update for github action

.github/workflows/develop.yml

@@ -0,0 +1,85 @@
+name: CI/CD - develop
+
+on: 
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+env:
+  IMAGE: ghcr.io/$(echo $GITHUB_REPOSITORY | tr '[A-Z]' '[a-z]')/aimingmed-ai-backend
+
+jobs:
+
+  build:
+    name: Build Docker Image
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: main
+      - name: Log in to GitHub Packages
+        run: echo ${GITHUB_TOKEN} | docker login -u ${GITHUB_ACTOR} --password-stdin ghcr.io
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Pull image
+        run: |
+          docker pull ${{ env.IMAGE }}:latest || true
+      - name: Build image
+        run: |
+          docker build \
+            --cache-from ${{ env.IMAGE }}:latest \
+            --tag ${{ env.IMAGE }}:latest \
+            --file ./app/backend/Dockerfile.prod \
+            "./app/backend"
+      - name: Push image
+        run: |
+          docker push ${{ env.IMAGE }}:latest
+
+  test:
+    name: Test Docker Image
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          ref: main
+      - name: Log in to GitHub Packages
+        run: echo ${GITHUB_TOKEN} | docker login -u ${GITHUB_ACTOR} --password-stdin ghcr.io
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - name: Pull image
+        run: |
+          docker pull ${{ env.IMAGE }}:latest || true
+      - name: Build image
+        run: |
+          docker build \
+            --cache-from ${{ env.IMAGE }}:latest \
+            --tag ${{ env.IMAGE }}:latest \
+            --file ./app/backend/Dockerfile.prod \
+            "./app/backend"
+      - name: Run container
+        run: |
+          docker run \
+            -d \
+            --name backend \
+            -e PORT=8765 \
+            -e ENVIRONMENT=dev \
+            -e TESTING=0 \
+            -p 8004:8765 \
+            ${{ env.IMAGE }}:latest
+      - name: Pytest
+        run: docker exec backend pipenv run python -m pytest .
+      # - name: Flake8
+      #   run: docker exec backend pipenv run python -m flake8 .
+      # - name: Black
+      #   run: docker exec backend pipenv run python -m black . --check
+      # - name: isort
+      #   run: docker exec backend pipenv run python -m isort . --check-only

Pipfile

@@ -0,0 +1,11 @@
+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+
+[dev-packages]
+
+[requires]
+python_version = "3.8"

app/README.md

@@ -0,0 +1,50 @@
+# How to work with this app repository
+
+Build the images:
+
+```bash
+docker compose up --build -d
+```
+
+I
+
+# Run the tests for backend:
+
+```bash
+docker compose exec backend pipenv run python -m pytest --disable-warnings --cov="."
+```
+
+Lint:
+
+```bash
+docker compose exec backend pipenv run flake8 .
+```
+
+Run Black and isort with check options:
+
+```bash
+docker compose exec backend pipenv run black . --check
+docker compose exec backend pipenv run isort . --check-only
+```
+
+Make code changes with Black and isort:
+
+```bash
+docker compose exec backend pipenv run black .
+docker compose exec backend pipenv run isort .
+```
+
+# Postgres
+
+Want to access the database via psql?
+
+```bash
+docker compose exec -it database psql -U postgres
+```
+
+Then, you can connect to the database and run SQL queries. For example:
+
+```sql
+# \c web_dev
+# \dt
+```

app/backend/Dockerfile

@@ -10,7 +10,7 @@ ENV PYTHONUNBUFFERED 1
 
 # install system dependencies
 RUN apt-get update \
-    && apt-get -y install build-essential netcat-traditional gcc postgresql \
+    && apt-get -y install build-essential netcat-traditional gcc \
     && apt-get clean
 
 # install python dependencies

app/backend/Dockerfile.prod

@@ -0,0 +1,84 @@
+###########
+# BUILDER #
+###########
+
+# pull official base image
+FROM python:3.11-slim AS builder
+
+
+# set working directory
+WORKDIR /usr/src/app
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+
+# install system dependencies
+RUN apt-get update \
+    && apt-get -y install build-essential netcat-traditional gcc \
+    && apt-get clean
+
+# install python dependencies
+RUN pip install --upgrade pip setuptools wheel -i https://pypi.tuna.tsinghua.edu.cn/simple
+RUN pip wheel --no-cache-dir --no-deps --wheel-dir /usr/src/app/wheels -i https://pypi.tuna.tsinghua.edu.cn/simple pipenv
+RUN pip install --no-cache-dir --find-links=/usr/src/app/wheels pipenv
+COPY ./Pipfile .
+RUN pipenv install --deploy
+
+# add app
+COPY . /usr/src/app
+RUN pipenv run pip install black==23.12.1 flake8==7.0.0 isort==5.13.2
+# RUN pipenv run flake8 .
+# RUN pipenv run black --exclude=migrations . --check
+# RUN pipenv run isort . --check-only
+
+#########
+# FINAL #
+#########
+
+# pull official base image
+FROM python:3.11-slim
+
+# create directory for the app user
+RUN mkdir -p /home/app
+
+# create the app user
+RUN addgroup --system app && adduser --system --group app
+
+
+# create the appropriate directories
+ENV HOME=/home/app
+ENV APP_HOME=/home/app/backend
+RUN mkdir $APP_HOME
+WORKDIR $APP_HOME
+
+# set environment variables
+ENV PYTHONDONTWRITEBYTECODE=1
+ENV PYTHONUNBUFFERED=1
+ENV ENVIRONMENT=prod
+ENV TESTING=0
+
+# install system dependencies
+RUN apt-get update \
+    && apt-get -y install build-essential netcat-traditional gcc \
+    && apt-get clean
+
+# install python dependencies
+COPY --from=builder /usr/src/app/wheels /wheels
+COPY --from=builder /usr/src/app/Pipfile .
+RUN pip install --upgrade pip setuptools wheel -i https://pypi.tuna.tsinghua.edu.cn/simple
+RUN pip install --no-cache /wheels/*
+RUN pipenv install --deploy
+RUN pipenv run pip install "uvicorn[standard]==0.26.0"
+
+# add app
+COPY . $APP_HOME
+
+# chown all the files to the app user
+RUN chown -R app:app $APP_HOME
+
+# change to the app user
+USER app
+
+# run gunicorn
+CMD pipenv run gunicorn --bind 0.0.0.0:$PORT backend.main:app -k uvicorn.workers.UvicornWorker

