Merge pull request #1891 from sanger/move-ont-pools-to-fetch

Y24-345 - Ont Pools store migration from axios to native fetch to reduce dependencies and increase maintainability.

src/api/JsonApi.js

@@ -305,6 +305,78 @@ const splitDataByParent = ({
   }, {})
 }
 
+/**
+ * Extract the includes from the relationships
+ * If the relationship is an array, then extract all the includes
+ * If the relationship is an object, then extract the include
+ * If the includes have their own relationships, then extract those
+ * @param {Object} relationships - the list of relationships to be extracted
+ * @param {Array} included - the list of included resources
+ * @param {Number} depth - the depth of the extraction
+ * @param {Number} maximumDepth - the maximum depth of the extraction. This is to prevent stack overflow error. Default is 3 (enough to get all data out for standard response). Othwerwise it gets stuck in an endless loop e.g. tags and tag sets.
+ * @returns {Array} - the list of extracted includes
+ */
+const extractIncludes = ({ relationships, included, depth = 1, maximumDepth = 3 }) => {
+  if (depth > maximumDepth) {
+    return []
+  }
+
+  const rawIncludes = Object.values(relationships).reduce((result, { data }) => {
+    // prevents failure with empty relationships
+    if (!data) {
+      return [...result]
+    }
+
+    if (Array.isArray(data)) {
+      return [...result, ...data.map((item) => findIncluded(item, included))]
+    } else {
+      return [...result, findIncluded(data, included)]
+    }
+  }, [])
+
+  // we need to run through it again as includes can also have relationships
+  // this is a recursive function
+  // we could do this in findIncluded but that is used elsewhere
+  const includes = rawIncludes.flatMap((includes) => {
+    if (includes.relationships) {
+      return [
+        includes,
+        ...extractIncludes({ relationships: includes.relationships, included, depth: depth + 1 }),
+      ]
+    } else {
+      return includes
+    }
+  })
+
+  // we need to remove includes with no id as this indicates it is part of the data
+  return includes.filter((item) => item.id)
+}
+
+/**
+ * Find the first n items in the data and return them
+ * Also extract the includes related to the found data
+ * @param {Object} data - the data object to be searched
+ * @param {Number} first - the number of items to return
+ * @param {Boolean} all - return all the data
+ * @param {Boolean} get - is this a get request? find returns data as an object and get returns an array
+ * @returns {Object} - the found data and the included resources
+ */
+const find = ({ data, all = false, first = 1, get = false } = {}) => {
+  const foundData = all ? data.data : data.data.slice(0, first)
+
+  // we need to extract the includes from the found data
+  const included = foundData.flatMap(({ relationships }) => {
+    return extractIncludes({ relationships, included: data.included })
+  })
+
+  // we need to remove the duplicates from included
+  // if we are only extracting a single record and find is used data needs to be an object
+  return {
+    data: foundData.length === 1 && !get ? foundData[0] : foundData,
+    included: [...new Set(included)],
+  }
+}
+
 export {
   extractAttributes,
   mapRelationships,
@@ -324,6 +396,8 @@ export {
   populateBy,
   splitDataByParent,
   dataToObjectByPlateNumber,
+  extractIncludes,
+  find,
 }
 
 export default deserialize

src/store/traction/ont/pools/actions.js

@@ -1,5 +1,4 @@
-import { handleResponse } from '@/api/v1/ResponseHelper'
-import { handleResponse as handleResponseV2 } from '@/api/v2/ResponseHelper'
+import { handleResponse } from '@/api/v2/ResponseHelper'
 import { groupIncludedByResource } from '@/api/JsonApi'
 import { wellFor, wellToIndex } from './wellHelpers'
 import { validate, valid, payload } from './pool'
@@ -152,15 +151,15 @@ export default {
       return { success: true, errors: [] }
     }
 
-    const request = rootState.api.v1.traction.ont.pools
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.find({
       id: id,
       include:
         'libraries.tag.tag_set,libraries.source_plate.wells.requests,libraries.source_tube.requests,libraries.request,tube',
     })
     const response = await handleResponse(promise)
 
-    const { success, data: { data, included = [] } = {}, errors = [] } = response
+    const { success, body: { data, included = [] } = {}, errors = [] } = response
 
     if (success) {
       const {
@@ -205,10 +204,11 @@ export default {
       }
     }
 
