CDCS Docker

This repository contains docker-compose files to build and deploy CDCS containers.

Prerequisites

Install Docker first, then install Docker Compose.

Build a CDCS image

1. Customize the build

Update the values in the .env file:

cd build
vim .env

Below is the list of environment variables to set and their description.

Variable	Description
PROJECT_NAME	Name of the CDCS/Django project to build (e.g. mdcs, nmrr)
IMAGE_NAME	Name of the image to build (e.g. mdcs, nmrr)
IMAGE_VERSION	Version of the image to build (e.g. latest, 2.10.0)
CDCS_REPO	URL of the CDCS repository to clone to build the image (e.g. https://github.com/usnistgov/mdcs.git)
BRANCH	Branch/Tag of the repository to pull to build the image (e.g. master, 2.10.0)
PIP_CONF	Pip configuration file to use to build the image
PYTHON_VERSION	Version of the Python image to use as a base image for the CDCS image

2. Build the image

cdcs-docker/build$ docker-compose build --no-cache

3. Build a custom image (optional)

Different images may be needed for different deployment contexts (development/CI/production, docker-compose/K8s, ...).

The custom build configuration allows adding the following elements to an existing CDCS image, by editing the following files:

packages.txt: install additional linux packages (see example_packages.txt),
requirements.txt: install additional python packages (see example_requirements.txt),
settings.py: add settings to settings.py file (see example_settings.py).

To configure the image to build, edit the following variables in the .env file.

Variable	Description
BASE_IMAGE_NAME	Name of the base image (e.g. mdcs, nmrr)
BASE_IMAGE_VERSION	Version of the base image (e.g. latest, 2.10.0)
PROJECT_NAME	Name of the CDCS/Django project to build (e.g. mdcs, nmrr)
IMAGE_NAME	Name of the image to build (e.g. mdcs)
IMAGE_VERSION	Version of the image to build (e.g. latest, 2.10.0)

Then build the custom image.

cd build/custom
vim .env
vim packages.txt
vim requirements.txt
vim settings.py
docker-compose build --no-cache

Deploy a CDCS

1. Customize the deployment

Update the values in the .env file:

cd deploy
vim .env

Below is the list of environment variables that can be set and their description. Commented variables in the .env need to be uncommented and filled.

Variable	Description
PROJECT_NAME	Name of the CDCS/Django project to deploy (e.g. mdcs, nmrr)
IMAGE_NAME	Name of the CDCS image to deploy (e.g. mdcs, nmrr)
IMAGE_VERSION	Version of the CDCS image to deploy (e.g. latest, 2.10.0)
HOSTNAME	Hostname of the server (e.g. for local deployment, use the machine's IP address xxx.xxx.xxx.xxx)
SERVER_URI	URI of server (e.g. for local deployment, http://xxx.xxx.xxx.xxx)
ALLOWED_HOSTS	Comma-separated list of hosts (e.g. ALLOWED_HOSTS=127.0.0.1,localhost), see Allowed Hosts
SERVER_NAME	Name of the server (e.g. MDCS)
SETTINGS	Settings file to use during deployment (more info in the Settings section)
SERVER_CONF	Mount appropriate nginx file (e.g. `default` for http deployment using a uWSGI UNIX socket, `https` to enable SSL, or `gunicorn_http[s]`. The protocol of the `SERVER_URI` should be updated accordingly)
MONGO_PORT	MongoDB Port (default: 27017)
MONGO_ADMIN_USER	Admin user for MongoDB (should be different from `MONGO_USER`)
MONGO_ADMIN_PASS	Admin password for MongoDB
MONGO_USER	User for MongoDB (should be different from `MONGO_ADMIN_USER`)
MONGO_PASS	User password for MongoDB
MONGO_DB	Name of the Mongo database (e.g. cdcs)
POSTGRES_PORT	Postgres Port (default: 5432)
POSTGRES_USER	User for Postgres
POSTGRES_PASS	User password for Postgres
POSTGRES_DB	Name of the Postgres database (e.g. cdcs)
REDIS_PORT	Redis Port (default: 6379)
REDIS_PASS	Password for Redis
DJANGO_SECRET_KEY	Secret Key for Django (should be a "large random value")
NGINX_PORT_80	Expose port 80 on host machine for NGINX
NGINX_PORT_443	Expose port 443 on host machine for NGINX
MONGO_VERSION	Version of the MongoDB image
REDIS_VERSION	Version of the Redis image
POSTGRES_VERSION	Version of the Postgres image
NGINX_VERSION	Version of the NGINX image
WEB_SERVER	Web server for the CDCS (e.g. `uwsgi`, `gunicorn`)
PROCESSES	Number of uWSGI processes (default `--processes=8`) / Gunicorn workers to start (default `workers=cpu_count() * 2 + 1`)
THREADS	Number of uWSGI/Gunicorn threads per process/worker (default 8)
MONITORING_SERVER_URI	(optional) URI of an APM server for monitoring

A few additional environment variables are provided to the CDCS container. The variables below are computed based on the values of other variables. If changed, some portions of the docker-compose.yml might need to be updated to stay consistent.