app/backend/Pipfile

@@ -4,13 +4,13 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-fastapi = "*"
+fastapi = "==0.115.9"
-pydantic = "*"
+starlette = "==0.45.3"
-uvicorn = "*"
+uvicorn = "==0.26.0"
 pydantic-settings = "==2.1.0"
-python-decouple = "*"
+gunicorn = "==21.0.1"
+python-decouple = "==3.8"
 pyyaml = "==6.0.1"
-pip = "==24.0.0"
 docker = "*"
 chromadb = "*"
 sentence-transformers = "*"

app/backend/Pipfile.lock

@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "05c19a932e8fd2238dab9a8ea53ef955cea73016b068887c8a410b33ec4c5ce8"
+            "sha256": "22c986576b1b18ff70ae1fefc20957d1758705ed23f84388376db2a6a478a99e"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -271,16 +271,16 @@
         },
         "chromadb": {
             "hashes": [
-                "sha256:4a604f212312c5c10b7470104de45123b75eb7239e1599b22127aa9a414ca78e",
+                "sha256:32daa01014acf98570eeb31e966b641a4d79a2fdc1f750caa5dfc1ba24d9991c",
-                "sha256:51d6adf1859774535f7ab6c6b5492f514970aa26a3e636861dbc7766418d6c08",
+                "sha256:37e8071e3bc40f0a67730f9483ca1d3e8a67d32a3409cd1beaacfb76336eb98c",
-                "sha256:55d514189998734470f700a9d7094ee578949e5df9f891a177e690413071f234",
+                "sha256:844a2a3bd624149093be84b9c3e2b070fa21da129c8563c790be64c4bf0d9f5f",
-                "sha256:582c5307a03a766bf321a023ce9e3c34b0cb7427658e102aacf6742c9d900a5d",
+                "sha256:9c4e72dba33b6fd2da55f044498b298169724cae5113538fa18b3458427ecea8",
-                "sha256:9d7a0c59c5ce95c78f711cf435526b6fdde5158d015132c04af8cb3b04c742d0",
+                "sha256:ee927adfe618e170320b6da25b39a01282142350de70b9b76ab98aa7af7d2f34",
-                "sha256:a29e12c4ac0fdfb12b3ee22ea3c66d2fa4e3516ee9fe3cad0f44b3086d1c50c4"
+                "sha256:f6789b573f510815218b25027f8471b6c132acc2f2d2a53ff42e3e76d9d248ac"
             ],
             "index": "pypi",
             "markers": "python_version >= '3.9'",
-            "version": "==1.0.3"
+            "version": "==1.0.4"
         },
         "click": {
             "hashes": [
@@ -435,6 +435,15 @@
             "markers": "python_version >= '3.9'",
             "version": "==1.71.0"
         },
+        "gunicorn": {
+            "hashes": [
+                "sha256:949880781d74f55eda34eb1a552f9c83db6edb42f2bd4f87c09e2a66b13922ea",
+                "sha256:b18fa5a9b22becdffc29d2586b914225a69624bb3e3a064cb04decfb2f34bfe8"
+            ],
+            "index": "pypi",
+            "markers": "python_version >= '3.5'",
+            "version": "==21.0.1"
+        },
         "h11": {
             "hashes": [
                 "sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d",
@@ -730,11 +739,11 @@
         },
         "langsmith": {
             "hashes": [
-                "sha256:060956aaed5f391a85829daa0c220b5e07b2e7dd5d33be4b92f280672be984f7",
+                "sha256:4666595207131d7f8d83418e54dc86c05e28562e5c997633e7c33fc18f9aeb89",
-                "sha256:0bdeda73cf723cbcde1cab0f3459f7e5d5748db28a33bf9f6bdc0e2f4fe0ee1e"
+                "sha256:54ac8815514af52d9c801ad7970086693667e266bf1db90fc453c1759e8407cd"
             ],
             "markers": "python_version >= '3.9' and python_version < '4.0'",
-            "version": "==0.3.27"
+            "version": "==0.3.28"
         },
         "markdown-it-py": {
             "hashes": [
@@ -1276,15 +1285,6 @@
             "markers": "python_version >= '3.9'",
             "version": "==11.1.0"
         },
-        "pip": {
-            "hashes": [
-                "sha256:ba0d021a166865d2265246961bec0152ff124de910c5cc39f1156ce3fa7c69dc",
-                "sha256:ea9bd1a847e8c5774a5777bb398c19e80bcd4e2aa16a4b301b718fe6f593aba2"
-            ],
-            "index": "pypi",
-            "markers": "python_version >= '3.7'",
-            "version": "==24.0"
-        },
         "posthog": {
             "hashes": [
                 "sha256:1ac0305ab6c54a80c4a82c137231f17616bef007bbf474d1a529cda032d808eb",
@@ -1330,7 +1330,6 @@
                 "sha256:7471657138c16adad9322fe3070c0116dd6c3ad8d649300e3cbdfe91f4db4ec3",
                 "sha256:a082753436a07f9ba1289c6ffa01cd93db3548776088aa917cc43b63f68fa60f"
             ],
-            "index": "pypi",
             "markers": "python_version >= '3.9'",
             "version": "==2.11.3"
         },
@@ -2030,6 +2029,7 @@
                 "sha256:2cbcba2a75806f8a41c722141486f37c28e30a0921c5f6fe4346cb0dcee1302f",
                 "sha256:dfb6d332576f136ec740296c7e8bb8c8a7125044e7c6da30744718880cdd059d"
             ],
+            "index": "pypi",
             "markers": "python_version >= '3.9'",
             "version": "==0.45.3"
         },
@@ -2194,12 +2194,12 @@
                 "standard"
             ],
             "hashes": [
-                "sha256:023dc038422502fa28a09c7a30bf2b6991512da7dcdb8fd35fe57cfc154126f4",
+                "sha256:48bfd350fce3c5c57af5fb4995fded8fb50da3b4feb543eb18ad7e0d54589602",
-                "sha256:404051050cd7e905de2c9a7e61790943440b3416f49cb409f965d9dcd0fa73e9"
+                "sha256:cdb58ef6b8188c6c174994b2b1ba2150a9a8ae7ea5fb2f1b856b94a815d6071d"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.9'",
+            "markers": "python_version >= '3.8'",
-            "version": "==0.34.0"
+            "version": "==0.26.0"
         },
         "uvloop": {
             "hashes": [