-    const request = rootState.api.v1.traction.ont.plates
-    const promise = request.get({ filter: filter, include: 'wells.requests' })
+    const request = rootState.api.v2.traction.ont.plates
+    const promise = request.get({ filter, include: 'wells.requests' })
     const response = await handleResponse(promise)
-    let { success, data: { data, included = [] } = {}, errors = [] } = response
+
+    let { success, body: { data, included = [] } = {}, errors = [] } = response
     const { wells, requests } = groupIncludedByResource(included)
 
     // We will be return a successful empty list if no plates match the filter
@@ -245,10 +245,10 @@ export default {
       }
     }
 
-    const request = rootState.api.v1.traction.ont.tubes
-    const promise = request.get({ filter: filter, include: 'requests' })
+    const request = rootState.api.v2.traction.ont.tubes
+    const promise = request.get({ filter, include: 'requests' })
     const response = await handleResponse(promise)
-    let { success, data: { data, included = [] } = {}, errors = [] } = response
+    let { success, body: { data, included = [] } = {}, errors = [] } = response
     const { requests } = groupIncludedByResource(included)
 
     // We will be return a successful empty list if no tubes match the filter
@@ -290,12 +290,12 @@ export default {
    * @param rootState the vuex rootState object. Provides access to the current state
    * @param commit the vuex commit object. Provides access to mutations
    */
-  fetchOntRequests: async ({ commit, rootState }, filter, page) => {
-    const request = rootState.api.v1.traction.ont.requests
+  fetchOntRequests: async ({ commit, rootState }, filter = {}, page = {}) => {
+    const request = rootState.api.v2.traction.ont.requests
     const promise = request.get({ page, filter })
     const response = await handleResponse(promise)
 
-    const { success, data: { data, meta = {} } = {}, errors = [] } = response
+    const { success, body: { data, meta = {} } = {}, errors = [] } = response
 
     if (success) {
       commit('setRequests', data)
@@ -308,6 +308,7 @@ export default {
    * Validate a pool for the given barcode exists
    * @param rootState the vuex state object. Provides access to current state
    * @param barcode the barcode applied to the pool search
+   * There doesn't seem to be a test for this. Maybe e2e?
    */
   validatePoolBarcode: async ({ rootState }, barcode) => {
     // Here we want to make sure the barcode exists
@@ -318,10 +319,10 @@ export default {
       }
     }
 
-    const request = rootState.api.v1.traction.ont.pools
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.get({ filter: { barcode } })
     const response = await handleResponse(promise)
-    let { success, data: { data } = {} } = response
+    let { success, body: { data } = {} } = response
 
     // We will be returned a successful empty list if no pools match the barcode
     // Therefore we want to return success false, if we don't have any pools
@@ -336,16 +337,16 @@ export default {
    * @param rootState the vuex rootState object. Provides access to the current state
    * @param commit the vuex commit object. Provides access to mutations
    */
-  fetchOntPools: async ({ commit, rootState }, filter, page) => {
-    const request = rootState.api.v1.traction.ont.pools
+  fetchOntPools: async ({ commit, rootState }, filter = {}, page = {}) => {
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.get({
       page,
       filter,
       include: 'tube,libraries.tag,libraries.request',
     })
     const response = await handleResponse(promise)
 
-    const { success, data: { data, included = [], meta = {} } = {}, errors = [] } = response
+    const { success, body: { data, included = [], meta = {} } = {}, errors = [] } = response
     const { tubes, libraries, tags, requests } = groupIncludedByResource(included)
 
     if (success) {
@@ -367,15 +368,16 @@ export default {
    */
   // For the component, the included relationships are not required
   // However, the functionality does not appear to work without them
+  // no unit tests?
   populateOntPools: async ({ commit, rootState }, filter) => {
-    const request = rootState.api.v1.traction.ont.pools
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.get({
       filter: filter,
       include: 'tube,libraries.tag,libraries.request',
     })
     const response = await handleResponse(promise)
 
