Merge pull request #2087 from sanger/develop

Release 10.9.3

.github/workflows/generate_pages.yml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup node
         uses: actions/setup-node@v4

.release-version

@@ -1 +1 @@
-10.9.2
+10.9.3

package.json

@@ -25,18 +25,18 @@
   },
   "dependencies": {
     "@sanger/ui-styling": "^4.1.0",
-    "@vitejs/plugin-vue": "^5.1.4",
+    "@vitejs/plugin-vue": "^5.2.0",
     "autoprefixer": "^10.4.20",
     "axios": "^1.7.7",
     "csv-parse": "^5.5.6",
     "global": "^4.4.0",
     "lodash-es": "^4.17.21",
     "pinia": "^2.2.6",
-    "postcss": "^8.4.47",
+    "postcss": "^8.4.49",
     "swrv": "^1.0.4",
-    "tailwindcss": "3.4.14",
-    "vite": "^5.4.10",
-    "vue": "^3.5.12",
+    "tailwindcss": "3.4.15",
+    "vite": "^5.4.11",
+    "vue": "^3.5.13",
     "vue-router": "^4.4.5",
     "vue3-selecto": "^1.12.3",
     "vuex": "^4.1.0"
@@ -46,20 +46,20 @@
     "@pinia/testing": "^0.1.7",
     "@vue/test-utils": "^2.4.6",
     "clean-jsdoc-theme": "^4.3.0",
-    "cypress": "^13.15.2",
+    "cypress": "^13.16.0",
     "cypress-file-upload": "^5.0.8",
     "dotenv": "^16.4.5",
-    "eslint": "^9.14.0",
+    "eslint": "^9.15.0",
     "eslint-config-prettier": "^9.1.0",
     "eslint-plugin-cypress": "^4.1.0",
-    "eslint-plugin-vue": "^9.30.0",
-    "globals": "^15.11.0",
+    "eslint-plugin-vue": "^9.31.0",
+    "globals": "^15.12.0",
     "jsdoc": "^4.0.4",
     "jsdom": "^25.0.1",
     "npm-run-all": "^4.1.5",
     "postcss-cli": "^11.0.0",
     "prettier": "3.3.3",
     "rollup-plugin-visualizer": "^5.12.0",
-    "vitest": "^2.1.4"
+    "vitest": "^2.1.5"
   }
 }

src/api/Config.js

@@ -91,6 +91,9 @@ const config = [
           {
             name: 'smrt_link_versions',
           },
+          {
+            name: 'library_batches',
+          },
         ],
       },
       {

src/components/pacbio/PacbioPoolEdit.vue

@@ -150,6 +150,7 @@ const {
   selectedUsedAliquots,
   createPool,
   updatePool,
+  validatePoolAttribute,
   updateUsedAliquotFromCsvRecord,
 } = usePacbioPoolCreateStore()
 const { showAlert } = useAlert()
@@ -230,7 +231,7 @@ const poolSetter = (attr) => {
     },
     set(newValue) {
       pool[attr] = newValue
-      updatePool(pool, attr)
+      validatePoolAttribute(attr)
     },
   })
 }

src/components/reception/MultiBarcode.vue

@@ -66,6 +66,9 @@
         Import {{ labwareData.foundBarcodes.size }} labware into {{ props.pipeline }} from
         {{ reception.text }}
       </p>
+      <p data-testid="workflow-location-text" class="text-left">
+        {{ workflowLocationText }}
+      </p>
       <div class="flex flex-row space-x-8 mt-5">
         <traction-button
           id="reset"
@@ -105,6 +108,7 @@ import { createBarcodeLabels, createBasicTubeBarcodeLabel } from '@/lib/LabelPri
 import { createReceptionResource, createMessages } from '@/services/traction/Reception.js'
 import { getCurrentDate } from '@/lib/DateHelpers.js'
 import DataFetcher from '@/components/DataFetcher.vue'
+import { scanInBarcodesToLocation } from '@/services/labwhere/helpers.js'
 
 const props = defineProps({
   pipeline: {
@@ -119,6 +123,18 @@ const props = defineProps({
     type: Object,
     default: () => ({}),
   },
+  workflowLocationText: {
+    type: String,
+    default: '',
+  },
+  userCode: {
+    type: String,
+    default: '',
+  },
+  locationBarcode: {
+    type: String,
+    default: '',
+  },
 })
 const emit = defineEmits(['importStarted', 'importFinished', 'reset'])
 