Variable	Description
DJANGO_SETTINGS_MODULE	`DJANGO_SETTINGS_MODULE` (set using the values of `PROJECT_NAME` and `SETTINGS`)
MONGO_HOST	Mongodb hostname (set to `${PROJECT_NAME}_cdcs_mongo`)
POSTGRES_HOST	Postgres hostname (set to `${PROJECT_NAME}_cdcs_postgres`)
REDIS_HOST	REDIS hostname (set to `${PROJECT_NAME}_cdcs_redis`)

SAML2

Configure SAML2 authentication by providing values for the following environment variables in the saml2/.env file. See saml2/.env.example for an example of SAML2 configuration with a Keycloak server.

Variable	Description
ENABLE_SAML2_SSO_AUTH	Enable SAML2 authentication (e.g. `ENABLE_SAML2_SSO_AUTH=True`)
SAML_ATTRIBUTE_MAP_DIR	Points to a directory which has the attribute maps in Python modules (see attribute_map_dir)
SAML_ATTRIBUTES_MAP_IDENTIFIER	SAML attribute map supported name-format (see attribute_map_dir)
SAML_ATTRIBUTES_MAP_UID	SAML attribute mapping to uid
SAML_ATTRIBUTES_MAP_UID_FIELD	SAML attribute mapping uid field name
SAML_ATTRIBUTES_MAP_EMAIL	SAML attribute mapping to email
SAML_ATTRIBUTES_MAP_EMAIL_FIELD	SAML attribute mapping email field name
SAML_ATTRIBUTES_MAP_CN	SAML attribute mapping to common name
SAML_ATTRIBUTES_MAP_CN_FIELD	SAML attribute mapping common name field name
SAML_ATTRIBUTES_MAP_SN	SAML attribute mapping to surname
SAML_ATTRIBUTES_MAP_SN_FIELD	SAML attribute mapping surname field name
SAML_DJANGO_USER_MAIN_ATTRIBUTE	Django field to use to find user and create session (see user attributes and account linking)
SAML_USE_NAME_ID_AS_USERNAME	Use SAML2 name id as username (see user attributes and account linking)
SAML_CREATE_UNKNOWN_USER	Create user if not found in Django database (see user attributes and account linking)
SAML_KEY_FILE	Path to private key (see key_file)
SAML_CERT_FILE	Path to the public key (see cert_file)
SAML_METADATA_REMOTE_URL	Url to remote SAML metadata file (see metadata)
SAML_METADATA_REMOTE_CERT	(Optional) Certificate for the remote (see metadata)
SAML_METADATA_LOCAL	Path to local SAML metadata file (see metadata)
SAML_XMLSEC_BIN_PATH	Full path to xmlsec1 binary program (see xmlsec_binary)
SAML_WANT_RESPONSE_SIGNED	Set to `True` if responses must be signed (see want_response_signed)
SAML_WANT_ASSERTIONS_SIGNED	Set to `True` if assertions must be signed (see want_assertions_signed)
SAML_LOGOUT_REQUESTS_SIGNED	Set to `True` if logout requests must be signed (see logout_requests_signed)
SAML_LOGOUT_RESPONSES_SIGNED	Set to `True` if logout responses must be signed (see logout_responses_signed)
SAML_SIGNING_ALGORITHM	Signing algorithm (see signing_algorithm)
SAML_DIGEST_ALGORITHM	Digest algorithm (see digest_algorithm)
CONTACT_PERSON_N	Contact information for person N (see contact_person)
ORGANIZATION_NAME_N	Organization name N (see organization)
ORGANIZATION_DISPLAY_NAME_N	Organization display name N (see organization)
ORGANIZATION_URL_N	Organization url N (see organization)

Contact Person and Organization environment variables

Environment variables ending with suffix _N are expecting N to be a sequence of integers starting at 1. For example, if two contact persons need to be added to the SAML configuration, the following variables should be set:

CONTACT_PERSON_1=
CONTACT_PERSON_2=

Contact Person

A contact person environment variable is expecting a comma separated list of values in the following order:

given name,
surname,
company,
email address,
type (technical, support, administrative, billing or other).

