Refactor of GetDigitalSpecimenComplete service and setup of data mapper to UI

.github/workflows/.trivyignore

@@ -21,4 +21,7 @@ CVE-2026-33671
 
 # Vulnerability in image dependency libpng that is included in the image and we cannot fix Apr-1-2026
 CVE-2026-33416
-CVE-2026-33636
+CVE-2026-33636
+
+# lodash-es is pinned as a dependency on a vulnerable version in formik and cannot be upgraded by us Apr-3-2026
+CVE-2026-4800

package.json

@@ -29,22 +29,22 @@
     "@tanstack/match-sorter-utils": "^8.19.4",
     "@tanstack/react-query": "^5.90.20",
     "@tanstack/react-table": "^8.20.5",
-    "axios": "^1.13.5",
+    "axios": "^1.15.0",
     "bootstrap": "^5.3.3",
     "bootstrap-css": "^4.0.0-alpha.5",
     "classnames": "^2.5.1",
     "cytoscape": "3.30.4",
     "date-fns": "^4.1.0",
     "date-fns-tz": "^3.2.0",
-    "formik": "^2.4.6",
+    "formik": "^2.4.9",
     "i18next": "^24.0.5",
     "intro.js": "^7.2.0",
     "intro.js-react": "^1.0.0",
     "json-schema-to-typescript": "^15.0.3",
     "jsonpath": "^1.1.1",
     "keycloak-js": "^26.0.7",
     "leaflet": "^1.9.4",
-    "lodash": "^4.17.21",
+    "lodash": "^4.18.1",
     "moment": "^2.30.1",
     "msw": "^2.6.7",
     "openseadragon": "^5.0.0",

src/hooks/useDigitalSpecimen.ts

@@ -0,0 +1,24 @@
+import { useQuery } from '@tanstack/react-query';
+import { getDigitalSpecimenComplete } from 'services/digitalSpecimenService/getDigitalSpecimenComplete';
+import { mapDigitalSpecimen } from 'utils/DataMappers/digitalSpecimenDataMapper';
+
+/* Base constants */
+const staleTime = 1000 * 60 * 5; // How long until the time is stale
+const gcTime = 1000 * 60 * 10; // Cache time: How long to store it in the cache
+
+/* useQuery hook to retrieve the complete Digital Specimen data object by calling the getDigitalSpecimenComplete service */
+export const useDigitalSpecimenComplete = ({ doi, version }:
+    { doi: string, version?: number }) => {
+    return useQuery({
+        queryKey: ['digitalSpecimen', doi, version],
+        queryFn: () => getDigitalSpecimenComplete({ doi, version }),
+        select: (data) => {
+            return {
+                ...data,
+                ...mapDigitalSpecimen(data),
+            }
+        },
+        staleTime,
+        gcTime
+    });
+};

src/services/digitalSpecimenService/getDigitalSpecimenComplete.ts

@@ -0,0 +1,40 @@
+import apiClient from '../apiClient';
+
+/**
+ * Service that retrieves the complete digital specimen details through the apiClient
+ * Takes doi and version as a parameter object
+ * @returns An array with complete digital specimen data on specimen, media and annotations
+ */
+export const getDigitalSpecimenComplete = async ({ doi, version }:
+    { doi: string, version?: number }) => {
+    let endPoint: string;
+
+    if (version) {
+        endPoint = `digital-specimen/v1/${doi}/${version}/full`;
+    } else {
+        endPoint = `digital-specimen/v1/${doi}/full`;
+    }
+    try {
+        /* Call service and wait for response */
+        const response = await apiClient.get(endPoint, {
+            params: {
+                doi,
+                version
+            }
+        });
+
+        /* Throw error if response is not as expected */
+        if(!response.data?.data) {
+            throw new Error('Incorrect response format');
+        }
+
+        /* Return response data */
+        return response.data;
+    } catch (error) {
+        /* If error, throw error with generic error message */
+        console.error('Error fetching the digital specimen:', error);
+
+        /* Rethrow error for useQuery */
+        throw error;
+    }
+}

src/utils/DataMappers/digitalSpecimenDataMapper.ts

@@ -0,0 +1,62 @@
+/* Import schemas */
+import DIGITAL_SPECIMEN_SCHEMA_MAP from "./schemas/DigitalSpecimenSchema";
+
+/* Import types */
+import { DigitalSpecimenUIModel, SchemaMap, UIProperty } from "./types/dataMapperTypes";
+
+/**
+ * Function to get the accepted identification or the first one it can find
+ * @param ds The digital specimen object
+ * @returns Either the accepted identification, the first identification it can find or null in the edge case that there is none
+ */
+const getAcceptedIdentification = (ds: any) => {
+    const identifications = ds["ods:hasIdentifications"];
+
+    /* Find verified identification or fallback to first identification */
+    const primary = identifications?.find((item: any) => item["ods:isVerifiedIdentification"]) 
+        ?? identifications?.[0];
+
+    /* Return the taxon identification or null if for some reason there is no identification*/
+    return primary?.["ods:hasTaxonIdentifications"]?.[0] ?? null;
+}
+
+/**
+ * Function to retrieve the primary event once
+ * @param ds The digital specimen object
+ * @returns Either the primary event if there is one or null
+ */
+const getPrimaryEvent = (ds: any) => {
+    return ds["ods:hasEvents"]?.[0] ?? null;
+}
+
+/**
+ * Transforms raw Digital Specimen data into a UI-ready model 
+ * based on the DIGITAL_SPECIMEN_SCHEMA_MAP definitions.
+ * It is executed in the useDigitalSpecimen hook immediately when the call is being done.
+ */
+export const mapDigitalSpecimen = (rawData: any): DigitalSpecimenUIModel | null => {
+    const ds = rawData?.data?.attributes?.digitalSpecimen;
+    if (!ds) return null;
+
+    /* Find acceptedIdentification or second best option */
+    const acceptedIdentification = getAcceptedIdentification(ds);
+    const primaryEvent = getPrimaryEvent(ds);
+
+    return Object.fromEntries(
+        Object.entries(DIGITAL_SPECIMEN_SCHEMA_MAP as SchemaMap).map(([groupKey, fields]) => {
+            const mappedFields: Record<string, UIProperty> = Object.fromEntries(
+                Object.entries(fields).map(([fieldKey, config]) => [
+                    fieldKey,
+                    {
+                        label: config.label,
+                        value: config.resolve(ds, {acceptedIdentification, primaryEvent}),
+                        isHtml: Boolean(config.isHtml),
+                        type: config.type || 'base',
+                    }
+                ])
+            );
+
+            return [groupKey, mappedFields];
+        })
+    ) as unknown as DigitalSpecimenUIModel;
+};