Installation

Important

Ubuntu (20.04 LTS is recommended)

See also

If you’ve never set up a server before, DigitalOcean provides an extensive variety of tutorials that we highly recommend. Several of the steps below were adapted from their tutorials.

Initial Server Setup With Ubuntu 20.04

Django, PostgreSQL, NGINX, Gunicorn, and Ubuntu 20.04

It’s recommended to visit these tutorials to understand some of the rational behind the steps below.

The following instructions provide guidance on installing MeDNA-Metadata on Ubuntu 20.04.

Important

Instances of youruser need to be replaced with a relevant username. For example, references to /home/youruser/ must be adjusted to the active Ubuntu username. The simplest solution would be to use the same username throughout the setup process, as long as it is not the root username. Never use root. For more information, see the aforementioned Initial Server Setup With Ubuntu 20.04.

Clone the Repository

To clone the most recent stable release as read-only:

git clone -b stable/1.0.2 https://github.com/Maine-eDNA/medna-metadata.git

To clone the development branch:

git clone -b main git@github.com:Maine-eDNA/medna-metadata.git

Docker Setup

Install Requirements

Ubuntu 20.04

Deploying with docker requires docker and docker-compose. Docker-compose must be able to run at least version 3.8. DigitalOcean provides tutorials on How to Install and Use Docker on Ubuntu 20.04 and How To Install and Use Docker Compose on Ubuntu 20.04.

After following DigitalOcean’s tutorials, create a symbolic link of the installation to the docker-compose command

sudo ln -s ~/.docker/cli-plugins/docker-compose /usr/bin/docker-compose

Important

This allows you to call docker-compose from the command line, and is highly recommended to avoid future headaches.

The docker/ directory has medna.env.txt and medna.env.db.txt, which contain all environmental variables for docker deployment. These files are necessary for docker. Other files that affect docker are:

entrypoint.sh

.dockerignore

contents of docker/ directory

settings in medna_metadata/settings.py

Navigate to the docker/ directory

cd medna-metadata/docker/

Make a copy of medna.env.txt and medna.env.db.txt in the same docker/ directory with the .txt extension removed (e.g., medna.env.db, medna.env)

cp medna.env.txt medna.env
cp medna.env.db.txt medna.env.db

medna.env:

####################################################################
# django general settings; loaded in settings.py
# The secret key must be a large random value and it must be kept secret.
# https://docs.djangoproject.com/en/4.0/ref/settings/#std:setting-SECRET_KEY
# https://docs.djangoproject.com/en/4.0/ref/settings/#std-setting-TIME_ZONE
# List of time zones: https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
####################################################################
DJANGO_SECRET_KEY=your_secret_key
DJANGO_ALLOWED_HOSTS=localhost 127.0.0.1 your_ip_address [::1]
DJANGO_ALLAUTH_HOST=your_domain
DJANGO_SETTINGS_MODULE=medna_metadata.settings
DJANGO_DEBUG=False
DJANGO_LOG_LEVEL=info
TIME_ZONE=America/New_York

####################################################################
# Creates a superuser account (a user who has all permissions).
# https://docs.djangoproject.com/en/4.0/ref/django-admin/#createsuperuser
####################################################################
DJANGO_SUPERUSER_PASSWORD=your_superuser_password
DJANGO_SUPERUSER_EMAIL=your_superuser_email@domain.com
DJANGO_SUPERUSER_USERNAME=your_superuser_email@domain.com