-    const { success, data: { data, included = [] } = {}, errors = [] } = response
+    const { success, body: { data, included = [] } = {}, errors = [] } = response
     const { tubes, libraries, tags, requests } = groupIncludedByResource(included)
 
     if (success) {
@@ -397,7 +399,7 @@ export default {
   fetchOntTagSets: async ({ commit, rootState }) => {
     const request = rootState.api.v2.traction.ont.tag_sets
     const promise = request.get({ include: 'tags' })
-    const response = await handleResponseV2(promise)
+    const response = await handleResponse(promise)
 
     const { success, body: { data, included = [] } = {}, errors = [] } = response
 
@@ -421,9 +423,9 @@ export default {
   }) => {
     validate({ libraries })
     if (!valid({ libraries })) return { success: false, errors: 'The pool is invalid' }
-    const request = rootState.api.v1.traction.ont.pools
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.create({ data: payload({ libraries, pool }), include: 'tube' })
-    const { success, data: { included = [] } = {}, errors } = await handleResponse(promise)
+    const { success, body: { included = [] } = {}, errors } = await handleResponse(promise)
     const { tubes: [tube = {}] = [] } = groupIncludedByResource(included)
     const { attributes: { barcode = '' } = {} } = tube
     return { success, barcode, errors }
@@ -440,7 +442,7 @@ export default {
   }) => {
     validate({ libraries })
     if (!valid({ libraries })) return { success: false, errors: 'The pool is invalid' }
-    const request = rootState.api.v1.traction.ont.pools
+    const request = rootState.api.v2.traction.ont.pools
     const promise = request.update(payload({ libraries, pool }))
     const { success, errors } = await handleResponse(promise)
     return { success, errors }

src/store/traction/ont/pools/mutations.js

@@ -74,6 +74,7 @@ export default {
    * Populated the result with the response
    * @param {Object} state The VueXState object
    * @param {Object} Response A response object
+   * I am wondering why we need to do this. Refactor needed.
    **/
   populatePoolingLibraries: (state, data) => {
     const newLibraries = dataToObjectById({ data, includeRelationships: true })

tests/data/index.js

@@ -1,4 +1,3 @@
-import Enzymes from './enzymes'
 import Libraries from './libraries'
 import Requests from './requests'
 import RunNoLibrary from './runNoLibrary'
@@ -31,27 +30,17 @@ import PacbioSequencingPlate from './pacbioSequencingPlate'
 import PacbioWell from './pacbioWell'
 import PacbioWells from './pacbioWells'
 import PacbioWellLibrary from './pacbioWellLibrary'
-import TractionOntRequests from './tractionOntRequests'
 import TractionTubeWithContainerMaterials from './tractionTubeWithContainerMaterials'
 import TractionTubesWithPacbioPools from './tractionTubesWithPacbioPools'
 import TractionPlates from './tractionPlates'
 import AutoTagStore from './autoTagStore.json'
-import OntAutoTagStore from './ontAutoTagStore.json'
 import OntPlatesRequest from './ontPlatesRequest.json'
-import OntTubesRequest from './ontTubesRequest.json'
-import OntPlates from './ontPlates.json'
-import OntPlateRequest from './ontPlateRequest.json'
 import OntRequestsRequest from './ontRequestsRequest'
-import OntTubeRequest from './ontTubeRequest.json'
 import OntRun from './ontRun.json'
-import tractionOntLibraries from './tractionOntLibraries'
-import TractionOntPool from './tractionOntPool.json'
-import TractionOntPools from './tractionOntPools.json'
 import PacbioRunWithWellDefaults from './pacbioRunWithWellDefaults'
 import StorePools from './StorePools.json'
 
 export default {
-  Enzymes,
   Libraries,
   Requests,
   RunNoLibrary,
@@ -84,22 +73,13 @@ export default {
   PacbioWell,
   PacbioWells,
   PacbioWellLibrary,
-  tractionOntLibraries,
-  TractionOntRequests,
-  TractionOntPool,
-  TractionOntPools,
   TractionTubeWithContainerMaterials,
   TractionTubesWithPacbioPools,
   TractionPlates,
   AutoTagStore,
-  OntAutoTagStore,
   OntPlatesRequest,
-  OntPlates,
-  OntPlateRequest,
   OntRequestsRequest,
   OntRun,
-  OntTubeRequest,
-  OntTubesRequest,
   PacbioRunWithWellDefaults,
   StorePools,
 }