TAX-107 | Adaptar geoserver y cliente a nuevo modelo de datos

Author: oscarfonts

README.md

@@ -51,6 +51,14 @@ Para importar el backbone de GBIF, ejecutar ./prepare-db.sh en devops/prepare-db
 Puede tardar 10mn en descargar.
 
 
+### Generar árbol taxonómico y geoarrow
+
+```
+export JWT_TOKEN=$(curl http://localhost:8000/api/v1/auth/jwt/create --data '{"email": "info@geomatico.es", "password": "1234"}' -H 'content-type: application/json' | jq -r .access)
+curl -X POST http://localhost/api/v1/manage/generate-resources/ -H "Accept: application/json" -H "Authorization: Bearer $JWT_TOKEN" | jq -r
+```
+
+
 ## Base de datos en Staging
 
 Ahora mismo la base de datos se persiste entre despliegues. Si en algún momento en necesario resetearla, se puede hacer entrando en el servidor.

client/package-lock.json

@@ -5,7 +5,7 @@
   "main": "./dist/main.js",
   "engines": {
     "npm": ">=10.0.0 <11.0.0",
-    "node": ">=20.0.0 <21.0.0"
+    "node": ">=20.0.0 <23.0.0"
   },
   "scripts": {
     "test": "npm run lint && karma start karma.config.js",

client/package.json

@@ -4,10 +4,10 @@ import {getDateLabel, getPlaceLabel} from './PopUpContent';
 describe('PopUpContent', () => {
   it('returns expected date labels"', async () => {
     // WHEN / THEN
-    expect(getDateLabel({})).to.equal(undefined);
-    expect(getDateLabel({year: 2000, day: 20})).to.equal('2000');
-    expect(getDateLabel({year: 2000, month: 2})).to.equal('2000-02');
-    expect(getDateLabel({year: 2000, month: 2, day: 7})).to.equal('2000-02-07');
+    expect(getDateLabel({}, '')).to.equal(undefined);
+    expect(getDateLabel({eventDate: new Date('2020-10-20Z')}, 'ca')).to.equal('20/10/2020');
+    expect(getDateLabel({eventDate: new Date('2020-10-20Z')}, 'en')).to.equal('10/20/2020');
+    expect(getDateLabel({eventDate: new Date('2020-10-20Z')}, 'es')).to.equal('20/10/2020');
   });
 
   it('returns expected place labels"', async () => {

client/src/components/PopUpContent.spec.ts

@@ -28,12 +28,14 @@ export type SelectedFeature = {
  * Required WFS properties to fill the popup.
  */
 const PROPERTIES = [
-  WFS_PROPERTY.year, WFS_PROPERTY.month, WFS_PROPERTY.day,
+  WFS_PROPERTY.eventDate,
   WFS_PROPERTY.municipality, WFS_PROPERTY.county, WFS_PROPERTY.stateProvince,
   WFS_PROPERTY.scientificName
 ];
 
-export const getPlaceLabel = (properties: WfsProperties): string | undefined => {
+type PopupWfsProperties = Partial<Pick<WfsProperties, 'eventDate' | 'municipality' | 'county' | 'stateProvince' | 'scientificName'>>;
+
+export const getPlaceLabel = (properties: PopupWfsProperties): string | undefined => {
   const parts = [properties.municipality, properties.county, properties.stateProvince].filter(Boolean);
   if (parts.length === 0) {
     return undefined;
@@ -44,21 +46,13 @@ export const getPlaceLabel = (properties: WfsProperties): string | undefined =>
   return `${parts.join(', ')} (${last})`;
 };
 
-export const getDateLabel = (properties: WfsProperties): string | undefined => {
-  if (properties.year === undefined) {
-    return;
-  } else if (!properties.month) {
-    return `${properties.year}`;
-  }
-  return [properties.year, properties.month, properties.day]
-    .filter(Boolean)
-    .map(part => String(part).padStart(2, '0'))
-    .join('-');
+export const getDateLabel = (properties: PopupWfsProperties, lang: string): string | undefined => {
+  return properties.eventDate?.toLocaleDateString(lang);
 };
 
 const PopUpContent: FC<PopUpContentProps> = ({selectedFeature, isTactile, museuId}) => {
-  const {t} = useTranslation();
-  const [wfsProperties, setWfsProperties] = useState<WfsProperties>();
+  const {t, i18n: {language}} = useTranslation();
+  const [wfsProperties, setWfsProperties] = useState<PopupWfsProperties>();
 
   const getMoreInfoUrl = (selectedFeature: SelectedFeature) => {
     const split = selectedFeature?.catalognumber?.split(' ');
@@ -75,7 +69,7 @@ const PopUpContent: FC<PopUpContentProps> = ({selectedFeature, isTactile, museuI
 
