Merge pull request #179 from wtsi-npg/devel

Release 1.4.0

CHANGELOG.md

@@ -3,7 +3,22 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## [Unreleased]
+## [1.4.0] - 2023-08-16
+
+### Added
+
+* Tests for bulk retrieval of QC states
+* Third dimension for describing wells added to QC Schema to support multi-plate runs
+
+### Changed
+
+* Browser URLs now use id_product to identify items to show in the QC Viewer instead of the combination of run, label (and plate number)
+* More strict validation of checksums (id_product) when sent to backend API
+
+### Fixed
+
+* A bug that disregarded the value of the `sequencing_outcomes_only`
+argument in what is now the `get_qc_states_by_id_product_list` function
 
 ## [1.3.0] - 2023-08-02
 

alembic/README.md

@@ -16,7 +16,8 @@ What you need:
 - the URL for that database set in `ALEMBIC_DB_URL`
 
 Set `ALEMBIC_DB_URL` env. variable to the SQLAlchemy URL for the database you
-want to operate on. The format is `driver://user:pass@host:port/dbname`.
+want to operate on. The format is `driver://user:pass@host:port/dbname`, where
+for MySQL and our software stack the driver is `mysql+pymysql`.
 
 Ensure `alembic` in on your PATH. Create a revision:
 

alembic/versions/36952df5b8ba_add_ability_to_record_plate_number.py

@@ -0,0 +1,50 @@
+"""Add ability to record plate number
+
+Revision ID: 36952df5b8ba
+Revises: dd60c67ad3e5
+Create Date: 2023-08-03 13:32:06.820978
+
+"""
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "36952df5b8ba"
+down_revision = "dd60c67ad3e5"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    sql = """
+    INSERT INTO sub_product_attr (`attr_name`, `description`)
+    VALUES ('plate_number', 'An optional PacBio plate number')
+    """
+    op.execute(sql)
+
+    sql = """
+    ALTER TABLE sub_product
+      ADD COLUMN `id_attr_three` INT DEFAULT NULL AFTER `value_attr_two`,
+      ADD COLUMN `value_attr_three` VARCHAR(20) DEFAULT NULL AFTER `id_attr_three`,
+      ADD KEY `ix_sub_product_id_attr_three` (`id_attr_three`),
+      ADD KEY `ix_sub_product_value_attr_three` (`value_attr_three`),
+      ADD CONSTRAINT `fk_subproduct_attr3` FOREIGN KEY (`id_attr_three`)
+          REFERENCES `sub_product_attr` (`id_attr`);
+    """
+    op.execute(sql)
+
+
+def downgrade() -> None:
+    sql = """
+    ALTER TABLE sub_product
+        DROP KEY `ix_sub_product_id_attr_three`,
+        DROP KEY `ix_sub_product_value_attr_three`,
+        DROP CONSTRAINT `fk_subproduct_attr3`,
+        DROP COLUMN `value_attr_three`,
+        DROP COLUMN `id_attr_three`;
+    """
+    op.execute(sql)
+
+    sql = """
+    DELETE FROM sub_product_attr WHERE attr_name='plate_number';
+    """
+    op.execute(sql)

frontend/package.json

@@ -1,6 +1,6 @@
 {
   "name": "npg-longue-vue",
-  "version": "1.3.0",
+  "version": "1.4.0",
   "description": "UI for LangQC",
   "author": "Kieron Taylor <kt19@sanger.ac.uk>",
   "license": "GPL-3.0-or-later",

frontend/src/components/ClaimWidget.vue

@@ -18,12 +18,12 @@ const props = defineProps({
 let client = new LangQc();
 
 function claimHandler() {
-    const [runName, wellLabel] = focusWell.getRunAndLabel;
-    if (!(runName && wellLabel)) {
-        throw new Error('Claim environment misconfigured, no run name or well label');
+    const id = focusWell.getIdProduct;
+    if (!id) {
+        throw new Error('Claim environment misconfigured, needs an id_product');
     }
 
