Merge branch 'main' into make-some-tables-unclickable

README.md

@@ -40,3 +40,6 @@ The new version is not deployed yet.
 :mag_right: [Class diagram](documentation/class_diagram.md) See the relations of relevant tables. Notice that it omits some unimportant tables and does not show most columns.
 
 :earth_africa: [Map features](documentation/frontend/components/maps/README.md) Maps' functionality and development notes
+
+**DeepWiki documentation for the NOW database can be found here:** 
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/nowcommunity/nowdatabase)

backend/src/api-tests/species/data.ts

@@ -45,7 +45,7 @@ export const newSpeciesBasis: EditDataType<SpeciesDetailsType & EditMetaData> =
   genus_name: 'Petenyia',
   species_name: 'dubiatest',
   unique_identifier: '-',
-  taxonomic_status: null,
+  taxonomic_status: '',
   common_name: null,
   sp_author: 'Bachmayer & Wilson, 1970',
   strain: null,

backend/src/routes/crossSearch.ts

@@ -132,8 +132,8 @@ router.get(`/export/:columnfilters/:sorting`, async (req, res) => {
   })
   res.attachment(`cross_search${currentDateAsString()}.csv`) // filename will get overwritten in frontend when fetching data from this route
 
-  // quoteColumns is needed to make sure linebreaks do not mess up the data
-  const stream = format({ headers: true, quoteColumns: true }).transform(
+  // this should match the csvConfig in frontend exportRows() function as closely as possible
+  const stream = format({ delimiter: ',', headers: true, quoteColumns: true }).transform(
     transformFunction as FormatterRowTransformFunction<FormatterRow, FormatterRow>
   )
 

backend/src/services/locality.ts

@@ -1,11 +1,20 @@
-import { EditDataType, EditMetaData, LocalityDetailsType, User, Role } from '../../../frontend/src/shared/types'
+import {
+  EditDataType,
+  EditMetaData,
+  LocalityDetailsType,
+  User,
+  Role,
+  LocalitySpeciesDetailsType,
+  Editable,
+  SpeciesDetailsType,
+} from '../../../frontend/src/shared/types'
 import { validateLocality } from '../../../frontend/src/shared/validators/locality'
+import { validateSpecies } from '../../../frontend/src/shared/validators/species'
 import { ValidationObject, referenceValidator } from '../../../frontend/src/shared/validators/validator'
 import Prisma from '../../prisma/generated/now_test_client'
 import { AccessError } from '../middlewares/authorizer'
 import { fixBigInt } from '../utils/common'
 import { logDb, nowDb } from '../utils/db'
-import { logger } from '../utils/logger'
 import { getReferenceDetails } from './reference'
 
 const getIdsOfUsersProjects = async (user: User) => {
@@ -200,6 +209,7 @@ export const getLocalityDetails = async (id: number, user: User | undefined) =>
   return JSON.parse(fixBigInt(result)!) as LocalityDetailsType
 }
 
+// also validates possible new species that were added to this locality
 export const validateEntireLocality = async (editedFields: EditDataType<Prisma.now_loc> & EditMetaData) => {
   const keys = Object.keys(editedFields)
   const errors: ValidationObject[] = []
@@ -207,6 +217,17 @@ export const validateEntireLocality = async (editedFields: EditDataType<Prisma.n
     const error = validateLocality(editedFields as EditDataType<LocalityDetailsType>, key as keyof LocalityDetailsType)
     if (error.error) errors.push(error)
   }
+  if ('now_ls' in editedFields) {
+    for (const species of editedFields.now_ls as Array<Editable<LocalitySpeciesDetailsType>>) {
+      if (species.rowState === 'new') {
+        const keys = Object.keys(species.com_species)
+        for (const key of keys) {
+          const newSpeciesError = validateSpecies(species.com_species, key as keyof SpeciesDetailsType)
+          if (newSpeciesError.error) errors.push(newSpeciesError)
+        }
+      }
+    }
+  }
   let error = null
   if ('references' in editedFields && editedFields.references) {
     error = referenceValidator(editedFields.references)
@@ -251,12 +272,10 @@ export const filterDuplicateLocalitySpecies = async (
       // Logic is flipped for filter as we want to skip the ones the check matches
       return !(localityDetailsSpeciesIds.includes(localitySpecies.species_id) && localitySpecies.rowState === 'new')
     }
-
-    // code shouldn't get here ever
-    logger.info(
-      `Filter already existing species: localitySpecies didn't have species_id. Skipping. ${JSON.stringify(localitySpecies)}`
-    )
-    return false
+    // if localitySpecies doesn't have species_id (i.e. it was created with the "add new species" button in Species tab),
+    // it will never be filtered out. However, due to the taxonomy check for the "add new species" button,
+    // it should not let the user create a duplicate species in this way.
+    return true
   })
 
   return updatedLocalityNow_ls

backend/src/services/species.ts

@@ -94,14 +94,13 @@ export const getSpeciesDetails = async (id: number) => {
       now_sau: {
         include: {
           now_sr: {
-            select: {
+            include: {
               ref_ref: {
-                select: {
+                include: {
                   ref_authors: true,
                   ref_journal: true,
                 },
               },
-              rid: true,
             },
           },
         },

backend/src/services/write/locality.ts

@@ -49,9 +49,9 @@ export const writeLocality = async (
   try {
     await writeHandler.start()
 
-    const filteredLocality = await filterDuplicateLocalitySpecies(locality, user)
-    if (updateOrAdd === 'update' && filteredLocality) {
-      locality.now_ls = filteredLocality
+    const filteredLocalities = await filterDuplicateLocalitySpecies(locality, user)
+    if (updateOrAdd === 'update' && filteredLocalities && filteredLocalities.length > 0) {
+      locality.now_ls = filteredLocalities
     }
 
     if (updateOrAdd === 'add') {

backend/src/services/write/species.ts

@@ -11,7 +11,7 @@ const getSpeciesWriteHandler = (type: ActionType) => {
     dbName: NOW_DB_NAME,
     table: 'com_species',
     idColumn: 'species_id',
-    allowedColumns: getFieldsOfTables(['com_species', 'now_ls', 'now_sau', 'now_lau']),
+    allowedColumns: getFieldsOfTables(['com_species', 'now_ls', 'now_sau', 'now_lau', 'com_taxa_synonym']),
     type,
   })
 }

cypress/e2e/locality.cy.js

@@ -1,3 +1,162 @@
+before('Reset database', () => {
+  cy.request(Cypress.env('databaseResetUrl'))
+})
+
+describe('Adding species in Locality -> Species tab for an existing locality', () => {
+  beforeEach('Login as admin', () => {
+    cy.login('testSu')
+  })
+
+  it('works with valid, unique species', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+
+    cy.contains('Add new Species').click()
+    cy.get('[name=order_name]').type('Rodentia')
+    cy.get('[name=family_name]').type('Gliridae')
+    cy.get('[name=genus_name]').type('Simplomys')
+    cy.get('[name=species_name]').type('someSpecies')
+    cy.get('[name=unique_identifier]').type('veryunique')
+    cy.contains('Save').click()
+    cy.contains('somespecies')
+
+    cy.addReferenceAndSave()
+    cy.contains('Edited item successfully.')
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('somespecies')
+  })
+
+  it('works through "copy species taxonomy" button', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+    cy.contains('Add new Species').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=add-button-21426]').click()
+    cy.contains('Close').click()
+    cy.get('[name=species_name]').clear()
+    cy.get('[name=species_name]').type('Newspecies')
+    cy.contains('Save').click()
+
+    cy.addReferenceAndSave()
+    cy.contains('Edited item successfully.')
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('newspecies')
+  })
+
+  it('does not work with invalid species', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('Order with spaces')
+    cy.get('[name=family_name]').type('newfamily')
+    cy.get('[name=genus_name]').type('newgenus')
+    cy.get('[name=species_name]').type('newspecies')
+    cy.get('[name=unique_identifier]').type('veryunique')
+    cy.contains('Save').click()
+    cy.contains('Order must not contain any spaces, unless the value is "incertae sedis".')
+  })
+
+  it('does not work if the species has already been added', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+
+    // adding species that already exists in the database
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('Rodentia')
+    cy.get('[name=family_name]').type('Gliridae')
+    cy.get('[name=genus_name]').type('Simplomys')
+    cy.get('[name=species_name]').type('Simplicidens')
+    cy.get('[name=unique_identifier]').type('-')
+    cy.contains('Save').click()
+    cy.contains('The taxon already exists in the database.')
+
+    // add new, unique species
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('neworder')
+    cy.get('[name=family_name]').type('newfamily')
+    cy.get('[name=genus_name]').type('newgenus')
+    cy.get('[name=species_name]').type('newspecies')
+    cy.get('[name=unique_identifier]').type('-')
+    cy.contains('Save').click()
+
+    cy.addReferenceAndSave()
+    cy.contains('Edited item successfully.')
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+    cy.contains('Neworder')
+
+    // adding species that has been added earlier through "add new species" button
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('neworder')
+    cy.get('[name=family_name]').type('newfamily')
+    cy.get('[name=genus_name]').type('newgenus')
+    cy.get('[name=species_name]').type('newspecies')
+    cy.get('[name=unique_identifier]').type('-')
+    cy.contains('Save').click()
+    cy.contains('The taxon already exists in the database.')
+  })
+
+  it('does not work with species with invalid taxonomic order', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+
+    // adding species that already exists in the database
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('Rodentia')
+    cy.get('[name=family_name]').type('Soricidae')
+    cy.get('[name=genus_name]').type('Simplomys')
+    cy.get('[name=species_name]').type('Simplicidens')
+    cy.get('[name=unique_identifier]').type('unique')
+    cy.contains('Save').click()
+    cy.contains('Family Soricidae belongs to order Eulipotyphla, not Rodentia.')
+    cy.contains('Genus Simplomys belongs to family Gliridae, not Soricidae.')
+
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('Carnivora')
+    cy.get('[name=family_name]').type('Canidae')
+    cy.get('[name=genus_name]').type('Simplomys')
+    cy.get('[name=species_name]').type('Simplicidens')
+    cy.get('[name=unique_identifier]').type('moreunique')
+    cy.contains('Save').click()
+    cy.contains('Genus Simplomys belongs to family Gliridae, not Canidae.')
+
+    cy.contains('Add new Species').click()
+    cy.clearNewSpeciesForm()
+    cy.get('[name=order_name]').type('Artiodactyla')
+    cy.get('[name=family_name]').type('Bovidae')
+    cy.get('[name=genus_name]').type('Amblycoptus')
+    cy.get('[name=species_name]').type('indet.')
+    cy.get('[name=unique_identifier]').type('uniquest')
+    cy.contains('Save').click()
+    cy.contains('Genus Amblycoptus belongs to family Soricidae, not Bovidae.')
+  })
+
+  it('does not work through "copy species taxonomy" button if nothing is changed', () => {
+    cy.visit(`/locality/20920?tab=2`)
+    cy.contains('Lantian-Shuijiazui')
+    cy.get('[id=edit-button]').click()
+    cy.contains('Add new Species').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=add-button-21052]').click()
+    cy.contains('Close').click()
+    cy.contains('Save').click()
+    cy.contains('The taxon already exists in the database.')
+  })
+})
+
 describe('Creating a new locality', () => {
   beforeEach('Login as admin', () => {
     cy.login('testSu')
@@ -30,13 +189,8 @@ describe('Creating a new locality', () => {
     cy.get('[id=dec_long-textfield]').type('103.67')
     cy.get('[id=dms_lat-textfield]').should('have.value', '49 4 12 N')
     cy.get('[id=dms_long-textfield]').should('have.value', '103 40 12 E')
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('Edited item successfully.')
     cy.contains('Bugat')
     cy.get('[id=delete-button]').should('exist')
@@ -150,15 +304,8 @@ describe('Creating a new locality', () => {
     cy.get('[id=dec_lat-textfield]').type('49.07')
     cy.get('[id=dec_long-textfield]').type('103.67')
     cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
-
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
 
