Separated fractal-data from vizarr

zonia3000 · zonia3000 · commit dbbd5b0f77b0 · 2025-06-20T12:03:03.000+02:00
diff --git a/.env.example b/.env.example
@@ -1,7 +1,6 @@
 PORT=3000
 BIND_ADDRESS=0.0.0.0
 FRACTAL_SERVER_URL=http://localhost:8000
-VIZARR_STATIC_FILES_PATH=/path/to/vizarr/dist
-BASE_PATH=/vizarr
+BASE_PATH=/data
 AUTHORIZATION_SCHEME=fractal-server
 CACHE_EXPIRATION_TIME=60
diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml
@@ -22,7 +22,7 @@ jobs:
         run: echo ${{ secrets.GITHUB_TOKEN }} | docker login ghcr.io -u ${{ github.actor }} --password-stdin
 
       - name: Build the Docker image
-        run:  docker build . --tag ghcr.io/fractal-analytics-platform/fractal-vizarr-viewer:${{ github.event_name == 'workflow_dispatch' && inputs.tag || 'dev' }}
+        run:  docker build . --tag ghcr.io/fractal-analytics-platform/fractal-data:${{ github.event_name == 'workflow_dispatch' && inputs.tag || 'dev' }}
 
       - name: Push the Docker Image
-        run: docker push ghcr.io/fractal-analytics-platform/fractal-vizarr-viewer:${{ github.event_name == 'workflow_dispatch' && inputs.tag || 'dev' }}
+        run: docker push ghcr.io/fractal-analytics-platform/fractal-data:${{ github.event_name == 'workflow_dispatch' && inputs.tag || 'dev' }}
diff --git a/.github/workflows/github_release.yaml b/.github/workflows/github_release.yaml
@@ -78,12 +78,12 @@ jobs:
         run: npm pack
 
       - name: Extract the package
-        run: tar -xzf fractal-vizarr-viewer-*.tgz
+        run: tar -xzf fractal-data-*.tgz
 
       - name: Repack the package removing parent folder
-        run: tar -C package -czf node-${{ matrix.node-version }}-fractal-vizarr-viewer-${{ github.ref_name }}.tar.gz dist package.json node_modules LICENSE
+        run: tar -C package -czf node-${{ matrix.node-version }}-fractal-data-${{ github.ref_name }}.tar.gz dist package.json node_modules LICENSE
 
       - name: Release
         uses: softprops/action-gh-release@v2.2.1
         with:
-          files: node-${{ matrix.node-version }}-fractal-vizarr-viewer-${{ github.ref_name }}.tar.gz
+          files: node-${{ matrix.node-version }}-fractal-data-${{ github.ref_name }}.tar.gz
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,7 @@ Note: Numbers like (#123) point to closed Pull Requests on the fractal-vizarr-vi
 
 # Unreleased
 
+* Separated fractal-data from vizarr, renamed repository to `fractal-data` (\#64);
 * Added `BIND_ADDRESS` environment variable, defaulting to `0.0.0.0` for IPv4 binding (\#64);
 
 # 0.3.2
diff --git a/Dockerfile b/Dockerfile
@@ -1,17 +1,8 @@
 FROM node:20
 
-WORKDIR /
+RUN mkdir /fractal-data
 
-RUN git clone https://github.com/hms-dbmi/vizarr.git
-WORKDIR /vizarr
-
-RUN git checkout eb2b77fed92a08c78c5770144bc7ccf19e9c7658
-RUN npx -y pnpm install
-RUN npx pnpm run build
-
-RUN mkdir /fractal-vizarr-viewer
-
-WORKDIR /fractal-vizarr-viewer
+WORKDIR /fractal-data
 
 ADD src src
 ADD package* .
@@ -20,6 +11,4 @@ ADD tsconfig.json .
 RUN npm install
 RUN npm run build
 
-ENV VIZARR_STATIC_FILES_PATH=/vizarr/dist
-
-CMD ["node", "/fractal-vizarr-viewer/dist/app.js"]
+CMD ["node", "/fractal-data/dist/app.js"]
diff --git a/README.md b/README.md
diff --git a/fractal-data-cookie-flow.png b/fractal-data-cookie-flow.png
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,5 +1,5 @@
 {
-  "name": "fractal-vizarr-viewer",
+  "name": "fractal-data",
   "version": "0.3.2",
   "description": "",
   "main": "dist/app.js",
diff --git a/src/app.ts b/src/app.ts
@@ -20,7 +20,7 @@ app.use((req, _, next) => {
 const authorizer = getAuthorizer();
 
