refactor(website): replace hardcoded wasapPageConfig references with config struct referenced by organism name

website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx

@@ -13,47 +13,47 @@ import { LabeledField } from './utils/LabeledField';
 import { RadioSelect } from './utils/RadioSelect';
 import { getCladeLineages } from '../../../lapis/getCladeLineages';
 import { Inset } from '../../../styles/Inset';
-import { wastewaterConfig } from '../../../types/wastewaterConfig';
 import { recentDaysDateRangeOptions } from '../../../util/recentDaysDateRangeOptions';
 import { type PageStateHandler } from '../../../views/pageStateHandlers/PageStateHandler';
-import {
-    type WasapFilter,
-    type WasapAnalysisMode,
-    defaultManualFilter,
-    defaultVariantFilter,
-    defaultResistanceFilter,
-    defaultUntrackedFilter,
-    type WasapBaseFilter,
-    type WasapAnalysisFilter,
-} from '../../../views/pageStateHandlers/WasapPageStateHandler';
 import { GsTextFilter } from '../../genspectrum/GsTextFilter';
+import type {
+    WasapAnalysisFilter,
+    WasapAnalysisMode,
+    WasapBaseFilter,
+    WasapFilter,
+    WasapPageConfig,
+} from '../../views/wasap/wasapPageConfig';
 
 /**
  * The root filter control for the W-ASAP dashboard.
  * Uses sub filter components for the different modes, in the 'filters' directory.
  */
 export function WasapPageStateSelector({
+    config,
     pageStateHandler,
     initialBaseFilterState,
     initialAnalysisFilterState,
 }: {
+    config: WasapPageConfig;
     pageStateHandler: PageStateHandler<WasapFilter>;
     initialBaseFilterState: WasapBaseFilter;
     initialAnalysisFilterState: WasapAnalysisFilter;
 }) {
     const [baseFilterState, setBaseFilterState] = useState(initialBaseFilterState);
 
     const [manualFilter, setManualFilter] = useState(
-        initialAnalysisFilterState.mode === 'manual' ? initialAnalysisFilterState : defaultManualFilter,
+        initialAnalysisFilterState.mode === 'manual' ? initialAnalysisFilterState : config.filterDefaults.manual,
     );
     const [variantFilter, setVariantFilter] = useState(
-        initialAnalysisFilterState.mode === 'variant' ? initialAnalysisFilterState : defaultVariantFilter,
+        initialAnalysisFilterState.mode === 'variant' ? initialAnalysisFilterState : config.filterDefaults.variant,
     );
     const [resistanceFilter, setResistanceFilter] = useState(
-        initialAnalysisFilterState.mode === 'resistance' ? initialAnalysisFilterState : defaultResistanceFilter,
+        initialAnalysisFilterState.mode === 'resistance'
+            ? initialAnalysisFilterState
+            : config.filterDefaults.resistance,
     );
     const [untrackedFilter, setUntrackedFilter] = useState(
-        initialAnalysisFilterState.mode === 'untracked' ? initialAnalysisFilterState : defaultUntrackedFilter,
+        initialAnalysisFilterState.mode === 'untracked' ? initialAnalysisFilterState : config.filterDefaults.untracked,
     );
 
     const [selectedAnalysisMode, setSelectedAnalysisMode] = useState(initialAnalysisFilterState.mode);
@@ -73,12 +73,13 @@ export function WasapPageStateSelector({
 
     // data for the 'untracked' analysis mode - loaded here already so it's available when the mode is selected
     const cladeLineageQueryResult = useQuery({
+        enabled: config.enabledAnalysisModes.includes('untracked'),
         queryKey: ['cladeLineages'],
         queryFn: () =>
             getCladeLineages(
-                wastewaterConfig.wasap.covSpectrum.lapisBaseUrl,
-                wastewaterConfig.wasap.covSpectrum.cladeField,
-                wastewaterConfig.wasap.covSpectrum.lineageField,
+                config.clinicalLapis.lapisBaseUrl,
+                config.clinicalLapis.cladeField,
+                config.clinicalLapis.lineageField,
                 true,
             ),
     });
@@ -90,7 +91,7 @@ export function WasapPageStateSelector({
                 <LabeledField label='Sampling location'>
                     <GsTextFilter
                         placeholderText='Sampling location'
-                        lapisField={wastewaterConfig.wasap.locationNameField}
+                        lapisField={config.locationNameField}
                         lapisFilter={{}}
                         onInputChange={({ locationName }) => {
                             setBaseFilterState({ ...baseFilterState, locationName });
@@ -101,8 +102,8 @@ export function WasapPageStateSelector({
 
