Merge pull request #77 from samply/release/v0.4.0

Release Version v.0.4.0
samply · Mar 28, 2024 · a41d8a8 · a41d8a8
2 parents 9c7856d + 739839a
commit a41d8a8
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Showing 26 changed files with 2,743 additions and 256 deletions.
diff --git a/.eslintignore b/.eslintignore
@@ -0,0 +1,3 @@
+node_modules
+dist
+.eslintrc.cjs
diff --git a/.eslintrc.cjs b/.eslintrc.cjs
@@ -1,38 +1,42 @@
 module.exports = {
-    plugins: ['@typescript-eslint/eslint-plugin', 'eslint-plugin-tsdoc', 'jsdoc'],
+    plugins: [
+        "@typescript-eslint/eslint-plugin",
+        "eslint-plugin-tsdoc",
+        "jsdoc",
+    ],
     extends: [
-      'plugin:@typescript-eslint/recommended',
-      'plugin:svelte/recommended',
-      'plugin:svelte/prettier', 
-      'eslint-config-prettier',
-      'prettier',
-      "plugin:jsdoc/recommended-typescript-error",
+        "plugin:@typescript-eslint/recommended",
+        "plugin:svelte/recommended",
+        "plugin:svelte/prettier",
+        "eslint-config-prettier",
+        "prettier",
+        "plugin:jsdoc/recommended-typescript-error",
     ],
-    parser: '@typescript-eslint/parser',
+    parser: "@typescript-eslint/parser",
     parserOptions: {
-        project: './tsconfig.json',
-        extraFileExtensions: ['.svelte'],
+        project: "./tsconfig.json",
+        extraFileExtensions: [".svelte"],
     },
     overrides: [
-      {
-        files: ['*.svelte'],
-        parser: 'svelte-eslint-parser',
-        parserOptions: {
-            parser: '@typescript-eslint/parser',
-        }
-      }
+        {
+            files: ["*.svelte"],
+            parser: "svelte-eslint-parser",
+            parserOptions: {
+                parser: "@typescript-eslint/parser",
+            },
+        },
     ],
     settings: {
-      'svelte/typescript': import('typescript'),
+        "svelte/typescript": import("typescript"),
     },
     rules: {
-      '@typescript-eslint/no-explicit-any': 'error',
-      '@typescript-eslint/explicit-function-return-type': ['error', { allowExpressions: true }],
-      'svelte/no-at-html-tags': 'off',
-      'jsdoc/check-syntax': 2,
-      "jsdoc/check-param-names": 2,
-
-
+        "@typescript-eslint/no-explicit-any": "error",
+        "@typescript-eslint/explicit-function-return-type": [
+            "error",
+            { allowExpressions: true },
+        ],
+        "svelte/no-at-html-tags": "off",
+        "jsdoc/check-syntax": 2,
+        "jsdoc/check-param-names": 2,
     },
-    ignorePatterns: ['**/dist/**'],
-  };
+};
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -21,7 +21,7 @@ jobs:
       - name: "Build @samply/lens"
         run: npm run build
       - name: "Publish @samply/lens"
-        run: cd dist && npm publish --access public
+        run: npm publish --access public
         env:
           NODE_AUTH_TOKEN: ${{secrets.NPM_TOKEN}}
 

diff --git a/.gitignore b/.gitignore
@@ -27,3 +27,5 @@ TODO
 # Deployment Files
 .env
 docker-compose.override.yml
+*.priv.pem
+traefik.yaml
diff --git a/.husky/commit-msg b/.husky/commit-msg
@@ -0,0 +1,4 @@
+#!/usr/bin/env sh
+. "$(dirname -- "$0")/_/husky.sh"
+
+npx --no-install commitlint --edit
diff --git a/README.md b/README.md
@@ -32,6 +32,16 @@ npm start
 
 to start a development server, that will typically be available at [http://localhost:5173](http://localhost:5173). For further available npm scripts, you can review the [package.json](./package.json)
 