For example:

CONTACT_PERSON_1=Firstname1,Lastname1,Example Co.,[email protected],technical

Organization

Each section of the SAML organization configuration is stored in a separate environment variable. Each variable is expecting a comma separated pair composed of:

label,
language code.

Below is an example from the Pysaml2 documentation and how to represent it in the CDCS using environment variables.

Example from the documentation:

"organization": {
    "name": [
        ("Example Company", "en"),
        ("Exempel AB", "se")
    ],
    "display_name": ["Exempel AB"],
    "url": [
        ("http://example.com", "en"),
        ("http://exempel.se", "se"),
    ],
}

Equivalent CDCS configuration using environment variables:

ORGANIZATION_NAME_1=Example Company,en
ORGANIZATION_NAME_2=Exempel AB,se
ORGANIZATION_DISPLAY_NAME_1=Exempel AB,se
ORGANIZATION_URL_1=http://example.com,en
ORGANIZATION_URL_2=http://exemple.se,se

hdl.net PID Integration

CDCS supports integration of a hdl.net server to issue and resolve PIDs for data and blobs. This requires some setting of environment variables at deploy time to configure effectively. Please see the file ./deploy/handle/.env.example for more details.

Variable	Description
`ENABLE_HANDLE_PID`	Controls whether CDCS is configured to use a handle server for PIDs. If so, all the values below should be set to values specific for your handle server config (contact your handle server administrator for any help). If you enable Handle integration but don't set these values correctly; it's very likely things won't work.
`HANDLE_NET_LOOKUP_URL`	The URL of the handle server to display links (e.g. https://hdl.handle.net)
`HANDLE_NET_REGISTRATION_URL`	The URL of the handle server for registering records (e.g. https://my-handle-net.domain)
`ID_PROVIDER_PREFIXES`	Prefixes to use when creating handles for data and blobs in CDCS. Comma-separated values.
`HANDLE_NET_USER`	Handle server authentication for a user that has admin rights to list and create handles on the provided prefix. The value provided here will be encoded as "300:{HANDLE_NET_PREFIX}/{HANDLE_NET_USER}" when it is sent to the handle server, so this value should be just the suffix of the admin handle
`HANDLE_NET_SECRET_KEY`	The "secret key" for the admin user specified above. This should be provided as plain text and not encoded in any way. This value corresponds to the secret key that would be used if you were creating a handle via batch file
`PID_PATH`	The location in the default schema in which to store and search for PID values. Should be provided in "dot" notation, with attributes indicated using the "@" character. For example, if your PIDs are stored in an attribute named "pid" on the root element named "Resource", the PID_PATH value should be "Resource.@pid"
`AUTO_SET_PID`	Whether to auto-create PIDs for records that are curated or uploaded without them. Should likely be True if you're using PIDs at all
`HANDLE_NET_RECORD_INDEX`	Starting index for records when minting handles
	The following are admin settings for the handle config. The default values are probably fine, but they should match any example batch files you have for creating handles on your handle server
`HANDLE_NET_ADMIN_INDEX`	The admin index value (default: `100`)
`HANDLE_NET_ADMIN_TYPE`	The admin type (default: `HS_ADMIN`)
`HANDLE_NET_ADMIN_DATA_FORMAT`	The admin data format (default: `admin`)
`HANDLE_NET_ADMIN_DATA_INDEX`	The admin data index value (default: `200`)
`HANDLE_NET_ADMIN_DATA_PERMISSIONS`	The admin data permissions (default: `011111110011`)

Settings

Starting from MDCS/NMRR 2.14, repositories of these two projects will have settings ready for deployment (not production).

The deployment can be further customized by mounting additional settings to the deployed containers:

Option 1: Use settings from the image. This option is recommended if the settings in your image are already well formatted for deployment.
- Update the docker-compose.yml file and comment the line that mounts the settings:
```
# - ./cdcs/${SETTINGS}.py:/srv/curator/${PROJECT_NAME}/${SETTINGS}.py
```
- set the SETTINGS variable to settings.
Option 2: Use default settings from the CDCS image and customize them. Custom settings can be used to provide CI or production configurations. For example:
- Create a custom_settings.py file (see ci_settings.py or test_settings.py as examples),
- set the SETTINGS variable to custom_settings.
Option 3: Override settings from the image. This will ignore settings already present in the CDCS image. This option is recommended for MDCS/NMRR 2.14 and below.
- Update the docker-compose.yml file and change the line that mounts the settings to:
```
- ./cdcs/${PROJECT_NAME}.settings.py:/srv/curator/${PROJECT_NAME}/settings.py
```
- set the SETTINGS variable to settings.