+    cy.addReferenceAndSave()
     cy.contains('Edited item successfully.')
     cy.contains('Bugat')
     cy.contains('8.676')
@@ -314,11 +461,8 @@ describe("Locality's coordinate selection map works", () => {
     cy.contains('Central Finland').first().click() // first item on the list
     cy.contains('Latitude: 63.05484, Longitude: 24.75291')
     cy.contains('Save').click()
-    cy.contains('Finalize entry').click()
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.visit(`/locality/20920?tab=1`)
     cy.contains('63.05484')
     cy.contains('24.75291')

cypress/e2e/species.cy.js

@@ -19,13 +19,7 @@ describe('Creating a species', () => {
     cy.get('[id=species_name-textfield]').type('testSpecies')
     cy.get('[id=unique_identifier-textfield]').type('{backspace}testUniqueIdentifier')
     cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+    cy.addReferenceAndSave()
 
     // tests that values are capitalised and trimmed properly
     cy.contains('Testsuperorder')
@@ -66,12 +60,7 @@ describe('Editing a species', () => {
     cy.get('[id=subfamily_name-textfield]').type('heimo')
 
     cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+    cy.addReferenceAndSave()
     cy.contains('Saved species entry successfully.')
     cy.contains('Modifiedgenus')
     cy.contains('modifiedspecies')
@@ -101,14 +90,8 @@ describe('Editing a species', () => {
 
     cy.get('[id=species_name-textfield]').type('newSpecies')
     cy.contains('Species: This field is required').should('not.exist')
-    cy.get('[id=write-button]').click()
-
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
 
+    cy.addReferenceAndSave()
     cy.contains('Saved species entry successfully.')
     cy.contains('Newgenus')
     cy.contains('newspecies')
@@ -126,8 +109,7 @@ describe('Taxonomy checks work', () => {
 
   it('Creating a species that already exists in database does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-21052]').click()
     cy.contains('Close').click()
     cy.get('[id=write-button]').click()
@@ -136,8 +118,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid main taxonomy values do not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-21052]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier') // change identifier so it's not a duplicate species
@@ -158,8 +139,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid superorder/order pair does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-21052]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -172,8 +152,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid order/suborder/family trio does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-84357]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -187,8 +166,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid suborder/family pair does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-84357]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -201,8 +179,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid family/subfamily/genus trio does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-23065]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -216,8 +193,7 @@ describe('Taxonomy checks work', () => {
 
   it('Invalid subfamily/genus pair does not work', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-23065]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -230,8 +206,7 @@ describe('Taxonomy checks work', () => {
 
   it('When genus is indet. species has to be indet.', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-21052]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')
@@ -246,8 +221,7 @@ describe('Taxonomy checks work', () => {
 
   it('When genus is gen. species has to be sp.', () => {
     cy.visit('/species/new')
-    cy.get('[id=copy_existing_taxonomy_button]').contains('Copy existing taxonomy')
-    cy.get('[id=copy_existing_taxonomy_button]').click()
+    cy.get('[data-cy=copy_existing_taxonomy_button]').click()
     cy.get('[data-cy=add-button-21052]').click()
     cy.contains('Close').click()
     cy.get('[id=unique_identifier-textfield]').type('{backspace}new identifier')

cypress/e2e/timeBound.cy.js

@@ -17,12 +17,8 @@ describe('Creating time bound', () => {
     cy.get('[id=write-button]').should('be.disabled')
     cy.get('[id=age-textfield]').first().type('20')
     cy.contains('Age (Ma): This field is required').should('not.exist')
-    cy.get('[id=write-button]').click()
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('Edited item successfully.')
   })
 })
@@ -38,13 +34,8 @@ describe('Editing time bound', () => {
     cy.get('[id=edit-button]').click()
     cy.get('[id=age-textfield]').first().type('{backspace}{backspace}{backspace}{backspace}{backspace}1.5')
     cy.contains('This field is required').should('not.exist')
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('Edited item successfully.')
     cy.contains('1.5')
   })

cypress/e2e/timeUnit.cy.js

@@ -16,13 +16,8 @@ describe('Creating a time unit', () => {
     cy.get('[data-cy=add-button-11]').first().click()
     cy.get('[id=low_bnd-tableselection]').first().click() // Select Lower Bound Button
     cy.get('[data-cy=add-button-14]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('Testing Time Unit Creation')
     cy.contains('ALMAAsianlandmammalage')
     cy.contains('C2N-o')
@@ -130,13 +125,8 @@ describe('Creating a time unit', () => {
     cy.get('[id=sequence-tableselection]').should('have.value', 'ALMAAsianlandmammalage')
     cy.contains('C2N-o')
     cy.contains('C2N-y')
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('C2N-o')
     cy.contains('C2N-y')
     cy.contains('Creating new time-unit').should('not.exist')
@@ -151,13 +141,8 @@ describe('Creating a time unit', () => {
     cy.get('[data-cy=add-button-11]').first().click()
     cy.get('[id=low_bnd-tableselection]').first().click()
     cy.get('[data-cy=add-button-14]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('C2N-o')
     cy.contains('C2N-y')
     cy.get('[id=edit-button]').click()
@@ -165,13 +150,8 @@ describe('Creating a time unit', () => {
     cy.get('[data-cy=add-button-CalatayudTeruellocalbiozone]').first().click()
     cy.get('[id=low_bnd-tableselection]').first().click()
     cy.get('[data-cy=add-button-49]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('CalatayudTeruellocalbiozone')
     cy.contains('Langhian/Serravallian')
   })
@@ -189,13 +169,8 @@ describe('Editing a time unit', () => {
     cy.get('[id=tu_display_name-textfield]').should('be.disabled') // name field is disabled when editing
     cy.get('[id=sequence-tableselection]').first().click()
     cy.get('[data-cy=add-button-ALMAAsianlandmammalage]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('ALMAAsianlandmammalage')
   })
 