   const scientificNameLabel = wfsProperties?.scientificName || selectedFeature.species?.name;
   const placeLabel = wfsProperties && getPlaceLabel(wfsProperties);
-  const dateLabel = wfsProperties && getDateLabel(wfsProperties);
+  const dateLabel = wfsProperties && getDateLabel(wfsProperties, language);
 
   return <Card variant="outlined">
     <CardContent>

client/src/components/PopUpContent.tsx

@@ -32,27 +32,17 @@ export const MAPSTYLES: Array<MapStyle> = [
     id: 'mapstyles/landcover.json',
     label: 'landCover',
     thumbnail: 'images/landcover.png'
-  },
-  {
-    id: 'mapstyles/temperature.json',
-    label: 'temperature',
-    thumbnail: 'images/temperature.png'
-  },
-  {
-    id: 'mapstyles/rain.json',
-    label: 'rain',
-    thumbnail: 'images/rain.png'
   }
 ];
 
 export const INITIAL_MAPSTYLE_URL = MAPSTYLES[1].id;
 
 export const ARROW_FIELDS = [
-  'id', 'catalognumber', 'domain', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus',
-  'species', 'subspecies', 'basisofrecord', 'institutioncode', 'year'
+  'id', 'catalognumber', 'basisofrecord', 'institutioncode', 'year',
+  'domain', 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species', 'subspecies'
 ];
 
-export const FILTER_BY = ['institutioncode', 'basisofrecord'];
+export const FILTER_BY = ['basisofrecord', 'institutioncode'];
 
 export const INITIAL_TAXONOMIC_LEVEL = TaxonomicLevel.kingdom;
 export const INITIAL_TAXONOMIC_NAME = 'Animalia';

client/src/config.ts

@@ -55,7 +55,7 @@ describe('wfs', () => {
     const params = validateUrlAndGetParams(format, urlString);
     expect(params.get('cql_filter')).to.equal('family_id = 1 ' +
       'AND institution_id = 2 AND basis_of_record_id = 3 AND genus IN (1,3) ' +
-      'AND year >= 1920 AND year <= 2010 ' +
+      'AND eventDate DURING 1920-01-01T00:00:00Z/2010-12-31T23:59:59Z ' +
       'AND BBOX(geometry,0.5,42.7,0.6,42.8)');
   });
 
@@ -164,18 +164,17 @@ describe('wfs', () => {
     // GIVEN
     const featureId = 42;
     const propertyNames = [
-      WFS_PROPERTY.year, WFS_PROPERTY.month, WFS_PROPERTY.day,
+      WFS_PROPERTY.eventDate,
       WFS_PROPERTY.municipality, WFS_PROPERTY.county, WFS_PROPERTY.stateProvince,
       WFS_PROPERTY.scientificName
     ];
     const response = {
       features: [{
         properties: {
-          year: 2023,
-          month: 11,
+          eventDate: '2023-11-01Z',
           county: 'Burjassot',
-          state_province: 'Valencia',
-          scientific_name: 'Ornithorhynchus anatinus'
+          stateProvince: 'Valencia',
+          scientificName: 'Ornithorhynchus anatinus'
         }
       }]
     };
@@ -185,13 +184,11 @@ describe('wfs', () => {
     const properties = await getWfsFeatureProperties(featureId, propertyNames);
 
     // THEN
-    expect(properties?.year).to.equal(response.features[0].properties.year);
-    expect(properties?.month).to.equal(response.features[0].properties.month);
-    expect(properties?.day).to.equal(undefined);
+    expect(properties?.eventDate).to.eql(new Date(response.features[0].properties.eventDate));
     expect(properties?.municipality).to.equal(undefined);
     expect(properties?.county).to.equal(response.features[0].properties.county);
-    expect(properties?.stateProvince).to.equal(response.features[0].properties.state_province);
-    expect(properties?.scientificName).to.equal(response.features[0].properties.scientific_name);
+    expect(properties?.stateProvince).to.equal(response.features[0].properties.stateProvince);
+    expect(properties?.scientificName).to.equal(response.features[0].properties.scientificName);
   });
 
   const validateUrlAndGetParams = (expectedFormat: string, urlString: string): URLSearchParams => {

client/src/wfs/wfs.spec.ts

@@ -1,26 +1,50 @@
 import {BBOX, Filters, Range, SubtaxonVisibility, TaxonomicLevel} from '../commonTypes';
+import {FeatureCollection, Point} from 'geojson';
 import {GEOSERVER_BASE_URL} from '../config';
 
 const FORMAT_GEOJSON = 'application/json';
 export const WFS_TYPENAME = 'taxomap:taxomap';
 
