Snow Owl is also available as Docker images. The images use centos:7 as the base image.

A list of all published Docker images and tags is available at Docker Hub.

These images are free to use under the Apache 2.0 license. They contain open source features only.

Pulling the image

Obtaining Snow Owl for Docker is as simple as issuing a docker pull command against the Docker Hub registry.

docker pull snow-owl-oss:latest

Running Snow Owl from the command line

Development mode

Snow Owl can be quickly started for development or testing use with the following command:

docker run -p 8080:8080 snow-owl-oss:latest

Production mode

The following example brings up Snow Owl instance with its dedicated Elasticsearch node. To bring up the cluster, use the docker-compose.yml and just type:

docker-compose up

The node snowowl listens on localhost:8080 while it talks to the elasticsearch node over a Docker network.

To stop the cluster, type docker-compose down. Data volumes/mounts will persist, so it's possible to start the stack again with the same data using docker-compose up`.

Configuring Snow Owl with Docker

Snow Owl loads its configuration from files under /usr/share/snowowl/config/. These configuration files are documented in the Configure Snow Owl pages.

The image offers several methods for configuring Snow Owl settings with the conventional approach being to provide customized files, that is to say, snowowl.yml. It's also possible to use environment variables to set options:

• A. Bind-mounted configuration

  Create your custom config file and mount this over the image's corresponding file.

  For example, bind-mounting a custom_snowowl.yml with docker run can be

  accomplished with the parameter:

-v full_path_to/custom_snowowl.yml:/usr/share/snowowl/configuration/snowowl.yml

• B. Customized image

  In some environments, it may make more sense to prepare a custom image containing

  your configuration. A Dockerfile to achieve this may be as simple as:

FROM snow-owl-oss:{version}
COPY --chown=snowowl:snowowl snowowl.yml /usr/share/snowowl/configuration/

You could then build and try the image with something like:

docker build --tag=snow-owl-oss-custom .
docker run -ti -v /usr/share/snowowl/resources snow-owl-oss-custom

Notes for production use and defaults

We have collected a number of best practices for production use. Any Docker parameters mentioned below assume the use of docker run.

By default, Snow Owl runs inside the container as user snowowl using uid:gid 1000:1000.

• If you are bind-mounting a local directory or file, ensure it is readable by

  this user, while the <> additionally require

  write access. A good strategy is to grant group access to gid 1000 or 0 for

  the local directory. As an example, to prepare a local directory for storing

  data through a bind-mount:

  mkdir sodatadir
  chmod g+rwx sodatadir
  chgrp 1000 sodatadir

• It is important to ensure increased ulimits for nofile

  and nproc are available for the Snow Owl containers.

  Verify the init system

  for the Docker daemon is already setting those to acceptable values and, if

  needed, adjust them in the Daemon, or override them per container, for example

  using docker run:

  --ulimit nofile=65535:65535

NOTE: One way of checking the Docker daemon defaults for the aforementioned ulimits is by running:

  docker run --rm centos:7 /bin/bash -c 'ulimit -Hn && ulimit -Sn && ulimit -Hu && ulimit -Su'

• Swapping needs to be disabled for performance and stability. This can be achieved through any of the methods mentioned in the system settings.

• The image exposes TCP ports 8080 and 2036.

• Use the SO_JAVA_OPTS environment variable to set heap size. For example, to use 16GB use SO_JAVA_OPTS="-Xms16g -Xmx16g" with docker run.

• Pin your deployments to a specific version of the Snow Owl OSS Docker image. For example, snow-owl-oss:7.2.0.

• Consider centralizing your logs by using a different https://docs.docker.com/engine/admin/logging/overview/[logging driver]. Also note that the default json-file logging driver is not ideally suited for production use.

Snow Owl uses SLF4J and Logback for logging.

The logging configuration file (serviceability.xml) can be used to configure Snow Owl logging. The logging configuration file location depends on your installation method, by default it is located in the ${SO_HOME}/configuration folder.

Extensive information on how to customize logging and all the supported appenders can be found on the Logback documentation.

This section includes information on how to setup Snow Owl and get it running, including:

• Downloading

• Installing

• Starting

• Configuring

Java (JVM) Version

Snow Owl is built using Java, and requires at least Java 11 in order to run. Only Oracle’s Java and the OpenJDK are supported. The same JVM version should be used on all Snow Owl nodes and clients.

We recommend installing Java version 11.0.x or a later version in the Java 11 release series. We recommend using a supported LTS version of Java.

