Address Darwin Core export review comments

backend/src/routes/locality.ts

@@ -12,19 +12,10 @@ import { AccessError, requireOneOf } from '../middlewares/authorizer'
 import { deleteLocality, writeLocality } from '../services/write/locality'
 import { buildDwcLocalityArchiveZipBuffer } from '../services/dwcArchiveExportLocalities'
 import { currentDateAsString } from '../../../frontend/src/shared/currentDateAsString'
+import { parseNumericIds } from './utils/exportFilters'
 
 const router = Router()
 
-const parseNumericIds = (value: unknown): number[] | undefined => {
-  if (value === undefined) return undefined
-  if (!Array.isArray(value)) throw new Error('ids must be an array.')
-  return value.map(id => {
-    const parsed = typeof id === 'number' ? id : typeof id === 'string' ? parseInt(id, 10) : NaN
-    if (!Number.isInteger(parsed)) throw new Error('ids must contain only integers.')
-    return parsed
-  })
-}
-
 router.get('/all', async (req, res) => {
   const localities = await getAllLocalities(req.user)
   return res.status(200).send(fixBigInt(localities))
@@ -45,7 +36,7 @@ router.post('/export/dwc-archive', requireOneOf([Role.Admin]), async (req, res)
   try {
     return await sendDwcArchive(parseNumericIds((req.body as { ids?: unknown }).ids), res)
   } catch (error) {
-    return res.status(403).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
+    return res.status(400).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
   }
 })
 

backend/src/routes/occurrence.ts

@@ -45,7 +45,7 @@ const resolveOccurrenceKeysForExport = async (req: Request): Promise<DwcOccurren
 }
 
 const handleExportFilterError = (error: unknown, res: Response) => {
-  return res.status(403).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
+  return res.status(400).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
 }
 
 router.get('/export/dwc-archive/progress/:exportId', requireOneOf([Role.Admin]), (req, res) => {

backend/src/routes/species.ts

@@ -6,19 +6,10 @@ import { deleteSpecies, writeSpecies } from '../services/write/species'
 import { requireOneOf } from '../middlewares/authorizer'
 import { buildDwcArchiveZipBuffer } from '../services/dwcArchiveExport'
 import { currentDateAsString } from '../../../frontend/src/shared/currentDateAsString'
+import { parseNumericIds } from './utils/exportFilters'
 
 const router = Router()
 
-const parseNumericIds = (value: unknown): number[] | undefined => {
-  if (value === undefined) return undefined
-  if (!Array.isArray(value)) throw new Error('ids must be an array.')
-  return value.map(id => {
-    const parsed = typeof id === 'number' ? id : typeof id === 'string' ? parseInt(id, 10) : NaN
-    if (!Number.isInteger(parsed)) throw new Error('ids must contain only integers.')
-    return parsed
-  })
-}
-
 router.get('/all', async (_req, res) => {
   const species = await getAllSpecies()
   return res.status(200).send(fixBigInt(species))
@@ -44,7 +35,7 @@ router.post('/export/dwc-archive', requireOneOf([Role.Admin]), async (req, res)
   try {
     return await sendDwcArchive(parseNumericIds((req.body as { ids?: unknown }).ids), res)
   } catch (error) {
-    return res.status(403).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
+    return res.status(400).send({ error: error instanceof Error ? error.message : 'Invalid export filters.' })
   }
 })
 

backend/src/routes/utils/exportFilters.ts

@@ -0,0 +1,11 @@
+export const parseNumericIds = (value: unknown): number[] | undefined => {
+  if (value === undefined) return undefined
+  if (!Array.isArray(value)) throw new Error('ids must be an array.')
+
+  return value.map(id => {
+    const parsed = typeof id === 'number' ? id : typeof id === 'string' && /^-?\d+$/.test(id) ? Number(id) : Number.NaN
+
+    if (!Number.isSafeInteger(parsed)) throw new Error('ids must contain only integers.')
+    return parsed
+  })
+}

backend/src/services/crossSearch.ts

@@ -268,11 +268,13 @@ export const getFilteredCrossSearchOccurrenceKeys = async (
   )) as Array<Array<Partial<CrossSearch>>>
 
   const keysById = new Map<string, { lid: number; speciesId: number }>()
-  for (const row of resultPages.flat()) {
+  for (const page of resultPages) {
+    for (const row of page) {
       if (typeof row.lid_now_loc !== 'number' || typeof row.species_id_com_species !== 'number') continue
       const key = { lid: row.lid_now_loc, speciesId: row.species_id_com_species }
       keysById.set(`${key.lid}:${key.speciesId}`, key)
     }
+  }
 
   return { occurrenceKeys: [...keysById.values()] }
 }

backend/src/services/dwcDataPackageExport.ts

@@ -38,6 +38,20 @@ const occurrenceIdForRow = (lid: number, speciesId: number): string => `NOW:OCC:
 type LocalityForDwcDpExport = Parameters<typeof mapLocalityToMeasurementRows>[0]
 type OccurrenceForDwcDpExport = Parameters<typeof mapOccurrenceToOccurrenceRow>[0]
 