@@ -274,13 +249,8 @@ describe('Editing a time unit', () => {
     cy.get('[id=sequence-tableselection]').should('have.value', 'CalatayudTeruellocalbiozone')
     cy.contains('C2N-y')
     cy.contains('MioceneLate-low')
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('CalatayudTeruellocalbiozone')
     cy.contains('C2N-y')
     cy.contains('MioceneLate-low')
@@ -292,13 +262,8 @@ describe('Editing a time unit', () => {
     cy.get('[id=edit-button]').click()
     cy.get('[id=sequence-tableselection]').first().click()
     cy.get('[data-cy=add-button-easternparatethys]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('Bahean')
     cy.contains('easternparatethys')
     cy.get('[id=edit-button]').click()
@@ -307,13 +272,8 @@ describe('Editing a time unit', () => {
     cy.get('[data-cy=add-button-CalatayudTeruellocalbiozone]').first().click()
     cy.get('[id=up_bnd-tableselection]').first().click()
     cy.get('[data-cy=add-button-14]').first().click()
-    cy.get('[id=write-button]').click()
-    cy.get('[id=write-button]').should('be.disabled')
-    cy.contains('button', 'Add existing reference').click()
-    cy.get('button[data-cy^="add-button"]').first().click()
-    cy.contains('button', 'Close').click()
-    cy.get('[id=write-button]').should('not.be.disabled')
-    cy.get('[id=write-button]').click()
+
+    cy.addReferenceAndSave()
     cy.contains('CalatayudTeruellocalbiozone')
     cy.contains('C2N-o')
   })

cypress/support/commands.js

@@ -27,7 +27,7 @@
 Cypress.Commands.add('login', username => {
   cy.clearLocalStorage()
   cy.visit('/login')
-  cy.contains('Login').click()
+  cy.get('[data-cy="login-button"]', { timeout: 10000 }).should('be.visible').click()
   cy.get('[data-cy="username-basic"]').type(username)
   cy.get('[data-cy="password-basic"]').type('test')
   cy.get('[data-cy="login-button"]').click()
@@ -42,3 +42,28 @@ Cypress.Commands.add('pageForbidden', url => {
 Cypress.Commands.add('resetDatabase', () => {
   cy.task('resetDatabase')
 })
+
+// use this once you have edited some data and want to save it
+Cypress.Commands.add('addReferenceAndSave', () => {
+  cy.get('[id=write-button]').click()
+  cy.get('[id=write-button]').should('be.disabled')
+  cy.contains('button', 'Add existing reference').click()
+  cy.get('button[data-cy^="add-button"]').first().click()
+  cy.contains('button', 'Close').click()
+  cy.get('[id=write-button]').should('not.be.disabled')
+  cy.get('[id=write-button]').click()
+})
+
+Cypress.Commands.add('clearNewSpeciesForm', () => {
+  cy.get('[name=order_name]').clear()
+  cy.get('[name=family_name]').clear()
+  cy.get('[name=genus_name]').clear()
+  cy.get('[name=species_name]').clear()
+  cy.get('[name=subclass_or_superorder_name]').clear()
+  cy.get('[name=suborder_or_superfamily_name]').clear()
+  cy.get('[name=subfamily_name]').clear()
+  cy.get('[name=unique_identifier]').clear()
+  cy.get('[name=taxonomic_status]').clear()
+  cy.get('[name=sp_comment]').clear()
+  cy.get('[name=sp_author]').clear()
+})

documentation/backend/cross_search_export.md

@@ -1,3 +1,3 @@
 ### Cross Search Export
 
-Cross search has a [`/export` route](../../backend/src/routes/crossSearch.ts) which is used by the ["Export Table"](../../../frontend/src/components/CrossSearch/CrossSearchExportButton.tsx) button in a cross-search table view. This route uses the same parameter parsing and validation function as the `/all` route, and it also uses the same SQL query, but with LIMIT set to undefined. The resulting data is [streamed](https://developer.mozilla.org/en-US/docs/Web/API/Streams_API) to the user, where the browser will download it as a csv file. See the "Exporting" section in [TableView docs](../frontend/components/TableView.md) for more information.
+Cross search has a [`/export` route](../../backend/src/routes/crossSearch.ts) which is used by the ["Export Table"](../../frontend/src/components/CrossSearch/CrossSearchExportMenuItem.tsx) button in a cross-search table view. This route uses the same parameter parsing and validation function as the `/all` route, and it also uses the same SQL query, but with LIMIT set to undefined. The resulting data is [streamed](https://developer.mozilla.org/en-US/docs/Web/API/Streams_API) to the user, where the browser will download it as a csv file. See the "Exporting" section in [TableView docs](../frontend/components/TableView.md) for more information.

documentation/entities/reference_types.md

@@ -1,12 +1,15 @@
-Current reference types & their field labels / field names (29.09.2024)
+# Reference types
 
-As of 29.09.2024 there is no UI to add more entries however you can do it by altering the db itself.
+Note: This file is old and should be checked and updated.
 
-In the test_data/sqlfiles/now_test.sql code related to adding reference types is around rows 3665-3700 and the fields for the data types are added around rows 3175-3525.
+Current reference types & their field labels / field names
 
-Do concider other options before you try to alter the data by hand.
+In the `test_data/sqlfiles/now_test.sql` file, code related to adding reference types is around rows 3665-3700 and the fields for the data types are added around rows 3175-3525.
+
+Do consider other options before you try to alter the data by hand.
 
 ## Existing fields & their ids
+
     title_primary 1
     authors_primary 2
     date_primary 3
@@ -265,4 +268,5 @@ Mandatory fields: title_primary OR gen_notes, date_primary, authors_primary, exa
 exact_date / exact_date
 
 Mandatory fields: title_primary OR title_secondary OR title_series OR gen_notes, date_primary, authors_primary OR authors_secondary OR authors_series, exact_date, journal
-* In old php test version instead of journal, journal_id had to be defined. That seems odd, since when creating a new journal, journal_id will not initally be defined. So that will not be done here.
+
+- In old php test version instead of journal, journal_id had to be defined. That seems odd, since when creating a new journal, journal_id will not initially be defined. So that will not be done here.

documentation/entities/species.md

@@ -1,4 +1,4 @@
-# Localities
+# Species
 
 ## Required fields
 

documentation/entities/time_bound.md

@@ -1,4 +1,4 @@
-### Time Bound
+### Time Bounds
 
 A Time Bound can be given the following information:
 

documentation/entities/time_unit.md

@@ -1,4 +1,4 @@
-### Time Unit
+### Time Units
 
 A Time Unit can be given the following information:
 

frontend/src/components/CrossSearch/CrossSearchExportMenuItem.tsx

@@ -14,7 +14,7 @@ export const CrossSearchExportMenuItem = ({ handleClose }: { handleClose: () =>
   const token = useUser().token
   const fetchOptions = token ? { headers: { Authorization: `Bearer ${token}` } } : {}
 
-  const filename = `cross_search${currentDateAsString()}.csv`
+  const filename = `locality-species-${currentDateAsString()}.csv`
 
   const fetchCSVFile = async () => {
     setLoading(true)

frontend/src/components/DetailView/StagingView.tsx

@@ -25,6 +25,7 @@ export const StagingView = <T extends MRT_RowData>() => {
         <SelectingTable<Reference, T>
           buttonText="Add existing reference"
           data={data}
+          title="References"
           isError={isError}
           columns={referenceTableColumns}
           idFieldName="rid"

frontend/src/components/DetailView/common/ContactModal.tsx

@@ -22,7 +22,6 @@ export const ContactModal = ({
     setOpen(false)
   }
 
-  return <></>
   return (
     <Box>
       <Button onClick={() => setOpen(true)} variant="outlined" startIcon={<EmailIcon />} className="button">

frontend/src/components/DetailView/common/EditingForm.tsx

@@ -3,6 +3,7 @@ import { EditingModal } from './EditingModal'
 import { useForm } from 'react-hook-form'
 import { Editable, EditDataType } from '@/shared/types'
 import { useDetailContext } from '../Context/DetailContext'
+import { useEffect } from 'react'
 
 export type EditingFormField = { name: string; label: string; required?: boolean; type?: 'number' | 'string' }
 
@@ -11,6 +12,10 @@ Renders a button, that will open EditingModal, which can be used
 to add a new entry to a list, or edit existing one.
 If using for adding new, provide arrayFieldName.
 For editing existing row, use existingObject and editAction.
+
+If you want to autofill the form's fields once the user e.g. clicks a button, 
+pass the updated values into the replacedValues prop. The form will be reset and uses those values.
+The copyTaxonomyButton prop is used only in Locality -> Species tab.
 */
 export const EditingForm = <T extends object, ParentType extends object>({
   dataCy,
@@ -19,6 +24,8 @@ export const EditingForm = <T extends object, ParentType extends object>({
   editAction,
   existingObject,
   arrayFieldName,
+  replacedValues,
+  copyTaxonomyButton,
 }: {
   dataCy?: string
   buttonText: string
@@ -26,15 +33,22 @@ export const EditingForm = <T extends object, ParentType extends object>({
   arrayFieldName?: keyof ParentType
   editAction?: (newObject: T) => void
   existingObject?: T | undefined
+  replacedValues?: T | undefined
+  copyTaxonomyButton?: JSX.Element | undefined
 }) => {
   const getDefaultValues: () => { [x: string]: unknown } = () => {
     if (!existingObject) return {}
     return existingObject
   }
-  const { register, trigger, formState, getValues } = useForm({ defaultValues: getDefaultValues() })
+  const { register, trigger, formState, getValues, reset } = useForm({ defaultValues: getDefaultValues() })
   const { errors } = formState
   const { editData, setEditData } = useDetailContext<ParentType>()
 
