Test PACS Q/R

jennydaman · PintoGideon · commit a7b1ea4789f0 · 2024-08-23T12:04:00.000-04:00
diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "miniChRIS"]
 	path = testing/miniChRIS
 	url = https://github.com/FNNDSC/miniChRIS-docker.git
+[submodule "testing/sample_dicoms"]
+	path = testing/sample_dicoms
+	url = https://github.com/FNNDSC/sample_dicom_downloader.git
diff --git a/README.md b/README.md
@@ -22,18 +22,11 @@ npm run dev:public
 
 ## Development
 
-We support development on **Linux** only.
-
-#### 0. Have the [_ChRIS_ backend](https://github.com/FNNDSC/ChRIS_ultron_backEnd) running (Optional)
-
-For local development, use [Docker Compose](https://docs.docker.com/compose/) and [miniChRIS-docker](https://github.com/FNNDSC/miniChRIS-docker). Open a terminal and run
-
-```shell
-git clone https://github.com/FNNDSC/miniChRIS-docker.git
-cd miniChRIS-docker
-./minichris.sh
-```
+There are two modes of development:
 
+- "local": runs the _ChRIS_ backend locally. Requires Docker, and uses more disk space + slower startup time.
+- "public": use the global, public testing server. This is the easier option, especially for non-Linux OS.
+ 
 <details>
 <summary>
   <strong>
@@ -64,51 +57,28 @@ $ ./unmake.sh
 If your backend is accessible from a host other than localhost, e.g. you are using a cloud or remote development
 server, run `cp .env .env.development.local` then edit `.env.development.local` with your backend API URL.
 
-#### 1. Install Dependencies
+### 1. Dependencies
 
 You need Node version 20 or 21.
 
 ```shell
 git clone https://github.com/FNNDSC/ChRIS_ui.git
 cd ChRIS_ui
-npm i
-```
-
-<details>
-<summary>
-<strong>
-Alternatively, using Docker (click to expand)
-</strong>
-</summary>
-
-These instructions are no longer supported.
-
-Open a new terminal on your system and follow these steps:
-
-```bash
-git clone https://github.com/FNNDSC/ChRIS_ui.git
-cd ChRIS_ui
-docker build -t localhost/fnndsc/chris_ui:dev -f Dockerfile_dev .
-docker run --rm -it -v $PWD:/home/localuser -p 3000:3000 -u $(id -u):$(id -g) --userns=host --name chris_ui localhost/fnndsc/chris_ui:dev
+npm ci
 ```
 
-Open [http://localhost:3000](http://localhost:3000) to view it in the browser.
-
-</details>
-
-
-#### 2. Run the development server
+### 2. Run the development server
 
-If you are running and have configured a backend in step 0, run
+Either using the "public" server:
 
 ```shell
-npm run dev
+npm run dev:public
 ```
 
-Otherwise, you can use our public testing backend instance. Run
+Or, start a local backend and run the "local" server:
 
 ```shell
-npm run dev:public
+npm run dev:local
 ```
 
 ## Build for production
@@ -142,16 +112,15 @@ npm test
 
 ### End-to-End Tests
 
-> [!IMPORTANT]
-> End-to-end (E2E) tests are configured to run against our public testing backend instance, which is prepopulated with data.
-
-E2E tests are located under `tests/`.
+End-to-end tests are located under `tests/`.
 
-Playwright requires some system dependencies. On first run, you will be prompted to install these dependencies.
-With Playwright installed, run
+The end-to-end testing framework, Playwright, requires some system dependencies.
+On first run, you will be prompted to install these dependencies.
 
 ```shell
-npm run test:e2e
+npm run test:e2e  # run tests using "public" backend
+
+npm run test:e2e:local  # run tests using "local" backend
 ```
 
