Bacpop 186 v9 db

README.md

@@ -1,35 +1,10 @@
-# beebop
-
-## Docker Quick Start
-
-Run the dockerised app along with proxy and all dependencies:
-
-```
-    ./scripts/run_docker_decrypt
-```
-
-You may need to update your version of Docker and Docker Compose: see [here](https://docs.docker.com/engine/install/ubuntu/) for instructions on updating on Ubuntu. 
-
-By default this will configure the nginx proxy for host localhost. To deploy with a different hostname, pass it as an argument, e.g.
-```
-./scripts/run_docker_decrypt beebop.dide.ic.ac.uk
-```
-
-This will also populate app config with secrets from the vault. If you are not running the script for the first time,
-or not for the first time since running the app outside docker, you can omit this step by running the `run_docker` script.
-
-Bring down the app with
-```
-    ./scripts/stop_docker
-```
+# Beebop
 
 Docker images are built on CI using `./proxy/docker/build`, `./app/server/docker/build`. If you want
 to generate them from changed local sources you can run those same scripts locally to build images.
 
-To target a branch of `beebop_py`, set `API_IMAGE` in `scripts/common`.
-
-When running locally in docker, the backend is serving from `beebop_beebop-server_1`, and the front end from the proxy
-container `beebop_proxy_1`.
+To target a branch of `beebop_py`, set `API_IMAGE` in `scripts/common`. If there is a dev image available,
+that can be targeting by adding `-dev` to the image name.
 
 ## Local development
 
@@ -47,7 +22,7 @@ docker --version
 
 
 If you run the application for the first time (or for the first time after running in docker), you need to replace the 
-secrets in the config file in `app/server/src/resources` first. 
+secrets in the config file in `app/server/src/resources` first.
 Login to the vault:
 ```
 export VAULT_ADDR=https://vault.dide.ic.ac.uk:8200
@@ -64,6 +39,12 @@ To start all required components, run:
 ./scripts/run_test
 ```
 
+To run dependencies and server only, run:
+```
+./scripts/run_test server-only
+```
+*Note: These scripts call `run_dependencies` which downloads ref databases only. To download full databases, remove `--refs` from the `./scripts/download_databases --refs` command in `run_dependencies`*
+
 The website can be viewed at http://localhost:5173/ . You can stop the application with `./scripts/stop_test`.
 
 The `run_test` script uses [pm2](https://github.com/Unitech/pm2) to manage running the client and server applications.

app/client-v2/package.json

@@ -40,7 +40,7 @@
   },
   "devDependencies": {
     "@pinia/testing": "^0.1.3",
-    "@playwright/test": "^1.42.0",
+    "@playwright/test": "^1.49.1",
     "@rushstack/eslint-patch": "^1.3.3",
     "@testing-library/jest-dom": "^6.4.2",
     "@testing-library/user-event": "^14.5.2",

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

@@ -4,7 +4,6 @@ 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(),

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

@@ -698,7 +698,33 @@ describe("projectStore", () => {
           [MOCK_PROJECT_SAMPLES[0].hash]: MOCK_PROJECT_SAMPLES[0].sketch,
           [MOCK_PROJECT_SAMPLES[1].hash]: MOCK_PROJECT_SAMPLES[1].sketch,
           [MOCK_PROJECT_SAMPLES[2].hash]: MOCK_PROJECT_SAMPLES[2].sketch
-        }
+        },
+        amrForMetadataCsv: [
+          {
+            "Chloramphenicol Resistance": "Probably",
+            "Cotrim Resistance": "Probably not",
+            "Erythromycin Resistance": "Probably not",
+            ID: "sample1-test-hash",
+            "Penicillin Resistance": "Unlikely",
+            "Tetracycline Resistance": "Highly unlikely"
+          },
+          {
+            "Chloramphenicol Resistance": "Probably",
+            "Cotrim Resistance": "Almost certainly",
+            "Erythromycin Resistance": "Almost certainly",
+            ID: "sample2-test-hash",
+            "Penicillin Resistance": "Highly unlikely",
+            "Tetracycline Resistance": "Highly unlikely"
+          },
+          {
+            "Chloramphenicol Resistance": "Probably",
+            "Cotrim Resistance": "Unlikely",
+            "Erythromycin Resistance": "Probably not",
+            ID: "sample3-test-hash",
+            "Penicillin Resistance": "Probably",
+            "Tetracycline Resistance": "Highly unlikely"
+          }
+        ]
       });
     });
     it("should get download url & download when downloadZip is called", async () => {