@@ -247,12 +263,23 @@ async function importLabware() {
       labwareData.foundBarcodes,
       labwareData.attributes,
     )
+    const importedBarcodes = Array.from(labwareData.foundBarcodes)
+    const messages =
+      createMessages({
+        barcodes: importedBarcodes,
+        response,
+        reception: props.reception,
+      }) || []
 
-    const messages = createMessages({
-      barcodes: Array.from(labwareData.foundBarcodes),
-      response,
-      reception: props.reception,
-    })
+    if (importedBarcodes.length > 0) {
+      messages.push(
+        await scanInBarcodesToLocation(
+          props.userCode,
+          props.locationBarcode,
+          importedBarcodes.join('\n'),
+        ),
+      )
+    }
 
     // we create a different alert for each message
     messages.forEach(({ type, text }) => {

src/components/reception/MultiplexedLibraryBarcode.vue

@@ -81,6 +81,9 @@
           Import {{ labwareData.foundBarcodes.size }} labware into {{ props.pipeline }} from
           {{ reception.text }}
         </p>
+        <p data-testid="workflow-location-text" class="text-left">
+          {{ workflowLocationText }}
+        </p>
         <div class="flex flex-row space-x-8 mt-5">
           <traction-button
             id="reset"
@@ -121,6 +124,7 @@ import { createBarcodeLabels, createBasicTubeBarcodeLabel } from '@/lib/LabelPri
 import { createReceptionResource, createMessages } from '@/services/traction/Reception.js'
 import { getCurrentDate } from '@/lib/DateHelpers.js'
 import DataFetcher from '@/components/DataFetcher.vue'
+import { scanInBarcodesToLocation } from '@/services/labwhere/helpers.js'
 
 const props = defineProps({
   pipeline: {
@@ -135,6 +139,18 @@ const props = defineProps({
     type: Object,
     default: () => ({}),
   },
+  workflowLocationText: {
+    type: String,
+    default: '',
+  },
+  userCode: {
+    type: String,
+    default: '',
+  },
+  locationBarcode: {
+    type: String,
+    default: '',
+  },
 })
 const emit = defineEmits(['importStarted', 'importFinished', 'reset'])
 
@@ -278,13 +294,23 @@ async function importLabware() {
       labwareData.foundBarcodes,
       labwareData.attributes,
     )
-
+    const importedBarcodes = Array.from(labwareData.foundBarcodes)
     const messages = createMessages({
-      barcodes: Array.from(labwareData.foundBarcodes),
+      barcodes: importedBarcodes,
       response,
       reception: props.reception,
     })
 
+    if (importedBarcodes.length > 0) {
+      messages.push(
+        await scanInBarcodesToLocation(
+          props.userCode,
+          props.locationBarcode,
+          importedBarcodes.join('\n'),
+        ),
+      )
+    }
+
     // we create a different alert for each message
     messages.forEach(({ type, text }) => {
       showAlert(text, type)

src/components/saphyr/SaphyrEnzymeModal.vue

@@ -24,7 +24,7 @@
 </template>
 
 <script>
-import handlePromise from '@/api/v1/PromiseHelper'
+import handleResponse from '@/api/v2/ResponseHelper'
 
 export default {
   name: 'SaphyrEnzymeModal',
@@ -42,7 +42,7 @@ export default {
   },
   computed: {
     api() {
-      return this.$store.getters.api.v1
+      return this.$store.getters.api.v2
     },
     enzymeRequest() {
       return this.api.traction.saphyr.enzymes
@@ -76,17 +76,20 @@ export default {
     },
     async getEnzymeOptions() {
       const promise = this.enzymeRequest.get()
-      const response = await handlePromise(promise)
+      const {
+        success,
+        errors,
+        body: { data },
+      } = await handleResponse(promise)
 
-      if (response.successful) {
-        const enzymes = response.deserialize.enzymes
-        const enzymeOptions = enzymes.map((enzyme) =>
-          Object.assign({ value: parseInt(enzyme.id), text: enzyme.name }),
+      if (success) {
+        const enzymeOptions = data.map((enzyme) =>
+          Object.assign({ value: parseInt(enzyme.id), text: enzyme.attributes.name }),
         )
         enzymeOptions.unshift({ value: null, text: 'Please select an option' })
         this.enzymeOptions = enzymeOptions
       } else {
-        this.message = response.errors.message
+        this.message = errors
       }
     },
     async provider() {

src/lib/csv/pacbio.js

@@ -57,12 +57,15 @@ const filterUndefinedValues = (record) =>
   Object.fromEntries(Object.entries(record).filter(([, value]) => value !== undefined))
 