                 <DynamicDateFilter
                     label='Sampling date'
-                    lapis={wastewaterConfig.wasap.lapisBaseUrl}
-                    dateFieldName={wastewaterConfig.wasap.samplingDateField}
+                    lapis={config.lapisBaseUrl}
+                    dateFieldName={config.samplingDateField}
                     generateOptions={recentDaysDateRangeOptions}
                     value={baseFilterState.samplingDate}
                     onChange={(newDateRange?) => setBaseFilterState({ ...baseFilterState, samplingDate: newDateRange })}
@@ -139,10 +140,11 @@ export function WasapPageStateSelector({
                     setSelectedAnalysisMode(e.target.value as WasapAnalysisMode);
                 }}
             >
-                <option value='manual'>Manual</option>
-                <option value='resistance'>Resistance Mutations</option>
-                <option value='variant'>Variant Explorer</option>
-                <option value='untracked'>Untracked Mutations</option>
+                {config.enabledAnalysisModes.map((mode) => (
+                    <option key={mode} value={mode}>
+                        {modeLabel(mode)}
+                    </option>
+                ))}
             </select>
             <Inset className='p-2'>
                 {(() => {
@@ -154,22 +156,25 @@ export function WasapPageStateSelector({
                                 <VariantExplorerFilter
                                     pageState={variantFilter}
                                     setPageState={setVariantFilter}
-                                    clinicalSequenceLapisBaseUrl={wastewaterConfig.wasap.covSpectrum.lapisBaseUrl}
+                                    clinicalSequenceLapisBaseUrl={config.clinicalLapis.lapisBaseUrl}
+                                    clinicalSequenceLapisLineageField={config.clinicalLapis.lineageField}
                                 />
                             );
                         case 'resistance':
                             return (
                                 <ResistanceMutationsFilter
                                     pageState={resistanceFilter}
                                     setPageState={setResistanceFilter}
+                                    resistanceMutationSets={config.resistanceMutationSets}
                                 />
                             );
                         case 'untracked':
                             return (
                                 <UntrackedFilter
                                     pageState={untrackedFilter}
                                     setPageState={setUntrackedFilter}
-                                    clinicalSequenceLapisBaseUrl={wastewaterConfig.wasap.covSpectrum.lapisBaseUrl}
+                                    clinicalSequenceLapisBaseUrl={config.clinicalLapis.lapisBaseUrl}
+                                    clinicalSequenceLapisLineageField={config.clinicalLapis.lineageField}
                                     cladeLineageQueryResult={cladeLineageQueryResult}
                                 />
                             );
@@ -180,3 +185,16 @@ export function WasapPageStateSelector({
         </div>
     );
 }
+
+function modeLabel(mode: WasapAnalysisMode): string {
+    switch (mode) {
+        case 'manual':
+            return 'Manual';
+        case 'resistance':
+            return 'Resistance Mutations';
+        case 'variant':
+            return 'Variant Explorer';
+        case 'untracked':
+            return 'Untracked Mutations';
+    }
+}

website/src/components/pageStateSelectors/wasap/filters/ManualAnalysisFilter.browser.spec.tsx

@@ -4,7 +4,7 @@ import { render } from 'vitest-browser-react';
 import { ManualAnalysisFilter } from './ManualAnalysisFilter';
 import { DUMMY_LAPIS_URL, type LapisRouteMocker } from '../../../../../routeMocker';
 import { it } from '../../../../../test-extend';
-import type { WasapManualFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
+import type { WasapManualFilter } from '../../../views/wasap/wasapPageConfig';
 
 describe('ManualAnalysisFilter', () => {
     const defaultPageState: WasapManualFilter = {

website/src/components/pageStateSelectors/wasap/filters/ManualAnalysisFilter.tsx

@@ -1,7 +1,7 @@
 import { mutationType, type MutationType } from '@genspectrum/dashboard-components/util';
 
-import { type WasapManualFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
 import { GsMutationFilter } from '../../../genspectrum/GsMutationFilter';
+import type { WasapManualFilter } from '../../../views/wasap/wasapPageConfig';
 import { SequenceTypeSelector } from '../utils/SequenceTypeSelector';
 
 export function ManualAnalysisFilter({

website/src/components/pageStateSelectors/wasap/filters/ResistanceMutationsFilter.browser.spec.tsx

@@ -3,7 +3,8 @@ import { render } from 'vitest-browser-react';
 
 import { ResistanceMutationsFilter } from './ResistanceMutationsFilter';
 import { it } from '../../../../../test-extend';
-import type { WasapResistanceFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
+import { wastewaterOrganismConfigs } from '../../../../types/wastewaterConfig';
+import type { WasapResistanceFilter } from '../../../views/wasap/wasapPageConfig';
 
 describe('ResistanceMutationsFilter', () => {
     const defaultPageState: WasapResistanceFilter = {
@@ -12,11 +13,17 @@ describe('ResistanceMutationsFilter', () => {
         resistanceSet: '3CLpro',
     };
 
