sillsdev · jmgrady · Sep 12, 2020 · Jul 16, 2020 · Jul 16, 2020 · Jul 16, 2020
diff --git a/.env.backend.auth.template b/.env.backend.auth.template
diff --git a/.env.backend.template b/.env.backend.template
diff --git a/.gitignore b/.gitignore
@@ -11,13 +11,17 @@
 
 # Production
 /build
-production.yml
 
-# Misc
-.DS_Store
+# Generated Docker files for development use
+docker-compose.yml
 .env.backend
-.env.backend.auth
+.env.frontend
 .env*.local
+nginx/scripts
+nginx/conf.d
+
+# Misc
+.DS_Store
 Session.vim
 /*.js
 
@@ -56,7 +60,9 @@ mongo_database
 .vagrant/
 
 # Python
+__pycache__
 *.pyc
+venv
 
 # Auto-generated SSL keys and certificate requests
 deploy/site_info/
@@ -67,12 +73,15 @@ deploy/roles_galaxy/
 # Host file to be used for ad hoc testing/development
 deploy/*.hosts
 deploy/*.hosts.yml
+docker_deploy/*.hosts.yml
 
 # Playbooks for ad hoc testing/development
 deploy/_playbook*.yml
+docker_deploy/_playbook*.yml
 
 # Emacs backup files (this is Jim's fault)
 *~
+\#*#
 
 # JetBrains Rider
 .idea
diff --git a/Backend/Dockerfile b/Backend/Dockerfile
@@ -15,6 +15,8 @@ FROM mcr.microsoft.com/dotnet/core/aspnet:3.1
 
 ENV ASPNETCORE_URLS=http://+:5000
 ENV COMBINE_IS_IN_CONTAINER=1
+ENV ASPNETCORE_ENVIRONMENT=Production
+ENV DOTNET_PRINT_TELEMETRY_MESSAGE=false
 
 # Set the home directory to the app user's home.
 ENV HOME=/home/app

diff --git a/Backend/launch.sh b/Backend/launch.sh
diff --git a/Dockerfile b/Dockerfile
@@ -11,25 +11,23 @@ COPY . ./
 RUN npm run build
 
 # Production environment.
-FROM nginx:stable-alpine
+FROM staticfloat/nginx-certbot
 
 WORKDIR /app
 
 # Args used to configure frontend build.
-ARG COMBINE_CAPTCHA_REQUIRED
-ARG COMBINE_CAPTCHA_SITE
+#ARG COMBINE_CAPTCHA_REQUIRED
+#ARG COMBINE_CAPTCHA_SITE
 
 ENV NGINX_HOST_DIR /usr/share/nginx/html
 
 COPY --from=builder /app/build ${NGINX_HOST_DIR}
 
 # Configure frontend.
-COPY nginx/generate_config.sh ./
-RUN ./generate_config.sh > ${NGINX_HOST_DIR}/config.js \
-    && rm generate_config.sh
+#COPY nginx/generate_config.sh ./
+#RUN ./generate_config.sh > ${NGINX_HOST_DIR}/config.js \
+#    && rm generate_config.sh
 
 # Copy default self-signed certificate.
 # Overwrite this with real certificate for authentication in production.
 COPY nginx/certs /ssl
-
-COPY nginx/nginx.conf /etc/nginx/conf.d/default.conf
diff --git a/README.md b/README.md
@@ -203,22 +203,6 @@ environment variable and then run:
 
 The exit code will be set to `0` on success and non-`0` otherwise.
 
-#### Docker
-
-Copy `.env.backend.auth.template` to `.env.backend.auth` add fill in the username and
-password environment variables.
-
-```batch
-> docker-compose build --parallel
-> docker-compose up --abort-on-container-exit
-```
-
-This will create the user and exit. If successful, the exit code will be `0`,
-otherwise an error will be logged and the exit code will be non-`0`.
-
-**Important**: Remove the `COMBINE_*` environment variables from
-`.env.backend.auth` so that subsequent launches will start up the backend.
-
 ### (Development Only) Grant an Existing User Admin Rights
 
 To grant an _existing_ user database administrator rights (all permissions for
@@ -247,93 +231,133 @@ To generate a full report of the licenses used in production:
 
 ### Requirements
 
+#### Docker
+
 Install [Docker](https://docs.docker.com/get-docker/).
 
 (Linux Only) Install [Docker Compose](https://docs.docker.com/compose/install/)
 separately. This is included by default in Docker Desktop for Windows and macOS.
 
-### Build and Run
+#### Python
 
-For more information see the
-[Docker Compose docs](https://docs.docker.com/compose/).
+A Python script, `docker_setup.py` is used to configure the files needed to run
+*TheCombine* in Docker containers.
 
-Copy `.env.backend.template` to `.env.backend` and fill in the environment
-variables.
+##### Windows Only
 
-```batch
-> docker-compose build --parallel
-> docker-compose up --detach
-```
+* Navigate to the [Python 3.8.5 Downloads](https://www.python.org/downloads/release/python-385/) page.
 
-Browse to https://localhost.
+* Download and run the appropriate installer - it is most likely the installer labeled
+    *Windows x86-64 executable installer*
 
-> By default self-signed certificates are included, so you will need to accept
-> a warning in the browser. See [SSL Certificates](#ssl-certificates) for
-> production deployment.
+* Once Python is installed, create an isolated Python 
+  [virtual environment](https://docs.python.org/3/library/venv.html) using the 
+  [`py`](https://docs.python.org/3/using/windows.html#getting-started) launcher
+  installed globally into the `PATH`. 
 
