Bacpop-194 All Beebop changes for multi-db

README.md

@@ -159,3 +159,8 @@ npx playwright test
 ```
 from `app/client-v2/`.
 To close all components once ready, run `./scripts/stop_test` from root.
+
+### Adding new species
+
+1. Add new database to [mrcdata](https://mrcdata.dide.ic.ac.uk/beebop).
+2. Add new species to `args.json` in *beebop_py*

app/client-v2/e2e/home.spec.ts

@@ -1,17 +1,12 @@
 import { test, expect, Page } from "@playwright/test";
-import { randomProjectName } from "./utils.js";
+import { createProject, randomProjectName } from "./utils.js";
 
 test.beforeEach(async ({ page }) => {
   await page.goto("");
 });
 
 const addProjectNavigateHome = async (page: Page, name: string) => {
-  await page.getByLabel("Create project").click();
-  await page.getByLabel("Create", { exact: true }).click();
-  await page.getByLabel("Select a Species").click();
-  await page.getByLabel("Streptococcus pneumoniae").click();
-  await page.getByLabel("Name").fill(name);
-  await page.getByLabel("Create", { exact: true }).click();
+  await createProject(page, name)
 
   await expect(page.getByText(name)).toBeVisible();
 

app/client-v2/e2e/projectPostRun.spec.ts

@@ -1,12 +1,11 @@
 import { expect, test } from "@playwright/test";
-import { randomProjectName, uploadFiles } from "./utils.js";
+import { createProject, randomProjectName, uploadFiles } from "./utils.js";
 
 let projectName: string;
 test.beforeEach(async ({ page }) => {
   await page.goto("");
   projectName = randomProjectName();
-  await page.getByPlaceholder("Create new Project").fill(projectName);
-  await page.getByPlaceholder("Create new Project").press("Enter");
+  await createProject(page, projectName);
 });
 
 test("can run project and view results", async ({ page }) => {
@@ -89,12 +88,3 @@ test("can run project multiple times", async ({ page }) => {
   await expect(page.getByText("GPSC7")).toBeVisible();
   await expect(page.getByText("GPSC4")).toBeVisible();
 });
-
-test("can export project data as csv", async ({ page }) => {
-  uploadFiles(page);
-
-  const downloadPromise = page.waitForEvent("download");
-  await page.getByLabel("Export").click();
-  const download = await downloadPromise;
-  expect(download.suggestedFilename()).toBe(`${projectName}.csv`);
-});

app/client-v2/e2e/projectPreRun.spec.ts

@@ -1,10 +1,11 @@
 import { expect, test } from "@playwright/test";
-import { randomProjectName, uploadFiles } from "./utils.js";
+import { createProject, randomProjectName, uploadFiles } from "./utils.js";
 
+let projectName: string;
 test.beforeEach(async ({ page }) => {
   await page.goto("");
-  await page.getByPlaceholder("Create new Project").fill(randomProjectName());
-  await page.getByPlaceholder("Create new Project").press("Enter");
+  projectName = randomProjectName();
+  await createProject(page, projectName);
 });
 
 test("upload multiple files and display amr information", async ({ page }) => {
@@ -36,3 +37,12 @@ test("shows progress bar whilst uploading files & gone after full uploaded", asy
 
   await expect(page.getByRole("progressbar")).not.toBeVisible();
 });
+
+test("can export project data as csv", async ({ page }) => {
+  uploadFiles(page);
+
+  const downloadPromise = page.waitForEvent("download");
+  await page.getByLabel("Export").click();
+  const download = await downloadPromise;
+  expect(download.suggestedFilename()).toBe(`${projectName}.csv`);
+});

app/client-v2/e2e/utils.ts

@@ -8,3 +8,12 @@ export const uploadFiles = async (page: Page, files = ["e2e/fastaFiles/good_1.fa
   const fileChooser = await fileChooserPromise;
   await fileChooser.setFiles(files);
 };
+
+export const createProject = async (page: Page, name: string, species = "Streptococcus pneumoniae") => {
+  await page.getByLabel("Create project").click();