+  useEffect(() => {
+    if (replacedValues) reset(replacedValues)
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, [replacedValues])
+
   const onSave = async () => {
     const result = await trigger()
     if (!result) return false
@@ -52,9 +66,11 @@ export const EditingForm = <T extends object, ParentType extends object>({
   return (
     <EditingModal {...{ dataCy, buttonText, onSave }}>
       <Box sx={{ display: 'flex', flexDirection: 'column', gap: '1em' }}>
+        {copyTaxonomyButton}
         {formFields.map(field => (
           <TextField
             key={field.name}
+            slotProps={{ inputLabel: { shrink: true } }}
             {...register(field.name, {
               required: field.required ? 'This field is required' : false,
               ...(field.type === 'number' && {

frontend/src/components/DetailView/common/SelectingTable.tsx

@@ -12,9 +12,11 @@ give an array in prop "selectedValues" that contains the string values
 that already exist in editdata
 */
 export const SelectingTable = <T extends MRT_RowData, ParentType extends object>({
+  dataCy,
   buttonText,
   data,
   columns,
+  title,
   editingAction,
   tableRowAction,
   fieldName,
@@ -23,9 +25,11 @@ export const SelectingTable = <T extends MRT_RowData, ParentType extends object>
   isError,
   useObject,
 }: {
+  dataCy?: string
   buttonText: string
   data: T[] | undefined
   columns: MRT_ColumnDef<T>[]
+  title: string
   editingAction?: (object: T) => void
   tableRowAction?: (row: T) => void
   fieldName: keyof ParentType
@@ -69,11 +73,12 @@ export const SelectingTable = <T extends MRT_RowData, ParentType extends object>
   if (isError) return <Box>Error fetching data for the selecting table.</Box>
   if (!data) return <CircularProgress />
   return (
-    <EditingModal buttonText={buttonText}>
+    <EditingModal buttonText={buttonText} dataCy={dataCy}>
       {data ? (
         <TableView<T>
           data={filteredData}
           columns={columns}
+          title={title}
           isFetching={false}
           visibleColumns={visibleColumns}
           selectorFn={editingAction ?? defaultEditingAction}

frontend/src/components/DetailView/common/UpdateTab.tsx

@@ -1,4 +1,4 @@
-import { ReferenceOfUpdate, UpdateLog } from '@/shared/types'
+import { AnyReference, ReferenceOfUpdate, UpdateLog } from '@/shared/types'
 import { useDetailContext } from '@/components/DetailView/Context/DetailContext'
 import { EditingModal } from '@/components/DetailView/common/EditingModal'
 import { SimpleTable } from '@/components/DetailView/common/SimpleTable'
@@ -18,9 +18,10 @@ const makeNameList = (names: Array<string | null>) => {
   return names[0] ?? ''
 }
 
-const ReferenceList = ({ references, big }: { references: ReferenceOfUpdate[]; big: boolean }) => {
+const ReferenceList = ({ references, big }: { references: AnyReference[]; big: boolean }) => {
   const getReferenceText = (ref: ReferenceOfUpdate) => {
     // php version: html/include/database.php -> referenceCitation()
+    //const ref = referenceOfUpdate.ref_ref
     const authors = makeNameList(ref.ref_authors.map(author => author.author_surname))
     const issue = ref.issue ? ` (${ref.issue}) ` : ''
     if (ref.ref_type_id === 1) {
@@ -37,6 +38,7 @@ const ReferenceList = ({ references, big }: { references: ReferenceOfUpdate[]; b
     // All other types
     return `${authors} ${ref.date_primary ? `(${ref.date_primary}). ` : ''} ${ref.title_primary?.concat('. ') ?? ''}${ref.title_secondary?.concat('. ') ?? ''}${ref.title_series?.concat('. ') ?? ''}${ref.gen_notes?.concat('.') ?? ''}`
   }
+
   return (
     <Stack>
       {references.map(ref => (
@@ -44,7 +46,7 @@ const ReferenceList = ({ references, big }: { references: ReferenceOfUpdate[]; b
           key={ref.rid}
           sx={{ padding: '0.4em', margin: '0.5em', maxWidth: big ? '50em' : '30em', backgroundColor: 'lightblue' }}
         >
-          <div style={{ wordWrap: 'break-word', whiteSpace: 'normal' }}>{getReferenceText(ref)}</div>
+          <div style={{ wordWrap: 'break-word', whiteSpace: 'normal' }}>{getReferenceText(ref.ref_ref)}</div>
           {big && (
             <div>
               <Link to={`/reference/${ref.rid}`}>View</Link>
@@ -90,10 +92,7 @@ export const UpdateTab = <T, UpdateType extends MRT_RowData & { updates: UpdateL
       accessorKey: refFieldName as string,
       header: 'Reference',
       Cell: ({ row }: { row: MRT_Row<UpdateType> }) => (
-        <ReferenceList
-          references={(row.original[refFieldName] as { ref_ref: ReferenceOfUpdate }[]).map(item => item.ref_ref)}
-          big={false}
-        />
+        <ReferenceList references={row.original[refFieldName]} big={false} />
       ),
     },
     {
@@ -105,7 +104,7 @@ export const UpdateTab = <T, UpdateType extends MRT_RowData & { updates: UpdateL
           coordinator={row.original[`${prefix}_coordinator`] as string}
           updates={row.original.updates}
           comment={row.original[`${prefix}_comment` as keyof UpdateType] as string}
-          references={row.original[refFieldName] as { ref_ref: ReferenceOfUpdate }[]}
+          references={row.original[refFieldName]}
         />
       ),
     },
@@ -118,7 +117,7 @@ export const UpdateTab = <T, UpdateType extends MRT_RowData & { updates: UpdateL
   )
 }
 
-const DetailsModal = <RefType extends { ref_ref: ReferenceOfUpdate }>({
+const DetailsModal = ({
   updates,
   references,
   comment,
@@ -127,7 +126,7 @@ const DetailsModal = <RefType extends { ref_ref: ReferenceOfUpdate }>({
   coordinator,
 }: {
   updates: UpdateLog[]
-  references: RefType[]
+  references: AnyReference[]
   comment: string
   date: Date
   authorizer: string
@@ -179,11 +178,7 @@ const DetailsModal = <RefType extends { ref_ref: ReferenceOfUpdate }>({
       </Card>
       <Divider />
       <h3>References</h3>
-      {references.length === 0 ? (
-        <Box>Update has no references.</Box>
-      ) : (
-        <ReferenceList references={references.map(ref => ref.ref_ref)} big />
-      )}
+      {references.length === 0 ? <Box>Update has no references.</Box> : <ReferenceList references={references} big />}
       <Divider />
       <h3>Changed database values</h3>
       <SimpleTable columns={columns} data={updates} />

frontend/src/components/DetailView/common/defaultValues.ts

@@ -119,7 +119,7 @@ export const emptyLocality = {
 } as unknown as LocalityDetailsType
 
 export const emptySpecies = {
-  class_name: '',
+  class_name: 'Mammalia',
   order_name: '',
   family_name: '',
   subclass_or_superorder_name: '',
@@ -128,7 +128,7 @@ export const emptySpecies = {
   genus_name: '',
   species_name: '',
   unique_identifier: '-',
-  taxonomic_status: null,
+  taxonomic_status: '',
   common_name: '',
   sp_author: '',
   strain: null,

frontend/src/components/DetailView/components.tsx

@@ -8,12 +8,13 @@ import { useDetailContext } from './Context/DetailContext'
 import { EditDataType, Editable, Reference, Species } from '@/shared/types'
 import { useState, useEffect, Fragment } from 'react'
 import { referenceValidator } from '@/shared/validators/validator'
-import { checkTaxonomy, convertTaxonomyFields } from '../../util/taxonomyFunctions'
-import { useLazyGetAllSpeciesQuery, useLazyGetAllSynonymsQuery } from '@/redux/speciesReducer'
+import { checkSpeciesTaxonomy, convertSpeciesTaxonomyFields } from '../../util/taxonomyUtilities'
+import { useGetAllSpeciesQuery, useGetAllSynonymsQuery } from '@/redux/speciesReducer'
 import { useNotify } from '@/hooks/notification'
 import { countryBoundingBoxes } from '@/country_data/countryBoundingBoxes'
 import { boundingBoxSplit, isPointInBoxes } from '@/util/isPointInBox'
 import { OutOfBoundsWarningModal, OutOfBoundsWarningModalState } from './OutOfBoundsWarningModal'
+import { skipToken } from '@reduxjs/toolkit/query'
 
 export const WriteButton = <T,>({
   onWrite,
@@ -28,8 +29,8 @@ export const WriteButton = <T,>({
     useDetailContext<T>()
   const [loading, setLoading] = useState(false)
   const { notify } = useNotify()
-  const [getSpeciesData] = useLazyGetAllSpeciesQuery()
-  const [getSynonyms] = useLazyGetAllSynonymsQuery()
+  const { data: speciesData } = useGetAllSpeciesQuery(!taxonomy ? skipToken : undefined)
+  const { data: synonymData } = useGetAllSynonymsQuery(!taxonomy ? skipToken : undefined)
 
   // For coordinate out of bounds warning
   const [warningModalState, setWarningModalState] = useState<OutOfBoundsWarningModalState>({
@@ -50,6 +51,11 @@ export const WriteButton = <T,>({
     return !isPointInBoxes(dec_lat, dec_long, boundingBoxSplit(countryBoundingBoxes[country]))
   }
 
+  useEffect(() => {
+    if (taxonomy && (!speciesData || !synonymData)) setLoading(true)
+    else setLoading(false)
+  }, [speciesData, synonymData])
+
   /*  validates all fields when entering new/editing mode
       to disable write button when unvisited tabs have
       validation errors (e.g. missing required fields) */
@@ -107,23 +113,21 @@ export const WriteButton = <T,>({
     // @ts-expect-error Reason: Typescript doesn't recognise that references do exist. Unable to find a way around it. Fix if extra time
   }, [mode, editData.references])
 
