Refactor tests & add create & delete tests for species

backend/package.json

@@ -6,7 +6,7 @@
   "scripts": {
     "dev": "npx tsx watch --clear-screen=false src/index.ts",
     "build": "tsc",
-    "test": "node --import tsx --test src/api-tests/**/*.ts",
+    "test": "node --import tsx --test src/api-tests/**/*test.ts",
     "start": "node build/index.js",
     "lint": "eslint . --ext ts,tsx --report-unused-disable-directives --max-warnings 0",
     "prisma": "prisma generate --schema prisma/schema.prisma && prisma generate --schema prisma/schema_log.prisma"

backend/src/api-tests/locality/create.test.ts

@@ -3,7 +3,7 @@ import assert from 'node:assert/strict'
 import { before, describe, it } from 'node:test'
 import { LocalityDetailsType, SpeciesDetailsType } from '../../../../frontend/src/backendTypes'
 import { LogRow } from '../../services/writeOperations/types'
-import { newLocalityBasis } from '../data'
+import { newLocalityBasis } from './data'
 import { login, send, testLogRows } from '../utils'
 
 let createdLocality: LocalityDetailsType | null = null
@@ -35,7 +35,8 @@ describe('Creating new locality works', () => {
   it('Species update also logged correctly', async () => {
     const speciesId = createdLocality!.now_ls.find(ls => ls.com_species.species_name === 'Newspecies')?.species_id
     const speciesResult = await send<SpeciesDetailsType>(`species/${speciesId}`, 'GET')
-    const update = speciesResult.body.now_sau[0]
+    const update = speciesResult.body.now_sau.find(update => update.sau_comment === 'new locality test update')
+    assert(update, 'Species update not found')
     update.species_id === speciesId
     const logRows = update.updates
     const expectedLogRows: Partial<LogRow>[] = [

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

@@ -1,4 +1,4 @@
-import { Reference, SpeciesDetailsType } from '../../../frontend/src/backendTypes'
+import { Reference, SpeciesDetailsType } from '../../../../frontend/src/backendTypes'
 
 export const newLocalityBasis = {
   bfa_max: 'bahean',
@@ -175,6 +175,7 @@ export const newLocalityBasis = {
       rowState: 'new',
     },
   ],
+  comment: 'new locality test update',
 }
 
 export const editedLocality = {

backend/src/api-tests/locality/delete.test.ts

@@ -2,7 +2,6 @@
 import assert from 'node:assert/strict'
 import { describe, it, before } from 'node:test'
 import { login, send } from '../utils'
-import { LocalityDetailsType } from '../../../../frontend/src/backendTypes'
 
 describe('Deleting a locality works', async () => {
   before(async () => {
@@ -11,7 +10,7 @@ describe('Deleting a locality works', async () => {
   await it('Deleting works', async () => {
     const deleteResult = await send<{ id: number }>('locality/28518', 'DELETE')
     assert(deleteResult.status === 200)
-    const getResult = await send<LocalityDetailsType>('locality/28518', 'GET')
-    assert(getResult.status === 404, 'Locality status was not 404 after deletion')
+    const getResult = await send('locality/28518', 'GET')
+    assert(getResult.status === 404, 'Locality response status was not 404 after deletion')
   })
 })

backend/src/api-tests/locality/update.test.ts

@@ -3,7 +3,7 @@ import assert from 'node:assert/strict'
 import { before, describe, it } from 'node:test'
 import { LocalityDetailsType } from '../../../../frontend/src/backendTypes'
 import { LogRow } from '../../services/writeOperations/types'
-import { editedLocality } from '../data'
+import { editedLocality } from './data'
 import { login, send, testLogRows } from '../utils'
 