+const LOOKUP_EXPORT_CHUNK_SIZE = 1000
+
+const chunk = <T>(values: T[], size: number): T[][] => {
+  const chunks: T[][] = []
+  for (let index = 0; index < values.length; index += size) {
+    chunks.push(values.slice(index, index + size))
+  }
+  return chunks
+}
+
+const sortOccurrenceKeys = (occurrenceKeys: DwcOccurrenceKey[]): DwcOccurrenceKey[] => {
+  return [...occurrenceKeys].sort((a, b) => a.lid - b.lid || a.speciesId - b.speciesId)
+}
+
 export const DWC_DP_EVENT_HEADERS = [
   'eventID',
   'parentEventID',
@@ -334,7 +348,7 @@ const FIELD_DESCRIPTIONS: Record<string, string> = {
   taxonID: 'Stable NOW taxon identifier; this joins to dwc-a-taxa/taxon.csv in the full export.',
   scientificName: 'Scientific name assembled from curated NOW taxonomic fields.',
   scientificNameAuthorship: 'Scientific name authorship where curated.',
-  taxonRank: 'Taxonomic rank when available; currently reserved for future enrichment.',
+  taxonRank: 'Taxonomic rank derived from curated NOW taxonomic fields when available.',
   identificationVerificationStatus: 'Curated identification status or qualifier.',
   assertionID: 'Stable assertion identifier derived from the source database field and owning event or occurrence.',
   verbatimAssertionType:
@@ -913,15 +927,26 @@ const fetchOccurrencesForDwcDataPackageExport = async (
 ): Promise<OccurrenceForDwcDpExport[]> => {
   if (occurrenceKeys && occurrenceKeys.length === 0) return []
   const { nowDb } = await import('../utils/db')
-  const occurrences = await nowDb.now_ls.findMany({
+
-    where: occurrenceKeys
+  if (occurrenceKeys) {
-      ? {
+    const occurrences: OccurrenceForDwcDpExport[] = []
-          OR: occurrenceKeys.map(key => ({
+    for (const keys of chunk(sortOccurrenceKeys(occurrenceKeys), LOOKUP_EXPORT_CHUNK_SIZE)) {
+      const chunkOccurrences = await nowDb.now_ls.findMany({
+        where: {
+          OR: keys.map(key => ({
             lid: key.lid,
             species_id: key.speciesId,
           })),
+        },
+        orderBy: [{ lid: 'asc' }, { species_id: 'asc' }],
+        select: occurrenceSelect,
+      })
+      occurrences.push(...(chunkOccurrences as unknown as OccurrenceForDwcDpExport[]))
     }
-      : undefined,
+    return occurrences
+  }
+
+  const occurrences = await nowDb.now_ls.findMany({
     orderBy: [{ lid: 'asc' }, { species_id: 'asc' }],
     select: occurrenceSelect,
   })

backend/src/unit-tests/exportFilters.test.ts

@@ -0,0 +1,21 @@
+import { describe, expect, it } from '@jest/globals'
+import { parseNumericIds } from '../routes/utils/exportFilters'
+
+describe('parseNumericIds', () => {
+  it('accepts integer ids as numbers or strings', () => {
+    expect(parseNumericIds([12, '34'])).toEqual([12, 34])
+  })
+
+  it('rejects partially numeric strings', () => {
+    expect(() => parseNumericIds(['12abc'])).toThrow('ids must contain only integers.')
+  })
+
+  it('rejects decimals', () => {
+    expect(() => parseNumericIds([12.3])).toThrow('ids must contain only integers.')
+    expect(() => parseNumericIds(['12.3'])).toThrow('ids must contain only integers.')
+  })
+
+  it('rejects non-array id payloads', () => {
+    expect(() => parseNumericIds('12')).toThrow('ids must be an array.')
+  })
+})

frontend/src/components/Occurrence/OccurrenceDwcExportMenuItem.tsx

@@ -39,6 +39,7 @@ export const OccurrenceDwcExportMenuItem = ({ handleClose }: { handleClose: () =
         progressUrl: `${BACKEND_URL}/occurrence/export/dwc-archive/progress/${exportId}`,
         filename,
         fetchOptions: filteredFetchOptions,
+        progressFetchOptions: fetchOptions,
         notify,
         setNotificationMessage,
         startMessage: 'Generating DwC-A occurrence ZIP export...',

frontend/src/util/exportProgress.ts

@@ -9,6 +9,7 @@ type DownloadExportParams = {
   url: string
   filename: string
   fetchOptions?: RequestInit
+  progressFetchOptions?: RequestInit
   notify: Notify
   setNotificationMessage: (message: string) => void
   startMessage: string
@@ -30,6 +31,7 @@ export const downloadExportFileWithProgress = async ({
   url,
   filename,
   fetchOptions = {},
+  progressFetchOptions,
   notify,
   setNotificationMessage,
   startMessage,
@@ -53,7 +55,7 @@ export const downloadExportFileWithProgress = async ({
     if (!progressUrl) return false
 
     try {
-      const response = await fetch(progressUrl, fetchOptions)
+      const response = await fetch(progressUrl, progressFetchOptions ?? fetchOptions)
       if (!response.ok) return false
 
       const progress = (await response.json()) as ExportProgress