The version of Java that Snow Owl will use can be configured by setting the JAVA_HOME environment variable.

Snow Owl ships with good defaults and requires very little configuration.

Config files location

Snow Owl has three configuration files:

• snowowl.yml for configuring Snow Owl

• serviceability.xml for configuring Snow Owl logging

• elasticsearch.yml for configuring the underlying Elasticsearch instance in case of embedded deployments

These files are located in the config directory, whose default location depends on whether or not the installation is from an archive distribution (tar.gz or zip) or a package distribution (Debian or RPM packages).

For the archive distributions, the config directory location defaults to $SO_PATH_HOME/configuration. The location of the config directory can be changed via the SO_PATH_CONF environment variable as follows:

SO_PATH_CONF=/path/to/my/config ./bin/startup

Alternatively, you can export the SO_PATH_CONF environment variable via the command line or via your shell profile.

For the package distributions, the config directory location defaults to /etc/snowowl. The location of the config directory can also be changed via the SO_PATH_CONF environment variable, but note that setting this in your shell is not sufficient. Instead, this variable is sourced from /etc/default/snowowl (for the Debian package) and /etc/sysconfig/snowowl (for the RPM package). You will need to edit the SO_PATH_CONF=/etc/snowowl entry in one of these files accordingly to change the config directory location.

Config file format

The configuration format is YAML. Here is an example of changing the path of the data directory:

path:
    data: /var/lib/snowowl

Settings can also be flattened as follows:

path.data: /var/lib/snowowl

Environment variable substitution

Environment variables referenced with the ${...} notation within the configuration file will be replaced with the value of the environment variable, for instance:

repository.host: ${HOSTNAME}
repository.port: ${SO_REPOSITORY_PORT}

While Snow Owl requires very little configuration, there are a number of settings which need to be considered before going into production.

The following settings must be considered before going to production:

Elasticsearch settings

By default, Snow Owl includes the OSS version of Elasticsearch and runs it in embedded mode to store terminology data and make it available for search. This is convenient for single node environments (eg. for evaluation, testing and development), but it might not be sufficient when you go into production.

To configure Snow Owl to connect to an Elasticsearch cluster, change the clusterUrl property in the snowowl.yml configuration file:

repository:
  index:
    clusterUrl: http://your.es.cluster:9200 # the ES cluster URL
    clusterUsername: snowowl # Optional username to connect to a protected ES cluster
    clusterPassword: snowowl_password # Optional password to connect to a protected ES cluster

The value for this setting should be a valid HTTP URL point to the HTTP API of your Elasticsearch cluster, which by default runs on port 9200.

Path settings

If you are using the .zip or .tar.gz archives, the data and logs directories are sub-folders of $SO_HOME. If these important folders are left in their default locations, there is a high risk of them being deleted while upgrading Snow Owl to a new version.

In production use, you will almost certainly want to change the locations of the data and log folders.

path:
  data: /var/data/snowowl

The RPM and Debian distributions already use custom paths for data and logs.

Network settings

To allow clients to connect to Snow Owl, make sure you open access to the following ports:

• 8080/TCP:: Used by Snow Owl Server's REST API for HTTP access

• 8443/TCP:: Used by Snow Owl Server's REST API for HTTPS access

• 2036/TCP:: Used by the Net4J binary protocol connecting Snow Owl clients to the server

Setting the heap size

By default, Snow Owl tells the JVM to use a heap with a minimum and maximum size of 2 GB. When moving to production, it is important to configure heap size to ensure that Snow Owl has enough heap available.

To configure the heap size settings, change the -Xms and -Xmx settings in the SO_JAVA_OPTS environment variable.

# Set the minimum and maximum heap size to 12 GB.
SO_JAVA_OPTS="-Xms12g -Xmx12g" ./bin/startup

The value for these setting depends on the amount of RAM available on your server and whether you are running Elasticsearch on the some node as Snow Owl (either embedded or as a service) or running it in its own cluster. Good rules of thumb are:

• Set the minimum heap size (Xms) and maximum heap size (Xmx) to be equal to each other.

• Too much heap can subject to long garbage collection pauses.

• Set Xmx to no more than 50% of your physical RAM, to ensure that there is enough physical RAM left for kernel file system caches.

• Snow Owl connecting to a remote Elasticsearch cluster requires less memory, but make sure you still allocate enough for your use cases (classification, batch processing, etc.).