+    const resistanceMutationSets = wastewaterOrganismConfigs.covid.resistanceMutationSets;
+
     it('renders with initial resistance set', async () => {
         const mockSetPageState = vi.fn();
 
         const { getByRole } = render(
-            <ResistanceMutationsFilter pageState={defaultPageState} setPageState={mockSetPageState} />,
+            <ResistanceMutationsFilter
+                pageState={defaultPageState}
+                setPageState={mockSetPageState}
+                resistanceMutationSets={resistanceMutationSets}
+            />,
         );
 
         const select = getByRole('combobox');
@@ -27,7 +34,11 @@ describe('ResistanceMutationsFilter', () => {
         const mockSetPageState = vi.fn();
 
         const { getByRole } = render(
-            <ResistanceMutationsFilter pageState={defaultPageState} setPageState={mockSetPageState} />,
+            <ResistanceMutationsFilter
+                pageState={defaultPageState}
+                setPageState={mockSetPageState}
+                resistanceMutationSets={resistanceMutationSets}
+            />,
         );
 
         const select = getByRole('combobox');

website/src/components/pageStateSelectors/wasap/filters/ResistanceMutationsFilter.tsx

@@ -1,13 +1,15 @@
-import { wastewaterConfig } from '../../../../types/wastewaterConfig';
-import { type WasapResistanceFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
+import type { ResistanceMutationSet } from '../../../views/wasap/resistanceMutations';
+import type { WasapResistanceFilter } from '../../../views/wasap/wasapPageConfig';
 import { LabeledField } from '../utils/LabeledField';
 
 export function ResistanceMutationsFilter({
     pageState,
     setPageState,
+    resistanceMutationSets,
 }: {
     pageState: WasapResistanceFilter;
     setPageState: (newState: WasapResistanceFilter) => void;
+    resistanceMutationSets: ResistanceMutationSet[];
 }) {
     return (
         <LabeledField label='Resistance mutation set'>
@@ -16,9 +18,9 @@ export function ResistanceMutationsFilter({
                 value={pageState.resistanceSet}
                 onChange={(e) => setPageState({ ...pageState, resistanceSet: e.target.value })}
             >
-                {wastewaterConfig.wasap.resistanceMutations.map((resistanceMutation) => (
-                    <option key={resistanceMutation.name} value={resistanceMutation.name}>
-                        {resistanceMutation.name}
+                {resistanceMutationSets.map((set) => (
+                    <option key={set.name} value={set.name}>
+                        {set.name}
                     </option>
                 ))}
             </select>

website/src/components/pageStateSelectors/wasap/filters/UntrackedFilter.browser.spec.tsx

@@ -6,7 +6,7 @@ import { render } from 'vitest-browser-react';
 import { UntrackedFilter } from './UntrackedFilter';
 import type { LapisRouteMocker } from '../../../../../routeMocker';
 import { it } from '../../../../../test-extend';
-import type { WasapUntrackedFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
+import type { WasapUntrackedFilter } from '../../../views/wasap/wasapPageConfig';
 
 const DUMMY_LAPIS_URL_2 = 'http://lapis2.dummy';
 
@@ -33,6 +33,7 @@ describe('UntrackedFilter - custom variants textarea', () => {
                 pageState={defaultPageState}
                 setPageState={mockSetPageState}
                 clinicalSequenceLapisBaseUrl={DUMMY_LAPIS_URL_2}
+                clinicalSequenceLapisLineageField='pangoLineage'
                 cladeLineageQueryResult={mockCladeLineageQueryResult}
             />,
         );

website/src/components/pageStateSelectors/wasap/filters/UntrackedFilter.tsx

@@ -1,11 +1,8 @@
 import { type UseQueryResult } from '@tanstack/react-query';
 
 import { Loading } from '../../../../util/Loading';
-import {
-    type ExcludeSetName,
-    type WasapUntrackedFilter,
-} from '../../../../views/pageStateHandlers/WasapPageStateHandler';
 import { GsLineageFilter } from '../../../genspectrum/GsLineageFilter';
+import type { ExcludeSetName, WasapUntrackedFilter } from '../../../views/wasap/wasapPageConfig';
 import { KnownVariantsExclusionInfo } from '../InfoBlocks';
 import { LabeledField } from '../utils/LabeledField';
 import { SequenceTypeSelector } from '../utils/SequenceTypeSelector';
@@ -19,13 +16,15 @@ interface UntrackedFilterProps {
      * This is _not_ the same as the LAPIS providing the wastewater amplicon sequences.
      */
     clinicalSequenceLapisBaseUrl: string;
+    clinicalSequenceLapisLineageField: string;
 }
 