app/backend/api/ping.py

@@ -1,7 +1,6 @@
 from fastapi import APIRouter, Depends
 
-from config import get_settings, Settings
+from config import Settings, get_settings
-
 
 router = APIRouter()
 
@@ -11,5 +10,5 @@ async def pong(settings: Settings = Depends(get_settings)):
     return {
         "ping": "pong!",
         "environment": settings.environment,
-        "testing": settings.testing
+        "testing": settings.testing,
-    }
+    }

app/backend/tests/api/test_chatbot.py

@@ -7,7 +7,7 @@ import unittest
 from unittest.mock import AsyncMock
 from fastapi import WebSocket, WebSocketDisconnect
 
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..')))
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..')))
 
-from app.backend.api.chatbot import websocket_endpoint, manager, llm_chat
+from api.chatbot import websocket_endpoint, manager, llm_chat
 

app/backend/tests/api/test_utils.py

@@ -4,9 +4,9 @@ import unittest
 from unittest.mock import AsyncMock, MagicMock
 from fastapi import WebSocket
 
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..', '..', '..')))
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..')))
 
-from app.backend.api.utils import ConnectionManager
+from api.utils import ConnectionManager
 
 class TestConnectionManager(unittest.IsolatedAsyncioTestCase):
     async def asyncSetUp(self):

app/backend/tests/conftest.py

@@ -1,10 +1,8 @@
-import os
-
 import pytest
 from starlette.testclient import TestClient
 
-import main
 from config import get_settings, Settings
+from main import create_application
 
 
 def get_settings_override():
@@ -14,10 +12,10 @@ def get_settings_override():
 @pytest.fixture(scope="module")
 def test_app():
     # set up
-    main.app.dependency_overrides[get_settings] = get_settings_override
+    app = create_application()
-    with TestClient(main.app) as test_client:
+    app.dependency_overrides[get_settings] = get_settings_override
-
+    with TestClient(app) as test_client:
         # testing
         yield test_client
 
-    # tear down
+    # tear down

app/docker-compose.yml

@@ -13,7 +13,6 @@ services:
     build:
       context: ./backend
       dockerfile: Dockerfile
-    platform: linux/amd64
     command: pipenv run uvicorn main:app --reload --workers 1 --host 0.0.0.0 --port 8000
     volumes:
       - ./backend:/usr/src/app
@@ -21,4 +20,4 @@ services:
       - "8004:8000"
     environment:
       - ENVIRONMENT=dev
-      - TESTING=0
+      - TESTING=0