-  const writeWithTaxonomyCheck = async () => {
+  const writeWithTaxonomyCheck = () => {
     let speciesEditData: EditDataType<Species> | undefined = undefined
 
     if (!mode.staging) {
-      const { data: speciesData } = await getSpeciesData(undefined, true)
-      const { data: synonyms } = await getSynonyms(undefined, true)
       if (!speciesData) {
         notify('Could not fetch species to check taxonomy data.', 'error')
         return
       }
-      if (!synonyms) {
+      if (!synonymData) {
         notify('Could not fetch synonyms to check taxonomy data.', 'error')
         return
       }
       // converts taxonomy fields to capitalized/lowercased
-      speciesEditData = convertTaxonomyFields(editData as EditDataType<Species>)
-      const errors = checkTaxonomy(speciesEditData, speciesData, synonyms)
+      speciesEditData = convertSpeciesTaxonomyFields(editData as EditDataType<Species>)
+      const errors = checkSpeciesTaxonomy(speciesEditData, speciesData, synonymData)
       if (errors.size > 0) {
         const errorMessage = [...errors].reduce((acc, currentError) => acc + `\n${currentError}`)
         notify(errorMessage, 'error', null)
@@ -144,10 +148,10 @@ export const WriteButton = <T,>({
     })
   }
 
-  const handleWriteButtonClick = async () => {
+  const handleWriteButtonClick = () => {
     if (taxonomy) {
       setLoading(true)
-      await writeWithTaxonomyCheck()
+      writeWithTaxonomyCheck()
       setLoading(false)
       return
     }
@@ -186,13 +190,13 @@ export const WriteButton = <T,>({
             !('dec_long' in (editData as object)) ||
             !('country' in (editData as object))
           ) {
-            void handleWriteButtonClick()
+            handleWriteButtonClick()
             return
           }
 
           const localityObject = editData as unknown as { dec_lat: number; dec_long: number; country: string }
           if (!isCoordinateOutOfBounds(localityObject.dec_lat, localityObject.dec_long, localityObject.country)) {
-            void handleWriteButtonClick()
+            handleWriteButtonClick()
             return
           }
 

frontend/src/components/Locality/LocalityTable.tsx

@@ -9,6 +9,7 @@ import { generateKml } from '@/util/kml'
 import { generateSvg } from '../Map/generateSvg'
 import { usePageContext } from '../Page'
 import { LocalitySynonymsModal } from './LocalitySynonymsModal'
+import { currentDateAsString } from '@/shared/currentDateAsString'
 
 const decimalCount = (num: number) => {
   const numAsString = num.toString()
@@ -403,7 +404,8 @@ export const LocalityTable = ({ selectorFn }: { selectorFn?: (newObject: Localit
     const url = URL.createObjectURL(blob)
     const a = document.createElement('a')
     a.href = url
-    a.download = 'localitiesWithSpecies.csv'
+
+    a.download = `localities-with-species-${currentDateAsString()}.csv`
     a.click()
   }
 
@@ -416,7 +418,7 @@ export const LocalityTable = ({ selectorFn }: { selectorFn?: (newObject: Localit
     const url = URL.createObjectURL(blob)
     const a = document.createElement('a')
     a.href = url
-    a.download = 'localities.kml'
+    a.download = `localities-${currentDateAsString()}.kml`
     a.click()
   }
 
@@ -427,7 +429,7 @@ export const LocalityTable = ({ selectorFn }: { selectorFn?: (newObject: Localit
     const url = URL.createObjectURL(blob)
     const a = document.createElement('a')
     a.href = url
-    a.download = 'map.svg'
+    a.download = `localities-map-${currentDateAsString()}.svg`
     a.click()
   }
 

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

@@ -192,6 +192,7 @@ export const LithologyTab = () => {
                 isError={isError}
                 columns={selectingTableColumns}
                 data={sedimentaryStructuresData}
+                title="Sedimentary structures"
                 fieldName="now_ss"
                 idFieldName="ss_value"
                 editingAction={(newSed: SedimentaryStructureValues) => {

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

@@ -38,6 +38,7 @@ export const MuseumTab = () => {
           <SelectingTable<Museum, LocalityDetailsType>
             buttonText="Select Museum"
             data={museumData}
+            title="Museums"
             isError={isError}
             columns={columns}
             fieldName="now_mus"

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

@@ -43,6 +43,7 @@ export const ProjectTab = () => {
           <SelectingTable<Project, LocalityDetailsType>
             buttonText="Select Project"
             data={projectData}
+            title="Projects"
             columns={columns}
             isError={isError}
             idFieldName="pid"

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

@@ -1,17 +1,105 @@
-import { LocalityDetailsType, LocalitySpecies, Species, SpeciesDetailsType } from '@/shared/types'
+import {
+  Editable,
+  EditDataType,
+  LocalityDetailsType,
+  LocalitySpecies,
+  Species,
+  SpeciesDetailsType,
+} from '@/shared/types'
 import { EditableTable } from '@/components/DetailView/common/EditableTable'
 import { EditingForm } from '@/components/DetailView/common/EditingForm'
 import { SelectingTable } from '@/components/DetailView/common/SelectingTable'
 import { Grouped } from '@/components/DetailView/common/tabLayoutHelpers'
 import { useDetailContext } from '@/components/DetailView/Context/DetailContext'
 import { useGetAllSpeciesQuery } from '@/redux/speciesReducer'
-import { Box } from '@mui/material'
+import { Box, CircularProgress } from '@mui/material'
 import { skipToken } from '@reduxjs/toolkit/query'
 import { MRT_ColumnDef } from 'material-react-table'
+import {
+  checkSpeciesTaxonomy,
+  convertSpeciesTaxonomyFields,
+  fixNullValuesInTaxonomyFields,
+} from '@/util/taxonomyUtilities'
+import { useNotify } from '@/hooks/notification'
+import { validateSpecies } from '@/shared/validators/species'
+import { smallSpeciesTableColumns } from '@/common'
+import { useState } from 'react'
+import { SynonymsModal } from '@/components/Species/SynonymsModal'
 
 export const SpeciesTab = () => {
   const { mode, editData, setEditData } = useDetailContext<LocalityDetailsType>()
   const { data: speciesData, isError } = useGetAllSpeciesQuery(mode.read ? skipToken : undefined)
+  const { notify } = useNotify()
+  const [replacedValues, setReplacedValues] = useState<EditDataType<Species> | undefined>()
+  const [selectedSpecies, setSelectedSpecies] = useState<string | undefined>()
+  const [modalOpen, setModalOpen] = useState<boolean>(false)
+
+  const handleRowActionClick = (row: Species) => {
+    setSelectedSpecies(row.species_id.toString())
+    setModalOpen(true)
+  }
+
+  const copyTaxonomyButton = (
+    <Box key="copy_existing_taxonomy_button">
+      <SelectingTable<Species, Species>
+        dataCy="copy_existing_taxonomy_button"
+        buttonText="Copy existing taxonomy"
+        title="Copy existing taxonomy"
+        data={speciesData}
+        isError={isError}
+        columns={smallSpeciesTableColumns}
+        fieldName="order_name" // this doesn't do anything here but is required
+        idFieldName="species_id"
+        useObject={true}
+        tableRowAction={handleRowActionClick}
+        editingAction={(selectedSpecies: Species) => {
+          const fixedSpecies = fixNullValuesInTaxonomyFields(selectedSpecies)
+          setReplacedValues({
+            subclass_or_superorder_name: fixedSpecies.subclass_or_superorder_name,
+            order_name: fixedSpecies.order_name!,
+            suborder_or_superfamily_name: fixedSpecies.suborder_or_superfamily_name,
+            family_name: fixedSpecies.family_name!,
+            subfamily_name: fixedSpecies.subfamily_name,
+            genus_name: fixedSpecies.genus_name!,
+            species_name: fixedSpecies.species_name!,
+            unique_identifier: fixedSpecies.unique_identifier!,
+            taxonomic_status: '',
+            sp_comment: '',
+            sp_author: '',
+          })
+        }}
+      />
+      <SynonymsModal open={modalOpen} onClose={() => setModalOpen(false)} selectedSpecies={selectedSpecies} />
+    </Box>
+  )
+
+  const convertAndCheckNewSpeciesTaxonomy = (newSpecies: EditDataType<Species>) => {
+    const errors = []
+    for (const field in newSpecies) {
+      const errorObject = validateSpecies(
+        newSpecies as unknown as EditDataType<SpeciesDetailsType>,
+        field as unknown as keyof EditDataType<SpeciesDetailsType>
+      )
+      const { error } = errorObject
+      if (error) errors.push(errorObject)
+    }
+    if (errors.length > 0) {
+      notify('Following validators failed: \n' + errors.map(e => `${e.name}: ${e.error}`).join('\n'), 'error')
+      return false
+    }
+
+    const convertedSpecies = convertSpeciesTaxonomyFields(newSpecies)
+    const everyLs = editData.now_ls.map(ls => ls.com_species) as unknown as Editable<Species>[]
+    const filteredLs = everyLs.filter(species => species.rowState === 'new')
+
+    const taxonomyErrors = checkSpeciesTaxonomy(convertedSpecies, speciesData!.concat(filteredLs), [])
+    if (taxonomyErrors.size > 0) {
+      const errorMessage = [...taxonomyErrors].reduce((acc, currentError) => acc + `\n${currentError}`)
+      notify(errorMessage, 'error', null)
+      return false
+    }
+    return convertedSpecies
+  }
 
   const speciesColumns: MRT_ColumnDef<Species>[] = [
     {
@@ -80,6 +168,14 @@ export const SpeciesTab = () => {
       accessorKey: 'com_species.taxonomic_status',
       header: 'Taxon status',
     },
+    {
+      accessorKey: 'com_species.sp_comment',
+      header: 'Comment',
+    },
+    {
+      accessorKey: 'com_species.sp_author',
+      header: 'Author',
+    },
   ]
   const formFields: { name: string; label: string; required?: boolean }[] = [
     { name: 'order_name', label: 'Order', required: true },
@@ -88,26 +184,36 @@ export const SpeciesTab = () => {
     { name: 'species_name', label: 'Species', required: true },
     { name: 'subclass_or_superorder_name', label: 'Subclass or Superorder' },
     { name: 'suborder_or_superfamily_name', label: 'Suborder or Superfamily' },
+    { name: 'subfamily_name', label: 'Subfamily or Tribe' },
     { name: 'unique_identifier', label: 'Unique Identifier', required: true },
     { name: 'taxonomic_status', label: 'Taxon status' },
+    { name: 'sp_comment', label: 'Comment' },
+    { name: 'sp_author', label: 'Author' },
   ]
 
