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refactor(website): read locationFields from YAML config instead of frontend constants #1123

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46 changes: 46 additions & 0 deletions backend/src/main/resources/application-dashboards-prod.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@ dashboards:
lapis:
url: "https://lapis.cov-spectrum.org/open/v2"
mainDateField: "date"
locationFields:
- "region"
- "country"
- "division"
lineageFields:
- "pangoLineage"
- "nextcladePangoLineage"
Expand All @@ -16,6 +20,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/h5n1"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -28,6 +35,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/h1n1pdm"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -40,6 +50,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/h3n2"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -52,6 +65,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/influenza-a"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -64,6 +80,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/influenza-b"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -76,6 +95,9 @@ dashboards:
lapis:
url: "https://api.loculus.genspectrum.org/b-victoria"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -88,6 +110,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/mpox"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -100,6 +125,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/west-nile"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -112,6 +140,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/rsv-a"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -124,6 +155,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/rsv-b"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -136,6 +170,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/ebola-sudan"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -148,6 +185,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/ebola-zaire"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -160,6 +200,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/cchf"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand Down Expand Up @@ -240,6 +283,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/measles"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand Down
43 changes: 43 additions & 0 deletions backend/src/main/resources/application-dashboards-staging.yaml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@ dashboards:
lapis:
url: "https://gs-staging-1.int.genspectrum.org/open/v2"
mainDateField: "date"
locationFields:
- "region"
- "country"
- "division"
externalNavigationLinks:
- url: "https://cov-spectrum.org"
label: "CoV-Spectrum"
Expand All @@ -13,6 +17,9 @@ dashboards:
lapis:
url: "https://api.loculus.staging.genspectrum.org/h5n1"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -25,6 +32,9 @@ dashboards:
lapis:
url: "https://api.loculus.staging.genspectrum.org/h1n1pdm"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -37,6 +47,9 @@ dashboards:
lapis:
url: "https://api.loculus.staging.genspectrum.org/h3n2"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -49,6 +62,9 @@ dashboards:
lapis:
url: "https://api.loculus.staging.genspectrum.org/influenza-a"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -61,6 +77,9 @@ dashboards:
lapis:
url: "https://api.loculus.staging.genspectrum.org/influenza-b"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "country"
- "division"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand Down Expand Up @@ -90,6 +109,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/mpox"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -102,6 +124,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/west-nile"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -114,6 +139,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/rsv-a"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -126,6 +154,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/rsv-b"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -138,6 +169,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/ebola-sudan"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -150,6 +184,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/ebola-zaire"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand All @@ -162,6 +199,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/cchf"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand Down Expand Up @@ -242,6 +282,9 @@ dashboards:
lapis:
url: "https://lapis.pathoplexus.org/measles"
mainDateField: "sampleCollectionDateRangeLower"
locationFields:
- "geoLocCountry"
- "geoLocAdmin1"
additionalFilters:
versionStatus: "LATEST_VERSION"
isRevocation: "false"
Expand Down
1 change: 1 addition & 0 deletions website/src/config.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ import { allOrganisms, type Organism } from './types/Organism.ts';
const lapisConfigSchema = z.object({
url: z.string(),
mainDateField: z.string(),
locationFields: z.array(z.string()),
additionalFilters: z.optional(z.record(z.string())),
});

Expand Down
10 changes: 5 additions & 5 deletions website/src/views/OrganismConstants.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -188,9 +188,6 @@ export const INSDC_ACCESSION_DOWNLOAD_FILES = ['insdcAccessionFull'];
export const LOCULUS_AUTHORS_FIELD = 'authors';
export const LOCULUS_AUTHORS_AFFILIATIONS_FIELD = 'authorAffiliations';

export const PATHOPLEXUS_LOCATION_FIELDS = ['geoLocCountry', 'geoLocAdmin1'];
export const GENSPECTRUM_LOCULUS_LOCATION_FIELDS = ['country', 'division'];

