Merge pull request #185 from afids/docker

Set up Docker compose

.dockerignore

@@ -0,0 +1,8 @@
+dist
+__pycache__
+Dockerfile
+compose
+compose.yaml
+.git
+uploads
+test

Dockerfile

@@ -0,0 +1,28 @@
+FROM debian:bullseye as packaging
+ENV PATH=/root/.local/bin:$PATH
+RUN echo "deb http://deb.debian.org/debian bullseye-backports main" > /etc/apt/sources.list.d/backports.list \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+        python3=3.9.2-3 \
+        python3-pip=20.3.4-4+deb11u1 \
+    && apt-get install -y -q --no-install-recommends -t bullseye-backports pipx=1.0.0-1~bpo11+1 \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
+    && pipx ensurepath \
+    && pipx install poetry==1.2.2
+WORKDIR /apps/afidsvalidator
+COPY . .
+RUN poetry build
+
+FROM debian:bullseye as deploy
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+        build-essential=12.9 \
+        gcc=4:10.2.1-1 \
+        python3=3.9.2-3 \
+        python3-dev=3.9.2-3 \
+        python3-pip=20.3.4-4+deb11u1 \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+WORKDIR /apps/afidsvalidator
+COPY --from=packaging /apps/afidsvalidator/dist/afidsvalidator-*-py3-none-any.whl /apps/wheels/
+RUN pip install --no-cache-dir `ls /apps/wheels/*.whl`[deploy]
+ENTRYPOINT ["uwsgi", "-w", "afidsvalidator.wsgi:app"]

afidsvalidator/__init__.py

@@ -3,11 +3,16 @@
 import os
 
 from flask import Flask
+from flask_migrate import Migrate
 
+from afidsvalidator.config import (
+    DevelopmentConfig,
+    ProductionConfig,
+    TestingConfig,
+)
 from afidsvalidator.model import db, login_manager
 from afidsvalidator.orcid import orcid_blueprint
 from afidsvalidator.views import validator
-from config import DevelopmentConfig, ProductionConfig, TestingConfig
 
 
 class ConfigException(Exception):
@@ -58,6 +63,8 @@ def create_app():
     app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
     db.init_app(app)
     login_manager.init_app(app)
+    migrate = Migrate(render_as_batch=True, compare_type=True)
+    migrate.init_app(app, db)
     app.register_blueprint(validator)
     app.register_blueprint(orcid_blueprint)
 

config.py → afidsvalidator/config.py

@@ -4,8 +4,7 @@
 
 from dotenv import load_dotenv
 
-basedir = os.path.abspath(os.path.dirname(__file__))
-load_dotenv(f"{basedir}/.env")
+load_dotenv()
 
 
 class Config(object):
@@ -21,7 +20,6 @@ class Config(object):
     )
 
     SQLALCHEMY_DATABASE_URI = os.environ.get("DATABASE_URL")
-    AFIDS_DIR = "afidsvalidator/afids-templates"
     SQLALCHEMY_TRACK_MODIFICATIONS = (
         os.environ.get("SQLALCHEMY_TRACK_MODIFICATIONS") or False
     )

afidsvalidator/views.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import os
 from dataclasses import dataclass
 from datetime import datetime, timezone
 from pathlib import Path
@@ -107,8 +106,10 @@ def render_validator(form, result="", placement_report=None):
     """Render the validator page."""
     form_choices = sorted(
         [
-            choice.capitalize()
-            for choice in os.listdir(current_app.config["AFIDS_DIR"])
+            choice.name.capitalize()
+            for choice in (
+                Path(current_app.root_path) / "afids-templates"
+            ).iterdir()
         ]
     )
     if placement_report:
@@ -178,7 +179,8 @@ def validate():
 
     # Need to pull from correct folder when more templates are added
     with open(
-        Path(current_app.config["AFIDS_DIR"])
+        Path(current_app.root_path)
+        / "afids-templates"
         / request.form["fid_species"].lower()
         / f"tpl-{fid_template}_afids.fcsv",
         "r",
@@ -211,11 +213,13 @@ def get_templates(species):
         ["Validate file structure"]
         + sorted(
             [
-                species_templates[4:].split("_")[0]
-                for species_templates in os.listdir(
-                    f"{current_app.config['AFIDS_DIR']}/{species.lower()}"
-                )
-                if "tpl" in species_templates
+                species_templates.name[4:].split("_")[0]
+                for species_templates in (
+                    Path(current_app.root_path)
+                    / "afids-templates"
+                    / species.lower()
+                ).iterdir()
+                if "tpl" in species_templates.name
             ],
             key=str.lower,
         )

afidsvalidator/wsgi.py

@@ -0,0 +1,3 @@
+from afidsvalidator import create_app
+
+app = create_app()

compose.yml

@@ -0,0 +1,26 @@
+services:
+  afidsvalidator:
+    build: .
+    environment:
+      DATABASE_URL: postgresql+psycopg2://postgres:example@postgres:5432
+      UWSGI_SOCKET: 0.0.0.0:5000
+      FLASK_ENV: development
+    ports: ["5000:5000"]
+    depends_on:
+      - postgres
+  postgres:
+    image: postgres:11
+    restart: unless-stopped
+    environment:
+      POSTGRES_PASSWORD: example
+    volumes:
+      - "./compose/postgres-db:/var/lib/postgresql/data"
+    ports: ["5432:5432"]
+  nginx:
+    image: nginx:latest
+    hostname: nginx
+    volumes:
+      - "./compose/nginx.conf:/etc/nginx/nginx.conf"
+    ports: ["5001:80"]
+    depends_on:
+      - afidsvalidator

compose/nginx.conf

@@ -0,0 +1,14 @@
+events {
+  worker_connections  4096;  ## Default: 1024
+}
+
+http {
+  server {
+    listen 80;
+    server_name nginx;
+    location / {
+      include uwsgi_params;
+      uwsgi_pass afidsvalidator:5000;
+    }
+  }
+}