+### Building the Library locally
+If you want to make changes to the lens library while integrating those changes directly in the local development version of your application, you need to tell npm to make lens locally available. For this use-case, we prepared to npm scripts:
+
+1) Run `npm run watch`, to start building the library on changes
+2) Open a second terminal
+3) Run `npm run link` which will make the library available locally
+4) In your own applications repository run `npm link @samply/lens`
+
+To controll that the linking of the local version worked, run `npm ls | grep lens` in your applications repository and verify that it refers to your local lens repository.
+
 ## Style Integration
 
 To import the default stylings, use 

diff --git a/commitlint.config.cjs b/commitlint.config.cjs
@@ -0,0 +1,7 @@
+module.exports = {
+    extends: ["@commitlint/config-conventional"],
+    rules: {
+        "body-max-line-length": [0, "always"],
+        "footer-max-line-length": [0, "always"],
+    },
+};
diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -19,16 +19,13 @@ services:
       - "default"
 
   spot:
-    # NOTE: This will be replaced by https://github.com/samply/spot soon.
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:main
     ports:
       - 8080:8080
     environment:
       BEAM_SECRET: "${LOCAL_BEAM_SECRET}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${LOCAL_BEAM_ID}
-      BEAM_BROKER_ID: ${BROKER_HOST}
-      BEAM_APP_ID: "focus"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_APP_ID: "focus.${LOCAL_BEAM_ID}.${BROKER_HOST}"
     depends_on:
       - "beam-proxy"
     profiles:

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -19,25 +19,36 @@ services:
       - /var/run/docker.sock:/var/run/docker.sock:ro
 
   traefik-forward-auth:
-    image: thomseddon/traefik-forward-auth:2
+    image: quay.io/oauth2-proxy/oauth2-proxy:latest
     environment:
       - http_proxy=${http_proxy}
       - https_proxy=${https_proxy}
-      - DEFAULT_PROVIDER=oidc
-      # TODO: https://login.bbmri-eric.eu/oidc/
-      - PROVIDERS_OIDC_ISSUER_URL=https://git.verbis.dkfz.de
-      - PROVIDERS_OIDC_CLIENT_ID=${OAUTH_CLIENT_ID}
-      - PROVIDERS_OIDC_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
-      - SECRET=${AUTHENTICATION_SECRET}
-      - COOKIE_DOMAIN=${GUI_HOST}
+      - OAUTH2_PROXY_PROVIDER=oidc
+      - OAUTH2_PROXY_SKIP_PROVIDER_BUTTON=true
+      - OAUTH2_PROXY_OIDC_ISSUER_URL=${OAUTH_ISSUER_URL}
+      - OAUTH2_PROXY_CLIENT_ID=${OAUTH_CLIENT_ID}
+      - OAUTH2_PROXY_CLIENT_SECRET=${OAUTH_CLIENT_SECRET}
+      - OAUTH2_PROXY_COOKIE_SECRET=${AUTHENTICATION_SECRET}
+      - OAUTH2_PROXY_COOKIE_DOMAINS=.${GUI_HOST}
+      - OAUTH2_PROXY_HTTP_ADDRESS=:4180
+      - OAUTH2_PROXY_REVERSE_PROXY=true
+      - OAUTH2_PROXY_WHITELIST_DOMAINS=.${GUI_HOST}
+      - OAUTH2_PROXY_UPSTREAMS=static://202
+      - OAUTH2_PROXY_EMAIL_DOMAINS=*
+      - OAUTH2_PROXY_ALLOWED_GROUPS=${ALLOWED_GROUPS}
+      # For some reason, login.verbis.dkfz.de does not have a "groups" scope but this comes automatically through a
+      # scope called microprofile-jwt. Remove the following line once we have a "groups" scope.
+      - OAUTH2_PROXY_SCOPE=openid profile email
     labels:
       - "traefik.enable=true"
-      - "traefik.http.middlewares.traefik-forward-auth.forwardauth.address=http://traefik-forward-auth:4181"
+      - "traefik.http.middlewares.traefik-forward-auth.forwardauth.address=http://traefik-forward-auth:4180"
       - "traefik.http.middlewares.traefik-forward-auth.forwardauth.authResponseHeaders=X-Forwarded-User"
-      - "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4181"
+      - "traefik.http.services.traefik-forward-auth.loadbalancer.server.port=4180"
+      - "traefik.http.routers.oauth2.rule=Host(`${GUI_HOST}`) && PathPrefix(`/oauth2/`)"
+      - "traefik.http.routers.oauth2.tls=true"
 