 /**
- * Parses the provides CSV contents and passes each record to the callback
- * Column headers are assumed to be provided in the first row
- * Each record will have keys corresponding to each
+ * Processes each record in the CSV content using the provided callback function.
+ *
+ * @param {string} csv - The CSV content as a string.
+ * @param {Function} callback - The callback function to process each record.
+ * @param {...any} args - Additional arguments to pass to the callback function.
+ * @returns {Array|Object} - The processed records or an error object if an error occurs.
  */
-const eachRecord = (csv, callback) => {
-  parse(csv, {
+const eachRecord = (csv, callback, ...args) => {
+  const records = parse(csv, {
     bom: true, // Strip any byte-order-markers
     delimiter: ',',
     columns: validateHeaders(normaliseHeaders),
@@ -71,8 +74,44 @@ const eachRecord = (csv, callback) => {
     trim: true,
     info: true,
     cast,
-    onRecord: filterUndefinedValues,
-  }).forEach(callback)
+  }).map(filterUndefinedValues)
+
+  let retRecords = []
+  for (const record of records) {
+    const result = callback(record, ...args)
+    // If callback does not return anything, we just add the record to the return
+    if (!result) {
+      retRecords.push(record)
+    } else if (result instanceof Error) {
+      // If callback returns an error, we return the error and the record
+      return { error: result.message, record }
+    } else {
+      // If callback returns a result, we add the record and the result to the return
+      retRecords.push({ ...record, result })
+    }
+  }
+  return retRecords
 }
+/*
+ * @param {string} csv - The CSV data as a string.
+ * @param {number} column - The index of the column to extract values from.
+ * @param {boolean} [hasHeader=true] - Whether the CSV data includes a header row.
+ * @returns {Array<string>} An array of values from the specified column.
+ *
+ * @example
+ * const csv = 'header1,header2,header3\nvalue1,value2,value3\nvalue4,value5,value6';
+ * const values = getColumnValues(csv, 1);
+ * console.log(values); // Output: ['value2', 'value5']
+ */
+const getColumnValues = (csv, column, hasHeader = true) => {
+  const lines = csv.split('\n').filter((line) => line.trim() !== '')
+  if (lines.length === 0) return []
 
-export { eachRecord }
+  const data = hasHeader ? lines.slice(1) : lines
+
+  return data.map((line) => {
+    const columns = line.split(',')
+    return column >= columns.length ? '' : columns[column]
+  })
+}
+export { eachRecord, getColumnValues }

src/lib/receptions/index.js

@@ -15,6 +15,39 @@ const defaultRequestOptions = () => ({
   data_type: null,
 })
 
+const WorkflowsLocations = {
+  Extractions: {
+    pipelines: ['ONT', 'PacBio'],
+    name: 'Extractions -80 samples',
+    location: 'Long Read DTOL Freezer 2/Shelf 3/Rack 3',
+    barcode: 'lw-drawer-2-30398',
+  },
+  ONT: {
+    pipelines: ['ONT'],
+    name: 'ONT -20 samples',
+    location: 'LRT020 Draw 1',
+    barcode: 'lw-drawer-1-37292',
+  },
+  OntFridgeSamples: {
+    pipelines: ['ONT'],
+    name: 'ONT Fridge samples',
+    location: 'LTR018 Shelf 1',
+    barcode: 'lw-shelf-1-30503',
+  },
+  Pacbio: {
+    pipelines: ['PacBio'],
+    name: 'Pacbio -20 samples',
+    location: 'LRT006 Draw 1',
+    barcode: 'lw-shelf-1-30472',
+  },
+  PacbioFridgeSamples: {
+    pipelines: ['PacBio'],
+    name: 'Pacbio Fridge samples',
+    location: 'LRT007 – Shelf 1',
+    barcode: 'lw-shelf-1-30451',
+  },
+}
+
 const ReceptionTypes = {
   Sequencescape: {
     name: 'sequencescape',
@@ -71,4 +104,4 @@ const Receptions = {
 }
 
 export default Receptions
-export { defaultRequestOptions }
+export { defaultRequestOptions, WorkflowsLocations }

src/services/labwhere/client.js

@@ -70,7 +70,7 @@ const scanBarcodesInLabwhereLocation = async (
   startPosition,
 ) => {
   if (!userCode || !labwareBarcodes) {
-    return { success: false, errors: ['Missing required parameters'] }
+    return { success: false, errors: ['Required parameters are missing for the Scan In operation'] }
   }
 
   const params = {