export const INFLUENZA_ACCESSION_DOWNLOAD_FIELDS = [
'insdcAccessionFull_seg1',
'insdcAccessionFull_seg2',
Expand All @@ -205,18 +202,20 @@ export const INFLUENZA_ACCESSION_DOWNLOAD_FIELDS = [
export const PATHOPLEXUS_HOST_FIELD = 'hostNameScientific';

type FiltersConfig = {
locationFields: string[];
dateRangeOptions: () => DateRangeOption[];
completenessSuffixes?: SuffixConfig[];
};

export function getPathoplexusFilters({
locationFields,
dateRangeOptions,
completenessSuffixes,
}: FiltersConfig): BaselineFilterConfig[] {
return [
{
type: 'location',
locationFields: PATHOPLEXUS_LOCATION_FIELDS,
locationFields,
label: 'Sampling location',
placeholderText: 'Sampling location',
},
Expand Down Expand Up @@ -289,13 +288,14 @@ export const INFLUENZA_COMPLETENESS_SUFFIXES = [
export const GENSPECTRUM_LOCULUS_HOST_FIELD = 'hostNameScientific';

export function getGenspectrumLoculusFilters({
locationFields,
dateRangeOptions,
completenessSuffixes,
}: FiltersConfig): BaselineFilterConfig[] {
return [
{
type: 'location',
locationFields: GENSPECTRUM_LOCULUS_LOCATION_FIELDS,
locationFields,
placeholderText: 'Sampling location',
label: 'Sampling location',
},
Expand Down
26 changes: 14 additions & 12 deletions website/src/views/cchf.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,6 @@ import {
type OrganismConstants,
PATHOPLEXUS_COMMON_DOWNLOAD_FIELDS,
PATHOPLEXUS_HOST_FIELD,
PATHOPLEXUS_LOCATION_FIELDS,
} from './OrganismConstants.ts';
import { compareSideBySideViewConstants } from './ViewConstants.ts';
import type { LineageFilterConfig } from '../components/pageStateSelectors/LineageFilterInput.tsx';
Expand All @@ -41,18 +40,9 @@ const dateRangeOptions = defaultDateRangeOptions(earliestDate);
class CchfConstants implements OrganismConstants {
public readonly organism = Organisms.cchf;
public readonly earliestDate = earliestDate;
public readonly baselineFilterConfigs: BaselineFilterConfig[] = [
...getPathoplexusFilters({
dateRangeOptions,
completenessSuffixes: [
{ suffix: 'M', suffixLabel: 'M' },
{ suffix: 'L', suffixLabel: 'L' },
{ suffix: 'S', suffixLabel: 'S' },
],
}),
];
public readonly baselineFilterConfigs: BaselineFilterConfig[];
public readonly mainDateField: string;
public readonly locationFields = PATHOPLEXUS_LOCATION_FIELDS;
public readonly locationFields: string[];
public readonly lineageFilters: LineageFilterConfig[] = [];
public readonly useVariantQuery = false;
public readonly hostField: string = PATHOPLEXUS_HOST_FIELD;
Expand Down Expand Up @@ -91,8 +81,20 @@ class CchfConstants implements OrganismConstants {
public readonly dataOrigins: DataOrigin[] = [dataOrigins.pathoplexus];

constructor(organismsConfig: OrganismsConfig) {
this.locationFields = organismsConfig.cchf.lapis.locationFields;
this.mainDateField = organismsConfig.cchf.lapis.mainDateField;
this.additionalFilters = organismsConfig.cchf.lapis.additionalFilters;
this.baselineFilterConfigs = [
...getPathoplexusFilters({
locationFields: this.locationFields,
dateRangeOptions,
completenessSuffixes: [
{ suffix: 'M', suffixLabel: 'M' },
{ suffix: 'L', suffixLabel: 'L' },
{ suffix: 'S', suffixLabel: 'S' },
],
}),
];
}
}

Expand Down
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