Add species delete route & service

backend/src/routes/species.ts

@@ -2,7 +2,7 @@ import { Request, Router } from 'express'
 import { getAllSpecies, getSpeciesDetails } from '../services/species'
 import { fixBigInt } from '../utils/common'
 import { EditMetaData, SpeciesDetailsType } from '../../../frontend/src/backendTypes'
-import { writeSpecies } from '../services/write/species'
+import { deleteSpecies, writeSpecies } from '../services/write/species'
 import { requireOneOf } from '../middlewares/authorizer'
 import { Role } from '../../../frontend/src/types'
 
@@ -17,7 +17,7 @@ router.get('/:id', async (req, res) => {
   const id = parseInt(req.params.id)
   const species = await getSpeciesDetails(id)
   if (!species) return res.status(404).send()
-  return res.status(200).send(fixBigInt(species))
+  return res.status(200).send(species)
 })
 
 router.put(
@@ -30,4 +30,10 @@ router.put(
   }
 )
 
+router.delete('/:id', requireOneOf([Role.Admin, Role.EditUnrestricted]), async (req, res) => {
+  const id = parseInt(req.params.id)
+  await deleteSpecies(id, req.user!)
+  res.status(200).send()
+})
+
 export default router

backend/src/services/species.ts

@@ -1,3 +1,5 @@
+import { SpeciesDetailsType } from '../../../frontend/src/backendTypes'
+import { fixBigInt } from '../utils/common'
 import { logDb, nowDb } from '../utils/db'
 
 export const getAllSpecies = async () => {
@@ -59,5 +61,5 @@ export const getSpeciesDetails = async (id: number) => {
     updates: logResult.filter(logRow => logRow.suid === sau.suid),
   }))
 
-  return { ...result, com_taxa_synonym: synonyms || [] }
+  return JSON.parse(fixBigInt({ ...result, com_taxa_synonym: synonyms || [] })!) as SpeciesDetailsType
 }

backend/src/services/write/species.ts

@@ -1,7 +1,20 @@
-import { EditDataType, Reference, SpeciesDetailsType } from '../../../../frontend/src/backendTypes'
+import { EditDataType, FixBigInt, Reference, SpeciesDetailsType, User } from '../../../../frontend/src/backendTypes'
 import { NOW_DB_NAME } from '../../utils/config'
 import { WriteHandler } from '../writeOperations/writeHandler'
 import { getFieldsOfTables } from '../../utils/db'
+import { ActionType } from '../writeOperations/types'
+import { getSpeciesDetails } from '../species'
+import { makeListRemoved } from '../writeOperations/utils'
+
+const getSpeciesWriteHandler = (type: ActionType) => {
+  return new WriteHandler({
+    dbName: NOW_DB_NAME,
+    table: 'com_species',
+    idColumn: 'species_id',
+    allowedColumns: getFieldsOfTables(['com_species', 'now_ls']),
+    type: type,
+  })
+}
 
 export const writeSpecies = async (
   species: EditDataType<SpeciesDetailsType>,
@@ -9,14 +22,7 @@ export const writeSpecies = async (
   references: Reference[] | undefined,
   authorizer: string
 ) => {
-  const writeHandler = new WriteHandler({
-    dbName: NOW_DB_NAME,
-    table: 'com_species',
-    idColumn: 'species_id',
-    allowedColumns: getFieldsOfTables(['com_species', 'now_ls']),
-    type: species.species_id ? 'update' : 'add',
-  })
-
+  const writeHandler = getSpeciesWriteHandler(species.species_id ? 'update' : 'add')
   try {
     await writeHandler.start()
 
@@ -40,3 +46,28 @@ export const writeSpecies = async (
     throw e
   }
 }
+
+export const deleteSpecies = async (species_id: number, user: User) => {
+  const species = (await getSpeciesDetails(species_id)) as EditDataType<FixBigInt<SpeciesDetailsType>>
+  species.now_sau[0].updates
+  if (!species) throw new Error('Species not found')
+
+  const writeHandler = getSpeciesWriteHandler('delete')
+  await writeHandler.start()
+  writeHandler.idValue = species.species_id
+
+  makeListRemoved(species.now_ls)
+  makeListRemoved(species.com_taxa_synonym)
+  makeListRemoved(species.now_sau)
+
+  try {
+    await writeHandler.applyListChanges('now_ls', species.now_ls, ['lid', 'species_id'])
+    await writeHandler.applyListChanges('com_taxa_synonym', species.com_taxa_synonym, ['synonym_id', 'species_id'])
+    await writeHandler.applyListChanges('now_sau', species.now_sau, ['suid'])
+    await writeHandler.deleteObject('com_species', species, ['species_id'])
+    await writeHandler.logUpdatesAndComplete(user.initials)
+  } catch (e) {
+    await writeHandler.end()
+    throw e
+  }
+}

backend/src/services/writeOperations/types.ts

@@ -14,6 +14,7 @@ export type AllowedTables =
   | 'now_tu_bound'
   | 'ref_ref'
   | 'now_tu_sequence'
+  | 'now_sau'
 
 export type PrimaryTables = 'now_loc' | 'com_species' | 'now_time_unit' | 'now_tu_bound'
 

frontend/src/backendTypes.d.ts

@@ -25,7 +25,7 @@ type EditDataType<T> = T extends object
 // Changes all bigints to number type including in nested objects
 export type FixBigInt<T> = {
   [K in keyof T]: T[K] extends bigint | null
-    ? number
+    ? number | null
     : T[K] extends (infer U)[]
       ? FixBigInt<U>[]
       : T[K] extends object
@@ -35,7 +35,7 @@ export type FixBigInt<T> = {
 
 export type SpeciesType = FixBigInt<Prisma.com_species>
 export type RowState = 'new' | 'removed' | 'cancelled' | 'clean'
-export type UpdateComment = { update_comment: string }
+
 // Use this for fields that include array that has to be edited by EditableTable.
 // For example see LocalityDetails: museums field
 export type Editable<T> = T & { rowState?: RowState }
@@ -69,7 +69,7 @@ export type LocalityDetailsType = Prisma.now_loc & {
   now_ss: SedimentaryStructure[]
 } & {
   now_coll_meth: CollectingMethod[]
-} & { now_lau: Array<LocalityUpdate> } & UpdateComment
+} & { now_lau: Array<LocalityUpdate> }
 export type UpdateLog = LogPrisma.log
 export type Locality = {
   lid: number
@@ -85,7 +85,7 @@ export type Locality = {
 export type Sequence = Prisma.now_tu_sequence
 export type SequenceDetailsType = Prisma.now_tu_sequence
 
-export type SpeciesDetailsType = SpeciesType & { now_ls: Array<SpeciesLocality> } & {
+export type SpeciesDetailsType = Prisma.com_species & { now_ls: Array<SpeciesLocality> } & {
   com_taxa_synonym: Array<SpeciesSynonym>
 } & { now_sau: Array<SpeciesUpdate> }