 let resultLocality: LocalityDetailsType | null = null

backend/src/api-tests/species/create.test.ts

@@ -0,0 +1,53 @@
+/* eslint-disable @typescript-eslint/no-floating-promises */
+import assert from 'node:assert/strict'
+import { before, describe, it } from 'node:test'
+import { LocalityDetailsType, SpeciesDetailsType } from '../../../../frontend/src/backendTypes'
+import { LogRow } from '../../services/writeOperations/types'
+import { newSpeciesBasis } from './data'
+import { login, send, testLogRows } from '../utils'
+
+let createdSpecies: SpeciesDetailsType | null = null
+
+describe.only('Creating new species works', () => {
+  before(async () => {
+    await login()
+  })
+
+  it('Request succeeds and returns valid number id', async () => {
+    const { body: resultBody } = await send<{ id: number }>('species', 'PUT', {
+      species: { ...newSpeciesBasis, comment: 'species test' },
+    })
+    const { id: createdId } = resultBody
+
+    assert(typeof createdId === 'number', `Invalid result returned on write: ${createdId}`)
+
+    const { body } = await send<SpeciesDetailsType>(`species/${createdId}`, 'GET')
+    createdSpecies = body
+  })
+
+  it('Contains correct data', () => {
+    const { species_name, now_ls } = createdSpecies!
+    assert(species_name === newSpeciesBasis.species_name, 'Name is different')
+    const locality = now_ls.find(ls => ls.now_loc.lid === 24750)
+    assert(!!locality, 'Locality in locality-species not found')
+  })
+
+  it('Locality-species change was updated also to locality', async () => {
+    const localityFound = createdSpecies!.now_ls.find(ls => ls.now_loc.loc_name.startsWith('Romany'))
+    assert(localityFound, 'Locality was not found in now_ls')
+    const speciesResult = await send<LocalityDetailsType>(`locality/24750`, 'GET')
+    const update = speciesResult.body.now_lau.find(lau => lau.lid === 24750 && lau.lau_comment === 'species test')
+    assert(update, 'Update not found')
+    const logRows = update.updates
+    const expectedLogRows: Partial<LogRow>[] = [
+      {
+        oldValue: null,
+        value: '24750',
+        type: 'add',
+        column: 'lid',
+        table: 'now_ls',
+      },
+    ]
+    testLogRows(logRows, expectedLogRows, 2)
+  })
+})

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

@@ -0,0 +1,107 @@
+import { EditDataType, SpeciesDetailsType } from '../../../../frontend/src/backendTypes'
+
+export const newSpeciesBasis: EditDataType<SpeciesDetailsType> = {
+  class_name: 'Mammalia',
+  order_name: 'Eulipotyphla',
+  family_name: 'Soricidae',
+  subclass_or_superorder_name: 'Eutheria',
+  suborder_or_superfamily_name: null,
+  subfamily_name: 'Soricinae',
+  genus_name: 'Petenyia',
+  species_name: 'dubia test',
+  unique_identifier: '-',
+  taxonomic_status: null,
+  common_name: null,
+  sp_author: 'Bachmayer & Wilson, 1970',
+  strain: null,
+  gene: null,
+  taxon_status: null,
+  diet1: 'a',
+  diet2: null,
+  diet3: null,
+  diet_description: null,
+  rel_fib: null,
+  selectivity: null,
+  digestion: null,
+  feedinghab1: null,
+  feedinghab2: null,
+  shelterhab1: null,
+  shelterhab2: null,
+  locomo1: null,
+  locomo2: null,
+  locomo3: null,
+  hunt_forage: null,
+  brain_mass: null,
+  sv_length: null,
+  activity: null,
+  sd_size: null,
+  sd_display: null,
+  tshm: null,
+  symph_mob: null,
+  relative_blade_length: null,
+  tht: null,
+  crowntype: null,
+  microwear: null,
+  horizodonty: null,
+  cusp_shape: null,
+  cusp_count_buccal: null,
+  cusp_count_lingual: null,
+  loph_count_lon: null,
+  loph_count_trs: null,
+  fct_al: null,
+  fct_ol: null,
+  fct_sf: null,
+  fct_ot: null,
+  fct_cm: null,
+  mesowear: null,
+  mw_or_high: null,
+  mw_or_low: null,
+  mw_cs_sharp: null,
+  mw_cs_round: null,
+  mw_cs_blunt: null,
+  mw_scale_min: null,
+  mw_scale_max: null,
+  mw_value: null,
+  pop_struc: null,
+  sp_status: false,
+  used_morph: null,
+  used_now: true,
+  used_gene: null,
+  sp_comment: null,
+  now_ls: [
+    {
+      rowState: 'new',
+      lid: 24750,
+      nis: null,
+      pct: null,
+      quad: null,
+      mni: null,
+      qua: null,
+      id_status: null,
+      orig_entry: null,
+      source_name: null,
+      mesowear: null,
+      mw_or_high: null,
+      mw_or_low: null,
+      mw_cs_sharp: null,
+      mw_cs_round: null,
+      mw_cs_blunt: null,
+      mw_scale_min: null,
+      mw_scale_max: null,
+      mw_value: null,
+      microwear: null,
+      dc13_mean: null,
+      dc13_n: null,
+      dc13_max: null,
+      dc13_min: null,
+      dc13_stdev: null,
+      do18_mean: null,
+      do18_n: null,
+      do18_max: null,
+      do18_min: null,
+      do18_stdev: null,
+    },
+  ],
+  now_sau: [],
+  com_taxa_synonym: [],
+}

backend/src/api-tests/species/delete.test.ts

@@ -0,0 +1,16 @@
+/* eslint-disable @typescript-eslint/no-floating-promises */
+import assert from 'node:assert/strict'
+import { describe, it, before } from 'node:test'
+import { login, send } from '../utils'
+
+describe('Deleting a species works', async () => {
+  before(async () => {
+    await login()
+  })
+  await it('Deleting returns correct status and after that is not found on request', async () => {
+    const deleteResult = await send<{ id: number }>('species/84357', 'DELETE')
+    assert(deleteResult.status === 200)
+    const getResult = await send('species/84357', 'GET')
+    assert(getResult.status === 404, 'Species response status was not 404 after deletion')
+  })
+})

