dev base project

update README

.gitignore

+.vscode
+.env
+
+# MacOS
+.DS_Store
+
+# Python
+__pycache__
+*.egg-info/

LICENSE

+MIT License
+
+Copyright (c) 2021 Institut Pasteur
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -4,3 +4,18 @@ From experiences acquired developing https://gitlab.pasteur.fr/metagenomics/meta
 
 * [FastAPI](https://fastapi.tiangolo.com/)
 * [SQLModel](https://sqlmodel.tiangolo.com/)
+
+## Run the project for DEV
+
+To run the application you need:
+
+* `Docker` : [Install instructions](https://docs.docker.com/install/)
+* `Docker Compose` : [Install instructions](https://docs.docker.com/compose/install/)
+
+From the root directory of the repository:
+
+```bash
+docker-compose up
+```
+
+Then you can visit the [documentation](http://localhost/docs) of the project.

backend/Dockerfile

+FROM python:3.9
+
+WORKDIR /app/
+
+# Install Poetry
+RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | POETRY_HOME=/opt/poetry python && \
+    cd /usr/local/bin && \
+    ln -s /opt/poetry/bin/poetry && \
+    poetry config virtualenvs.create false
+
+# Copy poetry.lock* in case it doesn't exist in the repo
+COPY ./app/pyproject.toml ./app/poetry.lock* /app/
+
+# Allow installing dev dependencies to run tests
+ARG INSTALL_DEV=false
+RUN bash -c "if [ $INSTALL_DEV == 'true' ] ; then poetry install --no-root ; else poetry install --no-root --no-dev ; fi"
+
+COPY ./app /app
+ENV PYTHONPATH=/app
+
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80"]

backend/app/app/__init__.py

+__version__ = '0.1.0'

backend/app/app/api/endpoints/genes.py

+from fastapi import APIRouter
+
+
+router = APIRouter()
+
+
+@router.get("/")
+async def genes():
+    """
+    """
+    return {
+        'data': {"genes": [1, 2, 3]}
+    }
+
+
+@router.get("/{gene_id}")
+async def gene(gene_id: str):
+    """
+    """
+    return {
+        'data': {"gene_id": gene_id}
+    }

backend/app/app/api/router.py

+from fastapi import APIRouter
+
+from app.api.endpoints import genes
+
+api_router = APIRouter()
+api_router.include_router(genes.router, prefix="/genes", tags=["Genes"])

backend/app/app/core/config.py

+from pydantic import BaseSettings
+
+
+class Settings(BaseSettings):
+    API_STR: str = "/api"
+
+
+settings = Settings()

backend/app/app/main.py

+import logging
+
+from fastapi import FastAPI
+
+from app.version import __version__
+from app.api.router import api_router
+from app.core.config import settings
+
+app = FastAPI(
+    title="FastGenes",
+    description="API for genes database.",
+    version=__version__,
+    docs_url="/docs",
+    openapi_url=f"{settings.API_STR}/openapi.json",
+)
+logger = logging.getLogger(__name__)
+
+
+app.include_router(
+    api_router,
+    prefix=settings.API_STR,
+)
\ No newline at end of file

backend/app/app/models/gene.py

+from typing import Optional
+
+from sqlmodel import Field, SQLModel
+
+
+class Gene(SQLModel, table=True):
+    gene_id: str = Field(primary_key=True)
+    sequence: str
+    length: int

backend/app/app/version.py

+version_info = (0, 1, 0)
+__version__ = '.'.join(str(c) for c in version_info)

backend/app/pyproject.toml

+[tool.poetry]
+name = "app"
+version = "0.1.0"
+description = ""
+authors = ["Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>"]
+
+[tool.poetry.dependencies]
+python = "^3.8"
+fastapi = "^0.70.0"
+sqlmodel = "^0.0.4"
+uvicorn = "^0.15.0"
+
+[tool.poetry.dev-dependencies]
+pytest = "^5.2"
+
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"

backend/tests/test_app.py

+from app import __version__
+
+
+def test_version():
+    assert __version__ == '0.1.0'

docker-compose.yaml

+version: '3'
+
+services:
+
+  backend:
+    container_name: fastgenes-backend
+    build:
+      context: ./backend
+      args:
+        INSTALL_DEV: ${INSTALL_DEV-true}
+    volumes:
+      - ./backend/app:/app
+    ports:
+      - "8888:8888"
+    command: uvicorn --reload --host 0.0.0.0 --port 8888 app.main:app
+    networks:
+      - main
+
+  nginx:
+    image: nginx:1.13.12-alpine
+    ports:
+      - "80:80"
+    depends_on:
+      - backend
+    volumes:
+      - ./nginx/dev/nginx.conf:/etc/nginx/nginx.conf:ro
+    networks:
+      - main
+
+networks:
+  main:
+    driver: bridge