 // Endpoint serving zarr files
-app.use(`${config.basePath}data`, async function (req, res) {
+app.use(`${config.basePath}files`, async function (req, res) {
   await serveZarrData(authorizer, req, res);
 });
 
@@ -29,13 +29,10 @@ app.use(`${config.basePath}alive`, async function (req, res) {
   await aliveEndpoint(req, res);
 });
 
-// Serving Vizarr static files
-app.use(`${config.basePath}`, express.static(config.vizarrStaticFilesPath));
-
 // Start server
 const server = app.listen(config.port, config.bindAddress, () => {
   logger.info(
-    "fractal-vizarr-viewer is listening at http://localhost:%d%s",
+    "fractal-data is listening at http://localhost:%d%s",
     config.port,
     config.basePath
   );
diff --git a/src/config.ts b/src/config.ts
@@ -26,7 +26,6 @@ function loadConfig(): Config {
   const port = process.env.PORT ? parseInt(process.env.PORT) : 3000;
   const bindAddress = process.env.BIND_ADDRESS || "0.0.0.0";
   const fractalServerUrl = getRequiredEnv("FRACTAL_SERVER_URL");
-  const vizarrStaticFilesPath = getRequiredEnv("VIZARR_STATIC_FILES_PATH");
 
   const validAuthorizationSchemes = [
     "fractal-server",
@@ -55,7 +54,7 @@ function loadConfig(): Config {
     ? parseInt(process.env.CACHE_EXPIRATION_TIME)
     : 60;
 
-  let basePath = process.env.BASE_PATH || "/vizarr";
+  let basePath = process.env.BASE_PATH || "/data";
   if (!basePath.endsWith("/")) {
     basePath += "/";
   }
@@ -64,7 +63,6 @@ function loadConfig(): Config {
   logger.debug("BIND_ADDRESS: %s", bindAddress);
   logger.debug("FRACTAL_SERVER_URL: %s", fractalServerUrl);
   logger.debug("BASE_PATH: %s", basePath);
-  logger.debug("VIZARR_STATIC_FILES_PATH: %s", vizarrStaticFilesPath);
   logger.debug("AUTHORIZATION_SCHEME: %s", authorizationScheme);
   logger.debug("CACHE_EXPIRATION_TIME: %d", cacheExpirationTime);
 
@@ -73,7 +71,6 @@ function loadConfig(): Config {
     bindAddress,
     fractalServerUrl,
     basePath,
-    vizarrStaticFilesPath,
     authorizationScheme: authorizationScheme as AuthorizationScheme,
     cacheExpirationTime,
     testingUsername,
diff --git a/src/types.ts b/src/types.ts
@@ -8,7 +8,6 @@ export type Config = {
   bindAddress: string;
   fractalServerUrl: string;
   basePath: string;
-  vizarrStaticFilesPath: string;
   authorizationScheme: AuthorizationScheme;
   cacheExpirationTime: number;
   testingUsername: string | null;
diff --git a/test/app.spec.ts b/test/app.spec.ts
@@ -17,8 +17,8 @@ vi.mock("../src/config.js", () => {
 import { serveZarrData } from "../src/data";
 import { Authorizer } from "../src/authorizer";
 
-describe("Serving vizarr data", () => {
-  const tmpDir = path.join(os.tmpdir(), "fractal-vizarr-app-test");
+describe("Serving data", () => {
+  const tmpDir = path.join(os.tmpdir(), "fractal-data-app-test");
 
   beforeAll(() => {
     // Create test files
diff --git a/test/mock.ts b/test/mock.ts
@@ -5,7 +5,7 @@ import { vi } from "vitest";
 export function mockConfig(config: Partial<Config>) {
   const getConfig = () =>
     ({
-      basePath: "/vizarr/",
+      basePath: "/data",
       fractalServerUrl: "http://localhost:8000",
       ...config,
     } as Config);

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`{`
`2`		`- "name": "fractal-vizarr-viewer",`
	`2`	`+ "name": "fractal-data",`
`3`	`3`	`"version": "0.3.2",`
`4`	`4`	`"description": "",`
`5`	`5`	`"main": "dist/app.js",`