####################################################################
# web_start.sh settings
# DJANGO_MANAGEPY_MIGRATE - build database tables; calls the migrate management cmd - https://docs.djangoproject.com/en/4.0/topics/migrations/
# DJANGO_DATABASE_FLUSH - empty database of all data; calls the flush management cmd - https://docs.djangoproject.com/en/4.0/ref/django-admin/#flush
# DJANGO_SUPERUSER_CREATE - create a superuser account; calls the createsuperuser management cmd - https://docs.djangoproject.com/en/4.0/ref/django-admin/#createsuperuser
# DJANGO_DEFAULT_GROUPS_CREATE - create default permissions groups; calls custom create_default_groups management cmd (admin, gradstudent, intern)
# DJANGO_DEFAULT_USERS_CREATE - create default user; calls custom create_default_user management cmd
# DJANGO_DATABASE_LOADDATA - load database with base data from fixtures; calls loaddata management cmd - https://docs.djangoproject.com/en/4.0/ref/django-admin/#loaddata
# DJANGO_COLLECT_STATIC - calls the collectstatic management cmd - https://docs.djangoproject.com/en/4.0/ref/contrib/staticfiles/
# entrypoint.sh settings
# ENTRYPOINT_DATABASE & ENTRYPOINT_MESSAGING - name of entrypoint to wait for; do not change these values unless updating entrypoint.sh and the type of messaging server or database
####################################################################
DJANGO_MANAGEPY_MIGRATE=on
DJANGO_DATABASE_FLUSH=on
DJANGO_SUPERUSER_CREATE=on
DJANGO_DEFAULT_GROUPS_CREATE=on
DJANGO_DEFAULT_USERS_CREATE=on
DJANGO_DATABASE_LOADDATA=on
DJANGO_COLLECT_STATIC=on
ENTRYPOINT_DATABASE=postgres
ENTRYPOINT_MESSAGING=rabbitmq

####################################################################
# django database settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/ref/settings/#databases
####################################################################
DJANGO_DATABASE_NAME=medna_metadata
DJANGO_DATABASE_TESTNAME=test_medna_metadata
DJANGO_DATABASE_USERNAME=your_db_user
DJANGO_DATABASE_PASSWORD=your_db_password
DJANGO_DATABASE_HOST=medna_metadata_pgdb
DJANGO_DATABASE_PORT=5432

####################################################################
# django database backup custom setting; loaded in settings.py
# setting DB_BACKUPS to True will automatically backup the full database
# daily at 4:30AM local time - this can be changed in medna_metadata/settings.py
# under CELERYBEAT_SCHEDULE
# https://django-dbbackup.readthedocs.io/en/master/index.html
####################################################################
DB_BACKUPS=False

####################################################################
# django smtp (email) settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/topics/email/
####################################################################
DJANGO_EMAIL_HOST_USER=your_email@domain.com
DJANGO_EMAIL_HOST_PASSWORD=your_email_password

####################################################################
# django-storages settings; loaded in settings.py
# https://django-storages.readthedocs.io/en/latest/backends/amazon-S3.html#amazon-s3
####################################################################
AWS_ACCESS_KEY_ID=your_access_key_id
AWS_SECRET_ACCESS_KEY=your_access_key
AWS_REGION=your_aws_region
AWS_STORAGE_BUCKET_NAME=your_storage_bucket_name
AWS_STORAGE_BUCKET_SUBFOLDER_NAME=your_storage_bucket_subfolder_name

####################################################################
# RabbitMQ docker settings
# https://www.rabbitmq.com/configure.html
# https://hub.docker.com/_/rabbitmq
####################################################################
RABBITMQ_DEFAULT_USER=your_rabbitmq_user
RABBITMQ_DEFAULT_PASS=your_rabbitmq_password
RABBITMQ_DEFAULT_VHOST=your_rabbitmq_vhost
RABBITMQ_HOST=medna_metadata_rabbitmq
RABBITMQ_PORT=5672

####################################################################
# Celery settings
# https://docs.celeryq.dev/en/stable/userguide/configuration.html
####################################################################
CELERY_RESULT_BACKEND=rpc
CELERY_BROKER_URL=pyamqp://your_rabbitmq_user:your_rabbitmq_password@medna_metadata_rabbitmq:5672/your_rabbitmq_vhost
CELERYD_NODES=worker
CELERYD_NUM_NODES=1
CELERY_BIN=/home/django/.virtualenvs/mednaenv/bin/celery
CELERY_APP=medna_metadata.celery.app
CELERYD_MULTI=multi
CELERYD_OPTS=''
CELERYD_PID_FILE=/var/run/celery/%n.pid
CELERYD_LOG_FILE=/var/log/celery/%n%I.log
CELERYD_LOG_LEVEL=INFO
CELERYBEAT_PID_FILE=/var/run/celery/beat.pid
CELERYBEAT_LOG_FILE=/var/log/celery/beat.log

####################################################################
# Gunicorn settings
# https://docs.gunicorn.org/en/stable/settings.html
# https://docs.gunicorn.org/en/stable/settings.html#logging
# https://github.com/benoitc/gunicorn/blob/master/examples/logging.conf
# https://stackoverflow.com/questions/36424335/how-to-perform-log-rotation-with-gunicorn
####################################################################
GUNICORN_CONFIG_FILE=/your/path/to/medna-metadata/docker/gunicorn-logging.conf

medna.env.db:

####################################################################
# PostGIS docker settings; loaded in settings.py
# https://registry.hub.docker.com/r/postgis/postgis/
####################################################################
POSTGRES_USER=your_db_user
POSTGRES_PASSWORD=your_db_password
POSTGRES_DB=medna_metadata

Open and update the environmental variables with desired settings in a text editor such as VIM

sudo vim medna.env

Write and exit the VIM text editor:

:wq!

