Merge pull request #222 from wtsi-npg/devel

Release PR for 2.1.0

.github/workflows/deploy-pages.yml

@@ -11,13 +11,13 @@ jobs:
       DB_URL: "mysql+pymysql://q:q@q/q"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: |
           pipx install poetry
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           architecture: 'x64'
@@ -27,14 +27,13 @@ jobs:
         run: |
           poetry env use '3.10'
           poetry install
-        
+
       - name: Build openapi.json
         run: |
           mkdir gh_pages
           poetry run python -c "from lang_qc.main import app; import json; output = open('gh-pages/openapi.json', 'w'); json.dump(app.openapi(), output); output.close()"
 
       - name: Deploy github pages
-        uses: JamesIves/github-pages-deploy-action@v4.3.3
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
-          branch: gh-pages
           folder: gh-pages

.github/workflows/lint.yml

@@ -12,13 +12,13 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: |
           pipx install poetry
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           architecture: 'x64'
@@ -41,7 +41,7 @@ jobs:
         run: |
           poetry run isort --check --diff --color .
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
         with:
           node-version: 18.x
 

.github/workflows/publish-docker.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
 
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Log in to registry
         run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin

.github/workflows/test.yml

@@ -11,9 +11,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           architecture: 'x64'
@@ -59,13 +59,13 @@ jobs:
           MYSQL_DATABASE: "langqc"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Poetry
         run: |
           pipx install poetry
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           architecture: 'x64'
@@ -82,10 +82,10 @@ jobs:
   test-frontend:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
-          node-version: '18'
+          node-version: '20'
       - run: npm install
         working-directory: ./frontend
       - run: npm run test

CHANGELOG.md

@@ -3,6 +3,40 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+
+## [2.1.0] - 2024-04-15
+
+### Changed
+
+* To simplify object instantiation and fields' assignment for some
+  of the response models, converted `PacBioWell` and `PacBioWellFull`
+  models to pydantic dataclasses.
+* Changed the response model for filtered by either QC status or run wells from
+  `PacBioWell` to `PacBioWellSummary`, the latter initially being identical
+  the former. In order to propagate information about a study to the tabbed
+  well summary view, added a new field, study_names, to the `PacBioWellSummary`
+  model.
+* Added a new event to the tabbed well summary view, to the button with the well
+  name. Mouse hover over this button displays study names associated with the
+  well.
+* Changed the colour scheme of the above mentioned button from grey to orange
+  if one of the studies associated with the well is the BIOSCAN study, which
+  the QC team needs to deal with slightly differently.
+* Added a new QC state 'On hold external'. Semantically the new state is similar
+  to the existing 'On hold' state. The intended purpose of the new QC state - to
+  highlight the wells, which are waiting for a completion of some off-site
+  process (example - deplexing at http://mbrave.net/).
+
+### Added
+
+* A new response model `PacBioWellSummary`, which replaces `PacBioWell`
+  in the latest's capacity of the response model for a PacBio well
+  summary.
+* A new field, `study_names`, a potentially empty sorted array of
+  unique study names, is added to the response model for a PacBio
+  well summary.
+
 ## [2.0.0] - 2024-02-20
 
 ### Changed

README.md

@@ -7,6 +7,17 @@ subjects other than development, testing and deployment.
 - [The QC process](docs/qc_process.md)
 - [The QC database schema](docs/qc_schema_explained.md)
 
+## Prepare for release
+
+Prior to merging to the master branch:
+
+- Update CHANGELOG.md
+- Update the hardcoded version in
+    - frontend/package.json
+    - lang_qc/__init__.py
+    - pyproject.toml
+- If needed, update the Copyright year in frontend/src/App.vue
+
 ## Install and run locally
 
 You can install the package with `pip install .` from the repository's root.

alembic/versions/2.1.0_extend_qc_state_dict.py

@@ -0,0 +1,24 @@
+"""extend_qc_state_dict
+
+Revision ID: 2.1.0
+Revises: 2.0.0
+Create Date: 2024-03-19 12:31:26.359652
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "2.1.0"
+down_revision = "2.0.0"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.execute(
+        "INSERT INTO qc_state_dict (state, outcome) VALUES ('On hold external', NULL)"
+    )
+
+
+def downgrade() -> None:
+    op.execute("DELETE FROM qc_state_dict WHERE state='On hold external'")

frontend/Dockerfile

@@ -1,4 +1,4 @@
-FROM node:18-alpine as base-stage
+FROM node:20-alpine as base-stage
 
