diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml new file mode 100644 index 0000000..70811e4 --- /dev/null +++ b/.github/workflows/docker.yaml @@ -0,0 +1,43 @@ +name: 🚢 Docker + +on: + push: + branches: + - main + pull_request: + +env: + BRANCH_NAME: ${{ github.head_ref || github.ref_name }} + +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + docker: + name: 🚢 Docker + runs-on: ubuntu-latest + steps: + - name: ⬇️ Checkout repo + uses: actions/checkout@v4 + + - name: ⎔ Setup node + uses: actions/setup-node@v4 + + - name: 📥 Install deps + run: npm install --frozen-lockfile + + - name: 🔨 Build image + run: ./scripts/build + + - name: 🔥 Smoke test + run: ./scripts/smoke-test + + - name: Login to Docker Hub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_TOKEN }} + + - name: 🚢 Push image + run: ./scripts/push diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..f288702 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md index 31d0a27..8635510 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ [![🔨 Build](https://github.com/seroanalytics/seroviz/actions/workflows/build.yml/badge.svg)](https://github.com/seroanalytics/seroviz/actions/workflows/build.yml) [![🔎 Test](https://github.com/seroanalytics/seroviz/actions/workflows/test.yml/badge.svg)](https://github.com/seroanalytics/seroviz/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/seroanalytics/seroviz/graph/badge.svg?token=2DH6NUOXRe)](https://codecov.io/gh/seroanalytics/seroviz) +![Docker Image Version](https://img.shields.io/docker/v/seroanalytics/seroviz?logo=docker) +![GitHub License](https://img.shields.io/github/license/seroanalytics/seroviz) Client-side React application for visualising serological data. diff --git a/package.json b/package.json index b504093..d824aa6 100644 --- a/package.json +++ b/package.json @@ -19,6 +19,7 @@ "typescript": "^4.9.5", "web-vitals": "^2.1.4" }, + "license": "GPL-3.0", "scripts": { "start": "react-scripts start", "build": "react-scripts build", diff --git a/scripts/build b/scripts/build index f7045df..0ffdba6 100755 --- a/scripts/build +++ b/scripts/build @@ -7,5 +7,7 @@ HERE=$(dirname $0) npm run build docker build --pull \ - --tag $TAG_SHA \ + --tag $DOCKER_COMMIT_TAG \ . + +docker tag $DOCKER_COMMIT_TAG $DOCKER_BRANCH_TAG diff --git a/scripts/common b/scripts/common index 1d5d463..eeddd12 100644 --- a/scripts/common +++ b/scripts/common @@ -17,5 +17,5 @@ else GIT_BRANCH=$(git symbolic-ref --short HEAD) fi -TAG_SHA="${PACKAGE_ORG}/${PACKAGE_NAME}:${GIT_SHA}" -TAG_BRANCH="${PACKAGE_ORG}/${PACKAGE_NAME}:${GIT_BRANCH}" +DOCKER_COMMIT_TAG="${PACKAGE_ORG}/${PACKAGE_NAME}:${GIT_SHA}" +DOCKER_BRANCH_TAG="${PACKAGE_ORG}/${PACKAGE_NAME}:${GIT_BRANCH}" diff --git a/scripts/push b/scripts/push index 39efa13..7e155d6 100755 --- a/scripts/push +++ b/scripts/push @@ -3,5 +3,7 @@ set -e HERE=$(dirname $0) . $HERE/common -docker tag $TAG_SHA $TAG_BRANCH -docker push $TAG_BRANCH +if [[ "$GIT_BRANCH" == "main" ]]; then + docker push $DOCKER_BRANCH_TAG + docker push $DOCKER_COMMIT_TAG +fi diff --git a/scripts/smoke-test b/scripts/smoke-test new file mode 100755 index 0000000..075ba37 --- /dev/null +++ b/scripts/smoke-test @@ -0,0 +1,35 @@ +#!