 For more information, consult the wiki:
diff --git a/package.json b/package.json
@@ -5,26 +5,35 @@
   "scripts": {
     "start": "sirv dist --host --port ${PORT:=8080} --single --etag --quiet",
     "__start": "# npm start command is used by s2i in OpenShift as the deployment command",
-    "dev": "npm run minichris:up && vite",
+    "dev": "npm run dev:local",
+    "dev:local": "npm run test:prepare && vite",
     "dev:public": "vite -c testing/publicCUBE/vite.config.ts",
     "build": "vite build",
     "test": "vitest",
+    "__test:prepare:comment": "# test:prepare runs CUBE locally and loads sample DICOM data into the PACS.",
+    "test:prepare": "npm run minichris:up && npm run get-dicoms && npm run minichris:wipe",
     "test:e2e": "playwright test -c playwright.config.ts",
+    "test:e2e:local": "npm run test:prepare && env TEST_LOCAL=yes npm run test:e2e",
     "test:report": "nyc report --reporter=text",
     "test:lcov": "nyc report --reporter=lcov",
     "test:ui": "playwright test -c playwright.config.ts --ui",
-    "test:codegen": "playwright codegen http://localhost:25173",
-    "test:codegen:mobile": "playwright codegen --device 'Pixel 5' http://localhost:25173",
-    "minichris:__comment": "The minichris:* commands are for running a ChRIS backend locally",
+    "test:ui:local": "npm run test:prepare && env TEST_LOCAL=yes npm run test:ui",
+    "test:codegen": "playwright codegen $(npm run -s get-running-url)",
+    "test:codegen:mobile": "playwright codegen --device 'Pixel 5' $(npm run -s get-running-url)",
+    "__minichris:comment": "# The minichris:* commands are for running a ChRIS backend locally",
     "minichris:up": "cd testing/miniChRIS && docker compose --profile pacs up -d && cd - && npm run chrisomatic",
     "minichris:down": "cd testing/miniChRIS && ./unmake.sh",
     "minichris:wipe": "./testing/miniChRIS/scripts/clear_pacsfiles.sh",
     "chrisomatic": "testing/chrisomatic.sh",
+    "get-dicoms": "./testing/get_dicoms.sh",
+    "list-mrns": "./testing/miniChRIS/scripts/list_mrns.sh",
     "lint": "biome lint .",
     "fix": "biome check --apply .",
     "fix:unsafe": "biome check --apply-unsafe .",
     "fmt": "biome format --write .",
     "preview": "vite preview",
+    "__helper_functions": "",
+    "get-running-url": "./testing/get_running_url.sh",
     "print-version": "./print_version.sh"
   },
   "dependencies": {
diff --git a/playwright.config.ts b/playwright.config.ts
@@ -1,3 +1,5 @@
+// See https://github.com/FNNDSC/ChRIS_ui/wiki/E2E-Testing-with-Playwright#local-tests
+
 import { defineConfig, devices, PlaywrightTestConfig } from "@playwright/test";
 
 const SAFARI_BROWSERS: PlaywrightTestConfig["projects"] = [];
diff --git a/testing/get_dicoms.sh b/testing/get_dicoms.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+HERE="$(dirname -- "$0")"
+
+set -ex
+
+cd "$HERE/sample_dicoms"
+make neuro
+cd -
+
+exec "$HERE/miniChRIS/scripts/upload2orthanc.sh" "$HERE/sample_dicoms/data"
diff --git a/testing/get_running_url.sh b/testing/get_running_url.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+URLS=(http://localhost:5173 http://localhost:25173)
+
+for url in "${URLS[@]}"; do
+  curl -o /dev/null "$url" > /dev/null 2>&1
+  if [ "$?" = "0" ]; then
+    echo "$url"
+    exit 0
+  fi
+done
+
+echo "UI is not running. Please run `npm run dev`"
+exit 1
diff --git a/testing/miniChRIS b/testing/miniChRIS
@@ -1 +1 @@
-Subproject commit bbf23ab1fbbb19296512bb35861e8272357099de
+Subproject commit 21ae7e6c0c2bc7f83390fb0a879e183deac0377d
diff --git a/testing/sample_dicoms b/testing/sample_dicoms
@@ -0,0 +1 @@
+Subproject commit 29cb5b7d207ede27aa8715c08cc17df6266b75e0
diff --git a/tests/NiivueDatasetViewer/firstPageLoads.spec.ts b/tests/NiivueDatasetViewer/firstPageLoads.spec.ts
@@ -27,7 +27,7 @@ async function gotoVolumeView({
 }) {
   test.skip(isFirefoxInGitHubActions(browserName), "GitHub Actions bug.");
   test.skip(
-    baseURL?.includes("localhost") || false,
+    baseURL?.includes("localhost:5173") || false,
     "Depends on global test server data.",
   );
   await page.goto("/");
diff --git a/tests/createAccount.spec.ts b/tests/createAccount.spec.ts
@@ -3,9 +3,7 @@ import createAccountHelper from "./helpers/createAccount.ts";
 import { faker } from "@faker-js/faker";
 