+  await page.getByLabel("Create", { exact: true }).click();
+  await page.getByLabel("Select a Species").click();
+  await page.getByLabel(species).click();
+  await page.getByLabel("Name").fill(name);
+  await page.getByLabel("Create", { exact: true }).click();
+};

app/client-v2/public/worker.js

@@ -13,26 +13,30 @@ function createFS(module, f) {
   module.FS.mount(module.FS.filesystems.WORKERFS, { files: [f] }, workdir);
 }
 
-async function computeSample(hash, file, filename) {
+async function computeSample(fileObject, sketchKmerArguments) {
+  const { file, hash, filename } = fileObject;
+  const { kmerMin, kmerMax, kmerStep } = sketchKmerArguments;
+
   const amrModule = await AMRprediction();
   const sketchModule = await WebSketch();
   //create working directory and mount file
   createFS(amrModule, file);
   createFS(sketchModule, file);
 
   const amr = amrModule.make_prediction_json(workdir + "/" + filename);
-  // sketch() takes the followings arguments: filepath, kmer_min, kmer_max, kmer_step,
-  // bbits, sketchsize64, codon_phased (boolean), use_rc (boolean)
-  const sketch = sketchModule.sketch(workdir + "/" + filename, 14, 29, 3, 14, 156, false, true);
+  // sketch() takes the followings arguments: 
+  // filepath, kmer_min, kmer_max, kmer_step, bbits, sketchsize64, codon_phased (boolean), use_rc (boolean)
+  const sketch = sketchModule.sketch(workdir + "/" + filename, kmerMin, kmerMax, kmerStep, 14, 156, false, true);
 
   return { hash, amr, sketch };
 }
 
 onmessage = async function (message) {
-  const hashedFiles = message.data;
+  const { hashedFiles, sketchKmerArguments } = message.data;
+
   const samples = [];
   for (const fileObject of hashedFiles) {
-    const { hash, amr, sketch } = await computeSample(fileObject.hash, fileObject.file, fileObject.filename);
+    const { hash, amr, sketch } = await computeSample(fileObject, sketchKmerArguments);
     samples.push({ hash, amr: JSON.parse(amr), sketch: JSON.parse(sketch), filename: fileObject.filename });
   }
   postMessage(samples);

app/client-v2/src/App.vue

@@ -1,9 +1,12 @@
 <script setup lang="ts">
 import AppNav from "@/layouts/AppNav.vue";
 import { useTheme } from "@/composables/useTheme";
+import { useSpeciesStore } from "./stores/speciesStore";
 
 const { setInitialTheme } = useTheme();
+const { setSpeciesConfig } = useSpeciesStore();
 setInitialTheme();
+setSpeciesConfig();
 </script>
 
 <template>

app/client-v2/src/__tests__/App.spec.ts

@@ -1,7 +1,10 @@
 import AppVue from "@/App.vue";
+import { useSpeciesStore } from "@/stores/speciesStore";
+import { createTestingPinia } from "@pinia/testing";
 import { render, screen } from "@testing-library/vue";
 import { defineComponent } from "vue";
 import { createRouter, createWebHistory } from "vue-router";
+import PrimeVue from "primevue/config";
 
 const mockedThemeValues = {
   setInitialTheme: vitest.fn(),
@@ -11,25 +14,31 @@
 vitest.mock("@/composables/useTheme", () => ({
   useTheme: () => mockedThemeValues
 }));
+vitest.mock("primevue/usetoast", () => ({
+  useToast: vitest.fn()
+}));
+
 const router = createRouter({
   history: createWebHistory(),
   routes: [{ path: "/about", component: defineComponent({ template: `<div>About Page</div>` }) }]
 });
 describe("App", () => {
-  it("should render about page(route) and call setInitialTheme on load of about page", async () => {
+  it("should render about page(route) and call setInitialTheme & setSpeciesConfig on load of about page", async () => {
     router.push("/about");
     await router.isReady();
 
     render(AppVue, {
       global: {
-        plugins: [router],
+        plugins: [router, createTestingPinia()],
         stubs: {
           AppNav: true
         }
       }
     });
 
+    const speciesStore = useSpeciesStore();
