pages/cchf/sequencing-efforts.astro

@@ -0,0 +1,6 @@
+---
+import GenericSequencingEffortsPage from '../../components/views/sequencingEfforts/GenericSequencingEffortsPage.astro';
+import { Organisms } from '../../types/Organism';
+---
+
+<GenericSequencingEffortsPage organism={Organisms.cchf} />

website/src/pages/cchf/single-variant.astro

@@ -0,0 +1,6 @@
+---
+import GenericAnalyzeSingleVariantPage from '../../components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro';
+import { Organisms } from '../../types/Organism';
+---
+
+<GenericAnalyzeSingleVariantPage organism={Organisms.cchf} />

website/src/types/Organism.ts

@@ -9,6 +9,7 @@ export const Organisms = {
     rsvB: 'rsvB' as const,
     mpox: 'mpox' as const,
     ebolaZaire: 'ebolaZaire' as const,
+    cchf: 'cchf' as const,
 };
 
 export const organismConfig = {
@@ -84,6 +85,15 @@ export const organismConfig = {
         menuListEntryDecoration: 'hover:decoration-wine',
         borderEntryDecoration: 'hover:border-wine',
     },
+    [Organisms.cchf]: {
+        organism: Organisms.cchf,
+        pathFragment: 'cchf',
+        label: 'Crimean-Congo Hemorrhagic Fever Virus',
+        backgroundColor: 'bg-oliveMuted',
+        backgroundColorFocus: 'group-hover:bg-olive',
+        menuListEntryDecoration: 'hover:decoration-olive',
+        borderEntryDecoration: 'hover:border-olive',
+    },
 };
 export const allOrganisms = Object.keys(organismConfig) as Organism[];
 export type Organism = keyof typeof organismConfig;

website/src/views/cchf.ts

@@ -0,0 +1,135 @@
+import { type DateRangeOption, dateRangeOptionPresets } from '@genspectrum/dashboard-components/util';
+
+import { type CompareSideBySideData, type DatasetAndVariantData, type Id } from './View.ts';
+import { type OrganismsConfig } from '../config.ts';
+import {
+    BaseView,
+    GenericCompareToBaselineView,
+    GenericCompareVariantsView,
+    GenericSequencingEffortsView,
+    GenericSingleVariantView,
+} from './BaseView.ts';
+import { getPathoplexusAdditionalSequencingEffortsFields, type ExtendedConstants } from './OrganismConstants.ts';
+import { compareSideBySideViewConstants } from './ViewConstants.ts';
+import type { LineageFilterConfig } from '../components/pageStateSelectors/LineageFilterInput.tsx';
+import { organismConfig, Organisms } from '../types/Organism.ts';
+import { type DataOrigin, dataOrigins } from '../types/dataOrigins.ts';
+import { GenericCompareSideBySideStateHandler } from './pageStateHandlers/CompareSideBySidePageStateHandler.ts';
+
+class CchfConstants implements ExtendedConstants {
+    public readonly organism = Organisms.cchf;
+    public readonly earliestDate = '1956-01-01';
+    public readonly defaultDateRange = dateRangeOptionPresets.lastYear;
+    public readonly dateRangeOptions: DateRangeOption[] = [
+        dateRangeOptionPresets.lastMonth,
+        dateRangeOptionPresets.last2Months,
+        dateRangeOptionPresets.last3Months,
+        dateRangeOptionPresets.last6Months,
+        dateRangeOptionPresets.lastYear,
+        { label: 'Since 2020', dateFrom: '2020-01-01' },
+        { label: '2010-2019', dateFrom: '2010-01-01', dateTo: '2019-12-31' },
+        { label: '2000-2009', dateFrom: '2000-01-01', dateTo: '2009-12-31' },
+        { label: 'Since 2000', dateFrom: '2000-01-01' },
+        { label: 'Before 2000', dateFrom: this.earliestDate, dateTo: '1999-12-31' },
+        { label: 'All times', dateFrom: this.earliestDate },
+    ];
+    public readonly mainDateField: string;
+    public readonly locationFields: string[];
+    public readonly lineageFilters: LineageFilterConfig[] = [];
+    public readonly useAdvancedQuery = false;
+    public readonly hostField: string;
+    public readonly authorsField: string | undefined;
+    public readonly authorAffiliationsField: string | undefined;
+    public readonly accessionDownloadFields;
+
+    public get additionalSequencingEffortsFields() {
+        return getPathoplexusAdditionalSequencingEffortsFields(this);
+    }
+
+    public readonly additionalFilters: Record<string, string> | undefined;
+    public readonly dataOrigins: DataOrigin[] = [dataOrigins.pathoplexus];
+
+    constructor(organismsConfig: OrganismsConfig) {
+        this.mainDateField = organismsConfig.cchf.lapis.mainDateField;
+        this.locationFields = organismsConfig.cchf.lapis.locationFields;
+        this.hostField = organismsConfig.cchf.lapis.hostField;
+        this.authorsField = organismsConfig.cchf.lapis.authorsField;
+        this.authorAffiliationsField = organismsConfig.cchf.lapis.authorAffiliationsField;
+        this.additionalFilters = organismsConfig.cchf.lapis.additionalFilters;
+        this.accessionDownloadFields = organismsConfig.cchf.lapis.accessionDownloadFields;
+    }
+}
+
+export class CchfAnalyzeSingleVariantView extends GenericSingleVariantView<CchfConstants> {
+    constructor(organismsConfig: OrganismsConfig) {
+        super(new CchfConstants(organismsConfig));
+    }
+}
+
+export class CchfCompareSideBySideView extends BaseView<
+    CompareSideBySideData,
+    CchfConstants,
+    GenericCompareSideBySideStateHandler
+> {
+    constructor(organismsConfig: OrganismsConfig) {
+        const constants = new CchfConstants(organismsConfig);
+        const defaultPageState = {
+            filters: new Map<Id, DatasetAndVariantData>([
+                [
+                    0,
+                    {
+                        datasetFilter: {
+                            location: {},
+                            dateRange: constants.defaultDateRange,
+                        },
+                        variantFilter: {
+                            lineages: {},
+                            mutations: {},
+                        },
+                    },
+                ],
+                [
+                    1,
+                    {
+                        datasetFilter: {
+                            location: {},
+                            dateRange: constants.defaultDateRange,
+                        },
+                        variantFilter: {
+                            lineages: {},
+                            mutations: {},
+                        },
+                    },
+                ],
+            ]),
+        };
+
+        super(
+            constants,
+            new GenericCompareSideBySideStateHandler(
+                constants,
+                defaultPageState,
+                organismConfig[constants.organism].pathFragment,
+            ),
+            compareSideBySideViewConstants,
+        );
+    }
+}
+
+export class CchfSequencingEffortsView extends GenericSequencingEffortsView<CchfConstants> {
+    constructor(organismsConfig: OrganismsConfig) {
+        super(new CchfConstants(organismsConfig));
+    }
+}
+
+export class CchfCompareVariantsView extends GenericCompareVariantsView<CchfConstants> {
+    constructor(organismsConfig: OrganismsConfig) {
+        super(new CchfConstants(organismsConfig));
+    }
+}
+
+export class CchfCompareToBaselineView extends GenericCompareToBaselineView<CchfConstants> {
+    constructor(organismsConfig: OrganismsConfig) {
+        super(new CchfConstants(organismsConfig));
+    }
+}