app/client-v2/src/__tests__/utils/projectCsvUtils.spec.ts

@@ -53,11 +53,11 @@ describe("projectCsvUtils", () => {
       const result = convertAmrForCsv(amr);
 
       expect(result).toEqual({
-        Penicillin: "word",
-        Chloramphenicol: "word",
-        Erythromycin: "word",
-        Tetracycline: "word",
-        Cotrim: "word"
+        "Penicillin Resistance": "word",
+        "Chloramphenicol Resistance": "word",
+        "Erythromycin Resistance": "word",
+        "Tetracycline Resistance": "word",
+        "Cotrim Resistance": "word"
       });
     });
   });

app/client-v2/src/components/ProjectView/CytoscapeCanvas.vue

@@ -29,14 +29,14 @@ onMounted(async () => {
         style: {
           width: "10px",
           height: "10px",
-          content: "data(key0)",
+          content: "data(d1)",
           "font-size": "7px",
           color: "#00CC66",
           "background-color": "rgba(45, 212, 191, 0.44)"
         }
       },
       {
-        selector: 'node[ref_query = "query"]',
+        selector: 'node[d2 = "query"]',
         style: {
           "background-color": "crimson",
           color: "crimson"

app/client-v2/src/components/ProjectView/NetworkTab.vue

@@ -20,6 +20,10 @@ const { data, error, isFetching } = useFetch(`${apiUrl}/networkGraphs/${store.pr
     <ProgressSpinner strokeWidth="8" class="w-4rem h-4rem" animationDuration=".5s" />
   </div>
   <div v-else-if="data?.data">
+    <InlineMessage severity="info" class="mb-2"
+      >These graphs are pruned versions of the full graphs. To view full graphs, download the zip file and view the
+      .graphml externally.</InlineMessage
+    >
     <InlineMessage severity="info" class="mb-2"
       >View in fullscreen, reset layout or use mouse, touchpad or touchscreen gestures on graphs to zoom in and out, or
       move nodes around.</InlineMessage

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

@@ -3,6 +3,7 @@ import { getApiUrl } from "@/config";
 import {
   AnalysisType,
   COMPLETE_STATUS_TYPES,
+  type AMRMetadataCsv,
   type AnalysisStatus,
   type ApiResponse,
   type ClusterInfo,
@@ -17,6 +18,7 @@ import { defineStore } from "pinia";
 import { Md5 } from "ts-md5";
 import { useSpeciesStore, type SketchKmerArguments } from "./speciesStore";
 import { toRaw } from "vue";
+import { convertAmrForCsv } from "@/utils/projectCsvUtils";
 
 const baseApi = mande(getApiUrl(), { credentials: "include" });
 
@@ -304,17 +306,26 @@ export const useProjectStore = defineStore("project", {
     buildRunAnalysisPostBody() {
       const sketches: Record<string, unknown> = {};
       const names: Record<string, unknown> = {};
+      const amrForMetadataCsv: AMRMetadataCsv[] = [];
       let projectHashKey = "";
       this.project.samples
         .sort((a, b) => a.filename.localeCompare(b.filename))
         .forEach((sample: ProjectSample) => {
           projectHashKey += sample.hash + sample.filename;
           sketches[sample.hash] = sample.sketch;
           names[sample.hash] = sample.filename;
+          amrForMetadataCsv.push({ ID: sample.hash, ...convertAmrForCsv(sample.amr!!) });
         }, "");
       const projectHash = Md5.hashStr(projectHashKey);
 
-      return { projectHash, names, sketches, projectId: this.project.id, species: this.project.species };
+      return {
+        projectHash,
+        names,
+        sketches,
+        projectId: this.project.id,
+        species: this.project.species,
+        amrForMetadataCsv
+      };
     },
 
     async downloadZip(type: AnalysisType, cluster: string) {

app/client-v2/src/types/projectTypes.ts

@@ -23,6 +23,17 @@ export interface AMR {
   species: boolean;
 }
 
+export interface AMRForCsv {
+  "Penicillin Resistance": string;
+  "Chloramphenicol Resistance": string;
+  "Erythromycin Resistance": string;
+  "Tetracycline Resistance": string;
+  "Cotrim Resistance": string;
+}
+
+export interface AMRMetadataCsv extends AMRForCsv {
+  ID: string;
+}
 export interface ProjectSample {
   hash: string;
   filename: string;

app/client-v2/src/utils/projectCsvUtils.ts

@@ -1,4 +1,4 @@
-import type { AMR, ProjectSample } from "@/types/projectTypes";
+import type { AMR, AMRForCsv, ProjectSample } from "@/types/projectTypes";
 import { convertProbabilityToWord } from "./amrDisplayUtils";
 
 export const downloadCsv = (samples: ProjectSample[], filename: string) => {
@@ -12,12 +12,12 @@ export const downloadCsv = (samples: ProjectSample[], filename: string) => {
   triggerCsvDownload(csvContent, `${filename}.csv`);
 };
 
