Merge pull request #66 from fractal-analytics-platform/vizarr-optional-endpoint

Made VIZARR_STATIC_FILES_PATH environment variable optional

Author: zonia3000

.env.example

@@ -2,5 +2,6 @@ PORT=3000
 BIND_ADDRESS=0.0.0.0
 FRACTAL_SERVER_URL=http://localhost:8000
 BASE_PATH=/data
+VIZARR_STATIC_FILES_PATH=/path/to/vizarr/dist
 AUTHORIZATION_SCHEME=fractal-server
 CACHE_EXPIRATION_TIME=60

CHANGELOG.md

@@ -4,6 +4,7 @@ Note: Numbers like (#123) point to closed Pull Requests on the fractal-vizarr-vi
 
 * 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);
+* Made `VIZARR_STATIC_FILES_PATH` environment variable optional (\#66);
 
 # 0.3.2
 

Dockerfile

@@ -1,5 +1,14 @@
 FROM node:20
 
+WORKDIR /
+
+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-data
 
 WORKDIR /fractal-data
@@ -11,4 +20,6 @@ ADD tsconfig.json .
 RUN npm install
 RUN npm run build
 
+ENV VIZARR_STATIC_FILES_PATH=/vizarr/dist
+
 CMD ["node", "/fractal-data/dist/app.js"]

README.md

@@ -4,10 +4,11 @@ Prototype to explore serving/viewing zarr data.
 
 This repository contains a simple server application made using [Express](https://expressjs.com/).
 
-The application has 2 endpoints:
+The application has 3 endpoints:
 
 - the endpoint `/files/{path-to-zarr}`, that serves the content of Zarr files checking user authorization.
 - the endpoint `/alive`, that returns the status of the service.
+- the optional endpoint `/vizarr`, that serves vizarr static files when the `VIZARR_STATIC_FILES_PATH` environment variable is set.
 
 > To run fractal-data you need to have an active instance of `fractal-server` and an active instance of `fractal-web`. You need to log-in to `fractal-web` from the browser using a user that has been authorized to see the vizarr files. Details about authorization are explained in the next section.
 
@@ -72,6 +73,7 @@ To start the application installed in this way see the section [Run fractal-data
 - `PORT`: the port where fractal-data app is served;
 - `BIND_ADDRESS`: specifies the IP address for the server to bind to; use `0.0.0.0` (IPv4) or `::` (IPv6) to listen on all interfaces, `127.0.0.1` (IPv4) or `::1` (IPv6) for localhost only; the default value is `0.0.0.0`;
 - `FRACTAL_SERVER_URL`: the base URL of fractal-server;
+- `VIZARR_STATIC_FILES_PATH`: path to the files generated running `npm run build` in Vizarr source folder; this variable is optional and, if present, it will be used to serve Vizarr static files from the `/vizarr` endpoint;
 - `BASE_PATH`: base path of fractal-data application;
 - `AUTHORIZATION_SCHEME`: defines how the service verifies user authorization. The following options are available:
   - `fractal-server`: the paths that can be accessed by each user are retrieved calling fractal-server API.
@@ -205,7 +207,7 @@ The output is located in the `dist` folder.
 
 ### Run fractal-data
 
-Then go back to fractal-data folder and run `npm run start` to start the project. The server will start on port 3000.
+Then go back to fractal-data folder and run `npm run start` to start the project. The server will start on port 3000. Remember to set the `VIZARR_STATIC_FILES_PATH`, to serve Vizarr static files from the `/vizarr` endpoint. Vizarr static files need to be served from the same port and domain of the fractal-data service, otherwise you will encounter CORS issues.
 
 ### Alive endpoint
 

src/app.ts

@@ -29,6 +29,14 @@ app.use(`${config.basePath}alive`, async function (req, res) {
   await aliveEndpoint(req, res);
 });
 
+// Serving Vizarr static files
+if (config.vizarrStaticFilesPath) {
+  app.use(
+    `${config.basePath}vizarr`,
+    express.static(config.vizarrStaticFilesPath)
+  );
+}
+
 // Start server
 const server = app.listen(config.port, config.bindAddress, () => {
   logger.info(

src/config.ts

@@ -59,13 +59,19 @@ function loadConfig(): Config {
     basePath += "/";
   }
 
+  const vizarrStaticFilesPath = process.env.VIZARR_STATIC_FILES_PATH;
+
   logger.debug("PORT: %s", port);
   logger.debug("BIND_ADDRESS: %s", bindAddress);
   logger.debug("FRACTAL_SERVER_URL: %s", fractalServerUrl);
   logger.debug("BASE_PATH: %s", basePath);
   logger.debug("AUTHORIZATION_SCHEME: %s", authorizationScheme);
   logger.debug("CACHE_EXPIRATION_TIME: %d", cacheExpirationTime);
 
+  if (vizarrStaticFilesPath) {
+    logger.debug("VIZARR_STATIC_FILES_PATH: %s", vizarrStaticFilesPath);
+  }
+
   return {
     port,
     bindAddress,
@@ -75,6 +81,7 @@ function loadConfig(): Config {
     cacheExpirationTime,
     testingUsername,
     testingPassword,
+    vizarrStaticFilesPath,
   };
 }
 

src/types.ts

@@ -12,6 +12,7 @@ export type Config = {
   cacheExpirationTime: number;
   testingUsername: string | null;
   testingPassword: string | null;
+  vizarrStaticFilesPath: string | undefined;
 };
 
 export type User = {