-    client.claimWell(runName, wellLabel)
+    client.claimWell(id)
         .then(
             (response) => {
                 focusWell.updateWellQcState(response);

frontend/src/components/QcWidget.vue

@@ -56,9 +56,9 @@ function syncWidgetToQcState() {
 }
 
 function submitQcState() {
-    let [name, well] = focusWell.getRunAndLabel;
+    const id_product = focusWell.getIdProduct;
 
-    client.setWellQcState(name, well, widgetQcSetting.value, widgetFinality.value)
+    client.setWellQcState(id_product, widgetQcSetting.value, widgetFinality.value)
         .then(
             (response) => {
                 focusWell.updateWellQcState(response);

frontend/src/components/WellTable.vue

@@ -28,7 +28,7 @@ defineEmits(['wellSelected'])
     <tr :key="wellObj.run_name + ':' + wellObj.label" v-for="wellObj in wellCollection">
       <td>{{ wellObj.run_name }}</td>
       <td class="well_selector">
-        <button v-on:click="$emit('wellSelected', { qcRun: wellObj.run_name, qcLabel: wellObj.label })">
+        <button v-on:click="$emit('wellSelected', { idProduct: wellObj.id_product })">
           {{ combineLabelWithPlate(wellObj.label, wellObj.plate_number) }}
         </button>
       </td>
@@ -48,4 +48,4 @@ defineEmits(['wellSelected'])
 #run_wells {
   width: 100%;
 }
-</style>
+</style>

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

@@ -10,6 +10,7 @@ describe('Clicking triggers POST and side-effects', () => {
     // A typical claim success
     fetch.mockResponse(
         JSON.stringify({
+            id_product: 'ABCDEF',
             qc_state: 'Claimed',
             outcome: null,
             is_preliminary: true,
@@ -31,6 +32,7 @@ describe('Clicking triggers POST and side-effects', () => {
                         initialState: {
                             focusWell: {
                                 well: {
+                                    id_product: 'ABCDEF',
                                     run_name: 'TEST',
                                     label: 'A1',
                                 }
@@ -56,7 +58,7 @@ describe('Clicking triggers POST and side-effects', () => {
         expect(wellStore.getQcValue).toEqual('Claimed');
 
         let request = fetch.mock.calls[0];
-        expect(request[0]).toEqual('/api/pacbio/run/TEST/well/A1/qc_claim');
+        expect(request[0]).toEqual('/api/pacbio/products/ABCDEF/qc_claim');
 
         let emits = widget.emitted();
         expect(emits.wellClaimed).toBeTruthy();

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

@@ -14,10 +14,9 @@ describe('QC widgets render with no prior QC state, i.e. pending/ready', () => {
                 initialState: {
                     focusWell: {
                         well: {
-                            run_info: {
-                                pac_bio_run_name: 'TEST',
-                                well_label: 'A1',
-                            }
+                            id_product: 'ABCDEF',
+                            run_name: 'TEST',
+                            label: 'A1',
                         }
                     },
                 },
@@ -107,10 +106,9 @@ describe('QC widget acquires state from prior outcome in run-table', () => {
                 initialState: {
                     focusWell: {
                         well: {
-                            run_info: {
-                                pac_bio_run_name: 'TEST',
-                                well_label: 'A1',
-                            },
+                            id_product: 'ABCDEF',
+                            run_name: 'TEST',
+                            label: 'A1',
                             qc_state: {
                                 qc_state: 'Claimed',
                                 is_preliminary: true,