website/src/views/routing.ts

@@ -1,5 +1,12 @@
 import type { OrganismConstants } from './OrganismConstants.ts';
 import type { View } from './View.ts';
+import {
+    CchfAnalyzeSingleVariantView,
+    CchfCompareSideBySideView,
+    CchfCompareToBaselineView,
+    CchfCompareVariantsView,
+    CchfSequencingEffortsView,
+} from './cchf.ts';
 import {
     CovidAnalyzeSingleVariantView,
     CovidCompareSideBySideView,
@@ -136,6 +143,13 @@ export class Routing {
                 [compareVariantsViewKey]: new EbolaZaireCompareVariantsView(organismsConfig),
                 [compareToBaselineViewKey]: new EbolaZaireCompareToBaselineView(organismsConfig),
             },
+            [Organisms.cchf]: {
+                [singleVariantViewKey]: new CchfAnalyzeSingleVariantView(organismsConfig),
+                [compareSideBySideViewKey]: new CchfCompareSideBySideView(organismsConfig),
+                [sequencingEffortsViewKey]: new CchfSequencingEffortsView(organismsConfig),
+                [compareVariantsViewKey]: new CchfCompareVariantsView(organismsConfig),
+                [compareToBaselineViewKey]: new CchfCompareToBaselineView(organismsConfig),
+            },
         } as const;
 
         this.externalPages = this.initializeExternalPages(organismsConfig);
@@ -159,6 +173,8 @@ export class Routing {
                 return Object.values(this.views[Organisms.mpox]);
             case Organisms.ebolaZaire:
                 return Object.values(this.views[Organisms.ebolaZaire]);
+            case Organisms.cchf:
+                return Object.values(this.views[Organisms.cchf]);
         }
     }
 

website/tests/compareVariants.spec.ts

@@ -13,6 +13,7 @@ const organismOptions = {
     [Organisms.rsvB]: { lineage: 'B.D.E.1', lineageFieldPlaceholder: 'Lineage' },
     [Organisms.mpox]: { lineage: 'F.1', lineageFieldPlaceholder: 'Lineage' },
     [Organisms.ebolaZaire]: { mutation: 'T18365C' },
+    [Organisms.cchf]: { mutation: 'M:G3565A' },
 };
 
 test.describe('The Compare Variants page', () => {

website/tests/sequencingEfforts.spec.ts

@@ -12,6 +12,7 @@ const organismOptions = {
     [Organisms.rsvB]: { location: 'USA' },
     [Organisms.mpox]: { location: 'USA' },
     [Organisms.ebolaZaire]: { location: 'USA' },
+    [Organisms.cchf]: { location: 'Turkey' },
 };
 
 test.describe('The Sequencing Efforts Page', () => {
@@ -24,8 +25,8 @@ test.describe('The Sequencing Efforts Page', () => {
 
                 await sequencingEffortsPage.goto(organism);
                 await sequencingEffortsPage.expectToSeeNoComponentErrors();
-                await sequencingEffortsPage.selectLocation(options.location);
                 await sequencingEffortsPage.selectDateRange('All times');
+                await sequencingEffortsPage.selectLocation(options.location);
                 await sequencingEffortsPage.submitFilters();
 
                 await expect(sequencingEffortsPage.diagramTitle('Number Sequences')).toBeVisible();