 COPY  package.json /code/longue_vue/
 

frontend/jsconfig.json

@@ -0,0 +1,3 @@
+{
+    "exclude": ["node_modules"]
+}

frontend/package.json

@@ -1,13 +1,14 @@
 {
   "name": "npg-longue-vue",
-  "version": "2.0.0",
+  "version": "2.1.0",
   "description": "UI for LangQC",
   "author": "Kieron Taylor <[email protected]>",
   "license": "GPL-3.0-or-later",
   "engines": {
     "node": ">=16.16.0",
     "npm": ">=8.11.0"
   },
+  "type": "module",
   "scripts": {
     "dev": "vite --port 3000",
     "build": "vite build",

frontend/src/App.vue

@@ -122,7 +122,7 @@ function notInWellsByRun() {
 
   </el-main>
 
-  <el-footer>Copyright Genome Research Ltd 2023 - client version: {{ VERSION.replace(/['"]+/g) + (DEVMODE ? "+DEV" : "")
+  <el-footer>Copyright Genome Research Ltd 2023, 2024 - client version: {{ VERSION.replace(/['"]+/g) + (DEVMODE ? "+DEV" : "")
   }}</el-footer>
 </template>
 

frontend/src/components/QcView.vue

@@ -5,7 +5,7 @@
 
     import { computed } from "vue";
     import groupMetrics from "../utils/metrics.js";
-    import combineLabelWithPlate from "../utils/text.js"
+    import { combineLabelWithPlate } from "../utils/text.js"
 
     const props = defineProps({
         // Well object representing one prepared input for the instrument

frontend/src/components/WellTable.vue

@@ -2,7 +2,11 @@
 /*
 * Renders a table for a list of wells and generates buttons for selecting wells
 */
-import combineLabelWithPlate from "../utils/text.js"
+import { combineLabelWithPlate, listStudiesForTooltip } from "../utils/text.js"
+import { ElTooltip, ElButton } from "element-plus";
+
+const tooltipDelay = 500
+const studyNameHighlight = 'BIOSCAN UK for flying insects'
 
 defineProps({
   wellCollection: Object
@@ -28,9 +32,17 @@ defineEmits(['wellSelected'])
     <tr :key="wellObj.id_product" v-for="wellObj in wellCollection">
       <td>{{ wellObj.run_name }}</td>
       <td class="well_selector">
-        <button v-on:click="$emit('wellSelected', { idProduct: wellObj.id_product })">
-          {{ combineLabelWithPlate(wellObj.label, wellObj.plate_number) }}
-        </button>
+        <el-tooltip placement="top" effect="light" :show-after="tooltipDelay"
+          :content="'<span>'.concat(listStudiesForTooltip(wellObj.study_names)).concat('</span>')"
+          raw-content
+        >
+          <el-button plain
+            :type="wellObj.study_names.includes(studyNameHighlight) ? 'warning' : 'info'"
+            v-on:click="$emit('wellSelected', { idProduct: wellObj.id_product })"
+          >
+            {{ combineLabelWithPlate(wellObj.label, wellObj.plate_number) }}
+          </el-button>
+        </el-tooltip>
       </td>
       <td>{{ wellObj.instrument_type }} {{ wellObj.instrument_name }}</td>
       <td>{{ wellObj.qc_state ? wellObj.qc_state.qc_state : '&nbsp;' }}</td>