 /**
- * These depend on how the database is generated. Make sure they always match whatever is done in `91-generate-dictionaries.sql`.
+ * These depend on how the database is generated.
  */
 export enum WFS_PROPERTY {
-  institutionCodeId = 'institution_id',
-  basisOfRecordId = 'basis_of_record_id',
-  year = 'year',
-  month = 'month',
-  day = 'day',
-  municipality = 'municipality',
-  county = 'county',
-  stateProvince = 'state_province',
   geometry = 'geometry',
-  scientificName = 'scientific_name'
+  institutionCode = 'institutionCode',
+  collectionCode = 'collectionCode',
+  catalogNumber = 'catalogNumber',
+  basisOfRecord = 'basisOfRecord',
+  taxonID = 'taxonID',
+  scientificName = 'scientificName',
+  decimalLatitude = 'decimalLatitude',
+  decimalLongitude = 'decimalLongitude',
+  eventDate = 'eventDate',
+  countryCode = 'countryCode',
+  stateProvince = 'stateProvince',
+  county = 'county',
+  municipality = 'municipality',
+  georeferenceVerificationStatus = 'georeferenceVerificationStatus',
+  identificationVerificationStatus = 'identificationVerificationStatus'
 }
 
-export type WfsProperties = { [key in (keyof typeof WFS_PROPERTY)]?: number | string | undefined }
+export type WfsProperties = {
+  geometry: Point,
+  institutionCode: string,
+  collectionCode: string,
+  catalogNumber: string,
+  basisOfRecord: string,
+  taxonID: number,
+  scientificName: string,
+  decimalLatitude: number,
+  decimalLongitude: number,
+  eventDate: Date,
+  countryCode: string,
+  stateProvince: string,
+  county: string,
+  municipality: string,
+  georeferenceVerificationStatus: string,
+  identificationVerificationStatus: string
+}
 
 /**
  * Returns the property name with the ID associated to the given taxonomic level.
@@ -57,7 +81,7 @@ const cqlTaxonIn = (subtaxonVisibility: SubtaxonVisibility | undefined) => {
 };
 
 const cqlYearBetween = (yearRange: Range | undefined) => yearRange
-  ? `${WFS_PROPERTY.year} >= ${yearRange[0]} AND ${WFS_PROPERTY.year} <= ${yearRange[1]}`
+  ? `${WFS_PROPERTY.eventDate} DURING ${yearRange[0]}-01-01T00:00:00Z/${yearRange[1]}-12-31T23:59:59Z`
   : undefined;
 
 const cqlBbox = (bbox: BBOX | undefined) =>
@@ -81,14 +105,15 @@ export const getWfsDownloadUrl = (
 
   const cqlFilters = [
     cqlPropertyEquals(getPropertyName(taxon.level), taxon.id),
-    cqlPropertyEquals(WFS_PROPERTY.institutionCodeId, institutionId),
-    cqlPropertyEquals(WFS_PROPERTY.basisOfRecordId, basisOfRecordId),
+    cqlPropertyEquals('institution_id', institutionId),
+    cqlPropertyEquals('basis_of_record_id', basisOfRecordId),
     cqlTaxonIn(subtaxonVisibility),
     cqlYearBetween(yearRange),
     // cql_filter and BBOX query params are mutually exclusive, BBOX needs to be introduced as part of the cql_filter
     cqlBbox(bbox)
   ];
   url.searchParams.append('cql_filter', cqlFilters.filter(Boolean).join(' AND '));
+  url.searchParams.append('propertyName', Object.values(WFS_PROPERTY).join(','));
 
   return url.toString();
 };
@@ -103,7 +128,7 @@ export const getWfsDownloadUrl = (
 export const getWfsFeatureProperties = async (
   id: number | undefined,
   propertyNames: WFS_PROPERTY[]
-): Promise<WfsProperties | undefined> => {
+): Promise<Partial<WfsProperties> | undefined> => {
   if (id === undefined) return undefined;
 
   const url = new URL(GEOSERVER_BASE_URL + '/wfs');
@@ -118,17 +143,11 @@ export const getWfsFeatureProperties = async (
   const response = await fetch(url);
   if (!response.ok) return undefined;
 
-  const featureCollection = await response.json();
+  const featureCollection = await response.json() as FeatureCollection<Point, WfsProperties>;
   if (!featureCollection.features) return undefined;
-
-  const properties = featureCollection.features[0].properties;
-  return properties && {
-    year: properties[WFS_PROPERTY.year],
-    month: properties[WFS_PROPERTY.month],
-    day: properties[WFS_PROPERTY.day],
-    stateProvince: properties[WFS_PROPERTY.stateProvince],
-    municipality: properties[WFS_PROPERTY.municipality],
-    county: properties[WFS_PROPERTY.county],
-    scientificName: properties[WFS_PROPERTY.scientificName]
-  };
+  const {properties} = featureCollection.features[0];
+  if(properties.eventDate) {
+    properties.eventDate = new Date(properties.eventDate);
+  }
+  return properties;
 };