Repeat these steps with medna.env.db.

Once settings are verified, run sudo docker-compose -f docker-compose.yml up -d --build from the docker/ directory to build and deploy medna-metadata from the Dockerfiles in docker/web/ and docker/nginx/, PostgreSQL with PostGIS, RabbitMQ, Celery, Gunicorn, and NGINX.:

cd medna-metadata/docker/
sudo docker-compose -f docker-compose.yml up -d --build

After the containers are up, it will take a moment for the application to set itself up. Once it is done, it will be accessible at http://localhost:8000

Manual Setup

Install Requirements

Ubuntu 20.04

Install Ubuntu Requirements:

cd medna-metadata
sudo bash requirements/ubuntu-requirements.sh

It will run the following installation commands:

# Ubuntu 20.04
# sudo bash ubuntu-requirements.sh
apt-get update && apt-get install -y --no-install-recommends apt-utils
# Django with Postgres, Nginx, and Gunicorn on Ubuntu 20.04
apt update && apt -y install \
 libpq-dev postgresql postgresql-contrib nginx curl vim netcat
# GDAL, GEOS, PROJ.4, python deps
apt-get -y install \
 binutils libproj-dev gdal-bin \
 python3-dev python3-pip python3-venv python3-wheel \
 rabbitmq-server
# PostGIS
apt -y install \
 postgis postgresql-12-postgis-3
# Certbot and Nginx plugin
apt -y install \
 certbot python3-certbot-nginx

Create a Virtual Environment and Set Environmental Variables

Create a virtual environment with venv:

sudo -H pip install --upgrade pip
sudo -H pip install virtualenvwrapper
sudo -H pip install virtualenv

Dotenv is a python library for reading in environmental variables from a file:

pip install django-dotenv

Add environmental variables to the bottom of bashrc, which reloads environmental variables anytime the server reboots.

The environmental variables required to run this application are listed in docker/bashrc.txt:

####################################################################
# django general settings; loaded in settings.py
# The secret key must be a large random value and it must be kept secret.
# https://docs.djangoproject.com/en/4.0/ref/settings/#std:setting-SECRET_KEY
# https://docs.djangoproject.com/en/4.0/ref/settings/#std-setting-TIME_ZONE
# List of time zones: https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
####################################################################
export DJANGO_SECRET_KEY='your_secret_key'
export DJANGO_ALLOWED_HOSTS='localhost www.yourdomain.com [::1]'
export DJANGO_ALLAUTH_HOST='your_domain'
export DJANGO_SETTINGS_MODULE=medna_metadata.settings
export DJANGO_DEBUG=False
export DJANGO_LOG_LEVEL='info'
export TIME_ZONE='America/New_York'

####################################################################
# django database settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/ref/settings/#databases
####################################################################
export DJANGO_DATABASE_NAME='medna_metadata'
export DJANGO_DATABASE_TESTNAME='test_medna_metadata'
export DJANGO_DATABASE_USERNAME='your_db_user'
export DJANGO_DATABASE_PASSWORD='your_db_password'
export DJANGO_DATABASE_HOST='localhost'
export DJANGO_DATABASE_PORT=''

####################################################################
# django database backup custom setting; loaded in settings.py
# setting DB_BACKUPS to True will automatically backup the full database
# daily at 4:30AM local time - this can be changed in medna_metadata/settings.py
# under CELERYBEAT_SCHEDULE
# https://django-dbbackup.readthedocs.io/en/master/index.html
####################################################################
export DB_BACKUPS=False

####################################################################
# django smtp (email) settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/topics/email/
####################################################################
export DJANGO_EMAIL_HOST_USER='your_email@domain.com'
export DJANGO_EMAIL_HOST_PASSWORD='your_email_password'

