diff --git a/README.md b/README.md
index 3f6c29130..f0cc7da1b 100644
--- a/README.md
+++ b/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.
diff --git a/app/client-v2/package-lock.json b/app/client-v2/package-lock.json
index aa3455e4e..eb3c0e72d 100644
--- a/app/client-v2/package-lock.json
+++ b/app/client-v2/package-lock.json
@@ -25,7 +25,7 @@
},
"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",
@@ -1190,18 +1190,18 @@
}
},
"node_modules/@playwright/test": {
- "version": "1.42.0",
- "resolved": "https://registry.npmjs.org/@playwright/test/-/test-1.42.0.tgz",
- "integrity": "sha512-2k1HzC28Fs+HiwbJOQDUwrWMttqSLUVdjCqitBOjdCD0svWOMQUVqrXX6iFD7POps6xXAojsX/dGBpKnjZctLA==",
+ "version": "1.49.1",
+ "resolved": "https://registry.npmjs.org/@playwright/test/-/test-1.49.1.tgz",
+ "integrity": "sha512-Ky+BVzPz8pL6PQxHqNRW1k3mIyv933LML7HktS8uik0bUXNCdPhoS/kLihiO1tMf/egaJb4IutXd7UywvXEW+g==",
"dev": true,
"dependencies": {
- "playwright": "1.42.0"
+ "playwright": "1.49.1"
},
"bin": {
"playwright": "cli.js"
},
"engines": {
- "node": ">=16"
+ "node": ">=18"
}
},
"node_modules/@rollup/pluginutils": {
@@ -5675,33 +5675,33 @@
}
},
"node_modules/playwright": {
- "version": "1.42.0",
- "resolved": "https://registry.npmjs.org/playwright/-/playwright-1.42.0.tgz",
- "integrity": "sha512-Ko7YRUgj5xBHbntrgt4EIw/nE//XBHOKVKnBjO1KuZkmkhlbgyggTe5s9hjqQ1LpN+Xg+kHsQyt5Pa0Bw5XpvQ==",
+ "version": "1.49.1",
+ "resolved": "https://registry.npmjs.org/playwright/-/playwright-1.49.1.tgz",
+ "integrity": "sha512-VYL8zLoNTBxVOrJBbDuRgDWa3i+mfQgDTrL8Ah9QXZ7ax4Dsj0MSq5bYgytRnDVVe+njoKnfsYkH3HzqVj5UZA==",
"dev": true,
"dependencies": {
- "playwright-core": "1.42.0"
+ "playwright-core": "1.49.1"
},
"bin": {
"playwright": "cli.js"
},
"engines": {
- "node": ">=16"
+ "node": ">=18"
},
"optionalDependencies": {
"fsevents": "2.3.2"
}
},
"node_modules/playwright-core": {
- "version": "1.42.0",
- "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.42.0.tgz",
- "integrity": "sha512-0HD9y8qEVlcbsAjdpBaFjmaTHf+1FeIddy8VJLeiqwhcNqGCBe4Wp2e8knpqiYbzxtxarxiXyNDw2cG8sCaNMQ==",
+ "version": "1.49.1",
+ "resolved": "https://registry.npmjs.org/playwright-core/-/playwright-core-1.49.1.tgz",
+ "integrity": "sha512-BzmpVcs4kE2CH15rWfzpjzVGhWERJfmnXmniSyKeRZUs9Ws65m+RGIi7mjJK/euCegfn3i7jvqWeWyHe9y3Vgg==",
"dev": true,
"bin": {
"playwright-core": "cli.js"
},
"engines": {
- "node": ">=16"
+ "node": ">=18"
}
},
"node_modules/possible-typed-array-names": {
diff --git a/app/client-v2/package.json b/app/client-v2/package.json
index 2893a95c2..c184976b1 100644
--- a/app/client-v2/package.json
+++ b/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",
diff --git a/app/client-v2/src/__tests__/App.spec.ts b/app/client-v2/src/__tests__/App.spec.ts
index 97c1e9867..abcb381fc 100644
--- a/app/client-v2/src/__tests__/App.spec.ts
+++ b/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(),
diff --git a/app/client-v2/src/__tests__/stores/projectStore.spec.ts b/app/client-v2/src/__tests__/stores/projectStore.spec.ts
index 5a10f1668..da991b487 100644
--- a/app/client-v2/src/__tests__/stores/projectStore.spec.ts
+++ b/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 () => {
diff --git a/app/client-v2/src/__tests__/utils/projectCsvUtils.spec.ts b/app/client-v2/src/__tests__/utils/projectCsvUtils.spec.ts
index f81117a8d..0848b6ed9 100644
--- a/app/client-v2/src/__tests__/utils/projectCsvUtils.spec.ts
+++ b/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"
});
});
});
diff --git a/app/client-v2/src/components/ProjectView/CytoscapeCanvas.vue b/app/client-v2/src/components/ProjectView/CytoscapeCanvas.vue
index 496551934..fead58185 100644
--- a/app/client-v2/src/components/ProjectView/CytoscapeCanvas.vue
+++ b/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"
diff --git a/app/client-v2/src/components/ProjectView/NetworkTab.vue b/app/client-v2/src/components/ProjectView/NetworkTab.vue
index a969c0329..6762eab80 100644
--- a/app/client-v2/src/components/ProjectView/NetworkTab.vue
+++ b/app/client-v2/src/components/ProjectView/NetworkTab.vue
@@ -20,6 +20,10 @@ const { data, error, isFetching } = useFetch(`${apiUrl}/networkGraphs/${store.pr
+ These graphs are pruned versions of the full graphs. To view full graphs, download the zip file and view the
+ .graphml externally.
