Development

.adonisrc.json

@@ -3,7 +3,8 @@
   "commands": [
     "./commands",
     "@adonisjs/core/build/commands/index.js",
-    "@adonisjs/repl/build/commands"
+    "@adonisjs/repl/build/commands",
+    "adonis5-swagger/build/commands"
   ],
   "exceptionHandlerNamespace": "App/Exceptions/Handler",
   "aliases": {
@@ -12,17 +13,30 @@
     "Database": "database",
     "Contracts": "contracts"
   },
-  "preloads": ["./start/routes", "./start/kernel"],
-  "providers": ["./providers/AppProvider", "@adonisjs/core"],
-  "aceProviders": ["@adonisjs/repl"],
+  "preloads": [
+    "./start/routes",
+    "./start/kernel"
+  ],
+  "providers": [
+    "./providers/AppProvider",
+    "@adonisjs/core",
+    "adonis5-swagger"
+  ],
+  "aceProviders": [
+    "@adonisjs/repl"
+  ],
   "tests": {
     "suites": [
       {
         "name": "functional",
-        "files": ["tests/functional/**/*.spec(.ts|.js)"],
+        "files": [
+          "tests/functional/**/*.spec(.ts|.js)"
+        ],
         "timeout": 60000
       }
     ]
   },
-  "testProviders": ["@japa/preset-adonis/TestsProvider"]
-}
+  "testProviders": [
+    "@japa/preset-adonis/TestsProvider"
+  ]
+}

.env.example

@@ -1,5 +1,5 @@
 PORT=3333
 HOST=0.0.0.0
-NODE_ENV=development
+NODE_ENV=production
 APP_KEY=NZu-mbqukZjV_65cT3ckDB21exh17-ws
-DRIVE_DISK=local
+DRIVE_DISK=local

.github/workflows/dev-build.yml

@@ -0,0 +1,86 @@
+
+# This worklflow will perform following actions when the code is pushed to development branch:
+# - Run test using Playwright
+# - Build the latest docker image in development which needs test to pass first.
+# - Push the latest docker image to Google Artifact Registry-Dev.
+# - Rollout the latest image in GKE.
+# 
+# Maintainers:
+#   - name: Nisha Sharma
+#   - email: [email protected]
+
+name: Build and Deploy to Dev
+
+on:
+  push:
+    branches: [development]
+
+env:
+  PROJECT_ID: ${{ secrets.GKE_PROJECT }}
+  GKE_CLUSTER_DEV: nmrxiv-dev
+  GKE_ZONE: europe-west3-a
+  DEPLOYMENT_NAME: nodejs-nmrxiv-nodejs-microservice
+  DOCKER_HUB_USERNAME : ${{ secrets.DOCKER_HUB_USERNAME  }}
+  DOCKER_HUB_PASSWORD : ${{ secrets.DOCKER_HUB_PASSWORD  }}
+  REPOSITORY_NAME: nodejs-microservice
+  REPOSITORY_NAMESPACE: nfdi4chem
+
+jobs:
+  e2etest:
+    uses: NFDI4Chem/nmrxiv-nodejs-microservice/.github/workflows/e2e.yml@development
+
+  setup-build-publish-deploy-dev:
+    name: Deploy to dev
+    if: github.ref == 'refs/heads/development'
+    runs-on: ubuntu-latest
+    needs: e2etest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Setup gcloud CLI
+      - name: Setup CLI
+        uses: google-github-actions/setup-gcloud@94337306dda8180d967a56932ceb4ddcf01edae7
+        with:
+          service_account_key: ${{ secrets.GKE_SA_KEY }}
+          project_id: ${{ secrets.GKE_PROJECT }}
+
+      # Configure docker to use the gcloud command-line tool as a credential helper
+      - name: Configure docker
+        run: |-
+          gcloud auth configure-docker europe-west3-docker.pkg.dev
+
+      # Get the GKE credentials
+      - name: Get GKE credentials
+        uses: google-github-actions/[email protected]
+        with:
+          cluster_name: ${{ env.GKE_CLUSTER_DEV }}
+          location: ${{ env.GKE_ZONE }}
+          credentials: ${{ secrets.GKE_SA_KEY }}
+
+      # Login to Docker Hub
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ env.DOCKER_HUB_USERNAME  }}
+          password: ${{ env.DOCKER_HUB_PASSWORD  }}
+
+      # Build and push image to Docker Hub
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          build-args: |
+            RELEASE_VERSION=dev-latest
+          tags: ${{ env.REPOSITORY_NAMESPACE }}/${{ env.REPOSITORY_NAME }}:dev-latest
+          username: ${{ env.DOCKER_HUB_USERNAME  }}
+          password: ${{ env.DOCKER_HUB_PASSWORD  }}
+
+      # Deploy the latest Docker image to the GKE cluster
+      - name: Deploy
+        run: |-
+          kubectl rollout restart deployment/$DEPLOYMENT_NAME
+          kubectl rollout status deployment/$DEPLOYMENT_NAME --timeout=300s
+          kubectl get services -o wide