####################################################################
# django-storages settings; loaded in settings.py
# https://django-storages.readthedocs.io/en/latest/backends/amazon-S3.html
####################################################################
export AWS_ACCESS_KEY_ID='your_access_key_id'
export AWS_SECRET_ACCESS_KEY='your_secret_access_key'
export AWS_REGION='your_aws_region'
export AWS_STORAGE_BUCKET_NAME='your_bucket'
export AWS_STORAGE_BUCKET_SUBFOLDER_NAME='your_bucket_subfolder'

####################################################################
# Celery settings
# https://docs.celeryq.dev/en/stable/userguide/configuration.html
####################################################################
export CELERY_RESULT_BACKEND='rpc'
export CELERY_BROKER_URL='pyamqp://your_rabbitmq_user:your_rabbitmq_password@localhost:5672/your_rabbitmq_vhost'

####################################################################
# virtualenv settings
# https://virtualenvwrapper.readthedocs.io/en/latest/install.html#python-interpreter-virtualenv-and-path
####################################################################
export WORKON_HOME=$HOME/.virtualenvs
export PROJECT_HOME=$HOME/medna-metadata
export VIRTUALENVWRAPPER_PYTHON=/usr/bin/python3
source /usr/local/bin/virtualenvwrapper.sh

These environmental variables must be updated with values specific to your deployment.

Open ~/.bashrc with a text editor such as VIM:

sudo vim ~/.bashrc

Scroll to the bottom of bashrc and type i to insert into the file. Write and exit the VIM text editor:

:wq!

Tip

To write and quit within the VIM text editor, [esc], :wq!, and [enter]

Load the environmental variables:

source ~/.bashrc

Make a copy of gunicorn.env.txt in the same docker/ directory with the .txt extension removed (e.g., gunicorn.env)

cp docker/gunicorn.env.txt docker/gunicorn.env

gunicorn.env:

####################################################################
# django general settings; loaded in settings.py
# The secret key must be a large random value and it must be kept secret.
# https://docs.djangoproject.com/en/4.0/ref/settings/#std:setting-SECRET_KEY
# https://docs.djangoproject.com/en/4.0/ref/settings/#std-setting-TIME_ZONE
# List of time zones: https://en.wikipedia.org/wiki/List_of_tz_database_time_zones
####################################################################
DJANGO_SECRET_KEY=your_secret_key
DJANGO_ALLOWED_HOSTS=localhost [::1]
DJANGO_ALLAUTH_HOST=your_domain
DJANGO_DEBUG=True
DJANGO_LOG_LEVEL=info
TIME_ZONE=America/New_York

####################################################################
# django database settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/ref/settings/#databases
####################################################################
DJANGO_DATABASE_NAME=medna_metadata
DJANGO_DATABASE_TESTNAME=test_medna_metadata
DJANGO_DATABASE_USERNAME=your_db_user
DJANGO_DATABASE_PASSWORD=your_db_password
DJANGO_DATABASE_HOST=localhost
DJANGO_DATABASE_PORT=''

####################################################################
# django database backup custom setting; loaded in settings.py
# setting DB_BACKUPS to True will automatically backup the full database
# daily at 4:30AM local time - this can be changed in medna_metadata/settings.py
# under CELERYBEAT_SCHEDULE
# https://django-dbbackup.readthedocs.io/en/master/index.html
####################################################################
DB_BACKUPS=False

####################################################################
# django smtp (email) settings; loaded in settings.py
# https://docs.djangoproject.com/en/4.0/topics/email/
####################################################################
DJANGO_EMAIL_HOST_USER=your_email@domain.com
DJANGO_EMAIL_HOST_PASSWORD=your_email_password

####################################################################
# django-storages settings; loaded in settings.py
# https://django-storages.readthedocs.io/en/latest/backends/amazon-S3.html
####################################################################
AWS_ACCESS_KEY_ID=your_access_key_id
AWS_SECRET_ACCESS_KEY=your_access_key
AWS_REGION=your_aws_region
AWS_STORAGE_BUCKET_NAME=your_storage_bucket_name
AWS_STORAGE_BUCKET_SUBFOLDER_NAME=your_storage_bucket_subfolder_name