The DJANGO_SETTINGS_MODULE environment variable can be set to select which settings to use. By default the docker-compose file sets it using the values of PROJECT_NAME and SETTINGS variables.

For more information about production deployment of a Django project, please check the Deployment Checklist

Web Server

The following web servers are available for the CDCS: uWSGI and Gunicorn.

The CDCS image contains a default configurations for each:

The default uWSGI configuration writes in a UNIX socket, that Nginx reads from. A socket file is mounted in both containers (cdcs_socket).
Gunicorn on the other hand, communicates with Nginx via a port (8000).

You can switch from one web server to the other by setting WEB_SERVER in the .env file to either uwsgi or gunicorn. The Nginx configuration is a little different depending on the web server, so SERVER_CONF needs to be updated accordingly: use default (HTTP deployment with uWSGI) or https (HTTPS deployment with uWSGI) for uWSGI, and gunicorn_http or gunicorn_https for Gunicorn.

2. Deploy the stack

docker-compose up -d

(Optional) For testing purposes, using the HTTPS protocol, you can then run the following script to generate and copy self-signed certificates to the container.

./docker_set_ssl.sh

3. Create a superuser

The superuser is the first user that will be added to the CDCS. This is the main administrator on the platform. Once it has been created, more users can be added using the web interface. Wait for the CDCS server to start, then run:

cdcs-docker/deploy$ ./docker_createsuperuser.sh ${username} ${password} ${email}

4. Initialize database

From CDCS 2.9, to prevent concurrency issues and avoid running database operations multiple times, some database initialization commands have been added. These commands need to be run once, after the initial deployment of the application.

To load the modules, run the following command:

./docker_loadmodules.sh

NOTE: If modules are added/removed from the project's INSTALLED_APPS, the commands needs to be run again.

To load the exporters, run the following command:

./docker_loadexporters.sh

5. Access

The CDCS is now available at the SERVER_URI set at deployment. Please read important deployment information in the troubleshoot section below.

6. Troubleshoot

Local deployment

DO NOT set HOSTNAME, SERVER_URI and ALLOWED_HOSTS to localhost or 127.0.0.1. Even if the system, starts properly, some features may not work (e.g. the search page may show an error instead of returning data). When deploying locally, use the computer's IP address to set those two variables, and use the same IP address when accessing the CDCS via a web browser: If your machine's IP address is xxx.xxx.xxx.xxx, and the default server configuration was used to deploy the system, access it by typing http://xxx.xxx.xxx.xxx in the address bar of the browser.

Find the IP of the local machine:

On Linux and MacOS: ifconfig
On Windows: ipconfig

Then update the .env file:

HOSTNAME=xxx.xxx.xxx.xxx
SERVER_URI=http://xxx.xxx.xxx.xxx
ALLOWED_HOSTS=xxx.xxx.xxx.xxx

NOTE: For testing purposes, ALLOWED_HOSTS can be set to *:

ALLOWED_HOSTS=*

Production deployment

Set SERVER_CONF to https
Update the file nginx/https.conf if necessary
Add HTTPS configuration to the mounted settings.py file
Have a look at the deployment checklist

Logs

Make sure every component is running properly by checking the logs. For example, to check the logs of an MDCS instance (PROJECT_NAME=mdcs), use the following commands:

docker logs -f mdcs_cdcs
docker logs -f mdcs_cdcs_nginx
docker logs -f mdcs_cdcs_mongo
docker logs -f mdcs_cdcs_postgres
docker logs -f mdcs_cdcs_redis

MongoDB RAM usage

From https://hub.docker.com/_/mongo

By default Mongo will set the wiredTigerCacheSizeGB to a value proportional to the host's total memory regardless of memory limits you may have imposed on the container. In such an instance you will want to set the cache size to something appropriate, taking into account any other processes you may be running in the container which would also utilize memory.

Having multiple mongodb containers on the same machine could be an issue as each of them will try to use the same amount of RAM from the host without taking into account the amount used by other containers. This could lead to the server running out of memory.

How to fix it?

The amount of RAM used by mongodb can be restricted by adding the --wiredTigerCacheSizeGB option to the mongodb command:

Example:

command: "--auth --wiredTigerCacheSizeGB 8"

More information on MongoDB RAM usage can be found in the doc

Additional components

Additional components can be added to the CDCS stack by providing docker-compose.yml files for those. Update the COMPOSE_FILE variable in the .env file to do so. More information can be found in on this option in the documentation.