   lens-web-components:
-    image: lens-web-components
+    image: samply/lens:main
     build: .
     labels:
       - "traefik.enable=true"
@@ -46,55 +57,39 @@ services:
       - "traefik.http.routers.lens.middlewares=traefik-forward-auth"
 
   spot:
-    image: docker.verbis.dkfz.de/ccp-private/central-spot
+    image: samply/rustyspot:main
     environment:
       BEAM_SECRET: "${LOCAL_BEAM_SECRET}"
-      BEAM_URL: http://beam-proxy:8081
-      BEAM_PROXY_ID: ${LOCAL_BEAM_ID}
-      BEAM_BROKER_ID: ${BROKER_HOST}
-      # TODO: Implement Switch between spot and focus
-      BEAM_APP_ID: "spot"
+      BEAM_PROXY_URL: http://beam-proxy:8081
+      BEAM_APP_ID: "focus.${LOCAL_BEAM_ID}.${BROKER_HOST}"
+      CORS_ORIGIN: "https://${GUI_HOST}"
     depends_on:
       - "beam-proxy"
     labels:
       - "traefik.enable=true"
       - "traefik.http.services.spot.loadbalancer.server.port=8080"
       - "traefik.http.middlewares.corsheaders.headers.accesscontrolallowmethods=GET,OPTIONS,POST"
+      - "traefik.http.middlewares.corsheaders.headers.accesscontrolallowheaders=content-type"
       - "traefik.http.middlewares.corsheaders.headers.accesscontrolalloworiginlist=https://${GUI_HOST}"
       - "traefik.http.middlewares.corsheaders.headers.accesscontrolallowcredentials=true"
       - "traefik.http.middlewares.corsheaders.headers.accesscontrolmaxage=-1"
-      - "traefik.http.routers.spot.rule=Host(`backend.${GUI_HOST}`)"
+      - "traefik.http.routers.spot.rule=Host(`backend.${GUI_HOST}`) && PathPrefix(`/prod`)"
+      - "traefik.http.middlewares.stripprefix_spot_prod.stripprefix.prefixes=/prod"
       - "traefik.http.routers.spot.tls=true"
-      - "traefik.http.routers.spot.middlewares=corsheaders,traefik-forward-auth"
+      - "traefik.http.routers.spot.middlewares=corsheaders,traefik-forward-auth,stripprefix_spot_prod"
 
   beam-proxy:
     image: docker.verbis.dkfz.de/cache/samply/beam-proxy:develop
     environment:
       BROKER_URL: https://${BROKER_HOST}
       PROXY_ID: ${LOCAL_BEAM_ID}.${BROKER_HOST}
-      # TODO: Same for focus here
-      APP_spot_KEY: ${LOCAL_BEAM_SECRET}
+      APP_focus_KEY: ${LOCAL_BEAM_SECRET}
       PRIVKEY_FILE: /run/secrets/proxy.pem
       ALL_PROXY: ${http_proxy}
     secrets:
       - proxy.pem
       - root.crt.pem
 
-  ## Only use this for test purposes
-  blaze:
-    image: samply/blaze:develop
-    ports:
-     - "8082:8080"
-    profiles: ["development"]
-
-  test-data-loader:
-    image: samply/test-data-loader
-    environment:
-      FHIR_STORE_URL: "http://blaze:8080/fhir"
-      PATIENT_COUNT: "2000"
-    command: sh -c "sleep 60 && /app/run.sh"
-    profiles: ["development"]
-
 secrets:
   proxy.pem:
     # TODO: Key in BBMRI was directly stored in lens directory!