####################################################################
# Celery settings
# https://docs.celeryq.dev/en/stable/userguide/configuration.html
####################################################################
CELERY_RESULT_BACKEND=rpc
CELERY_BROKER_URL=pyamqp://your_rabbitmq_user:your_rabbitmq_password@localhost:5672/your_rabbitmq_vhost
CELERYD_NODES=worker
CELERYD_NUM_NODES=1
CELERY_BIN=/your/path/to/bin/celery
CELERY_APP=medna_metadata.celery.app
CELERYD_MULTI=multi
CELERYD_OPTS=''
CELERYD_PID_FILE=/var/run/celery/%n.pid
CELERYD_LOG_FILE=/var/log/celery/%n%I.log
CELERYD_LOG_LEVEL=INFO
CELERYBEAT_PID_FILE=/var/run/celery/beat.pid
CELERYBEAT_LOG_FILE=/var/log/celery/beat.log

####################################################################
# Gunicorn settings
# https://docs.gunicorn.org/en/stable/settings.html
# https://docs.gunicorn.org/en/stable/settings.html#logging
# https://github.com/benoitc/gunicorn/blob/master/examples/logging.conf
# https://stackoverflow.com/questions/36424335/how-to-perform-log-rotation-with-gunicorn
####################################################################
GUNICORN_CONFIG_FILE=/your/path/to/medna-metadata/docker/gunicorn-logging.conf

Update the environmental variables with values specific to your deployment in a text editor such as VIM

sudo vim docker/gunicorn.env

Type i to insert into the file. Write and exit the VIM text editor:

:wq!

Warning

MeDNA-Metadata will not successfully deploy without setting these environmental variables.

Create and activate virtualenvwrapper:

mkvirtualenv --python /usr/bin/python3.8 mednaenv

Important

The version of python varies and you will have to check or install it.

Activate the virtual environment:

workon mednaenv

Install python requirements to the virtualenv:

pip install -U -r requirements/prod.txt

The following python libraries will install: .. literalinclude:: ../../requirements/base.txt

language:

env

-r base.txt

gunicorn==20.1.0

Create PostgreSQL database with PostGIS Extension

Create the database for your project:

sudo -u postgres psql -c "CREATE DATABASE medna_metadata;"

Create a database user and add them to the project with a secure password:

sudo -u postgres psql -c "CREATE USER youruser WITH PASSWORD 'yourdbpassword';"

Recommended settings from the Django project:

sudo -u postgres psql -c "ALTER ROLE youruser SET client_encoding TO 'utf8';"
sudo -u postgres psql -c "ALTER ROLE youruser SET default_transaction_isolation TO 'read committed';"
sudo -u postgres psql -c "ALTER ROLE youruser SET timezone TO 'UTC';"

Set youruser as the administrator for the medna_metadata database:

sudo -u postgres psql -c "GRANT ALL PRIVILEGES ON DATABASE medna_metadata TO youruser;"

Grant privileges to the youruser database user to create databases for Django tests:

sudo -u postgres psql -c "ALTER USER youruser CREATEDB NOSUPERUSER NOCREATEROLE;"

Add the PostGIS extension to medna_metadata:

sudo -i -u postgres psql -d medna_metadata -c "CREATE EXTENSION postgis;"

Tip

It would be advantageous here to use the same username as your selected Ubuntu username.

Migrate the Database Tables

Migrate the database schema to PostgreSQL from within the same directory as manage.py Within each app there is a migration directory which contains files which tell the database how to create the database tables. These have been pre-generated and added to this repository to simplify the process of deplying the medna-metadata application:

python manage.py migrate users
python manage.py migrate utility
python manage.py migrate field_site
python manage.py migrate sample_label
python manage.py migrate field_survey
python manage.py migrate wet_lab
python manage.py migrate freezer_inventory
python manage.py migrate bioinformatics

Now, if everything looked good (e.g., no error messages), complete the remaining migrations:

python manage.py migrate

Create Superuser

Creating a superuser adds an administrative user with full privileges to the MeDNA-Metadata project.

Create a superuser:

python manage.py createsuperuser

When prompted, enter in your preferred credentials (youremail, yourpassword).

Collect Static

Collecting static files will copy all static content into the directory specified in settings.py.

Collect static files:

python manage.py collectstatic

Test The Deployment

Temporarily create an exception for port 8000:

sudo ufw allow 8000

Test the project deployment:

python manage.py runserver 0.0.0.0:8000

In your web browser, visit the server’s IP address followed by :8000

http://youripaddress:8000

If you’re able to see a live project, then enter [CTRL-C] in to shut down the test deployment.