/usr/bin/env bash + +HERE=$(realpath "$(dirname $0)") +. $HERE/common + +wait_for() +{ + echo "waiting up to $TIMEOUT seconds for app" + start_ts=$(date +%s) + for i in $(seq $TIMEOUT); do + result="$(curl --write-out %{http_code} --silent --output /dev/null --insecure https://localhost 2>/dev/null)" + if [[ $result -eq "200" ]]; then + end_ts=$(date +%s) + echo "App available after $((end_ts - start_ts)) seconds" + exit 0 + fi + sleep 1 + echo "...still waiting" + done + return $result +} + +$HERE/run + +# The variable expansion below is 60s by default, or the argument provided +# to this script +TIMEOUT="${1:-60}" +sleep 2 # Wait for SSL to be ready +wait_for +RESULT=$? +if [[ $RESULT -ne 200 ]]; then + echo "App did not become available in time" + exit 1 +fi +exit 0 diff --git a/src/RootContext.ts b/src/RootContext.ts index ba4a1ab..5914a7e 100644 --- a/src/RootContext.ts +++ b/src/RootContext.ts @@ -20,7 +20,8 @@ export enum ActionType { DATASET_METADATA_FETCHED = "DATASET_METADATA_FETCHED", DATASET_SELECTED = "DATASET_SELECTED", SELECT_COVARIATE = "SELECT_COVARIATE", - UNSELECT_COVARIATE = "UNSELECT_COVARIATE" + UNSELECT_COVARIATE = "UNSELECT_COVARIATE", + SELECT_SCALE = "SELECT_SCALE" } export interface RootAction { diff --git a/src/components/ChooseScale.tsx b/src/components/ChooseScale.tsx new file mode 100644 index 0000000..a69ba32 --- /dev/null +++ b/src/components/ChooseScale.tsx @@ -0,0 +1,26 @@ +import React, {useContext} from "react"; +import {ActionType, RootContext, RootDispatchContext} from "../RootContext"; +import Form from "react-bootstrap/Form"; + +export default function ChooseScale() { + + const state = useContext(RootContext); + const dispatch = useContext(RootDispatchContext); + + const onSelect = (event: any) => { + dispatch({ + type: ActionType.SELECT_SCALE, + payload: event.target.value + }); + } + + return + Transform data by + + + + + + +} diff --git a/src/components/LinePlot.tsx b/src/components/LinePlot.tsx index ee33b3a..79edb60 100644 --- a/src/components/LinePlot.tsx +++ b/src/components/LinePlot.tsx @@ -42,16 +42,20 @@ export default function LinePlot({ const facetDefinition = facetDefinitions.join("+") + const covariateSettings = state.datasetSettings[state.selectedDataset].covariateSettings; + const scale = state.datasetSettings[state.selectedDataset].scale; useEffect(() => { - dataService(state.language, dispatch) - .getDataSeries(state.selectedDataset, - biomarker, facetDefinition, state.datasetSettings[state.selectedDataset].covariateSettings) - .then(data => { - if (data && data.data) { - setSeries(data.data) - } - }); - }, [state.language, dispatch, state.selectedDataset, biomarker, facetDefinition, state.datasetSettings]); + const fetchData = async () => { + const result = await dataService(state.language, dispatch) + .getDataSeries(state.selectedDataset, + biomarker, facetDefinition, covariateSettings, scale); + + if (result && result.data) { + setSeries(result.data) + } + } + fetchData(); + }, [state.language, dispatch, state.selectedDataset, biomarker, facetDefinition, covariateSettings, scale]); let series: any[] = []; diff --git a/src/components/SideBar.tsx b/src/components/SideBar.tsx index ceb1290..d0b362f 100644 --- a/src/components/SideBar.tsx +++ b/src/components/SideBar.tsx @@ -5,6 +5,7 @@ import {ActionType, RootContext, RootDispatchContext} from "../RootContext"; import CovariateOptions from "./CovariateOptions"; import SelectedCovariate from "./SelectedCovariate"; import ChooseDataset from "./ChooseDataset"; +import ChooseScale from "./ChooseScale"; export default function SideBar() { @@ -37,6 +38,7 @@ export default function SideBar() { className={"text-secondary"}>{state.datasetMetadata?.biomarkers.join(", ")} + {availableCovariates.length > 0 && Disaggregate by diff --git a/src/reducers/datasetReducer.ts b/src/reducers/datasetReducer.ts index 3245efe..d72708e 100644 --- a/src/reducers/datasetReducer.ts +++ b/src/reducers/datasetReducer.ts @@ -11,6 +11,8 @@ export const datasetReducer = (state: AppState, action: RootAction): AppState => return selectCovariate(state, action) case