-To view logs:
+    ```batch
+    > py -m venv venv
+    > venv\Scripts\activate
+    ```
+
+##### Linux Only
 
-```batch
-> docker-compose logs --follow
+To install Python 3 on Ubuntu, run the following commands:
+
+```bash
+$ sudo apt update
+$ sudo apt install python3 python3-venv
 ```
 
-To stop and remove any stored data:
+Create an isolated Python virtual environment
 
-```batch
-> docker-compose down --volumes
+```bash
+$ python3 -m venv venv
+$ venv/bin/activate
 ```
 
-### Configuration
+##### Python Packages
 
-#### SSL Certificates
-
-To update SSL certificates after images have been built and are running,
-find the `frontend` container name. By default this will be formatted as
-`<lowercase_parent_dir>_frontend_1`.
+With an active virtual environment, install `Jinja2`:
 
 ```batch
-> docker-compose images
-      Container             Repository         Tag       Image Id       Size
-------------------------------------------------------------------------------
-thecombine_backend_1    thecombine_backend    latest   73cf7b867c22   292.2 MB
-thecombine_database_1   mongo                 4.2      2b2cc1f48aed   387.8 MB
-thecombine_frontend_1   thecombine_frontend   latest   7cca1c1f1a5f   32.55 MB
+(venv) > python -m pip install Jinja2
 ```
 
-Copy new certificates from local filesystem into the container:
+#### Configure Docker
+
+Run the configuration script in an activated virtual environment.
 
 ```batch
-> docker cp new_cert.pem thecombine_frontend_1:/ssl/cert.pem
-> docker cp new_key.pem thecombine_frontend_1:/ssl/key.pem
+(venv) > python docker_setup.py 
 ```
 
-Restart the Docker Compose project:
+### Build and Run
 
-```batch
-> docker-compose down
-> docker-compose up --detatch
-```
+For information on *Docker Compose* see the
+[Docker Compose documentation](https://docs.docker.com/compose/).
 
-#### Modifying Build Arguments
+#### Step-by-step Instructions for Running *TheCombine* In Docker
 
-Create a file `production.yml`, and override build arguments as needed.
+1. Create the required docker files by running `docker_setup.py` from *TheCombine*'s project directory:
+2. The `docker_setup.py` will generate a file, `.env.backend`, that defines
+the environment variables needed by the Backend container.  If you have defined
+them as OS variables in the [Getting Started with Development](#getting-started-with-development) section above, then these variables will already be set.  If not,
+then you will need to edit `.env.backend` and provide values for the variables that
+are listed.
+3. Build the images for the Docker containers
 
-```yaml
-version: "3.8"
-services:
-  frontend:
-    build:
-      args:
-        - COMBINE_CAPTCHA_REQUIRED=false
-```
+   ```batch
+   > docker build -t combine/frontend:latest --pull -f Dockerfile .
+   > cd Backend
+   > docker build -t combine/backend:latest --pull -f Dockerfile .
+   > cd ..
+   ```
+4. Run `docker-compose` to start the containers
+   ```batch
+   > docker-compose up --detach
+   ```
+5. Browse to https://localhost.
+
+   *By default self-signed certificates are included, so you will need to accept a warning in the browser.*
+
+6. To view logs:
+
+   ```batch
+   > docker-compose logs --follow
+   ```
+
+7. To stop and remove any stored data:
 
-Use this file when building and launching the Docker Compose project.
+   ```batch
+   > docker-compose down --volumes
+   ```
+
+### Create a New Admin User (Docker Environment)
+
+Edit `.env.backend` as follows:
+ * Fill in the environment variables.
+ * Add the following environment variables and assign values to them:
+   - COMBINE_ADMIN_USERNAME
+   - COMBINE_ADMIN_PASSWORD
+ * Set the file permissions so that only you have read or write access.
+
+Run the following command to install the admin user in the *CombineDatabase*:
 
 ```batch
-> docker-compose -f docker-compose.yml -f production.yml build --parallel
-> docker-compose -f docker-compose.yml -f production.yml up --detach
+> docker-compose up --abort-on-container-exit
 ```
 
+This will create the user and exit. If successful, the exit code will be `0`,
+otherwise an error will be logged and the exit code will be non-`0`.
+
+**Important**: Remove the `COMBINE_ADMIN_*` environment variables from
+`.env.backend` so that subsequent launches will start up the backend.
+
+### Production
+
+The process for configuring and deploying *TheCombine* for production targets is described in ./docs/docker_deploy/README.md
+
 ## Learn More
 
 - [React](https://reactjs.org/)

diff --git a/deploy/roles/ansible_depends/tasks/main.yml b/deploy/roles/ansible_depends/tasks/main.yml
@@ -2,10 +2,6 @@
 # This role installs all the packages that must be on the target
 # machine in order to successfully use Ansible to manage the target.
 
-- name: Install python2-pip
-  package:
-    name: python-pip
-    state: present
 - name: Install python3
   package:
     name: python3

diff --git a/deploy/roles/mongodb/tasks/install.yml b/deploy/roles/mongodb/tasks/install.yml
@@ -20,7 +20,7 @@
     repo: "deb [arch=amd64] https://repo.mongodb.org/apt/ubuntu {{ ansible_distribution_release }}/mongodb-org/{{ mongodb_version }} multiverse"
     filename: mongodb-org-{{ mongodb_version }}
     update_cache: yes
-  when: ansible_distribution == 'Ubuntu' and ansible_distribution_release == 'bionic'
+  when: ansible_distribution == 'Ubuntu'
 
 - name: Install mongodb-org
   apt: