Occurrence details page now edits or creates occurrences through the locality route in backend, also add button to select species for occurrence

backend/src/services/write/locality.ts

@@ -82,6 +82,11 @@ export const writeLocality = async (
       localitySpecies.species_id = species_id as number
     }
 
+    for (const localitySpecies of locality.now_ls) {
+      if (localitySpecies.rowState === 'new' || localitySpecies.rowState === 'removed') continue
+      await writeHandler.updateObject('now_ls', localitySpecies, ['lid', 'species_id'])
+    }
+
     await writeHandler.applyListChanges('now_ls', locality.now_ls, ['lid', 'species_id'])
     await writeHandler.applyListChanges('now_mus', locality.now_mus, ['lid', 'museum'])
     await writeHandler.applyListChanges('now_ss', locality.now_ss, ['lid', 'sed_struct'])

frontend/src/components/Locality/Tabs/OccurrencesTab.tsx

@@ -248,16 +248,17 @@ export const OccurrencesTab = () => {
 
   return (
     <Grouped title={occurrenceLabels.informationSectionTitle}>
-      <Button
-        disabled={mode.new}
-        variant="contained"
-        onClick={() =>
-          window.open(`${window.location.origin}/occurrence/new?lid=${data.lid}&loc_name=${data.loc_name}`)
-        }
-      >
-        Create new occurrence
-      </Button>
-      {!mode.read && editingModal}
+      {!mode.read && (
+        <Button
+          disabled={mode.new}
+          variant="contained"
+          onClick={() =>
+            window.open(`${window.location.origin}/occurrence/new?lid=${data.lid}&loc_name=${data.loc_name}`)
+          }
+        >
+          Create new occurrence
+        </Button>
+      )}
       <EditableTable<Editable<LocalitySpecies>, LocalityDetailsType>
         columns={columns}
         field="now_ls"

frontend/src/components/Occurrence/OccurrenceDetails.tsx

@@ -1,15 +1,22 @@
 import { CircularProgress } from '@mui/material'
-import { useParams, useSearchParams } from 'react-router-dom'
+import { useNavigate, useParams, useSearchParams } from 'react-router-dom'
 import { DetailView, TabType } from '@/components/DetailView/DetailView'
 import { UpdateTab } from '@/components/DetailView/common/UpdateTab'
 import { OccurrenceCoreTab } from './Tabs/OccurrenceCoreTab'
 import { OccurrenceWearTab } from './Tabs/OccurrenceWearTab'
 import { OccurrenceIsotopeTab } from './Tabs/OccurrenceIsotopeTab'
-import { EditDataType, EditableOccurrenceData, OccurrenceDetailsType } from '@/shared/types'
+import {
+  EditDataType,
+  EditableOccurrenceData,
+  EditMetaData,
+  LocalityDetailsType,
+  OccurrenceDetailsType,
+} from '@/shared/types'
 import { validateOccurrence } from '@/shared/validators/occurrence'
 import { getErrorMessage, useNotify } from '@/hooks/notification'
 import { ValidationObject } from '@/shared/validators/validator'
-import { useEditOccurrenceMutation, useGetOccurrenceDetailsQuery } from '@/redux/api'
+import { useGetOccurrenceDetailsQuery } from '@/redux/api'
+import { useEditLocalityMutation, useGetLocalityDetailsQuery } from '@/redux/localityReducer'
 
 const validateOccurrenceDetail = (
   editData: EditDataType<OccurrenceDetailsType>,
@@ -66,10 +73,41 @@ const emptyOccurrence: OccurrenceDetailsType = {
   now_oau: [],
 }
 
+const occurrenceFields: Array<keyof EditableOccurrenceData> = [
+  'nis',
+  'pct',
+  'quad',
+  'mni',
+  'qua',
+  'id_status',
+  'orig_entry',
+  'source_name',
+  'body_mass',
+  'mesowear',
+  'mw_or_high',
+  'mw_or_low',
+  'mw_cs_sharp',
+  'mw_cs_round',
+  'mw_cs_blunt',
+  'mw_scale_min',
+  'mw_scale_max',
+  'mw_value',
+  'microwear',
+  'dc13_mean',
+  'dc13_n',
+  'dc13_max',
+  'dc13_min',
+  'dc13_stdev',
+  'do18_mean',
+  'do18_n',
+  'do18_max',
+  'do18_min',
+  'do18_stdev',
+]
+
 export const OccurrenceDetails = () => {
   const { id, lid, speciesId } = useParams()
   const [searchParams] = useSearchParams()
-  console.log(searchParams)
   const isNew = id === 'new'
   if (isNew) {
     document.title = 'New locality'
@@ -86,11 +124,15 @@ export const OccurrenceDetails = () => {
       skip: isNew,
     }
   )
+
   const { notify } = useNotify()
-  const [editOccurrenceRequest, { isLoading: mutationLoading }] = useEditOccurrenceMutation()
+  const navigate = useNavigate()
+  const [editLocalityRequest, { isLoading: mutationLoading }] = useEditLocalityMutation()
 
   const lidFromSearchParams = searchParams.get('lid')
   const locNameFromSearchParams = searchParams.get('loc_name')
+  const localityId = lidFromSearchParams ?? lid ?? ''
+  const { data: localityData } = useGetLocalityDetailsQuery(localityId)
 
   if (isError) return <div>Error loading occurrence data</div>
   if (isLoading || (!occurrenceData && !isNew) || mutationLoading) return <CircularProgress />
@@ -98,19 +140,58 @@ export const OccurrenceDetails = () => {
   const initialOccurrence = emptyOccurrence
 
   if (isNew) {
-    initialOccurrence.lid = parseInt(lidFromSearchParams!, 10)
-    initialOccurrence.loc_name = locNameFromSearchParams!
+    initialOccurrence.lid = parseInt(localityId, 10)
+    initialOccurrence.loc_name = locNameFromSearchParams ?? ''
   }
 
   if (occurrenceData) {
     document.title = `Occurrence - ${occurrenceData.lid}/${occurrenceData.species_id}`
   }
 
-  const onWrite = async (editData: EditDataType<OccurrenceDetailsType>) => {
+  const onWrite = async (editData: EditDataType<OccurrenceDetailsType> & EditMetaData) => {
     try {
-      console.log(editData)
-      await editOccurrenceRequest(editData).unwrap()
+      if (!localityData) throw new Error('Could not load the linked locality.')
+
+      const occurrenceSpeciesId = isNew ? editData.species_id : parsedSpeciesId
+      const existingOccurrence = localityData.now_ls.find(row => row.species_id === occurrenceSpeciesId)
+      const occurrenceData = occurrenceFields.reduce<Record<string, unknown>>((data, field) => {
+        if (field in editData) data[field] = editData[field]
+        return data
+      }, {})
+      const occurrence = {
+        ...(existingOccurrence ?? {}),
+        lid: localityData.lid,
+        species_id: occurrenceSpeciesId ?? existingOccurrence?.species_id,
+        ...occurrenceData,
+        ...(isNew
+          ? {
+              rowState: 'new' as const,
+              com_species: {
+                com_taxa_synonym: [],
+                now_sau: [],
+                species_id: editData.species_id,
+                family_name: editData.family_name,
+                genus_name: editData.genus_name,
+                species_name: editData.species_name,
+                unique_identifier: editData.unique_identifier,
+              },
+            }
+          : {}),
+      }
+
+      const nowLs = (
+        isNew
+          ? [...localityData.now_ls, occurrence]
+          : localityData.now_ls.map(row => (row.species_id === occurrenceSpeciesId ? occurrence : row))
+      ) as EditDataType<LocalityDetailsType>['now_ls']
+      await editLocalityRequest({
+        ...localityData,
+        now_ls: nowLs,
+        comment: editData.comment,
+        references: editData.references ?? [],
+      }).unwrap()
       notify('Occurrence entry finalized successfully.')
+      setTimeout(() => navigate(`/occurrence/${editData.lid}/${editData.species_id}`), 15)
     } catch (error) {
       notify(getErrorMessage(error, 'Could not finalize occurrence entry.'), 'error')
       throw error

frontend/src/components/Occurrence/Tabs/OccurrenceCoreTab.tsx

@@ -1,37 +1,51 @@
 import { useDetailContext } from '@/components/DetailView/Context/DetailContext'
 import { ArrayFrame, HalfFrames } from '@/components/DetailView/common/tabLayoutHelpers'
-import { OccurrenceDetailsType } from '@/shared/types'
+import { EditDataType, LocalityDetailsType, OccurrenceDetailsType, Species, SpeciesDetailsType } from '@/shared/types'
 import { Link } from 'react-router-dom'
 import { idStatusOptions, quantityOptions } from '../constants'
 import { useGetAllSpeciesQuery } from '@/redux/speciesReducer'
-import { buildTaxonomySuggestionOptions, TaxonomySuggestionFieldName } from '@/components/Species/taxonomySuggestions'
-import { useMemo } from 'react'
-import { TaxonomySuggestionField } from '@/components/Species/TaxonomySuggestionField'
+import { SelectingTable } from '@/components/DetailView/common/SelectingTable'
+import { MRT_ColumnDef } from 'material-react-table'
 
 const toText = (value: string | number | null | undefined) =>
   value === null || value === undefined || value === '' ? '-' : String(value)
-
+const speciesColumns: MRT_ColumnDef<Species>[] = [
+  {
+    accessorKey: 'order_name',
+    header: 'Order',
+  },
+  {
+    accessorKey: 'family_name',
+    header: 'Family',
+  },
+  {
+    accessorKey: 'genus_name',
+    header: 'Genus',
+  },
+  {
+    accessorKey: 'species_name',
+    header: 'Species',
+  },
+  {
+    accessorKey: 'subclass_or_superorder_name',
+    header: 'Subclass or Superorder',
+  },
+  {
+    accessorKey: 'suborder_or_superfamily_name',
+    header: 'Suborder or Superfamily',
+  },
+  {
+    accessorKey: 'unique_identifier',
+    header: 'Unique Identifier',
+  },
+  {
+    accessorKey: 'taxonomic_status',
+    header: 'Taxon status',
+  },
+]
 export const OccurrenceCoreTab = () => {
   const { data: speciesQueryData, isError } = useGetAllSpeciesQuery()
-  const { data, editData, mode, textField, dropdown } = useDetailContext<OccurrenceDetailsType>()
-
-  console.log(editData)
-  const taxonomySuggestionOptions = useMemo(
-    () => ({
-      subclass_or_superorder_name: buildTaxonomySuggestionOptions(speciesQueryData, 'subclass_or_superorder_name'),
-      order_name: buildTaxonomySuggestionOptions(speciesQueryData, 'order_name'),
-      suborder_or_superfamily_name: buildTaxonomySuggestionOptions(speciesQueryData, 'suborder_or_superfamily_name'),
-      family_name: buildTaxonomySuggestionOptions(speciesQueryData, 'family_name'),
-      subfamily_name: buildTaxonomySuggestionOptions(speciesQueryData, 'subfamily_name'),
-      genus_name: buildTaxonomySuggestionOptions(speciesQueryData, 'genus_name'),
-      species_name: buildTaxonomySuggestionOptions(speciesQueryData, 'species_name'),
-    }),
-    [speciesQueryData]
-  )
-
-  const taxonomySuggestionField = (field: TaxonomySuggestionFieldName) => (
-    <TaxonomySuggestionField field={field} options={taxonomySuggestionOptions[field]} />
-  )
+  const { data, editData, setEditData, mode, textField, dropdown } = useDetailContext<OccurrenceDetailsType>()
 
   return (
     <>
@@ -47,9 +61,35 @@ export const OccurrenceCoreTab = () => {
                   {toText(data.loc_name)}
                 </Link>,
               ],
-              ['Family', taxonomySuggestionField('family_name')],
-              ['Genus', taxonomySuggestionField('genus_name')],
-              ['Species', taxonomySuggestionField('species_name')],
+              !mode.read
+                ? [
+                    '',
+                    <SelectingTable
+                      key={'selecting-table'}
+                      buttonText="Select Species"
+                      data={speciesQueryData}
+                      title="Species"
+                      isError={isError}
+                      columns={speciesColumns}
+                      fieldName="species_id"
+                      idFieldName="species_id"
+                      useObject
+                      editingAction={(newSpecies: Species) => {
+                        setEditData({
+                          ...editData,
+                          family_name: newSpecies.family_name,
+                          genus_name: newSpecies.genus_name!,
+                          species_name: newSpecies.species_name!,
+                          species_id: newSpecies.species_id,
+                          unique_identifier: newSpecies.unique_identifier,
+                        })
+                      }}
+                    />,
+                  ]
+                : [],
+              ['Family', editData.family_name],
+              ['Genus', editData.genus_name],
+              ['Species', editData.species_name],
               ['ID status', dropdown('id_status', idStatusOptions, 'ID status')],
               ['Additional Information', textField('orig_entry', { type: 'text' })],
               ['Source name', textField('source_name', { type: 'text' })],

frontend/src/redux/localityReducer.ts

@@ -1,6 +1,6 @@
 import { api } from './api'
 import { addLocality } from '@/redux/userReducer'
-import { EditDataType, Locality, LocalityDetailsType } from '@/shared/types'
+import { EditDataType, EditMetaData, Locality, LocalityDetailsType } from '@/shared/types'
 
 const sanitizeLocalityProjects = (locality?: EditDataType<LocalityDetailsType>) => {
   if (!locality || !locality.now_plr) return [] as LocalityDetailsType['now_plr']
@@ -23,14 +23,14 @@ const localitiesApi = api.injectEndpoints({
       }),
       providesTags: result => (result ? [{ type: 'locality', id: result.lid }] : []),
     }),
-    editLocality: builder.mutation<{ id: number }, EditDataType<LocalityDetailsType>>({
+    editLocality: builder.mutation<{ id: number }, EditDataType<LocalityDetailsType> & EditMetaData>({
       query: locality => ({
         url: `/locality`,
         method: 'PUT',
         body: { locality },
       }),
       invalidatesTags: (result, _error, { lid }) =>
-        result ? [{ type: 'locality', id: lid }, 'localities', 'specieslist'] : [],
+        result ? [{ type: 'locality', id: lid }, 'localities', 'specieslist', 'occurrence'] : [],
       async onQueryStarted(locality, { dispatch, queryFulfilled }) {
         if (!locality.lid) {
           try {