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

@@ -7,24 +7,25 @@ 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'},
-        {run_name: 'TEST1', label: 'B1', plate_number: null, instrument_name: '1234', instrument_type: 'Revio'},
-        {run_name: 'TEST2', label: 'A1', plate_number: 1, instrument_name: '1234', instrument_type: 'Revio'},
+        {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'},
       ]
     }
   })
 
   test('There are three rows plus a header in the table', () => {
     const rows = table.findAll('tr')
     expect(rows.length).toEqual(4)
-
-    const columns = rows[1].findAll('td')
+    let columns = rows[1].findAll('td')
     expect(columns[0].text()).toEqual('TEST1')
     expect(columns[1].text()).toEqual('A1')
     expect(columns[2].text()).toEqual('Revio 1234')
     for (let col of columns.splice(3)) {
       expect(col.text()).toEqual('')
     }
+    columns = rows[3].findAll('td')
+    expect(columns[1].text()).toEqual('1-A1')
   })
 
   test('Non-null plate_number gives modified well labels', () => {
@@ -35,13 +36,11 @@ describe('Rows of data give rows in the table', () => {
   test('Clicking triggers event emits containing required data', async () => {
     const rows = table.findAll('tr')
     await rows[1].find('button').trigger('click')
-    expect(table.emitted().wellSelected[0][0]).toHaveProperty('qcLabel')
-    expect(table.emitted().wellSelected[0][0]).toHaveProperty('qcRun')
-    expect(table.emitted().wellSelected[0][0].qcRun).toEqual('TEST1')
-    expect(table.emitted().wellSelected[0][0].qcLabel).toEqual('A1')
+
+    expect(table.emitted().wellSelected[0][0]).toHaveProperty('idProduct')
+    expect(table.emitted().wellSelected[0][0].idProduct).toEqual('ABCDEF')
 
     await rows[2].find('button').trigger('click')
-    expect(table.emitted().wellSelected[1][0].qcRun).toEqual('TEST1')
-    expect(table.emitted().wellSelected[1][0].qcLabel).toEqual('B1')
+    expect(table.emitted().wellSelected[1][0].idProduct).toEqual('123456')
   })
-})
+})

frontend/src/stores/__tests__/focusWell.spec.js

@@ -10,16 +10,15 @@ describe('Check the getters', () => {
         wellStore = useWellStore();
     })
 
-    test('Get run name name and well label', () => {
-        expect(wellStore.getRunAndLabel).toStrictEqual([null, null]);
+    test('Get id_product', () => {
+        expect(wellStore.getIdProduct).toBeNull()
 
         wellStore.setFocusWell({
-            run_name: 'Whatever',
-            label: 'A1'
-        });
+            id_product: 'ABCDEF'
+        })
 
-        expect(wellStore.getRunAndLabel).toStrictEqual(['Whatever', 'A1']);
-    });
+        expect(wellStore.getIdProduct).toEqual('ABCDEF')
+    })
 
     test('getQcState', () => {
         expect(wellStore.getQcState).toBeNull();

frontend/src/stores/focusWell.js

@@ -28,14 +28,11 @@ export const useWellStore = defineStore('focusWell', {
         */
     }),
     getters: {
-        getRunAndLabel(state) {
-            if (!isNull(state.well)) {
-                return [
-                    state.well.run_name,
-                    state.well.label
-                ];
+        getIdProduct(state) {
+            if (state.well && !isNull(state.well.id_product)) {
+                return state.well.id_product
             } else {
-                return [null, null]
+                return null
             }
         },
         getQcState(state) {
@@ -71,8 +68,8 @@ export const useWellStore = defineStore('focusWell', {
         setFocusWell(well) {
             this.well = well;
         },
-        loadWellDetail(runName, label) {
-            apiClient.getWellPromise(runName, label).then(
+        loadWellDetail(id_product) {
+            apiClient.getWellPromise(id_product).then(
                 (well) => this.well = well
             ).catch(
                 (error) => {

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

@@ -69,13 +69,13 @@ describe('Example fake remote api call', () => {
             })
         )
 