 export function UntrackedFilter({
     pageState,
     setPageState,
     cladeLineageQueryResult: { isPending, isError, data: cladeLineages },
     clinicalSequenceLapisBaseUrl,
+    clinicalSequenceLapisLineageField,
 }: UntrackedFilterProps) {
     const defaultLineages = cladeLineages ? Object.values(cladeLineages) : [];
     defaultLineages.sort();
@@ -42,11 +41,11 @@ export function UntrackedFilter({
                     value={pageState.excludeSet}
                     onChange={(e) => setPageState({ ...pageState, excludeSet: e.target.value as ExcludeSetName })}
                 >
-                    <option value='nextstrain'>Nextstrain clades</option>
+                    <option value='predefined'>Nextstrain clades</option>
                     <option value='custom'>custom</option>
                 </select>
             </LabeledField>
-            {pageState.excludeSet === 'nextstrain' ? (
+            {pageState.excludeSet === 'predefined' ? (
                 isPending ? (
                     <Loading />
                 ) : isError ? (
@@ -74,7 +73,7 @@ export function UntrackedFilter({
                     <LabeledField label='Custom variant list'>
                         <gs-app lapis={clinicalSequenceLapisBaseUrl}>
                             <GsLineageFilter
-                                lapisField='pangoLineage'
+                                lapisField={clinicalSequenceLapisLineageField}
                                 lapisFilter={{}}
                                 placeholderText='Variant'
                                 value={pageState.excludeVariants}

website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.browser.spec.tsx

@@ -5,7 +5,7 @@ import { render } from 'vitest-browser-react';
 import { VariantExplorerFilter } from './VariantExplorerFilter';
 import { DUMMY_LAPIS_URL, type LapisRouteMocker } from '../../../../../routeMocker';
 import { it } from '../../../../../test-extend';
-import type { WasapVariantFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
+import type { WasapVariantFilter } from '../../../views/wasap/wasapPageConfig';
 
 const DUMMY_LAPIS_URL_2 = 'http://lapis2.dummy';
 
@@ -29,6 +29,7 @@ describe('VariantExplorerFilter', () => {
                     pageState={defaultPageState}
                     setPageState={mockSetPageState}
                     clinicalSequenceLapisBaseUrl={DUMMY_LAPIS_URL_2}
+                    clinicalSequenceLapisLineageField='pangoLineage'
                 />
             </gs-app>,
         );
@@ -52,6 +53,7 @@ describe('VariantExplorerFilter', () => {
                     pageState={defaultPageState}
                     setPageState={mockSetPageState}
                     clinicalSequenceLapisBaseUrl={DUMMY_LAPIS_URL_2}
+                    clinicalSequenceLapisLineageField='pangoLineage'
                 />
             </gs-app>,
         );
@@ -82,6 +84,7 @@ describe('VariantExplorerFilter', () => {
                     pageState={defaultPageState}
                     setPageState={mockSetPageState}
                     clinicalSequenceLapisBaseUrl={DUMMY_LAPIS_URL_2}
+                    clinicalSequenceLapisLineageField='pangoLineage'
                 />
             </gs-app>,
         );

website/src/components/pageStateSelectors/wasap/filters/VariantExplorerFilter.tsx

@@ -1,6 +1,6 @@
 import { Inset } from '../../../../styles/Inset';
-import { type WasapVariantFilter } from '../../../../views/pageStateHandlers/WasapPageStateHandler';
 import { GsLineageFilter } from '../../../genspectrum/GsLineageFilter';
+import type { WasapVariantFilter } from '../../../views/wasap/wasapPageConfig';
 import { SelectorHeadline } from '../../SelectorHeadline';
 import { DefineClinicalSignatureInfo } from '../InfoBlocks';
 import { LabeledField } from '../utils/LabeledField';
@@ -15,12 +15,14 @@ interface VariantExplorerFilterProps {
      * This is _not_ the same as the LAPIS providing the wastewater amplicon sequences.
      */
     clinicalSequenceLapisBaseUrl: string;
+    clinicalSequenceLapisLineageField: string;
 }
 
 export function VariantExplorerFilter({
     pageState,
     setPageState,
     clinicalSequenceLapisBaseUrl,
+    clinicalSequenceLapisLineageField,
 }: VariantExplorerFilterProps) {
     return (
         <>
@@ -33,7 +35,7 @@ export function VariantExplorerFilter({
                 <LabeledField label='Variant'>
                     <gs-app lapis={clinicalSequenceLapisBaseUrl}>
                         <GsLineageFilter
-                            lapisField='pangoLineage'
+                            lapisField={clinicalSequenceLapisLineageField}
                             lapisFilter={{}}
                             placeholderText='Variant'
                             value={pageState.variant}