+  if (!mode.read && !speciesData) return <CircularProgress />
+
   return (
     <Grouped title="Species">
       {!mode.read && (
         <Box display="flex" gap={1}>
-          <EditingForm<Species, LocalityDetailsType>
+          <EditingForm<EditDataType<Species>, LocalityDetailsType>
             buttonText="Add new Species"
             formFields={formFields}
-            editAction={(newSpecies: Species) => {
+            existingObject={{ unique_identifier: '-' }}
+            replacedValues={replacedValues}
+            copyTaxonomyButton={copyTaxonomyButton}
+            editAction={(newSpecies: EditDataType<Species>) => {
+              const convertedSpecies = convertAndCheckNewSpeciesTaxonomy(newSpecies)
+              if (!convertedSpecies) return
               setEditData({
                 ...editData,
                 now_ls: [
                   ...editData.now_ls,
                   {
                     lid: editData.lid,
-                    species_id: newSpecies.species_id,
-                    com_species: { ...(newSpecies as unknown as SpeciesDetailsType) },
+                    species_id: undefined,
+                    com_species: { ...(convertedSpecies as unknown as SpeciesDetailsType), class_name: 'Mammalia' },
                     rowState: 'new',
                   },
                 ],
@@ -117,6 +223,7 @@ export const SpeciesTab = () => {
           <SelectingTable<Species, LocalityDetailsType>
             buttonText="Select Species"
             data={speciesData}
+            title="Species"
             isError={isError}
             columns={speciesColumns}
             fieldName="now_ls"
@@ -129,7 +236,9 @@ export const SpeciesTab = () => {
                   {
                     lid: editData.lid,
                     species_id: newSpecies.species_id,
-                    com_species: { ...(newSpecies as unknown as SpeciesDetailsType) },
+                    com_species: {
+                      ...(fixNullValuesInTaxonomyFields(newSpecies) as SpeciesDetailsType),
+                    },
                     rowState: 'new',
                   },
                 ],

frontend/src/components/Museum/MuseumTable.tsx

@@ -64,7 +64,7 @@ export const MuseumTable = ({ selectorFn }: { selectorFn?: (museum: Museum) => v
 
   return (
     <TableView<Museum>
-      title="Museum"
+      title="Museums"
       selectorFn={selectorFn}
       idFieldName="museum"
       columns={columns}

frontend/src/components/Reference/Tabs/AuthorTab.tsx

@@ -124,6 +124,7 @@ export const AuthorTab: React.FC<AuthorTabProps> = ({ field_num_param, tab_name
             <SelectingTable<ReferenceAuthorType, ReferenceDetailsType>
               buttonText={`Select ${buttonText}`}
               data={authorData}
+              title="Authors"
               isError={isError}
               columns={authorColumns}
               fieldName="ref_authors"

frontend/src/components/Reference/Tabs/JournalTab.tsx

@@ -88,6 +88,7 @@ export const JournalTab: React.FC<JournalTabProps> = ({ tab_name = 'Journal' })
             <SelectingTable<ReferenceJournalType, ReferenceDetailsType>
               buttonText="Select Journal"
               data={journalData}
+              title="Journals"
               isError={isError}
               columns={journalColumns}
               fieldName="ref_journal"

frontend/src/components/Region/Tabs/CoordinatorTab.tsx

@@ -106,6 +106,7 @@ export const CoordinatorTab = () => {
           <SelectingTable<PersonDetailsType, RegionDetails>
             buttonText="Select Coordinator"
             data={personsData}
+            title="Coordinators"
             isError={isError}
             columns={personTableColumns}
             fieldName="now_reg_coord_people"

frontend/src/components/Sequence/SequenceTable.tsx

@@ -31,6 +31,7 @@ export const SequenceTable = ({ selectorFn }: { selectorFn?: (id: Sequence) => v
       selectorFn={selectorFn}
       idFieldName="sequence"
       columns={columns}
+      title="Sequences"
       isFetching={isFetching}
       visibleColumns={visibleColumns}
       clickableRows={false}

frontend/src/components/Species/SpeciesDetails.tsx

@@ -16,6 +16,7 @@ import { validateSpecies } from '@/shared/validators/species'
 import { emptySpecies } from '../DetailView/common/defaultValues'
 import { useNotify } from '@/hooks/notification'
 import { useEffect, useState } from 'react'
+import { fixNullValuesInTaxonomyFields } from '@/util/taxonomyUtilities'
 
 export const SpeciesDetails = () => {
   const { id } = useParams()
@@ -24,7 +25,7 @@ export const SpeciesDetails = () => {
     document.title = 'New species'
   }
   const [editSpeciesRequest, { isLoading: mutationLoading }] = useEditSpeciesMutation()
-  const { isError, isFetching, data } = useGetSpeciesDetailsQuery(id!, { skip: isNew })
+  const { isError, isFetching, data } = useGetSpeciesDetailsQuery(encodeURIComponent(id!), { skip: isNew })
   const { notify } = useNotify()
   const navigate = useNavigate()
   const [deleteMutation, { isSuccess: deleteSuccess, isError: deleteError }] = useDeleteSpeciesMutation()
@@ -40,15 +41,11 @@ export const SpeciesDetails = () => {
   }, [deleteSuccess, deleteError, notify, navigate])
 
   useEffect(() => {
-    // changes subclass, suborder, and subfamily from null to empty string to make validators work
+    // changes subclass, suborder, subfamily and taxonomic_status from null to empty string to make validators work
     // this should be removed if validators are improved in the future
     if (data) {
-      setModifiedData({
-        ...data,
-        subclass_or_superorder_name: data.subclass_or_superorder_name ?? '',
-        suborder_or_superfamily_name: data.suborder_or_superfamily_name ?? '',
-        subfamily_name: data.subfamily_name ?? '',
-      })
+      const fixedSpeciesData = fixNullValuesInTaxonomyFields(data)
+      setModifiedData(fixedSpeciesData as SpeciesDetailsType)
     }
   }, [data])
 

frontend/src/components/Species/Tabs/LocalityTab.tsx

@@ -50,6 +50,7 @@ export const LocalityTab = () => {
     <SelectingTable<Editable<Locality>, SpeciesDetailsType>
       buttonText="Select Locality"
       columns={columns}
+      title="Localities"
       isError={isError}
       data={localitiesData}
       fieldName="now_ls"

frontend/src/components/Species/Tabs/SynonymTab.tsx

@@ -4,9 +4,66 @@ import { Grouped } from '@/components/DetailView/common/tabLayoutHelpers'
 import { MRT_ColumnDef } from 'material-react-table'
 import { EditableTable } from '@/components/DetailView/common/EditableTable'
 import { EditingForm, EditingFormField } from '@/components/DetailView/common/EditingForm'
+import { useNotify } from '@/hooks/notification'
+import { validateSynonym } from '@/shared/validators/synonym'
+import { convertSynonymTaxonomyFields } from '@/util/taxonomyUtilities'
+import { useGetAllSpeciesQuery } from '@/redux/speciesReducer'
+import { skipToken } from '@reduxjs/toolkit/query'
+import { CircularProgress } from '@mui/material'
 
 export const SynonymTab = () => {
   const { mode, setEditData, editData } = useDetailContext<SpeciesDetailsType>()
+  const { data: speciesQueryData, isFetching } = useGetAllSpeciesQuery(mode.read ? skipToken : undefined)
+  const { notify } = useNotify()
+
+  const convertAndCheckNewSynonymTaxonomy = (newSynonym: EditDataType<SpeciesSynonym>) => {
+    const errors = []
+    for (const field in newSynonym) {
+      const errorObject = validateSynonym(
+        newSynonym as unknown as EditDataType<SpeciesSynonym>,
+        field as unknown as keyof EditDataType<SpeciesSynonym>
+      )
+      const { error } = errorObject
+      if (error) errors.push(errorObject)
+    }
+    if (errors.length > 0) {
+      notify('Following validators failed: \n' + errors.map(e => `${e.name}: ${e.error}`).join('\n'), 'error')
+      return false
+    }
+
+    const convertedSynonym = convertSynonymTaxonomyFields(newSynonym)
+    for (const existingSynonym of editData.com_taxa_synonym) {
+      if (
+        convertedSynonym.syn_genus_name === existingSynonym.syn_genus_name &&
+        convertedSynonym.syn_species_name === existingSynonym.syn_species_name
+      ) {
+        notify(
+          `${convertedSynonym.syn_genus_name} ${convertedSynonym.syn_species_name} \
+          has already been added as a synonym for this species.`,
+          'error',
+          null
+        )
+        return false
+      }
+    }
+
+    for (const existingSpecies of speciesQueryData!) {
+      if (
+        convertedSynonym.syn_genus_name === existingSpecies.genus_name &&
+        convertedSynonym.syn_species_name === existingSpecies.species_name
+      ) {
+        notify(
+          `${convertedSynonym.syn_genus_name} ${convertedSynonym.syn_species_name} \
+          has already been created as a separate species, adding it as a synonym is currently not allowed.`,
+          'error',
+          null
+        )
+        return false
+      }
+    }
+
+    return convertedSynonym
+  }
 
   const columns: MRT_ColumnDef<SpeciesSynonym>[] = [
     {
@@ -31,15 +88,17 @@ export const SynonymTab = () => {
 
   const editingForm = (
     <EditingForm<Species, SpeciesDetailsType>
-      buttonText="Add new Species"
+      buttonText="Add synonym"
       formFields={formFields}
       editAction={(newSynonym: EditDataType<SpeciesSynonym>) => {
+        const convertedSynonym = convertAndCheckNewSynonymTaxonomy(newSynonym)
+        if (!convertedSynonym) return
         setEditData({
           ...editData,
           com_taxa_synonym: [
             ...editData.com_taxa_synonym,
             {
-              ...newSynonym,
+              ...convertedSynonym,
               rowState: 'new',
             },
           ],
@@ -48,6 +107,8 @@ export const SynonymTab = () => {
     />
   )
 