MongoDB

In preparation for the release of CDCS 3.x, MongoDB becomes an optional component and will not be part of the default stack. It will need to be added for any CDCS 2.x deployment.

To add MongoDB to the CDCS stack, you can do the following:

Update the .env file to deploy MongoDB:

COMPOSE_FILE=docker-compose.yml:mongo/docker-compose.yml

🚧 Celery (WIP)

By default, CDCS images have been running the django web server but also celery worker and celery beat. It is now also possible to change this default behavior and run these services separately by selecting one of the following entrypoint:

docker-entrypoint.sh: starts the django server, celery worker and celery beat (default)
docker-entrypoint-django.sh: starts the django server only
docker-entrypoint-celery-worker.sh: starts the celery worker only
docker-entrypoint-celery-beat.sh: starts the celery beat only

The default behavior will continue to run these 3 services within the same container. To deploy the 3 services separately in a docker-compose deployment, you can do the following:

Update the file docker-compose.yml and set the default entrypoint of the cdcs service to only start the django server:

cdcs:
  entrypoint: /docker-entrypoint-django.sh

Then add celery worker and celery beat services to the CDCS stack, by updating the COMPOSE_FILE variable from the .env file:

COMPOSE_FILE=docker-compose.yml:celery/docker-compose.yml

⚠️ Concurrency Issue in CDCS < 2.9: Some CDCS applications make database modifications during their initialization. Starting Django and Celery services in parallel can make these scripts run multiple times, causing inconsistencies in the database. The issue needs to be resolved in the code of the CDCS apps. In the meantime, a startup delay has been implemented for celery services.

📄 The default entrypoint runs the scripts synchronously and does not have this issue.

Elasticsearch

Ongoing developments on the CDCS make use of Elasticsearch. To add Elasticsearch to the CDCS stack, you can do the following:

Update the .env file to deploy Elasticsearch:

COMPOSE_FILE=docker-compose.yml:elasticsearch/docker-compose.yml

Add and fill the following environment variables:

Variable	Description
ELASTIC_VERSION	Version of the Elasticsearch image (e.g. 7.16.2)

On linux, you will need to increase the available virtual memory.

Delete the containers and their data

To delete all the containers of the CDCS stack, run:

docker-compose down

To delete all containers and all the data, run:

docker-compose down -v

Upgrade the CDCS container

When a new version of a CDCS image becomes available, the system can be upgraded by doing the following steps:

Stop the stack

docker-compose stop

Update the version of the image in deploy/.env:

IMAGE_VERSION=3.6.0 # set the version of the new image

Restart the stack with the new image:

docker-compose up -d

Run the migration script (that will update static files and apply database migrations):

./docker_migrate.sh

NOTE: the script will do dry runs and ask for confirmation before applying the changes, but it is
recommended to create a back up of the databases before starting the migration.

Disclaimer

NIST Disclaimer

Name		Name	Last commit message	Last commit date
Latest commit History 77 Commits
build		build
deploy		deploy
.gitignore		.gitignore
LICENSE.md		LICENSE.md
README.md		README.md

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CDCS Docker

Prerequisites

Build a CDCS image

1. Customize the build

2. Build the image

3. Build a custom image (optional)

Deploy a CDCS

1. Customize the deployment

SAML2

Contact Person and Organization environment variables

hdl.net PID Integration

Settings

Web Server

2. Deploy the stack

3. Create a superuser

4. Initialize database

5. Access

6. Troubleshoot

Local deployment

Production deployment

Logs

MongoDB RAM usage

How to fix it?

Additional components

MongoDB

🚧 Celery (WIP)

Elasticsearch

Delete the containers and their data

Upgrade the CDCS container

Disclaimer

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Contributors 4

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usnistgov/cdcs-docker

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CDCS Docker

Prerequisites

Build a CDCS image

1. Customize the build

2. Build the image

3. Build a custom image (optional)

Deploy a CDCS

1. Customize the deployment

SAML2

Contact Person and Organization environment variables

hdl.net PID Integration

Settings

Web Server

2. Deploy the stack

3. Create a superuser

4. Initialize database

5. Access

6. Troubleshoot

Local deployment

Production deployment

Logs

MongoDB RAM usage

How to fix it?

Additional components

MongoDB

🚧 Celery (WIP)

Elasticsearch

Delete the containers and their data

Upgrade the CDCS container

Disclaimer

About

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Contributors 4

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