Merge branch 'master' into bugfix/pubmed-citations

Author: chreman

.babelrc.json

@@ -0,0 +1,12 @@
+{
+  "presets": [
+    [
+      "@babel/preset-env",
+      {
+        "targets": "> 0.25%, not dead"
+      }
+    ],
+    "@babel/preset-react",
+    "@babel/preset-typescript"
+  ]
+}

.github/workflows/backend.yml

@@ -0,0 +1,34 @@
+name: Backend CI
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  persistence-unit-tests:
+    name: Unit tests for persistence functions
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Cache pip dependencies
+        uses: actions/cache@v3
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Give execution permissions to script
+        run: chmod +x tests_runners/persistence/locally.sh
+
+      - name: Run tests
+        run: tests_runners/persistence/locally.sh

.github/workflows/frontend.yml

@@ -0,0 +1,57 @@
+name: Frontend CI
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  test:
+    name: Unit and snapshot tests
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Copy config file
+        run: cp config.example.js config.js
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18
+          cache: "npm"
+
+      - name: Clean node_modules and lockfile
+        run: rm -rf node_modules package-lock.json
+
+      - name: Install project dependencies
+        run: npm install
+
+      - name: Run tests
+        run: npm run test
+
+  build:
+    name: Build the project like on production deployment
+    needs: test
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Copy the config file for the vis
+        run: cp config.example.js config.js
+
+      - name: Setup Node.JS
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18
+          cache: "npm"
+
+      - name: Install all project dependencies
+        run: npm ci
+
+      - name: Build the project (prod)
+        run: npx webpack

.prettierignore

@@ -0,0 +1,17 @@
+# Folders that should not be checked by Prettier
+.github/
+.pytest_cache/
+.vscode/
+api_cache/
+checks/
+dist/
+doc/
+examples/
+local_dev/
+node_modules/
+server/
+
+# Exact files that should not be checked by Prettier
+.docker.test.env
+.flake8
+CHANGELOG.md

.prettierrc.json

@@ -0,0 +1,16 @@
+{
+  "printWidth": 80,
+  "tabWidth": 2,
+  "useTabs": false,
+  "semi": true,
+  "singleQuote": false,
+  "quoteProps": "consistent",
+  "jsxSingleQuote": false,
+  "trailingComma": "all",
+  "bracketSpacing": true,
+  "bracketSameLine": false,
+  "arrowParens": "always",
+  "proseWrap": "always",
+  "endOfLine": "lf",
+  "embeddedLanguageFormatting": "auto"
+}

babel.config.js

@@ -1,19 +1,16 @@
 services:
-
-  end2endtest:
+  integration_tests:
     build:
       context: ./server/workers/tests
       dockerfile: ./Dockerfile.tests
-    container_name: end2endtest
-    hostname: "end2endtest"
+    container_name: integration_tests
+    hostname: "integration_tests"
     environment:
       POSTGRES_USER: ${POSTGRES_USER}
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
-      POSTGRES_HOST: ${POSTGRES_HOST}
-      POSTGRES_PORT: ${POSTGRES_PORT}
-      POSTGRES_HOSTS: ${POSTGRES_HOST}
-      POSTGRES_PORTS: ${POSTGRES_PORT}
-      DEFAULT_DATABASE: ${POSTGRES_DATABASE}
+      POSTGRES_HOSTS: ${POSTGRES_HOSTS}
+      POSTGRES_PORTS: ${POSTGRES_PORTS}
+      DEFAULT_DATABASE: ${POSTGRES_DB}
       SERVICE_VERSION: "test_version"
     ports:
       - "7575:80"
@@ -23,46 +20,55 @@ services:
       - db
       - backend
     restart: "no"
-    entrypoint: ["pytest", '/app/workers/tests/test_end2end.py', '-s', '-rfA']
+    entrypoint:
+      ["pytest", "/app/workers/tests/integration-tests.py", "-s", "-rfA"]
     networks:
       - test
 