+  if (isFetching) return <CircularProgress />
+
   return (
     <>
       <Grouped title="Synonyms">

frontend/src/components/Species/Tabs/TaxonomyTab.tsx

@@ -1,13 +1,14 @@
 import { SpeciesDetailsType, Species } from '@/shared/types'
 import { ArrayFrame, HalfFrames } from '@/components/DetailView/common/tabLayoutHelpers'
 import { useDetailContext } from '@/components/DetailView/Context/DetailContext'
-import { emptyOption } from '@/components/DetailView/common/misc'
+import { fixNullValuesInTaxonomyFields } from '@/util/taxonomyUtilities'
 import { Box } from '@mui/material'
 import { SelectingTable } from '@/components/DetailView/common/SelectingTable'
 import { useGetAllSpeciesQuery } from '@/redux/speciesReducer'
 import { smallSpeciesTableColumns } from '@/common'
 import { SynonymsModal } from '../SynonymsModal'
 import { useState } from 'react'
+import { taxonStatusOptions } from '@/shared/taxonStatusOptions'
 
 export const TaxonomyTab = () => {
   const { textField, dropdown, bigTextField, editData, setEditData, mode } = useDetailContext<SpeciesDetailsType>()
@@ -21,10 +22,12 @@ export const TaxonomyTab = () => {
   }
 
   const copyTaxonomyButton = (
-    <Box key="copy_existing_taxonomy_button" id="copy_existing_taxonomy_button">
+    <Box key="copy_existing_taxonomy_button">
       <SelectingTable<Species, Species>
+        dataCy="copy_existing_taxonomy_button"
         buttonText="Copy existing taxonomy"
         data={speciesQueryData}
+        title="Species"
         isError={isError}
         columns={smallSpeciesTableColumns}
         fieldName="order_name" // this doesn't do anything here but is required
@@ -32,16 +35,17 @@ export const TaxonomyTab = () => {
         useObject={true}
         tableRowAction={handleRowActionClick}
         editingAction={(selectedSpecies: Species) => {
+          const fixedSpecies = fixNullValuesInTaxonomyFields(selectedSpecies)
           setEditData({
             ...editData,
-            subclass_or_superorder_name: selectedSpecies.subclass_or_superorder_name ?? '',
-            order_name: selectedSpecies.order_name ?? '',
-            suborder_or_superfamily_name: selectedSpecies.suborder_or_superfamily_name ?? '',
-            family_name: selectedSpecies.family_name ?? '',
-            subfamily_name: selectedSpecies.subfamily_name ?? '',
-            genus_name: selectedSpecies.genus_name ?? '',
-            species_name: selectedSpecies.species_name ?? '',
-            unique_identifier: selectedSpecies.unique_identifier ?? '',
+            subclass_or_superorder_name: fixedSpecies.subclass_or_superorder_name,
+            order_name: fixedSpecies.order_name!,
+            suborder_or_superfamily_name: fixedSpecies.suborder_or_superfamily_name,
+            family_name: fixedSpecies.family_name!,
+            subfamily_name: fixedSpecies.subfamily_name,
+            genus_name: fixedSpecies.genus_name!,
+            species_name: fixedSpecies.species_name!,
+            unique_identifier: fixedSpecies.unique_identifier!,
           })
         }}
       />
@@ -49,16 +53,6 @@ export const TaxonomyTab = () => {
     </Box>
   )
 
-  const taxonStatusOptions = [
-    emptyOption,
-    'family attrib of genus uncertain',
-    'genus attrib of species uncertain',
-    'informal species',
-    'species validity uncertain',
-    'taxonomic validity uncertain',
-    'NOW synonym',
-  ]
-
   const classification = [
     [
       'Class',

frontend/src/components/TableView/TableToolBar.tsx

@@ -12,6 +12,7 @@ import { usePageContext } from '../Page'
 
 export const TableToolBar = <T extends MRT_RowData>({
   table,
+  tableName,
   combinedExport,
   kmlExport,
   svgExport,
@@ -21,6 +22,7 @@ export const TableToolBar = <T extends MRT_RowData>({
   showNewButton,
 }: {
   table: MRT_TableInstance<T>
+  tableName: string
   combinedExport?: (lids: number[]) => Promise<void>
   kmlExport?: (table: MRT_TableInstance<T>) => void
   svgExport?: (table: MRT_TableInstance<T>) => void
@@ -87,7 +89,7 @@ export const TableToolBar = <T extends MRT_RowData>({
           ) : (
             <MenuItem
               onClick={() => {
-                exportRows(table)
+                exportRows(table, tableName)
                 handleClose()
               }}
             >

frontend/src/components/TableView/TableView.tsx

@@ -57,10 +57,9 @@ export const TableView = <T extends MRT_RowData>({
   idFieldName: keyof T
   checkRowRestriction?: (row: T) => boolean
   selectorFn?: (id: T) => void
-  // here
   tableRowAction?: (row: T) => void
   url?: string
-  title?: string
+  title: string
   combinedExport?: (lids: number[]) => Promise<void>
   kmlExport?: (table: MRT_TableInstance<T>) => void
   svgExport?: (table: MRT_TableInstance<T>) => void
@@ -259,6 +258,7 @@ export const TableView = <T extends MRT_RowData>({
           {title && <Box className="title">{title}</Box>}
           <TableToolBar<T>
             table={table}
+            tableName={title}
             combinedExport={combinedExport}
             kmlExport={kmlExport}
             svgExport={svgExport}

frontend/src/components/TableView/helpers.tsx

@@ -1,15 +1,17 @@
 import { MRT_RowData, MRT_TableInstance } from 'material-react-table'
 import { mkConfig, generateCsv, download } from 'export-to-csv'
 import { AcceptedData } from 'node_modules/export-to-csv/output/lib/types'
+import { currentDateAsString } from '@/shared/currentDateAsString'
 
 export type ExportFn<T> = (data: T) => { [k: string]: AcceptedData }
 
-export const exportRows = <T extends MRT_RowData>(table: MRT_TableInstance<T>) => {
+export const exportRows = <T extends MRT_RowData>(table: MRT_TableInstance<T>, tableName: string) => {
   const csvConfig = mkConfig({
     fieldSeparator: ',',
     decimalSeparator: '.',
     useKeysAsHeaders: true,
     quoteStrings: true, // If true, will wrap all values in double quotes
+    filename: `${tableName.toLowerCase()}-${currentDateAsString()}`,
   })
   const rowData = table.getPrePaginationRowModel().rows.map(row => {
     const r = {} as Record<string, AcceptedData>

frontend/src/components/TimeUnit/Tabs/LocalityTab.tsx

@@ -11,6 +11,15 @@ export const LocalityTab = () => {
   if (isError) return 'Error loading Localities.'
   if (!localitiesData) return <CircularProgress />
 
+  // changes min and max age values to checkmarks or X symbols, to show whether this time unit is set as the basis for min/max age or not
+  const modifiedData = localitiesData.map(locality => {
+    return {
+      ...locality,
+      min_age: locality.bfa_min === data.tu_name ? '\u2713' : '\u0058',
+      max_age: locality.bfa_max === data.tu_name ? '\u2713' : '\u0058',
+    }
+  })
+
   const columns = [
     {
       accessorKey: 'loc_name',
@@ -30,5 +39,5 @@ export const LocalityTab = () => {
     },
   ]
 
