deploy script

.aws/task-definition.json

@@ -0,0 +1,41 @@
+{
+  "family": "atlas-task-definition",
+  "containerDefinitions": [
+    {
+      "name": "atlas",
+      "image": "533266983284.dkr.ecr.us-east-1.amazonaws.com/atlas",
+      "cpu": 0,
+      "portMappings": [
+        {
+          "name": "atlas-container-port",
+          "containerPort": 8000,
+          "hostPort": 8000,
+          "protocol": "tcp",
+          "appProtocol": "http"
+        }
+      ],
+      "essential": true,
+      "environment": [],
+      "environmentFiles": [],
+      "mountPoints": [],
+      "volumesFrom": [],
+      "ulimits": [],
+      "systemControls": []
+    }
+  ],
+  "executionRoleArn": "arn:aws:iam::533266983284:role/ecsTaskExecutionRole",
+  "networkMode": "awsvpc",
+  "requiresCompatibilities": ["FARGATE"],
+  "cpu": "1024",
+  "memory": "3072",
+  "runtimePlatform": {
+    "cpuArchitecture": "X86_64",
+    "operatingSystemFamily": "LINUX"
+  },
+  "tags": [
+    {
+      "key": "project",
+      "value": "atlas"
+    }
+  ]
+}

.dockerignore

@@ -0,0 +1,168 @@
+# config files
+.github/
+.husky/
+.jest/
+.vscode/
+.editorconfig
+.eslintrc
+.git
+.gitignore
+.prettierignore
+.prettierrc
+.releaserc
+Dockerfile
+docker-compose.yml
+Jenkinsfile
+jest.config.js
+
+# documentation
+LICENSE
+CHANGELOG.md
+README.md
+
+# build files
+node_modules
+**/node_modules
+
+.git
+Dockerfile
+.DS_Store
+.gitignore
+.dockerignore
+
+/credentials
+/cache
+/store
+
+/node_modules
+
+# https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
+
+# General
+*.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+# https://raw.githubusercontent.com/github/gitignore/master/Python.gitignore
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

.github/workflows/aws-deploy.yml

@@ -0,0 +1,67 @@
+name: Deploy to Amazon ECS
+
+on:
+  push:
+    branches: ["main"]
+
+env:
+  AWS_REGION: us-east-1 # AWS region, e.g. us-west-1
+  ECR_REPOSITORY: atlas # Amazon ECR repository name
+  ECS_SERVICE: atlas-service # Amazon ECS service name
+  ECS_CLUSTER: atlas-cluster # Amazon ECS cluster name
+  ECS_TASK_DEFINITION: .aws/task-definition.json # Amazon ECS task definition
+  CONTAINER_NAME: atlas
+
+permissions:
+  id-token: write
+  contents: read
+
+jobs:
+  deploy:
+    name: Deploy
+    runs-on: ubuntu-latest
+    environment: production
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_PROD_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_PROD_KEY }}
+          aws-region: us-east-1
+
+      - name: Login to Amazon ECR
+        id: login-ecr
+        uses: aws-actions/amazon-ecr-login@v2
+
+      - name: Build, tag, and push image to Amazon ECR
+        id: build-image
+        env:
+          ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+          IMAGE_TAG: ${{ github.sha }}
+        run: |
+          # Build a docker container and
+          # push it to ECR so that it can
+          # be deployed to ECS.
+          docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG --build-arg GITHUB_HASH=${GITHUB_SHA::7} --build-arg GITHUB_BRANCH=${GITHUB_REF_NAME} .
+          docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
+          echo "image=$ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG" >> $GITHUB_OUTPUT
+
+      - name: Fill in the new image ID in the Amazon ECS task definition
+        id: task-def
+        uses: aws-actions/amazon-ecs-render-task-definition@v1
+        with:
+          task-definition: ${{ env.ECS_TASK_DEFINITION }}
+          container-name: ${{ env.CONTAINER_NAME }}
+          image: ${{ steps.build-image.outputs.image }}
+
+      - name: Deploy Amazon ECS task definition
+        uses: aws-actions/amazon-ecs-deploy-task-definition@v1
+        with:
+          task-definition: ${{ steps.task-def.outputs.task-definition }}
+          service: ${{ env.ECS_SERVICE }}
+          cluster: ${{ env.ECS_CLUSTER }}
+          wait-for-service-stability: true

.vscode/settings.json

@@ -23,5 +23,8 @@
   },
   "[github-actions-workflow]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode"
+  },
+  "[dockerfile]": {
+    "editor.defaultFormatter": "ms-azuretools.vscode-docker"
   }
 }

Dockerfile

@@ -0,0 +1,24 @@
+# Build step #1: build the React front end
+FROM node:18-alpine as build-step
+WORKDIR /app
+ENV PATH /app/node_modules/.bin:$PATH
+COPY client/package*.json ./
+RUN npm ci
+COPY client/ ./
+RUN npm run build
+
+# Build step #2: build the API with the client as static files
+FROM python:3.9
+WORKDIR /app
+COPY --from=build-step /app/dist ./build
+
+RUN mkdir ./api
+COPY server ./api
+RUN pip install -r ./api/requirements.txt
+RUN pip install gunicorn
+ENV FLASK_ENV production
+
+
+EXPOSE 8000
+WORKDIR /app/api
+CMD ["gunicorn", "-b", ":8000", "api:app"]

client/package.json

@@ -58,5 +58,6 @@
   "description": "tool for exploring scientific litreture ",
   "main": "postcss.config.js",
   "author": "A.Nakhaei",
-  "license": "ISC"
+  "license": "ISC",
+  "proxy": "http://localhost:8000"
 }

client/src/App.tsx

@@ -15,7 +15,7 @@ function App() {
           <SocketProvider>
             <Routes>
               <Route path='/' element={<Home />} />
-              <Route path='/login/:magicLink' element={<Home loggingIn={true} />} />
+              <Route path='/login/:email/:magicLink' element={<Home loggingIn={true} />} />
               <Route path='/dashboard' element={<Dashboard />} />
               <Route path='/table' element={<Table />} />
               <Route path='/test' element={<ArrageTable />} />