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

@@ -0,0 +1,74 @@
+/* eslint-disable @typescript-eslint/no-floating-promises */
+import assert from 'node:assert/strict'
+import { before, describe, it } from 'node:test'
+import { LocalityDetailsType } from '../../../../frontend/src/backendTypes'
+import { LogRow } from '../../services/writeOperations/types'
+import { editedLocality } from '../locality/data'
+import { login, send, testLogRows } from '../utils'
+
+let resultLocality: LocalityDetailsType | null = null
+
+describe('Locality write works', () => {
+  before(async () => {
+    await login()
+  })
+
+  it('Edits name, synonyms and locality species correctly', async () => {
+    const writeResult = await send<{ id: number }>('locality', 'PUT', { locality: editedLocality })
+
+    assert(writeResult.body.id === editedLocality.lid, `Invalid result returned on write: ${writeResult.body.id}`)
+
+    const { body } = await send<LocalityDetailsType>(`locality/${editedLocality.lid}`, 'GET')
+    resultLocality = body
+  })
+
+  it('Name changed correctly', () => {
+    assert(resultLocality!.loc_name === editedLocality.loc_name, 'Name was not changed correctly')
+  })
+
+  it('Added locality species is found', () => {
+    assert(
+      resultLocality!.now_ls.find(ls => ls.species_id === 21052 && ls.lid === 21050),
+      'Added locality species not found'
+    )
+  })
+
+  it('Locality species include exactly two entries', () => {
+    assert(resultLocality!.now_ls.length === 2, `Unexpected now_ls length: ${resultLocality!.now_ls.length}`)
+  })
+
+  it('Changes were logged correctly', () => {
+    const update = resultLocality!.now_lau
+    const lastUpdate = update[update.length - 1]
+
+    assert(lastUpdate.lau_comment === editedLocality.comment, 'Comment wrong')
+    assert(lastUpdate.now_lr[lastUpdate.now_lr.length - 1].rid === editedLocality.references[0].rid)
+
+    const logRows = lastUpdate.updates
+
+    const expectedLogRows: Partial<LogRow>[] = [
+      {
+        oldValue: 'Dmanisi',
+        value: editedLocality.loc_name,
+        type: 'update',
+        column: 'loc_name',
+        table: 'now_loc',
+      },
+      {
+        oldValue: '21050',
+        value: null,
+        type: 'delete',
+        column: 'lid',
+        table: 'now_ls',
+      },
+      {
+        oldValue: '85729',
+        value: null,
+        type: 'delete',
+        column: 'species_id',
+        table: 'now_ls',
+      },
+    ]
+    testLogRows(logRows, expectedLogRows, 5)
+  })
+})

backend/src/api-tests/utils.ts

@@ -15,6 +15,7 @@ export const send = async <T extends Record<string, unknown>>(
   if (token) headers.append('authorization', `bearer ${token}`)
   const options = { body: method !== 'GET' ? JSON.stringify(body) : undefined, method, headers }
   const response = await fetch(`${baseUrl}/${path}`, options)
+  if (response.status > 399) return { body: {} as T, status: response.status }
   const responseText = await response.text()
   if (!responseText) return { body: {} as T, status: response.status }
   return { body: JSON.parse(responseText) as T, status: response.status }
@@ -45,7 +46,7 @@ export const testLogRows = (logRows: UpdateLog[], expectedLogRows: Partial<LogRo
         row.old_data === expectedRow.oldValue &&
         row.new_data === expectedRow.value
     )
-    assert(!!receivedRow, 'Did not find relevant log row')
+    assert(!!receivedRow, `Did not find this expected logrow: ${JSON.stringify(expectedRow)}`)
     const debugLog = `Row: \n${JSON.stringify(receivedRow, null, 2)}\nExpected:\n${JSON.stringify(expectedRow)}`
     assert(receivedRow.new_data === expectedRow.value, `Log rows new data differs. ${debugLog}`)
     assert(receivedRow.old_data === expectedRow.oldValue, `Log rows old data differs. ${debugLog}`)