-export const convertAmrForCsv = (amr: AMR) => ({
-  Penicillin: convertProbabilityToWord(amr.Penicillin, "Penicillin"),
-  Chloramphenicol: convertProbabilityToWord(amr.Chloramphenicol, "Chloramphenicol"),
-  Erythromycin: convertProbabilityToWord(amr.Erythromycin, "Erythromycin"),
-  Tetracycline: convertProbabilityToWord(amr.Tetracycline, "Tetracycline"),
-  Cotrim: convertProbabilityToWord(amr.Trim_sulfa, "Cotrim")
+export const convertAmrForCsv = (amr: AMR): AMRForCsv => ({
+  "Penicillin Resistance": convertProbabilityToWord(amr.Penicillin, "Penicillin"),
+  "Chloramphenicol Resistance": convertProbabilityToWord(amr.Chloramphenicol, "Chloramphenicol"),
+  "Erythromycin Resistance": convertProbabilityToWord(amr.Erythromycin, "Erythromycin"),
+  "Tetracycline Resistance": convertProbabilityToWord(amr.Tetracycline, "Tetracycline"),
+  "Cotrim Resistance": convertProbabilityToWord(amr.Trim_sulfa, "Cotrim")
 });
 
 export const generateCsvContent = (data: Record<string, string>[]) => {

app/server/src/controllers/indexController.ts

@@ -14,10 +14,10 @@ export default (config) => {
         async runPoppunk(request, response, next) {
             await asyncHandler(next, async () => {
                 const poppunkRequest = request.body as BeebopRunRequest;
-                const {projectHash, projectId, names, sketches, species } = poppunkRequest;
+                const { projectHash, projectId, names, sketches, species, amrForMetadataCsv } = poppunkRequest;
                 const {redis} = request.app.locals;
                 await userStore(redis).saveHashAndSamplesRun(request, projectId, projectHash, names);
-                const apiRequest = { names, projectHash, sketches, species } as PoppunkRequest;
+                const apiRequest = { names, projectHash, sketches, species, amrForMetadataCsv } as PoppunkRequest;
                 await axios
                   .post(`${config.api_url}/poppunk`, apiRequest, {
                     headers: {

app/server/src/types/requestTypes.ts

@@ -5,8 +5,20 @@ export interface PoppunkRequest {
     projectHash: string,
     sketches: Record<string, never>
     species: string,
+    amrForMetadataCsv: AMRMetadataCsv[]
 }
 
+export interface AMRForCsv {
+    "Penicillin Resistance": string;
+    "Chloramphenicol Resistance": string;
+    "Erythromycin Resistance": string;
+    "Tetracycline Resistance": string;
+    "Cotrim Resistance": string;
+}
+
+export interface AMRMetadataCsv extends AMRForCsv {
+    ID: string;
+}
 export interface BeebopRunRequest extends PoppunkRequest {
     projectId: string,
 }

app/server/tests/integration/testSample.ts

@@ -13135,4 +13135,14 @@ export const testSample = (
     },
   },
   names: { fd38a3bc7197390fd3734240a67fb515: "7622_5#78.fa" },
+  amrForMetadataCsv: [
+    {
+      ID: "fd38a3bc7197390fd3734240a67fb515",
+      "Penicillin Resistance": "Highly unlikely",
+      "Chloramphenicol Resistance": "Unsure",
+      "Erythromycin Resistance": "Highly unlikely",
+      "Tetracycline Resistance": "Almost certainly",
+      "Cotrim Resistance": "Highly likely",
+    },
+  ],
 });

scripts/common

@@ -1,9 +1,9 @@
 #!/usr/bin/env bash
-export API_IMAGE="main"
+export API_IMAGE="main" # TODO revert back to main before merge into main
 
 NETWORK=beebop_nw
 VOLUME=beebop-storage
 NAME_REDIS=beebop-redis
 NAME_API=beebop-py-api
 NAME_WORKER=beebop-py-worker
-PORT=5000
+PORT=5000