Add instructions for Docker deployment

Changes to be committed:
	modified:   Dockerfile
	modified:   docker-compose.yml
	modified:   docs/deployment/dockerDeployment.md
	new file:   entrypoint.sh

Author: HadleyKing

Dockerfile

@@ -6,29 +6,22 @@ LABEL org.opencontainers.image.source=https://github.com/octocat/my-repo
 LABEL org.opencontainers.image.description="My container image"
 LABEL org.opencontainers.image.licenses=MIT
 
-# Note that this is just for debug / test purposes; should not be set via the setup for production
-# ENV DJANGO_SUPERUSER_PASSWORD="BioCompute123"
-# ENV DJANGO_SUPERUSER_USERNAME="BioComputeSuperUser"
-# ENV DJANGO_SUPERUSER_EMAIL="[email protected]"
 
 RUN apt-get -qq update && apt-get install -y python3.9 python3-dev python3-pip
 
 RUN python3 -m pip install --upgrade pip
 
 WORKDIR /biocompute_api
 
-COPY requirements.txt .
-
+COPY requirements.txt /biocompute_api/
 RUN python3 -m pip install -r requirements.txt
 
-COPY . ./
-
-WORKDIR /biocompute_api/
+COPY . /biocompute_api/
 
-# RUN python3 manage.py migrate
-# RUN python3 manage.py createsuperuser --no-input
+WORKDIR /biocompute_api
 
 EXPOSE 8000
-#CMD ["bash"]
-ENTRYPOINT ["python3", "manage.py", "runserver"]
-CMD ["0.0.0.0:8000"]
+
+ENTRYPOINT ["./entrypoint.sh"]
+
+CMD ["python3", "manage.py", "runserver", "0.0.0.0:8000"]

docker-compose.yml

@@ -1,24 +1,18 @@
-#cat docker-compose.yml
-
-version: '3.4'
 
 services:
   bco-api:
     platform: linux/amd64
     build: .
-    image: ghcr.io/biocompute-objects/bco_api:23.07
     container_name: bco-api
-    volumes:
-       - ./data/db.sqlite3:/biocompute_api/db.sqlite3
-       - ./data/server.conf:/biocompute_api/server.conf
+    # volumes:
+    #   - ./db.sqlite3:/biocompute_api/db.sqlite3
+    #   - ./.secrets:/biocompute_api/.secrets
     environment:
       TZ: 'America/New_York'
-      ENV DJANGO_SUPERUSER_PASSWORD: "BioCompute123"
-      ENV DJANGO_SUPERUSER_USERNAME: "BioComputeSuperUser"
-      ENV DJANGO_SUPERUSER_EMAIL: "[email protected]"
+
     ports:
       - "8000:8000"
-    read_only: true
+
     tmpfs:
       - /tmp
     restart: unless-stopped

docs/deployment/dockerDeployment.md

@@ -0,0 +1,88 @@
+# BCODB Docker Deployment
+
+
+### Requirements
+- Python 3: [3.10.6 reccomended](https://www.python.org/downloads/release/python-3106/)
+- [PyEnv](https://github.com/pyenv/pyenv) (optional but recommended for Mac/Linux)
+- Docker:
+    - [Docker Desktop for Linux](https://docs.docker.com/desktop/install/linux-install/)
+    - [Docker Desktop for Mac (macOS)](https://docs.docker.com/desktop/install/mac-install/)
+    - [Docker Desktop for Windows](https://docs.docker.com/desktop/install/windows-install/)
+
+
+## Clone the repository
+```
+git clone https://github.com/biocompute-objects/bco_api
+```
+
+**Make sure you are on the desired branch (Check for latest branch):**
+
+```
+git switch [DESIRED BRANCH TAG]
+```
+
+## Enter the repository
+```
+cd bco_api
+```
+## Configure the DB settings using the `.secrets` file:
+
+### OPTION 1: Generate the secrets file 
+
+In the project root copy the `.secrets.example` to `.secrets`
+
+```
+cp .secrets.example .secrets
+```
+#### Generate the DJANGO_KEY
+Generate a 32-bytes long PSK key using the `openssl` command or `PowerShell` command.
+
+##### Mac/Linux:
+```
+openssl rand -base64 32
+```
+##### Windows:
+```   
+[Convert]::ToBase64String((1..32 | ForEach-Object { Get-Random -Minimum 0 -Maximum 256 }) -as [byte[]])
+```
+
+Use a text editor to open the `.secrets` file and update the rest of the variables. For details on each of the variables see the [configuration](/docs/config.md) documentation. 
+
+### OPTION 2: Use the `local_deployment.secrets` file
+Fromt the project root:
+```
+cp admin_only/local_deployment.secrets .secrets
+```
+
+### Building the BCO API via Docker
+
+A docker file is provided to allow easy building of the BCO API.  This can be done from the root directory (the directory with Dockerfile in it) by running:
+
+`docker build -t bco_api:latest .`
+
+This will build a container named `bco_api` with the tag `latest`.
+
+The build process (via the `entrypoint.sh` script) will check for an existing database in the repository and run migrations. If no database is present one will be created and the test data will be loaded (taken from `config/fixtures/local_data.json`).
+
+### Running the container via Docker
+
+The BCO Api container can be run via docker on the command line in Linux/Windows by running:
+
+`docker run --rm --network host -it bco_api:latest`
+
+The BCO Api container can be run via docker on the command line in MacOS by running:
+
+`docker run --rm -p 8000:8000 -it bco_api:latest`
+
+This will expose the server at `http://127.0.0.1:8000`, whitch is where all of the default settings will expect to find the BCODB. 
+
+#### Overriding the port
+
+It is possible to override the port 8000 to whatever port is desired.  This is done by running the container with 8080 representing the desired port.
+
+`docker run --rm --network host -it bco_api:latest 0.0.0.0:8080`
+
+
+NOTE: The ip address of 0.0.0.0 is to allow the web serer to properly associate with 127.0.0.1 - if given 127.0.0.1 it will not allow communications outside of the container!
+
+You can also give it a specific network created with `docker network create` if you wanted to give assigned IP addresses.

entrypoint.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+# entrypoint.sh
+
+# Check if the SQLite database file exists and run migrations if it doesn't
+if [ ! -f "db.sqlite3" ]; then
+  echo "Database not found. Running migrations..."
+  python3 manage.py migrate
+  python3 manage.py loaddata config/fixtures/local_data.json
+else
+  echo "Database exists. Running migrations."
+  python3 manage.py migrate
+fi
+
+# Start the Django server
+exec "$@"