Test Gunicorn

Now test to see if the project can be deployed with Gunicorn:

gunicorn --bind 0.0.0.0:8000 medna_metadata.wsgi

See also

If you were able to visit the same page while deployed with Gunicorn, continue onward. If not, some helpful troubleshooting steps can be found in the DigitalOcean tutorial on setting up Django with PostgreSQL, Gunicorn, and Nginx.

Django with PostgreSQL, Gunicorn, and Nginx on Ubuntu 20.04

Create Gunicorn Socket and Service files (e.g., daemonizing!)

Leave the virtualenv:

deactivate

Create a systemd Socket file:

sudo vim /etc/systemd/system/gunicorn.socket

Write the following to the file:

[Unit]
Description=gunicorn socket

[Socket]
ListenStream=/run/gunicorn.sock

[Install]
WantedBy=sockets.target

Write and exit the VIM text editor:

:wq!

Create a systemd service file:

sudo vim /etc/systemd/system/gunicorn.service

Modify then write the following to the file:

[Unit]
Description=gunicorn daemon
Requires=gunicorn.socket
After=network.target

[Service]
User=youruser
Group=youruser
WorkingDirectory=/path/to/medna-metadata
EnvironmentFile=/path/to/medna-metadata/docker/gunicorn.env
ExecStart=/path/to/.virtualenvs/mednaenv/bin/gunicorn \
          --log-config ${GUNICORN_CONFIG_FILE} \
          --workers 3 \
          --timeout 300 \
          --bind unix:/run/gunicorn.sock \
          medna_metadata.wsgi:application

[Install]
WantedBy=multi-user.target

Warning

You will need to replace the User and Group to the correct Ubuntu username and group and modify the WorkingDirectory, EnvironmentFile, and ExecStart to the actual directory MeDNA-Metadata is in.

Write and exit the VIM text editor:

:wq!

Enable the socket and service:

sudo systemctl start gunicorn.socket
sudo systemctl enable gunicorn.socket

Check for the socket file’s status (it should be green):

sudo systemctl status gunicorn.socket

Check for the existence of the sock file:

file /run/gunicorn.sock

If there is no file, check the socket’s logs and troubleshoot:

sudo journalctl -u gunicorn.socket

Test the socket activation (should be grey & inactive):

sudo systemctl status gunicorn

Test the socket activation mechanism through curl:

curl --unix-socket /run/gunicorn.sock localhost

Now see if Gunicorn is “running”:

sudo systemctl status gunicorn

If you need to troubleshoot, check journalctl and daemon-reload and restart gunicorn when the service, socket, settings, or env files are edited:

sudo journalctl -u gunicorn
sudo systemctl daemon-reload
sudo systemctl restart gunicorn

Setup Celery and RabbitMQ 

Celery task management and the RabbitMQ messaging server are used for task queues within the backend application. This allows for things such as queues of data transformations and workers that will spawn as resources are available.

See also

Note

Celery and RabbitMQ should have already been installed with the requirements.txt and ubuntu-requirements.sh, but the commands are also provided here.

Install RabbitMQ messaging server:

sudo apt-get update
sudo apt-get install rabbitmq-server

Important

If you named your venv something other than mednaenv, use that here instead.

Activate the virtualenv:

workon mednaenv

Install Celery:

pip install -U "celery>=5.2.3"

Setup RabbitMQ 

Add a user and a virtual host:

sudo rabbitmqctl add_user youruser yourpassword
sudo rabbitmqctl add_vhost yourvhost
sudo rabbitmqctl set_user_tags youruser yourtag
sudo rabbitmqctl set_permissions -p yourvhost youruser ".*" ".*" ".*"

Warning

You will need to replace youruser, yourpassword, yourvhost, yourtag, to the password, username, tag and hostname of your choosing. These are specific to RabbitMQ and not dependent on other applications. What is chosen is used to construct your CELERY_BROKER_URL.

