Modify scripts to use fnndsc/utils container

Author: jennydaman

README.md

@@ -71,30 +71,8 @@ npm ci
 
 No extra dependencies are required when using the "public" server.
 
-If you intend on developing with the "local" server, you need to install extra dependencies which are used for downloading sample data files and utility scripts. These dependencies are:
-
-- [GNU coreutils](https://www.gnu.org/software/coreutils/)
-- [GNU bash](https://www.gnu.org/software/bash/)
-- [GNU parallel](https://www.gnu.org/software/parallel/)
-- [GNU make](https://www.gnu.org/software/make/)
-- [find](https://www.gnu.org/software/findutils/)
-- [curl](https://curl.se/)
-
-Here are the installation instructions for various Linux distros.
-
-```shell
-# for Ubuntu, Debian
-sudo apt install -y make parallel curl
-
-# for Arch Linux
-sudo pacman -S make parallel curl
-
-# for NixOS or home-manger
-nix-shell -p coreutils findutils bash gnumake parallel curl
-
-# MacOS or Linux using homebrew
-brew install coreutils findutils bash make parallel curl
-```
+If you intend on developing with the "local" server, you will need **Docker** and Docker Compose
+to run the backend and helper scripts.
 
 ### 2. Run the development server
 

biome.json

@@ -1,7 +1,7 @@
 {
   "$schema": "https://biomejs.dev/schemas/1.1.2/schema.json",
   "files": {
-    "include": ["src/**", "tests/**", "./*.{ts,json}"],
+    "include": ["src/**", "tests/**", "./*.ts", "./*.json", "testing/*.mjs"],
     "ignore": ["package-lock.json"]
   },
   "organizeImports": {

package.json

@@ -25,7 +25,7 @@
     "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",
+    "get-dicoms": "./testing/getDicoms.mjs",
     "list-mrns": "./testing/miniChRIS/scripts/list_mrns.sh",
     "lint": "biome lint .",
     "fix": "biome check --apply .",

testing/getDicoms.mjs

@@ -0,0 +1,62 @@
+#!/usr/bin/env node
+// Purpose: download sample DICOM files and upload them to Orthanc.
+
+import * as childProcess from "node:child_process";
+import * as os from "node:os";
+import * as path from "node:path";
+
+const UTILS_IMAGE = "ghcr.io/fnndsc/utils:fc56615";
+
+function main() {
+  runUtils("testing/sample_dicoms", ["make", "neuro"]);
+  runUtils("testing", [
+    "./miniChRIS/scripts/upload2orthanc.sh",
+    "./sample_dicoms/data",
+  ]);
+}
+
+main();
+
+/**
+ * Run a command using docker in the utils image.
+ *
+ * @param workDir {string} relative working directory
+ * @param args {string[]} command to run
+ */
+function runUtils(workDir, args) {
+  const { uid, gid } = os.userInfo();
+  childProcess.execFileSync(
+    "docker",
+    [
+      "run",
+      "--rm",
+      ...getTtyArgs(),
+      "--net=host",
+      "-u",
+      `${uid}:${gid}`,
+      "-v",
+      `${getHere()}:/ChRIS_ui`,
+      "-w",
+      path.join("/ChRIS_ui", workDir),
+      UTILS_IMAGE,
+      ...args,
+    ],
+    { stdio: "inherit" },
+  );
+}
+
+/**
+ * @returns {string} the directory of the NPM project
+ */
+function getHere() {
+  return childProcess
+    .execFileSync("npm", ["prefix"], { encoding: "utf-8" })
+    .trim();
+}
+
+/**
+ * @returns {string[]} tty-related flags to use for `docker run`
+ */
+function getTtyArgs() {
+  return process.env.GITHUB_CI ? [] : ["-t"];
+}