ActionType.UNSELECT_COVARIATE: return unselectCovariate(state, action) + case ActionType.SELECT_SCALE: + return selectScale(state, action) default: return state } @@ -34,7 +36,7 @@ const selectCovariate = (state: AppState, action: RootAction): AppState => { const newState = {...state} const settings = newState.datasetSettings[state.selectedDataset].covariateSettings if (settings.indexOf(action.payload) === -1) { - settings.push(action.payload) + newState.datasetSettings[state.selectedDataset].covariateSettings = [...settings, action.payload] } return newState } @@ -45,3 +47,9 @@ const unselectCovariate = (state: AppState, action: RootAction) => { newState.datasetSettings[state.selectedDataset].covariateSettings = settings.filter(v => v.name !== action.payload) return newState } + +const selectScale = (state: AppState, action: RootAction): AppState => { + const newState = {...state} + newState.datasetSettings[state.selectedDataset].scale = action.payload + return newState +} diff --git a/src/services/dataService.ts b/src/services/dataService.ts index c453804..c34c2bb 100644 --- a/src/services/dataService.ts +++ b/src/services/dataService.ts @@ -50,10 +50,11 @@ export class DataService { async getDataSeries(selectedDataset: string, biomarker: string, facetDefinition: string, - selectedCovariates: CovariateSettings[]) { + covariateSettings: CovariateSettings[], + scale: "log" | "natural" | "log2") { - const traces = selectedCovariates + const traces = covariateSettings .filter(v => v.display === "trace") .map(v => v.name).join("+") @@ -63,9 +64,11 @@ export class DataService { } if (traces.length > 0) { - queryString += `disaggregate=${encodeURIComponent(traces)}` + queryString += `disaggregate=${encodeURIComponent(traces)}&` } + queryString += `scale=${scale}` + return await this._api .ignoreSuccess() .withError(ActionType.ERROR_ADDED) diff --git a/test/components/ChooseDataset.test.tsx b/test/components/ChooseDataset.test.tsx index 3d4cb13..343cb9c 100644 --- a/test/components/ChooseDataset.test.tsx +++ b/test/components/ChooseDataset.test.tsx @@ -6,7 +6,6 @@ import { } from "../../src/RootContext"; import {render, screen, waitFor} from "@testing-library/react"; import {mockAppState, mockAxios, mockSuccess} from "../mocks"; -import {act} from "react"; import {userEvent} from "@testing-library/user-event"; describe("", () => { @@ -22,11 +21,11 @@ describe("", () => { let state = mockAppState(); const dispatch = jest.fn(); - act(() => render( + render( - )); + ); await waitFor(() => expect(dispatch.mock.calls.length).toBe(1)); @@ -45,11 +44,11 @@ describe("", () => { }); const dispatch = jest.fn(); - act(() => render( + render( - )); + ); expect(screen.getAllByLabelText("Choose dataset").length).toBe(1); const select = screen.getByRole("combobox") as HTMLSelectElement; @@ -67,11 +66,11 @@ describe("", () => { }); const dispatch = jest.fn(); - act(() => render( + render( - )); + ); expect(screen.queryByLabelText("Choose dataset")).toBe(null); expect(screen.queryByText("Go")).toBe(null); @@ -87,11 +86,11 @@ describe("", () => { const dispatch = jest.fn(); const user = userEvent.setup(); - act(() => render( + render( - )); + ); const select = screen.getByRole("combobox") as HTMLSelectElement; @@ -115,11 +114,11 @@ describe("", () => { const dispatch = jest.fn(); const user = userEvent.setup(); - act(() => render( + render( - )); + ); expect(screen.getByTestId("advanced-options")).toHaveClass("d-none"); const toggle = screen.getByText("Advanced options"); @@ -143,11 +142,11 @@ describe("", () => { const dispatch = jest.fn(); const user = userEvent.setup(); - act(() => render( + render( - )); + ); const