   db:
-    container_name: ${POSTGRES_HOST}
-    image: 'postgres:12.2-alpine'
+    container_name: ${POSTGRES_HOSTS}
+    image: "postgres:12.2-alpine"
     restart: "no"
-    hostname: ${POSTGRES_HOST}
+    hostname: ${POSTGRES_HOSTS}
     environment:
       POSTGRES_USER: ${POSTGRES_USER}
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
-      POSTGRES_PORT: ${POSTGRES_PORT}
-      DEFAULT_DATABASE: ${POSTGRES_DATABASE}
+      POSTGRES_PORT: ${POSTGRES_PORTS}
+      DEFAULT_DATABASE: ${POSTGRES_DB}
     command: postgres -c config_file=/etc/postgresql.conf -c hba_file=/etc/pg_hba.conf
     volumes:
       - ./server/workers/tests/test_data/pg_hba_test_local.conf:/etc/pg_hba.conf
       - ./server/workers/tests/test_data/postgresql_test_local.conf:/etc/postgresql.conf
     ports:
-      - "${POSTGRES_PORT}:${POSTGRES_PORT}"
+      - "${POSTGRES_PORTS}:${POSTGRES_PORTS}"
     networks:
       - test
 
   redis:
-      image: 'redis:6.0-alpine'
-      restart: unless-stopped
-      hostname: "${REDIS_HOST}"
-      # container_name: "${REDIS_HOST}"
-      environment:
-        REDIS_HOST: "${REDIS_HOST}"
-        REDIS_PORT: "${REDIS_PORT}"
-        REDIS_PASSWORD: "${REDIS_PASSWORD}"
-      command: ["redis-server", "/etc/redis/redis.conf", "--bind", "${REDIS_HOST}", "--port", "${REDIS_PORT}"]
-      volumes:
-          - 'redis:/var/lib/redis/data'
-          - ./local_dev/redis.conf:/etc/redis/redis.conf
-      ports:
+    image: "redis:6.0-alpine"
+    restart: unless-stopped
+    hostname: "${REDIS_HOST}"
+    # container_name: "${REDIS_HOST}"
+    environment:
+      REDIS_HOST: "${REDIS_HOST}"
+      REDIS_PORT: "${REDIS_PORT}"
+      REDIS_PASSWORD: "${REDIS_PASSWORD}"
+    command:
+      [
+        "redis-server",
+        "/etc/redis/redis.conf",
+        "--bind",
+        "${REDIS_HOST}",
+        "--port",
+        "${REDIS_PORT}",
+      ]
+    volumes:
+      - "redis:/var/lib/redis/data"
+      - ./local_dev/redis.conf:/etc/redis/redis.conf
+    ports:
       - "127.0.0.1:${REDIS_PORT}:${REDIS_PORT}"
-      networks:
-        - test
+    networks:
+      - test
 
   api:
     build:
@@ -81,13 +87,13 @@ services:
       FLASK_ENV: "${FLASK_ENV}"
       POSTGRES_USER: "${POSTGRES_USER}"
       POSTGRES_PASSWORD: "${POSTGRES_PASSWORD}"
-      POSTGRES_HOST: "${POSTGRES_HOST}"
-      DEFAULT_DATABASE: "${POSTGRES_DATABASE}"
+      POSTGRES_HOST: "${POSTGRES_HOSTS}"
+      DEFAULT_DATABASE: "${POSTGRES_DB}"
     command: ["python", "api/tests/mock_app.py"]
     depends_on:
       - redis
       - db
-    networks: 
+    networks:
       - test
 
   persistence:
@@ -101,11 +107,11 @@ services:
       SERVICE_VERSION: "test"
       BEHIND_PROXY: "false"
       FLASK_ENV: "development"
-      POSTGRES_HOSTS: ${POSTGRES_HOST}
-      POSTGRES_PORTS: ${POSTGRES_PORT}
+      POSTGRES_HOSTS: ${POSTGRES_HOSTS}
+      POSTGRES_PORTS: ${POSTGRES_PORTS}
       POSTGRES_USER: ${POSTGRES_USER}
       POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
-      DEFAULT_DATABASE: ${POSTGRES_DATABASE}
+      DEFAULT_DATABASE: ${POSTGRES_DB}
     volumes:
       - ./server/workers/tests/mock_app.py:/persistence/mock_app.py
     command: ["python", "mock_app.py"]