Stop RabbitMQ:

sudo systemctl stop rabbitmq-server

Check to verify it is actually stopped:

sudo rabbitmqctl cluster_status

Start it up again:

sudo systemctl start rabbitmq-server
sudo systemctl restart rabbitmq-server
sudo systemctl status rabbitmq-server

Warning

For Celery and RabbitMQ to function, the CELERY_RESULT_BACKEND and CELERY_BROKER_URL variables must be set in ~/.bashrc and docker/gunicorn.env. These variables should resemble the following:

CELERY_RESULT_BACKEND=’rpc’

CELERY_BROKER_URL=’pyamqp://youruser:yourpassword@localhost:port/yourvhost`

Create Celery Worker and Beat files (e.g., daemonizing!)

Like Gunicorn, celery should be run as a Systemd service.

First, open your environment file:

sudo vim docker/gunicorn.env

Update or add the following Celery config settings to your environment file:

CELERY_RESULT_BACKEND='your_result_backend'
CELERY_BROKER_URL='transport://your_rabbitmq_user:your_rabbitmq_password@hostname:port/your_rabbitmq_vhost'
CELERYD_NODES='worker'
CELERY_BIN='/path/to/.virtualenvs/mednaenv/bin/celery'
CELERY_APP='medna_metadata.celery.app'
CELERYD_MULTI='multi'
CELERYD_OPTS=''
CELERYD_PID_FILE='/var/run/celery/%n.pid'
CELERYD_LOG_FILE='/var/log/celery/%n%I.log'
CELERYD_LOG_LEVEL='INFO'
CELERYBEAT_PID_FILE='/var/run/celery/beat.pid'
CELERYBEAT_LOG_FILE='/var/log/celery/beat.log'

Write and exit the VIM text editor:

:wq!

Now we need to create the Celery log and run directories and update their permissions:

sudo mkdir /var/run/celery/
sudo mkdir /var/log/celery/

sudo chgrp yourgroup /var/run/celery/
sudo chgrp yourgroup /var/log/celery/

sudo chmod g+rwx /var/run/celery/
sudo chmod g+rwx /var/log/celery/

Create a Celery service file:

sudo vim /etc/systemd/system/celery.service

Modify then write the following to the file:

[Unit]
Description=Celery Service
After=network.target rabbitmq-server.service
Requires=rabbitmq-server.service

[Service]
Type=forking
User=youruser
Group=yourgroup
EnvironmentFile=/path/to/medna-metadata/docker/gunicorn.env
WorkingDirectory=/path/to/medna-metadata
Environment=DJANGO_SETTINGS_MODULE=medna_metadata.settings
ExecStart=/bin/sh -c '${CELERY_BIN} -A ${CELERY_APP} multi start ${CELERYD_NODES} \
    --pidfile=${CELERYD_PID_FILE} --logfile=${CELERYD_LOG_FILE} \
    --loglevel="${CELERYD_LOG_LEVEL}" ${CELERYD_OPTS}'
ExecStop=/bin/sh -c '${CELERY_BIN} multi stopwait ${CELERYD_NODES} \
    --pidfile=${CELERYD_PID_FILE} --logfile=${CELERYD_LOG_FILE} \
    --loglevel="${CELERYD_LOG_LEVEL}"'
ExecReload=/bin/sh -c '${CELERY_BIN} -A ${CELERY_APP} multi restart ${CELERYD_NODES} \
    --pidfile=${CELERYD_PID_FILE} --logfile=${CELERYD_LOG_FILE} \
    --loglevel="${CELERYD_LOG_LEVEL}" ${CELERYD_OPTS}'
Restart=always

[Install]
WantedBy=multi-user.target

Write and exit the VIM text editor:

:wq!

Warning

You will need to replace the User and Group to the correct Ubuntu username and group and modify the WorkingDirectory and EnvironmentFile to the actual directory MeDNA-Metadata is in.

We also need a celerybeat Systemd service for scheduling tasks.

Create a celerybeat file:

sudo vim /etc/systemd/system/celerybeat.service

Modify then write the following to the file:

[Unit]
Description=Celery Beat Service
After=network.target rabbitmq-server.service
Requires=rabbitmq-server.service

[Service]
Type=simple
User=youruser
Group=yourgroup
EnvironmentFile=/path/to/medna-metadata/docker/gunicorn.env
WorkingDirectory=/path/to/medna-metadata
Environment=DJANGO_SETTINGS_MODULE=medna_metadata.settings
ExecStart=/bin/sh -c '${CELERY_BIN} -A ${CELERY_APP} beat  \
    --pidfile=${CELERYBEAT_PID_FILE} \
    --logfile=${CELERYBEAT_LOG_FILE} --loglevel=${CELERYD_LOG_LEVEL}'
Restart=always

[Install]
WantedBy=multi-user.target

Write and exit the VIM text editor:

:wq!