frontend/src/components/__tests__/WellTable.spec.js

@@ -7,9 +7,33 @@ describe('Rows of data give rows in the table', () => {
   const table = mount(WellTable, {
     props: {
       wellCollection: [
-        {run_name: 'TEST1', label: 'A1', plate_number: null, instrument_name: '1234', instrument_type: 'Revio', id_product: 'ABCDEF'},
-        {run_name: 'TEST1', label: 'B1', plate_number: null, instrument_name: '1234', instrument_type: 'Revio', id_product: '123456'},
-        {run_name: 'TEST2', label: 'A1', plate_number: 1, instrument_name: '1234', instrument_type: 'Revio', id_product: '123457'},
+        {
+          run_name: 'TEST1',
+          label: 'A1',
+          plate_number: null,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: 'ABCDEF',
+          study_names: []
+        },
+        {
+          run_name: 'TEST1',
+          label: 'B1',
+          plate_number: null,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: '123456',
+          study_names: ['Study name 1', 'Study name 2']
+        },
+        {
+          run_name: 'TEST2',
+          label: 'A1',
+          plate_number: 1,
+          instrument_name: '1234',
+          instrument_type: 'Revio',
+          id_product: '123457',
+          study_names: ['BIOSCAN UK for flying insects']
+        },
       ]
     }
   })
@@ -40,7 +64,14 @@ describe('Rows of data give rows in the table', () => {
     expect(table.emitted().wellSelected[0][0]).toHaveProperty('idProduct')
     expect(table.emitted().wellSelected[0][0].idProduct).toEqual('ABCDEF')
 
-    await rows[2].find('button').trigger('click')
+    let wellButton = rows[2].find('button')
+    await wellButton.trigger('click')
     expect(table.emitted().wellSelected[1][0].idProduct).toEqual('123456')
+    expect(wellButton.classes('el-tooltip__trigger')).toBeTruthy()
+    expect(wellButton.classes('el-button--info')).toBeTruthy()
+
+    wellButton = rows[3].find('button')
+    expect(wellButton.classes('el-tooltip__trigger')).toBeTruthy()
+    expect(wellButton.classes('el-button--warning')).toBeTruthy()
   })
 })

frontend/src/utils/__tests__/text.spec.js

@@ -1,7 +1,7 @@
 import { describe, test, expect } from 'vitest'
-import combineLabelWithPlate from '../text'
+import { combineLabelWithPlate, listStudiesForTooltip } from '../text'
 
-describe('Text processing', () => {
+describe('Well label and plate display', () => {
   test('Print well label without plate number', () => {
     expect(combineLabelWithPlate('A1', undefined)).toEqual('A1')
     expect(combineLabelWithPlate('A1', null)).toEqual('A1')
@@ -11,3 +11,18 @@ describe('Text processing', () => {
     expect(combineLabelWithPlate('A1', 1)).toEqual('1-A1')
   })
 })
+
+describe('Study names tooltip', () => {
+  test('Display a warning in case of an empty study array', () => {
+    expect(listStudiesForTooltip([])).toEqual('No study info')
+  })
+
+  test('Display a single study name for an array of one study', () => {
+    expect(listStudiesForTooltip(['My single study'])).toEqual('My single study')
+  })
+
+  test('Display multiple lines for multiple studies', () => {
+    expect(listStudiesForTooltip(['Study One', 'Study two', 'Study 3'])).toEqual(
+      'Study One<br />Study two<br />Study 3')
+  })
+})

frontend/src/utils/text.js

@@ -1,9 +1,16 @@
 // Reusable text-mangling for the interface
 
-export default function combineLabelWithPlate(well, plate) {
+export { combineLabelWithPlate, listStudiesForTooltip }
+
+function combineLabelWithPlate(well, plate) {
   if (!plate) {
     return well
   } else {
     return `${plate}-${well}`
   }
 }
+
+function listStudiesForTooltip(study_names) {
+  let names = study_names.length == 0 ? ['No study info'] : study_names
+  return names.join('<br />')
+}

frontend/src/views/__tests__/WellsByRun.spec.js

@@ -38,6 +38,7 @@ for (let index = 0; index < 2; index++) {
     instrument_name: "1234",
     instrument_type: "Revio",
     id_product: `${index}23456`,
+    study_names: [`Study ${index}`, 'Another study'],
     ...someLinkGeneration
   })
 }
@@ -48,6 +49,7 @@ const secondaryRun = {
   instrument_name: '1234',
   instrument_type: 'Revio',
   id_product: 'ABCDEF',
+  study_names: [],
   ...someLinkGeneration
 }
 
@@ -141,7 +143,6 @@ describe('Does it work?', async () => {
     let buttons = wrapper.findAll('button')
     buttons[1].trigger('click')
     await flushPromises()
-
     expect(wrapper.get('#well_summary').exists()).toBe(true)
   })