View in fullscreen, reset layout or use mouse, touchpad or touchscreen gestures on graphs to zoom in and out, or
move nodes around. = {};
const names: Record = {};
+ const amrForMetadataCsv: AMRMetadataCsv[] = [];
let projectHashKey = "";
this.project.samples
.sort((a, b) => a.filename.localeCompare(b.filename))
@@ -311,10 +314,18 @@ export const useProjectStore = defineStore("project", {
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) {
diff --git a/app/client-v2/src/types/projectTypes.ts b/app/client-v2/src/types/projectTypes.ts
index e1574a407..6321915b0 100644
--- a/app/client-v2/src/types/projectTypes.ts
+++ b/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;
diff --git a/app/client-v2/src/utils/projectCsvUtils.ts b/app/client-v2/src/utils/projectCsvUtils.ts
index 47602a014..4925c2072 100644
--- a/app/client-v2/src/utils/projectCsvUtils.ts
+++ b/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, `${filename}.csv`);
};
-export const convertAmrForCsv = (amr: AMR) => ({
- Penicillin: convertProbabilityToWord(amr.Penicillin, "Penicillin"),
- Chloramphenicol: convertProbabilityToWord(amr.Chloramphenicol, "Chloramphenicol"),
- Erythromycin: convertProbabilityToWord(amr.Erythromycin, "Erythromycin"),
- Tetracycline: convertProbabilityToWord(amr.Tetracycline, "Tetracycline"),
- Cotrim: convertProbabilityToWord(amr.Trim_sulfa, "Cotrim")
+export const convertAmrForCsv = (amr: AMR): AMRForCsv => ({
+ "Penicillin Resistance": convertProbabilityToWord(amr.Penicillin, "Penicillin"),
+ "Chloramphenicol Resistance": convertProbabilityToWord(amr.Chloramphenicol, "Chloramphenicol"),
+ "Erythromycin Resistance": convertProbabilityToWord(amr.Erythromycin, "Erythromycin"),
+ "Tetracycline Resistance": convertProbabilityToWord(amr.Tetracycline, "Tetracycline"),
+ "Cotrim Resistance": convertProbabilityToWord(amr.Trim_sulfa, "Cotrim")
});
export const generateCsvContent = (data: Record[]) => {
diff --git a/app/server/src/controllers/indexController.ts b/app/server/src/controllers/indexController.ts
index c826a6d26..9e91f4880 100644
--- a/app/server/src/controllers/indexController.ts
+++ b/app/server/src/controllers/indexController.ts
@@ -14,10 +14,10 @@ export default (config) => {
async runPoppunk(request, response, next) {
await asyncHandler(next, async () => {
const poppunkRequest = request.body as BeebopRunRequest;
- const {projectHash, projectId, names, sketches, species } = poppunkRequest;
+ const { projectHash, projectId, names, sketches, species, amrForMetadataCsv } = poppunkRequest;
const {redis} = request.app.locals;
await userStore(redis).saveHashAndSamplesRun(request, projectId, projectHash, names);
- const apiRequest = { names, projectHash, sketches, species } as PoppunkRequest;
+ const apiRequest = { names, projectHash, sketches, species, amrForMetadataCsv } as PoppunkRequest;
await axios
.post(`${config.api_url}/poppunk`, apiRequest, {
headers: {
diff --git a/app/server/src/types/requestTypes.ts b/app/server/src/types/requestTypes.ts
index c759d7880..be3199594 100644
--- a/app/server/src/types/requestTypes.ts
+++ b/app/server/src/types/requestTypes.ts
@@ -5,8 +5,20 @@ export interface PoppunkRequest {
projectHash: string,
sketches: Record
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,
}
diff --git a/app/server/tests/integration/testSample.ts b/app/server/tests/integration/testSample.ts
index 0b1ffa881..c3e3ecbb8 100644
--- a/app/server/tests/integration/testSample.ts
+++ b/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",
+ },
+ ],
});
diff --git a/scripts/common b/scripts/common
index 403c69324..9004cca03 100755
--- a/scripts/common
+++ b/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
\ No newline at end of file
+PORT=5000