-  return <SimpleTable columns={columns} data={localitiesData} idFieldName="lid" url="locality" />
+  return <SimpleTable columns={columns} data={modifiedData} idFieldName="lid" url="locality" />
 }

frontend/src/redux/api.ts

@@ -57,6 +57,7 @@ export const api = createApi({
     'localities',
     'species',
     'specieslist',
+    'speciessynonyms',
     'reference',
     'references',
     'timeunits',

frontend/src/redux/localityReducer.ts

@@ -28,7 +28,8 @@ const localitiesApi = api.injectEndpoints({
         method: 'PUT',
         body: { locality },
       }),
-      invalidatesTags: (result, _error, { lid }) => (result ? [{ type: 'locality', id: lid }, 'localities'] : []),
+      invalidatesTags: (result, _error, { lid }) =>
+        result ? [{ type: 'locality', id: lid }, 'localities', 'specieslist'] : [],
     }),
     deleteLocality: builder.mutation<void, number>({
       query: id => ({

frontend/src/redux/speciesReducer.ts

@@ -7,18 +7,19 @@ const speciesApi = api.injectEndpoints({
       query: () => ({
         url: `/species/all`,
       }),
-      providesTags: result => (result ? [{ type: 'specieslist' }] : []),
+      providesTags: result => (result ? [{ type: 'specieslist' }, 'speciessynonyms'] : []),
     }),
     getAllSynonyms: builder.query<SpeciesSynonym[], void>({
       query: () => ({
         url: `/species/synonyms`,
       }),
+      providesTags: result => (result ? ['speciessynonyms'] : []),
     }),
     getSpeciesDetails: builder.query<SpeciesDetailsType, string>({
       query: id => ({
         url: `/species/${id}`,
       }),
-      providesTags: result => (result ? [{ type: 'species', id: result.species_id }] : []),
+      providesTags: result => (result ? [{ type: 'species', id: result.species_id }, 'speciessynonyms'] : []),
     }),
     editSpecies: builder.mutation<SpeciesDetailsType, EditDataType<SpeciesDetailsType>>({
       query: species => ({
@@ -27,7 +28,7 @@ const speciesApi = api.injectEndpoints({
         body: { species },
       }),
       invalidatesTags: (result, _error, { species_id }) =>
-        result ? [{ type: 'species', id: species_id }, 'specieslist'] : [],
+        result ? [{ type: 'species', id: species_id }, 'specieslist', 'speciessynonyms'] : [],
     }),
     deleteSpecies: builder.mutation<void, number>({
       query: id => ({
@@ -36,15 +37,14 @@ const speciesApi = api.injectEndpoints({
       }),
 
       invalidatesTags: (result, _error, species_id) =>
-        typeof result !== 'undefined' ? [{ type: 'species', id: species_id }, 'specieslist'] : [],
+        typeof result !== 'undefined' ? [{ type: 'species', id: species_id }, 'specieslist', 'speciessynonyms'] : [],
     }),
   }),
 })
 
 export const {
   useGetAllSpeciesQuery,
-  useLazyGetAllSpeciesQuery,
-  useLazyGetAllSynonymsQuery,
+  useGetAllSynonymsQuery,
   useGetSpeciesDetailsQuery,
   useEditSpeciesMutation,
   useDeleteSpeciesMutation,

frontend/src/shared/taxonStatusOptions.ts

@@ -0,0 +1,16 @@
+// cannot be imported from DetailView -> misc since files in shared folder cannot import from elsewhere in frontend
+const emptyOption = {
+  optionDisplay: 'No value',
+  display: '',
+  value: '',
+}
+
+export const taxonStatusOptions = [
+  emptyOption,
+  'family attrib of genus uncertain',
+  'genus attrib of species uncertain',
+  'informal species',
+  'species validity uncertain',
+  'taxonomic validity uncertain',
+  'NOW synonym',
+]

frontend/src/shared/types/data.ts

@@ -332,6 +332,7 @@ export type Species = {
   locomo2: string | null
   locomo3: string | null
   sp_comment: string | null
+  sp_author: string | null
 }
 
 export type RegionDetails = Prisma.now_reg_coord & { now_reg_coord_people: Array<RegionCoordinator> } & {
@@ -443,8 +444,12 @@ export type ReferenceOfUpdate = Prisma.ref_ref & {
   ref_journal: Prisma.ref_journal
 }
 
-export type LocalityReference = Prisma.now_lr & ReferenceOfUpdate
-export type SpeciesReference = Prisma.now_sr & ReferenceOfUpdate
+export type LocalityReference = Prisma.now_lr & { ref_ref: ReferenceOfUpdate }
+export type SpeciesReference = Prisma.now_sr & { ref_ref: ReferenceOfUpdate }
+export type TimeUnitReference = Prisma.now_tr & { ref_ref: ReferenceOfUpdate }
+export type TimeBoundReference = Prisma.now_br & { ref_ref: ReferenceOfUpdate }
+
+export type AnyReference = LocalityReference | SpeciesReference | TimeUnitReference | TimeBoundReference
 
 export type ReferenceJournalType = {
   journal_id?: number

frontend/src/shared/validators/species.ts

@@ -1,3 +1,4 @@
+import { taxonStatusOptions } from '../taxonStatusOptions'
 import { EditDataType, SpeciesDetailsType } from '../types'
 import { Validators, validator } from './validator'
 
@@ -80,6 +81,7 @@ export const validateSpecies = (
       name: 'Species',
       required: true,
       asString: (speciesName: string) => {
+        if (speciesName.indexOf(' ') !== -1) return 'Species name must not contain any spaces.'
         if (speciesName !== 'indet.' && editData.genus_name === 'indet.')
           return 'when the Genus is indet., Species must also be indet.'
         if (speciesName !== 'sp.' && editData.genus_name === 'gen.')
@@ -89,6 +91,14 @@ export const validateSpecies = (
         return
       },
     },
+    taxonomic_status: {
+      name: 'Taxonomic Status',
+      asString: (taxonomicStatus: string) => {
+        if (!taxonStatusOptions.slice(1).includes(taxonomicStatus) && taxonomicStatus !== '')
+          return `Taxonomic Status must be one of the following (or left empty): ${taxonStatusOptions.slice(1).join(', ')}.`
+        return
+      },
+    },
     unique_identifier: {
       name: 'Unique Identifier',
       required: true,

frontend/src/shared/validators/synonym.ts

@@ -0,0 +1,31 @@
+import { EditDataType, SpeciesSynonym } from '../types'
+import { Validators, validator } from './validator'
+
+export const validateSynonym = (
+  editData: EditDataType<SpeciesSynonym>,
+  fieldName: keyof EditDataType<SpeciesSynonym>
+) => {
+  const validators: Validators<Partial<EditDataType<SpeciesSynonym>>> = {
+    syn_genus_name: {
+      name: 'Synonym genus name',
+      required: true,
+      asString: (synGenusName: string) => {
+        if (synGenusName.indexOf(' ') !== -1) return 'Genus must not contain any spaces.'
+        return
+      },
+    },
+    syn_species_name: {
+      name: 'Synonym species name',
+      required: true,
+      asString: (synSpeciesName: string) => {
+        if (synSpeciesName !== 'indet.' && editData.syn_genus_name === 'indet.')
+          return 'when the Genus is indet., Species must also be indet.'
+        if (synSpeciesName !== 'sp.' && editData.syn_genus_name === 'gen.')
+          return 'when the Genus is gen., Species must be sp.'
+        return
+      },
+    },
+  }
+
+  return validator<EditDataType<SpeciesSynonym>>(validators, editData, fieldName)
+}

frontend/src/util/taxonomyUtilities.tsx

@@ -1,4 +1,4 @@
-import { EditDataType, Species, SpeciesSynonym } from '@/shared/types'
+import { EditDataType, Species, SpeciesDetailsType, SpeciesSynonym } from '@/shared/types'
 
 const generateMultipleParentsError = (
   invalidField: string,
@@ -11,7 +11,10 @@ Please contact the NOW administration to fix this taxonomy.`
 
 const isDuplicateTaxon = (newSpecies: EditDataType<Species>, existingSpecies: Species) => {
   if (
-    newSpecies.species_id !== existingSpecies.species_id &&
+    // the check for undefined species_id is here to make sure you cannot add two new,
+    // identical species at the same time (e.g. in Locality -> Species -> Add new species)
+    ((newSpecies.species_id === undefined && existingSpecies.species_id === undefined) ||
+      newSpecies.species_id !== existingSpecies.species_id) &&
     newSpecies.genus_name === existingSpecies.genus_name &&
     newSpecies.species_name === existingSpecies.species_name &&
     newSpecies.unique_identifier === existingSpecies.unique_identifier
@@ -133,7 +136,7 @@ const checkSubFamilyGenus = (newSpecies: EditDataType<Species>, existingSpecies:
   )
 }
 
-export const checkTaxonomy = (
+export const checkSpeciesTaxonomy = (
   newSpecies: EditDataType<Species>,
   existingSpeciesArray: Species[],
   synonyms: SpeciesSynonym[]
@@ -314,7 +317,7 @@ const convertTaxonomyField = (value: string | null | undefined) => {
   return convertedValue
 }
 
-export const convertTaxonomyFields = (species: EditDataType<Species>) => {
+export const convertSpeciesTaxonomyFields = (species: EditDataType<Species>) => {
   const speciesName = species.species_name
   let lowercasedSpeciesName = ''
   if (speciesName) {
@@ -336,3 +339,31 @@ export const convertTaxonomyFields = (species: EditDataType<Species>) => {
   }
   return convertedSpecies as EditDataType<Species>
 }
+
+export const fixNullValuesInTaxonomyFields = (species: Species | SpeciesDetailsType) => {
+  return {
+    ...species,
+    subclass_or_superorder_name: species.subclass_or_superorder_name ?? '',
+    suborder_or_superfamily_name: species.suborder_or_superfamily_name ?? '',
+    subfamily_name: species.subfamily_name ?? '',
+    taxonomic_status: species.taxonomic_status ?? '',
+  }
+}
+
+export const convertSynonymTaxonomyFields = (synonym: EditDataType<SpeciesSynonym>) => {
+  const synSpeciesName = synonym.syn_species_name
+  let lowercasedSynSpeciesName = ''
+  if (synSpeciesName) {
+    if (synSpeciesName !== 'indet.') {
+      lowercasedSynSpeciesName = synSpeciesName.toLowerCase()
+    } else {
+      lowercasedSynSpeciesName = synSpeciesName
+    }
+  }
+  const convertedSynonym = {
+    ...synonym,
+    syn_genus_name: convertTaxonomyField(synonym.syn_genus_name),
+    syn_species_name: lowercasedSynSpeciesName,
+  }
+  return convertedSynonym as EditDataType<SpeciesSynonym>
+}