Merge pull request #2010 from sanger/develop

Merge develop into master

.release-version

@@ -1 +1 @@
-10.7.8
+10.8.0

README.md

@@ -24,6 +24,8 @@ config required:
     VITE_SAMPLEEXTRACTION_BASE_URL=<url>
     VITE_LOG=false
 
+Replace `<url>` with relevant URLs
+
 ### Setup Steps
 
 Install the require dependencies:

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/components/qcResultsUpload/QcResultsUploadForm.vue

@@ -75,7 +75,7 @@ export default {
   },
   computed: {
     api() {
-      return this.$store.getters.api.v1
+      return this.$store.getters.api.v2
     },
     qcResultUploadsRequest: ({ api }) => api.traction.qc_results_uploads.create,
     border() {
@@ -113,17 +113,18 @@ export default {
       this.busy = true
       this.disableUpload = true
 
-      try {
-        const csv = await this.file.text()
-        const data = { csv: csv, usedBySelected: this.usedBySelected }
-        await createQcResultsUploadResource(this.qcResultUploadsRequest, data)
-        this.uploadSuccessful = true
+      const csv = await this.file.text()
+      const data = { csv: csv, usedBySelected: this.usedBySelected }
+      const { success, errors } = await createQcResultsUploadResource(
+        this.qcResultUploadsRequest,
+        data,
+      )
+      this.uploadSuccessful = success
 
+      if (success) {
         this.showAlert(`Successfully imported: ${this.file.name}`, 'success')
-      } catch (e) {
-        this.uploadSuccessful = false
-
-        this.showAlert(e, 'danger')
+      } else {
+        this.showAlert(errors || 'Unable to upload QC File', 'danger')
       }
       this.busy = false
     },

src/services/traction/QcResultsUpload.js

@@ -1,10 +1,21 @@
-import { handleResponse } from '@/api/v1/ResponseHelper'
-/*
-  UPDATE
-*/
+import { handleResponse } from '@/api/v2/ResponseHelper'
 
+/**
+ * Creates a QC results upload resource.
+ *
+ * @param {Function} request - The request function to be called.
+ * @param {Object} params - The parameters for the request.
+ * @param {string} params.csv - The CSV data to be uploaded.
+ * @param {boolean} params.usedBySelected - Indicates if the resource is used by the selected entity.
+ * @returns {Promise<Object>} The data from the response if successful.
+ * @throws {Object} The errors from the response if unsuccessful.
+ */
 const createQcResultsUploadResource = async (request, { csv, usedBySelected }) => {
-  const { success, data, errors } = await handleResponse(
+  const {
+    success,
+    body: { data = {} },
+    errors = [],
+  } = await handleResponse(
     request({
       data: {
         data: {
@@ -18,10 +29,6 @@ const createQcResultsUploadResource = async (request, { csv, usedBySelected }) =
     }),
   )
 
-  if (success) {
-    return data
-  } else {
-    throw errors
-  }
+  return { success, data, errors }
 }
 export { createQcResultsUploadResource }

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 })

src/views/pacbio/PacbioLibraryIndex.vue

@@ -173,7 +173,8 @@ const state = reactive({
 })
 
 //Define refs
-const sortBy = ref('created_at')
+// Sort By id descending by default
+const sortBy = ref('id')
 
 //Composables
 const { showAlert } = useAlert()