     expect(screen.getByText(/about page/i)).toBeVisible();
     expect(mockedThemeValues.setInitialTheme).toHaveBeenCalled();
+    expect(speciesStore.setSpeciesConfig).toHaveBeenCalled();
   });
 });

app/client-v2/src/__tests__/components/HomeView/CreateProjectButton.spec.ts

@@ -4,11 +4,12 @@ import { createRouter, createWebHistory } from "vue-router";
 import { defineComponent } from "vue";
 import PrimeVue from "primevue/config";
 import ToastService from "primevue/toastservice";
-import { MOCK_PROJECTS } from "@/mocks/mockObjects";
+import { MOCK_PROJECTS, MOCK_SPECIES } from "@/mocks/mockObjects";
 import userEvent from "@testing-library/user-event";
 import { server } from "@/mocks/server";
 import { http, HttpResponse } from "msw";
 import { projectIndexUri } from "@/mocks/handlers/projectHandlers";
+import { createTestingPinia } from "@pinia/testing";
 
 const router = createRouter({
   history: createWebHistory(),
@@ -20,7 +21,18 @@ const router = createRouter({
 const renderComponent = () => {
   render(CreateProjectButton, {
     global: {
-      plugins: [router, PrimeVue, ToastService]
+      plugins: [
+        router,
+        PrimeVue,
+        ToastService,
+        createTestingPinia({
+          initialState: {
+            species: {
+              species: MOCK_SPECIES
+            }
+          }
+        })
+      ]
     },
     props: {
       projects: MOCK_PROJECTS

app/client-v2/src/__tests__/stores/projectStore.spec.ts

@@ -1,14 +1,21 @@
 import { getApiUrl } from "@/config";
 import { assignResultUri, projectIndexUri, statusUri } from "@/mocks/handlers/projectHandlers";
-import { MOCK_PROJECT, MOCK_PROJECT_SAMPLES, MOCK_PROJECT_SAMPLES_BEFORE_RUN } from "@/mocks/mockObjects";
+import {
+  MOCK_PROJECT,
+  MOCK_PROJECT_SAMPLES,
+  MOCK_PROJECT_SAMPLES_BEFORE_RUN,
+  MOCK_SPECIES,
+  MOCK_SPECIES_CONFIG
+} from "@/mocks/mockObjects";
 import { server } from "@/mocks/server";
 import { useProjectStore } from "@/stores/projectStore";
+import { useSpeciesStore } from "@/stores/speciesStore";
 import {
-  type ProjectSample,
   AnalysisType,
   type AnalysisStatus,
-  type WorkerResponse,
-  type HashedFile
+  type HashedFile,
+  type ProjectSample,
+  type WorkerResponse
 } from "@/types/projectTypes";
 import { flushPromises } from "@vue/test-utils";
 import { HttpResponse, http } from "msw";
@@ -135,6 +142,16 @@ describe("projectStore", () => {
 
       expect(processFilesSpy).toHaveBeenCalledWith([newFileWithHash]);
     });
+    it("should show error toast and not call processFiles when onFilesUpload is called with 0 new files", async () => {
+      const store = useProjectStore();
+      store.toast.showErrorToast = vitest.fn();
+      store.project.samples = mockFilesWithHashes.map((file) => ({ hash: file.hash, filename: file.name }));
+      const processFilesSpy = vitest.spyOn(store, "processFiles");
+      store.onFilesUpload(mockFilesWithHashes[0]);
+
+      expect(store.toast.showErrorToast).toHaveBeenCalledWith("No new files to upload.");
+      expect(processFilesSpy).not.toHaveBeenCalled();
+    });
     it("should call batchFilesForProcessing and processFileBatches when processFiles is called", async () => {
       const mockHashedFileBatches = [[{ hash: "test-hash" }], [{ hash: "test-hash" }]] as HashedFile[][];
       const store = useProjectStore();
@@ -511,22 +528,27 @@ describe("projectStore", () => {
       expect(fileBatches.length).toBe(Math.ceil(mockFilesWithHashes.length / 5));
     });
 
-    it("should process file batches correctly when processFileBatches is called", async () => {
+    it("should process file batches correctly with species kmer args when processFileBatches is called", async () => {
       const mockFilesWithHashes = Array.from({ length: 98 }, (_, index) => ({