.github/workflows/e2e.yml

@@ -0,0 +1,29 @@
+name: e2e tests
+
+on:
+  workflow_call:
+
+jobs:
+    test:
+      runs-on: ubuntu-latest
+
+      strategy:
+        matrix:
+          node-version: [20.x]
+
+      steps:
+        - uses: actions/checkout@v3
+        - name: Use Node.js ${{ matrix.node-version }}
+          uses: actions/setup-node@v3
+          with:
+            node-version: ${{ matrix.node-version }}
+        - name: 'Create .env file'
+          run: |
+            touch .env
+            cp .env.example .env
+        - run: npm ci
+        - run: npm run build --if-present
+        - name: Install Playwright
+          run: npx playwright install --with-deps
+        - name: Run test
+          run: npm test

.github/workflows/release-please.yml

@@ -0,0 +1,68 @@
+
+# This worklflow will perform following actions when the code is pushed to main branch.
+# - Run end to end test
+# - Test linting.
+# - Trigger release-please action to create release which needs e2etest & lint to pass first.
+# 
+# Maintainers:
+#   - name: Nisha Sharma
+#   - email: [email protected]
+
+name: release-please 
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [20.x]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Use Node.js ${{ matrix.node-version }}
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node-version }}
+      - name: 'Create .env file'
+        run: |
+          touch .env
+          cp .env.example .env
+      - run: npm ci
+      - run: npm run build --if-present
+      - name: Install Playwright
+        run: npx playwright install --with-deps
+      - name: Run test
+        run: npm test
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v2
+        with:
+          node-version: 20.x
+      - name: Install dependencies
+        run: npm ci
+      - name: Run ESLint
+        run: npm run eslint
+      - name: Run Prettier
+        run: npm run prettier
+      - name: Check types
+        run: npm run check-types
+
+  release-please:
+    runs-on: ubuntu-latest
+    needs: ['lint', 'test']
+    steps:
+      - uses: google-github-actions/release-please-action@v3
+        with:
+          release-type: node
+          package-name: release-please-action
+          token: ${{ secrets.GITHUB_TOKEN }}
+          prerelease: true

Dockerfile

@@ -22,5 +22,7 @@ ENV HOST=0.0.0.0
 COPY --chown=node:node ./package*.json ./
 RUN npm ci --production
 COPY --chown=node:node --from=build /home/node/app/build .
+COPY --chown=node:node --from=build /home/node/app/docs ./docs
+COPY --chown=node:node --from=build /home/node/app/public ./public
 EXPOSE $PORT
 CMD [ "dumb-init", "node", "server.js" ]

README.md

@@ -1,3 +1,46 @@
+# API Service To Process Spectra from various data formats to NMRium format
+
+
+The API uses the [nmr-load-save](https://github.com/cheminfo/nmr-load-save) package to process the spectra and [playwright](https://playwright.dev/) to load the NMRium from the deployed wrapper [nmrium-react-wrapper](https://github.com/NFDI4Chem/nmrium-react-wrapper) and import the generated data to get the snapshots.
+
+## Secptra processing 
+
+Process and convert various data formats (from various manufacturers, JCAMP standard files, or NMReDATA format, Bruker) to NMRium format
+
+
+```http
+POST /spectra-parser
+```
+
+| Parameter | Type |Default| Description |
+| :--- | :--- | :--- | :--- |
+| `urls` | `string[]` || **Required**. Spectra files URLs   |
+| `snapshot` | `boolean` |`false`| **Optional**. Enable/dispable Spectra snapshot     |
+
+## Responses
+
+```javascript
+{
+  "data": {
+      "source": object[],
+      "spectra" : object[],
+      "molecules" : object[],
+      "version"    : number,
+   },
+  "images"    : {"id":string,"image":string}[]
+
+}
+The `source` attribute contains an array of spectra files relative paths.
+The `spectra` attribute contains an array of spectra (1D and 2D).
+The `molecules` attribute contains an array of molecules.
+The `version` attribute contains the current version of the data which is crucial for data migration in NMRium
+The `images` attribute contains a list of the images for the spectra which is processed and displayed by NMRium,
+  where each object contains two attributes the `id` is the spectrum id and an `image` as a Base64 format.
+  ```
+
+> **⚠ WARNING: Data Conversion.**  
+> Data should be converted from a **Typed Array** to a **Array**, without this step the NMRium will not be able to load the spectra. ```version``` object is important for NMRium data migration. 
+
 ## Maintained by
 This project is developed and maintained by the [NFDI4Chem partners](https://www.nfdi4chem.de/) at the [Friedrich Schiller University](https://www.uni-jena.de/en/) Jena, Germany. 
 The code for this web application is released under the [MIT license](https://opensource.org/licenses/MIT).

ace-manifest.json

@@ -95,6 +95,17 @@
       "args": [],
       "aliases": [],
       "flags": []
+    },
+    "swagger:generate": {
+      "settings": {
+        "loadApp": true
+      },
+      "commandPath": "adonis5-swagger/build/commands/GenerateSwaggerFile",
+      "commandName": "swagger:generate",
+      "description": "Generate swagger file",
+      "args": [],
+      "aliases": [],
+      "flags": []
     }
   },
   "aliases": {}