 test("Can create new user accounts", async ({ page, baseURL }) => {
-  if (!baseURL?.includes("localhost")) {
-    test.slow();
-  }
+  test.slow();
 
   const username = faker.internet.userName();
   const email = faker.internet.email();
diff --git a/tests/pacsQueryAndRetrieve.spec.ts b/tests/pacsQueryAndRetrieve.spec.ts
@@ -0,0 +1,75 @@
+/*
+ * Note: these tests are brittle because they depend on internal Patternfly v4
+ * class names. This is due to the lack of accessibility on the PACS pull page.
+ */
+
+import { test, expect } from "./fixtures/loggedIn.ts";
+
+test("Retrieve a single study and create a feed", async ({ page, baseURL }) => {
+  test.skip(
+    baseURL?.includes("localhost:25173") || false,
+    "Testing PACS Q/R cannot be done on the global test server.",
+  );
+
+  await page.goto("/pacs");
+
+  // When the page is done loading, the name of a PACS server should show up
+  // and it should be automatically selected.
+  await expect(page.getByText("MINICHRISORTHANC")).toBeVisible();
+
+  // Search for a patient by MRN
+  await page.getByLabel("Query").fill("1449c1d");
+  await page.getByLabel("Query").press("Enter");
+
+  await expect(
+    page.getByText("Patient Birth Date: July 1, 2009"),
+  ).toBeVisible();
+
+  // Expand the card and check study metadata
+  await page
+    .locator(".pf-v5-c-card__header-toggle > .pf-v5-c-button")
+    .first()
+    .click();
+  await expect(page.getByText("1 series, March 8, 2013")).toBeVisible();
+  await expect(page.getByText("98edede8b2")).toBeVisible(); // AccessionNumber
+
+  // Click the "Pull Study" button
+  await page.locator("div:nth-child(2) > .pf-v5-c-button").click();
+
+  // Assert that the study was pulled successfully
+  await expect(
+    page.locator(".pf-v5-c-progress__status > .pf-v5-c-progress__measure"),
+  ).toBeVisible();
+  await expect(
+    page.locator(".pf-v5-c-progress__status > .pf-v5-c-progress__measure"),
+  ).toHaveText("100%", { timeout: 20_000 });
+
+  // Click the "Create feed" button
+  await page
+    .locator(".flex-series-item > div > div > .pf-v5-c-button")
+    .first()
+    .click();
+
+  // Assert that the "Create a New Analysis" wizard appeared
+  await expect(
+    page.getByRole("heading", { name: "Create a New Analysis" }),
+  ).toBeVisible();
+  await page
+    .getByPlaceholder("e.g. Tractography Study")
+    .fill("Analyze patient 98edede8b2 from Playwright test");
+  await page.getByRole("button", { name: "Next", exact: true }).click();
+  // "Choose files" screen
+  await expect(page.getByText("Creating analysis from 1 item")).toBeVisible();
+  await page.getByRole("button", { name: "Next", exact: true }).click();
+  // "Choose pipeline" screen
+  await expect(page.getByRole("textbox", { name: "search" })).toBeVisible();
+  await page.getByRole("button", { name: "Next", exact: true }).click();
+  // "Review" screen
+
+  await page.getByRole("button", { name: "Create Analysis" }).click();
+  // wait for the wizard to close itself after feed is created
+  await expect(page.locator(".pf-v5-c-wizard")).not.toBeVisible();
+  await expect(
+    page.getByText("Analyze patient 98edede8b2 from Playwright test"),
+  ).toBeVisible();
+});

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+// See https://github.com/FNNDSC/ChRIS_ui/wiki/E2E-Testing-with-Playwright#local-tests`
	`2`	`+`
`1`	`3`	`import { defineConfig, devices, PlaywrightTestConfig } from "@playwright/test";`
`2`	`4`
`3`	`5`	`const SAFARI_BROWSERS: PlaywrightTestConfig["projects"] = [];`