         name: `sample${index + 1}.fasta`,
         text: () => Promise.resolve(`sample${index + 1}`)
       })) as unknown as File[];
-      const store = useProjectStore();
-      store.getOptimalWorkerCount = vitest.fn().mockReturnValue(8);
-      const batchPromise = vitest.spyOn(store, "computeAmrAndSketch").mockResolvedValue();
-      const hashedFileBatches = await store.batchFilesForProcessing(mockFilesWithHashes);
+      const speciesStore = useSpeciesStore();
+      speciesStore.sketchKmerArguments = MOCK_SPECIES_CONFIG;
+
+      const projectStore = useProjectStore();
+      projectStore.project.species = MOCK_SPECIES[0];
+
+      projectStore.getOptimalWorkerCount = vitest.fn().mockReturnValue(8);
+      const batchPromise = vitest.spyOn(projectStore, "computeAmrAndSketch").mockResolvedValue();
+      const hashedFileBatches = await projectStore.batchFilesForProcessing(mockFilesWithHashes);
 
-      await store.processFileBatches(hashedFileBatches);
+      await projectStore.processFileBatches(hashedFileBatches);
       await flushPromises();
 
-      expect(store.uploadingPercentage).toEqual(100);
+      expect(projectStore.uploadingPercentage).toEqual(100);
       hashedFileBatches.forEach((batch) => {
-        expect(batchPromise).toHaveBeenCalledWith(batch);
+        expect(batchPromise).toHaveBeenCalledWith(batch, MOCK_SPECIES_CONFIG[MOCK_SPECIES[0]]);
       });
     });
   });

app/client-v2/src/__tests__/stores/speciesStore.spec.ts

@@ -0,0 +1,69 @@
+import { speciesConfigIndexUri } from "@/mocks/handlers/configHandlers";
+import { MOCK_SPECIES_CONFIG } from "@/mocks/mockObjects";
+import { server } from "@/mocks/server";
+import { useSpeciesStore } from "@/stores/speciesStore";
+import { http, HttpResponse } from "msw";
+import { createPinia, setActivePinia } from "pinia";
+
+const mockToastAdd = vitest.fn();
+vitest.mock("primevue/usetoast", () => ({
+  useToast: vitest.fn(() => ({
+    add: mockToastAdd
+  }))
+}));
+
+describe("SpeciesStore", () => {
+  beforeEach(() => {
+    setActivePinia(createPinia());
+  });
+
+  describe("getters", () => {
+    it("should return correct SketchArguments when getSketchKmerArguments is called", () => {
+      const store = useSpeciesStore();
+      store.sketchKmerArguments = MOCK_SPECIES_CONFIG;
+
+      const result = store.getSketchKmerArguments("Streptococcus pneumoniae");
+
+      expect(result).toEqual(MOCK_SPECIES_CONFIG["Streptococcus pneumoniae"]);
+    });
+
+    it("should return undefined when getSketchKmerArguments is called with an invalid species", () => {
+      const store = useSpeciesStore();
+      store.sketchKmerArguments = {
+        "Streptococcus pneumoniae": {
+          kmerMax: 14,
+          kmerMin: 3,
+          kmerStep: 3
+        }
+      } as any;
+
+      const result = store.getSketchKmerArguments("Streptococcus agalactiae");
+
+      expect(result).toBeUndefined();
+    });
+  });
+  describe("actions", () => {
+    it("should set speciesConfig from api when setSpeciesConfig is called", async () => {
+      const store = useSpeciesStore();
+
+      await store.setSpeciesConfig();
+
+      expect(store.sketchKmerArguments).toEqual(MOCK_SPECIES_CONFIG);
+      expect(store.species).toEqual(Object.keys(MOCK_SPECIES_CONFIG));
+    });
+
+    it("should show error toast when setSpeciesConfig fails", async () => {
+      server.use(http.get(speciesConfigIndexUri, () => HttpResponse.error()));
+      const store = useSpeciesStore();
+
+      await store.setSpeciesConfig();
+
+      expect(mockToastAdd).toHaveBeenCalledWith({
+        severity: "error",
+        detail: "Failed to fetch sketch kmer arguments, please try again later",
+        life: 5000,
+        summary: "Error"
+      });
+    });
+  });
+});