-        client.claimWell('TRACTION-RUN-299', 'B1');
+        client.claimWell('ABCDEF');
 
         let request = fetch.mock.calls[3];
         expect(
             request[0]
         ).toEqual(
-            '/api/pacbio/run/TRACTION-RUN-299/well/B1/qc_claim'
+            '/api/pacbio/products/ABCDEF/qc_claim'
         );
 
         expect(
@@ -90,8 +90,8 @@ describe('Example fake remote api call', () => {
         client.getClientConfig();
         expect(fetch.mock.calls[4][0]).toEqual('/api/config');
 
-        client.getWellPromise('blah', 'A2');
-        expect(fetch.mock.calls[5][0]).toEqual('/api/pacbio/run/blah/well/A2');
+        client.getWellPromise('A12345');
+        expect(fetch.mock.calls[5][0]).toEqual('/api/pacbio/products/A12345/seq_level');
 
         client.getWellsForRunPromise('blah')
         expect(fetch.mock.calls[6][0]).toEqual('/api/pacbio/run/blah?page_size=100&page=1')

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

@@ -63,8 +63,8 @@ describe('Test query setting in URL', () => {
 })
 
 describe('Test QC param check', () => {
-  const testRun = {qcRun: 'test-run', qcLabel: 'A1'}
-  const alteredTestRun = {qcRun: 'test-run', qcLabel: 'B1'}
+  const testRun = {idProduct: 'AAAAAAAA'}
+  const alteredTestRun = {idProduct: 'BBBBBBBB'}
 
   test('No before, some after', () => {
     expect(qcQueryChanged(undefined, testRun)).toBe(true)

frontend/src/utils/langqc.js

@@ -84,8 +84,8 @@ export default class LangQc {
     );
   }
 
-  getWellPromise(name, well) {
-    return this.fetchWrapper(this.buildUrl(['run', name, 'well', well]));
+  getWellPromise(id_product) {
+    return this.fetchWrapper(this.buildUrl(['products', id_product, 'seq_level']));
   }
 
   getWellsForRunPromise(name) {
@@ -100,16 +100,16 @@ export default class LangQc {
     return this.fetchWrapper('/api/config');
   }
 
-  claimWell(name, well) {
+  claimWell(id_product) {
     return this.fetchWrapper(
-      this.buildUrl(['run', name, 'well', well, 'qc_claim']),
+      this.buildUrl(['products', id_product, 'qc_claim']),
       'POST'
     )
   }
 
-  setWellQcState(name, well, state, final = false) {
+  setWellQcState(id_product, state, final = false) {
     return this.fetchWrapper(
-      this.buildUrl(['run', name, 'well', well, 'qc_assign']),
+      this.buildUrl(['products', id_product, 'qc_assign']),
       'PUT',
       {
         qc_state: state,

frontend/src/utils/url.js

@@ -37,22 +37,26 @@ export function generateUrl(existingSettings, newSettings, path) {
 }
 
 export function qcQueryChanged(before, after) {
-  // Compares ?qcLabel and ?qcRun in the URL to tell when new data will be needed
-  // Invoke while watching vue-router.route.query
+  // Compares ?idProduct in the URL to tell when new data will
+  // be needed. Invoke while watching vue-router.route.query
   if (
-    (after.qcLabel || after.qcRun)
+    (after.idProduct)
     && (
+      // New page load
       before === undefined
       || (
-        !before['qcLabel'] && !before['qcRun']
+        // Focus removed in previous nav, e.g. go home
+        !before['idProduct']
       )
       || (
-        before.qcLabel && before.qcRun && (after.qcLabel != before.qcLabel || after.qcRun != before.qcRun)
+        // Change of focus within page
+        before.idProduct
+        && (after.idProduct != before.idProduct)
       )
     )
   ) {
     return true
-  } else if (before !== undefined && (before['qcLabel'] || before['qcRun'])) {
+  } else if (before !== undefined && (before['idProduct'])) {
     // In case all arguments are removed
     return true
   }