fileInput = screen.getByLabelText("Upload new dataset"); const testFile = new File(['hello'], 'hello.csv', {type: 'text/csv'}); diff --git a/test/components/ChooseScale.test.tsx b/test/components/ChooseScale.test.tsx new file mode 100644 index 0000000..35ec0dd --- /dev/null +++ b/test/components/ChooseScale.test.tsx @@ -0,0 +1,43 @@ +import React from "react"; +import {render, screen} from "@testing-library/react"; +import { + mockAppState, + mockDatasetSettings +} from "../mocks"; +import { + RootDispatchContext, + RootContext, + ActionType +} from "../../src/RootContext"; +import ChooseScale from "../../src/components/ChooseScale"; +import {userEvent} from "@testing-library/user-event"; + +describe("", () => { + + test("can change scale", async () => { + const dispatch = jest.fn(); + const state = mockAppState({ + selectedDataset: "d1", + datasetSettings: { + "d1": mockDatasetSettings() + } + }); + render( + + + + + ); + + const select = screen.getByRole("combobox") as HTMLSelectElement; + expect(select.value).toBe("natural"); + expect(select.item(1)!!.value).toBe("log"); + expect(select.item(2)!!.value).toBe("log2"); + await userEvent.selectOptions(select, "log"); + + expect(dispatch.mock.calls[0][0]).toEqual({ + type: ActionType.SELECT_SCALE, + payload: "log" + }); + }); +}); diff --git a/test/components/LinePlot.test.tsx b/test/components/LinePlot.test.tsx new file mode 100644 index 0000000..285136f --- /dev/null +++ b/test/components/LinePlot.test.tsx @@ -0,0 +1,186 @@ +import { + mockAppState, + mockAxios, mockDatasetMetadata, + mockDatasetSettings, + mockSuccess +} from "../mocks"; +import {render, waitFor} from "@testing-library/react"; +import { + RootContext, + RootDispatchContext +} from "../../src/RootContext"; +import React from "react"; +import LinePlot from "../../src/components/LinePlot"; +import {DataSeries} from "../../src/generated"; +import Plot from "react-plotly.js"; +import Mock = jest.Mock; + +jest.mock("react-plotly.js", () => jest.fn()); + +describe("", () => { + + beforeEach(() => { + mockAxios.reset(); + }); + + test("requests data for given biomarker", async () => { + mockAxios.onGet(`/dataset/d1/trace/ab/?scale=natural`) + .reply(200, mockSuccess([{ + name: "all", + model: { + x: [1.1, 2.2], + y: [3.3, 4.4] + }, + raw: { + x: [1, 2], + y: [3, 4] + } + }])); + + const dispatch = jest.fn(); + const state = mockAppState({ + selectedDataset: "d1", + datasetMetadata: mockDatasetMetadata(), + datasetSettings: { + "d1": mockDatasetSettings() + } + }); + render( + + + + + ); + + await waitFor(() => expect(mockAxios.history.get.length) + .toBe(1)); + + await waitFor(() => expect((Plot as Mock)) + .toBeCalledTimes(2)); + + const plot = Plot as Mock + expect(plot.mock.calls[1][0]).toEqual({ + data: [ + { + legendgroup: "all", + line: { + shape: "spline", + width: 2 + }, + marker: { + color: "#1f77b4" + }, + mode: "line", + name: "all", + showlegend: false, + type: "scatter", + x: [1.1, 2.2], + y: [3.3, 4.4] + }, + { + legendgroup: "all", + marker: { + color: "#1f77b4", + opacity: 0.5 + }, + mode: "markers", + name: "all", + showlegend: false, + type: "scatter", + x: [1, 2], + y: [3, 4] + }], + layout: { + legend: { + orientation: "v", + xanchor: "center" + }, + paper_bgcolor: "rgba(255,255,255, 0)", + title: "ab ", + xaxis: { + title: { + text: "day" + } + } + }, + style: { + height: "500", + minWidth: "400px", + width: "100%" + }, + useResizeHandler: true + }) + }); + + test("requests data for given facet variables", async () => { + mockAxios.onGet(`/dataset/d1/trace/ab/?filter=age%3A0%2Bsex%3AF&scale=natural`) + .reply(200, mockSuccess([{ + name: "all", + model: { + x: [1.1, 2.2], + y: [3.3, 4.4] + }, + raw: { + x: [1, 2], + y: [3, 4] + } + }])); + + const dispatch = jest.fn(); + const state = mockAppState({ + selectedDataset: "d1", + datasetMetadata: mockDatasetMetadata(), + datasetSettings: { + "d1": mockDatasetSettings() + } + }); + render( + + + + + ); + + await waitFor(() => expect(mockAxios.history.get.length) + .toBe(1)); + + await waitFor(() => expect((Plot as Mock)) + .toBeCalledTimes(2)); + + const plot = Plot as Mock + expect(plot.mock.calls[1][0].data).toEqual([ + { + legendgroup: "all", + line: { + shape: "spline", + width: 2 + }, + marker: { + color: "#1f77b4" + }, + mode: "line", + name: "all", + showlegend: false, + type: "scatter", + x: [1.1, 2.2], + y: [3.3, 4.4] + }, + { + legendgroup: "all", + marker: { + color: "#1f77b4", + opacity: 0.5 + }, + mode: "markers", + name: "all", + showlegend: false, + type: "scatter", + x: [1, 2], + y: [3, 4] + }]) + }); +}); diff --git a/test/components/SideBar.test.tsx b/test/components/SideBar.test.tsx index b80320b..d4c5a76 100644 --- a/test/components/SideBar.test.tsx +++ b/test/components/SideBar.test.tsx @@ -89,7 +89,7 @@ describe("", () => { ); - const selectDataset = await screen.findByRole("combobox") as HTMLSelectElement; + const selectDataset = screen.getAllByRole("combobox")[0] as HTMLSelectElement; await userEvent.selectOptions(selectDataset, "d2"); expect(dispatch.mock.calls[0][0]).toEqual({ diff --git a/test/integration/dataService.itest.ts b/test/integration/dataService.itest.ts index af90a81..9e357c3 100644 --- a/test/integration/dataService.itest.ts +++ b/test/integration/dataService.itest.ts @@ -59,7 +59,7 @@ describe("DataService", () => { test("it can fetch dataset metadata", async () => { const dispatch = jest.fn(); const sut = dataService("en", dispatch); - const res = await sut.getDataSeries("testpopulation", "ab_units", "", []) as GenericResponse; + const res = await sut.getDataSeries("testpopulation", "ab_units", "", [], "natural") as GenericResponse; expect(res.data!![0].name).toBe("all"); expect(res.data!![0].raw.x).toEqual([1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4]); expect(dispatch.mock.calls.length).toBe(0); @@ -68,7 +68,7 @@ describe("DataService", () => { test("it can fetch dataset metadata with facet definition", async () => { const dispatch = jest.fn(); const sut = dataService("en", dispatch); - const res = await sut.getDataSeries("testpopulation", "ab_units", "sex:F", []) as GenericResponse; + const res = await sut.getDataSeries("testpopulation", "ab_units", "sex:F", [], "natural") as GenericResponse; expect(res.data!!.length).toBe(1); expect(res.data!![0].name).toBe("sex:F"); @@ -83,7 +83,7 @@ describe("DataService", () => { name: "age", display: "trace", levels: ["0-5"] - }]) as GenericResponse; + }], "natural") as GenericResponse; expect(res.data!!.length).toBe(2); expect(res.data!![0].name).toBe("0-5"); diff --git a/test/rootReducer.test.ts b/test/rootReducer.test.ts index d00ec74..d4880a0 100644 --- a/test/rootReducer.test.ts +++ b/test/rootReducer.test.ts @@ -101,4 +101,18 @@ describe("rootReducer", () => { {type: ActionType.UNSELECT_COVARIATE, payload: "c1"}); expect(newState.datasetSettings["d1"].covariateSettings.length).toBe(0); }); + + + it("should select scale on SELECT_SCALE", () => { + const state = mockAppState({ + selectedDataset: "d1", + datasetSettings: { + "d1": mockDatasetSettings() + } + }); + expect(state.datasetSettings["d1"].scale).toBe("natural"); + const newState = rootReducer(state, + {type: ActionType.SELECT_SCALE, payload: "log"}); + expect(newState.datasetSettings["d1"].scale).toBe("log"); + }); });