Warning

You must replace the User and Group to the correct Ubuntu username and group and modify the WorkingDirectory and EnvironmentFile to the actual directory MeDNA-Metadata is in.

We can now start the celery and celerybeat services:

sudo systemctl daemon-reload
sudo systemctl start celery.service
sudo systemctl status celery.service

sudo systemctl start celerybeat.service
sudo systemctl status celerybeat.service

If any modifications are made to any tasks.py or medna_metadata/celery.py, restart celerybeat and celeryworker:

sudo systemctl restart celery.service && sudo systemctl restart celerybeat.service && sudo systemctl daemon-reload && sudo systemctl restart gunicorn

If you want these services to start automatically on boot, you can enable them as follows:

sudo systemctl enable celery.service
sudo systemctl enable celerybeat.service

Troubleshooting Celery 

If you are trying to troubleshoot celery or celerybeat, be sure to check system logs for error messages:

sudo cat /var/log/syslog
sudo tail /var/log/syslog -n 40

You can also check RabbitMQ logs:

sudo tail /var/log/rabbitmq/rabbit@medna-metadata.log -n 50

To view Celery tasks as they are sent by RabbitMQ:

celery -A medna_metadata worker --pool=solo -l info

[CTRL-C] to exit.

Collect Static Files

Any time there is a change made to the python code, run the following to reload changes:

git pull && python manage.py collectstatic --noinput --clear && sudo systemctl daemon-reload && sudo systemctl restart gunicorn.socket gunicorn.service

Configure Nginx 

Create a nginx config file:

sudo vim /etc/nginx/sites-available/medna-metadata

Modify and write the following:

server {
    listen 80;
    server_name youripaddress yourdomain.com;

    location = /favicon.ico { access_log off; log_not_found off; }
    location /static/ {
        root /path/to/medna-metadata;
        client_max_body_size 150M;
    }

    location / {
        include proxy_params;
        proxy_pass http://unix:/run/gunicorn.sock;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_connect_timeout 300s;
        proxy_read_timeout 300s;
        client_max_body_size 150M;
    }
}

Warning

You must edit the server_name and location to the actual IP address or domain name and to the actual directory MeDNA-Metadata is in.

Write and exit the VIM text editor:

:wq!

Enable the file by linking it to sites-enabled:

sudo ln -s /etc/nginx/sites-available/medna-metadata /etc/nginx/sites-enabled

Test the Nginx configuration for syntaix errors:

sudo nginx -t

If there are no errors, restart Nginx:

sudo systemctl restart nginx

Delete port 8000 and allow Nginx in the firewall:

sudo ufw delete allow 8000
sudo ufw allow 'Nginx Full'

Troubleshooting Nginx and Gunicorn 

See also

For more information on troubleshooting Nginx and Gunicorn, please see the following:

Django with PostgreSQL, NGINX, and Gunicorn on Ubuntu 20.04

SSL Certificates with Certbot

Run certbot:

sudo certbot --nginx -d yourdomain.com

Follow the prompt by enter in your email address, [A], [n], and [2].

Verify Certbot auto-renewal:

sudo certbot renew --dry-run

You should now be good to go and running with your desired server and domain.

Installation

Clone the Repository

Docker Setup

Install Requirements

Ubuntu 20.04

Manual Setup

Install Requirements

Ubuntu 20.04

Create a Virtual Environment and Set Environmental Variables

Create PostgreSQL database with PostGIS Extension

Migrate the Database Tables

Create Superuser

Collect Static

Test The Deployment

Test Gunicorn

Create Gunicorn Socket and Service files (e.g., daemonizing!)

Setup Celery and RabbitMQ

Setup RabbitMQ

Create Celery Worker and Beat files (e.g., daemonizing!)

Troubleshooting Celery

Collect Static Files

Configure Nginx

Troubleshooting Nginx and Gunicorn

SSL Certificates with Certbot

Setup Celery and RabbitMQ 

Setup RabbitMQ 

Troubleshooting Celery 

Configure Nginx 

Troubleshooting Nginx and Gunicorn 