You should rarely need to change Java Virtual Machine (JVM) options. If you do, the most likely change is setting the heap size.

The preferred method of setting JVM options (including system properties and JVM flags) is via the the SO_JAVA_OPTS environment variable. For instance:

export SO_JAVA_OPTS="$SO_JAVA_OPTS -Djava.io.tmpdir=/path/to/temp/dir"
./bin/startup

When using the RPM or Debian packages, SO_JAVA_OPTS can be specified in the system configuration file.

Snow Owl (with embedded Elasticsearch) uses a lot of file descriptors or file handles. Running out of file descriptors can be disastrous and will most probably lead to data loss. Make sure to increase the limit on the number of open files descriptors for the user running Snow Owl to 65,536 or higher.

For the .zip and .tar.gz packages, set ulimit -n 65536 as root before starting Snow Owl, or set nofile to 65536 in /etc/security/limits.conf.

RPM and Debian packages already default the maximum number of file descriptors to 65536 and do not require further configuration.

An orderly shutdown of Snow Owl ensures that Snow Owl has a chance to cleanup and close outstanding resources. For example, an instance that is shutdown in an orderly fashion will initiate an orderly shutdown of the embedded Elasticsearch instance, gracefully close and disconnect connections and perform other related cleanup activities. You can help ensure an orderly shutdown by properly stopping Snow Owl.

If you’re running Snow Owl as a service, you can stop Snow Owl via the service management functionality provided by your installation.

If you’re running Snow Owl directly, you can stop Snow Owl by sending Ctrl-C if you’re running Snow Owl in the console, or by invoking the provided shutdown script as follows:

$ ./bin/shutdown

Snow Owl security features enable you to easily secure your terminology server. You can password-protect your data as well as implement more advanced security measures such as role-based access control and auditing.

Realms

By default Snow Owl comes without any security features enabled and all read and write operations are unprotected. To configure a security realm, you can choose from the following built-in identity providers:

• Configure a file realm

• Configure an LDAP realm

Authentication

After configuring at least one security realm, Snow Owl will authenticate all incoming requests to ensure that the sender of the request is allowed to access the terminology server and its contents. To authenticate a request, the client must send an HTTP Basic or Bearer Authorization header with the request. The value should be a user/pass pair in case of using Basic authentication or a JWT token generated by Snow Owl if using the Bearer method.

Snow Owl sends an HTTP 401 Unauthorized response if a request needs to be authenticated.

Authorization

If supported by the security realm, Snow Owl will also check whether an authenticated user is permitted to perform the requested action on a given resource.

Within an organization, roles are created for various job functions. The permissions to perform certain operations are assigned to specific roles. Members, staff or other system users are assigned particular roles, and through those role assignments acquire the permissions needed to perform particular system functions. Since users are not assigned permissions directly, but only acquire them through their role (or roles), management of individual user rights becomes a matter of simply assigning appropriate roles to the user's account; this simplifies common operations, such as adding a user, or changing a user's department.

Rules

1. Role assignment: A subject can exercise a permission only if the subject has selected or been assigned a role.

2. Permission authorization: A subject can exercise a permission only if the permission is authorized for the subject's active role.

With rules 1 and 2, it is ensured that users can exercise only permissions for which they are authorized.

S = Subject = A person or automated agent R = Role = Job function or title which defines an authority level P = Permissions = An approval of a mode of access to a resource

Permissions

In Snow Owl a permission is a single value that represents both the operation the user would like to perform and the resource that is being accessed. The format is the following: <operation>:<resource>

Currently there are 7 operations supported by Snow Owl:

• browse - read the contents of a resource

• edit - write the contents of the resource, delete the resource

• import - import from external content and formats

• export - export to external content and formats

• version - create a version in a Code System, create a release

• promote - merge content from isolated branch environments to a Code System's development version

• classify - run classifiers and save their results

Resources represent the content that is being accessed by a client. A resource can be anything that can be resolved to a database entry. Currently, the following resource formats are allowed to be used in a permission:

• <repositoryId> - access the entire content available in a terminology repository

• <repositoryId>/<branch> - access the content available on a branch in a terminology repository

• <codeSystemId> - access all content of a Code System, including both the latest development and all previous releases

• <codeSystemId>/<versionId> - access a specific release of a Code System

There is a special * wild card character that can be used for both the operation and resource parts in a permission value to allow any operation to be performed on any or selected resources, or to allow certain operations to be performed on any available resources.

Examples:

• browse:snomedStore - browse all SNOMED CT Code Systems and their content

• edit:SNOMEDCT-UK-CL - edit the SNOMEDCT-UK-CL Code System

• export:SNOMEDCT-US/2019-03-01 - export the 2019-03-01 US Extension release

• *:SNOMEDCT - allow any operations to be performed on the SNOMEDCT Code System

• browse:* - allow read operations on all available resources

• *:* - administrator permission, the user can do anything with any of the available resources

Configuring Authorization

To configure authorization, please consult the security realm specific documentation:

• Configure a file realm

• Configure an LDAP realm

You can manage and authenticate users with the built-in file realm. All the data about the users for the file realm is stored in the users file. The file is located in SO_PATH_CONF and is read on startup.

You need to explicitly select the file realm in the snowowl.yml configuration file in order to use it for authentication.

identity:
  providers:
    - file:
        name: users

In the above configuration the file realm is using the users file to read your users from. Each row in the file represents a username and password delimited by : character. The passwords are BCrypt encrypted hashes. The default users file comes with a default snowowl user with the default snowowl password.

Users Command

To simplify file realm configuration, the Snow Owl CLI comes with a command to add a user to the file realm (snowowl users add). See the command help manual (-h option) for further details.

Authorization

The file security realm does NOT support the Authorization formats at the moment. If you are interested in configuring role-based access control for your users, it is recommended to switch to the LDAP security realm.

Most operating systems try to use as much memory as possible for file system caches and eagerly swap out unused application memory. This can result in parts of the JVM heap or even its executable pages being swapped out to disk.

Swapping is very bad for performance, and should be avoided at all costs. It can cause garbage collections to last for minutes instead of milliseconds and can cause services to respond slowly or even time out.

There are two approaches to disabling swapping. The preferred option is to completely disable swap, but if this is not an option, you can minimize swappiness.

Disable all swap files

Usually Snow Owl is the only service running on a box, and its memory usage is controlled by the JVM options. There should be no need to have swap enabled.

On Linux systems, you can disable swap temporarily by running:

sudo swapoff -a

To disable it permanently, you will need to edit the /etc/fstab file and comment out any lines that contain the word swap.

Configure swappiness

Another option available on Linux systems is to ensure that the sysctl value vm.swappiness is set to 1. This reduces the kernel’s tendency to swap and should not lead to swapping under normal circumstances, while still allowing the whole system to swap in emergency conditions.

# sysctl settings, to be added to /etc/sysctl.conf or equivalent
vm.swappiness = 1
vm.max_map_count = 262144

Snow Owl uses a number of thread pools for different types of operations. It is important that it is able to create new threads whenever needed. Make sure that the number of threads that the Snow Owl user can create is at least 4096.

This can be done by setting ulimit -u 4096 as root before starting Snow Owl, or by setting nproc to 4096 in /etc/security/limits.conf.

The package distributions when run as services under systemd will configure the number of threads for the Snow Owl process automatically. No additional configuration is required.

The method for starting Snow Owl varies depending on how you installed it.

Archive packages (.tar.gz, .zip)

If you installed Snow Owl with a .tar.gz or zip package, you can start Snow Owl from the command line.

Running Snow Owl from the command line

Snow Owl can be started from the command line as follows:

./bin/startup

By default, Snow Owl runs in the foreground, prints some of its logs to the standard output (stdout), and can be stopped by pressing Ctrl-C.

Running as a daemon

To run Snow Owl as a daemon, use the following command:

nohup ./bin/startup > /dev/null &

Log messages can be found in the $SO_HOME/serviceability/logs/ directory.

RPM packages

Snow Owl is not started automatically after installation. How to start and stop Snow Owl depends on whether your system uses SysV init or systemd (used by newer distributions). You can tell which is being used by running this command:

ps -p 1

Running Snow Owl with SysV init

Use the chkconfig command to configure Snow Owl to start automatically when the system boots up:

sudo chkconfig --add snowowl

Snow Owl can be started and stopped using the service command:

sudo -i service snowowl start
sudo -i service snowowl stop

If Snow Owl fails to start for any reason, it will print the reason for failure to STDOUT. Log files can be found in /var/log/snowowl/.

Running Snow Owl with systemd

To configure Snow Owl to start automatically when the system boots up, run the following commands:

sudo /bin/systemctl daemon-reload
sudo /bin/systemctl enable snowowl.service

Snow Owl can be started and stopped as follows:

sudo systemctl start snowowl.service
sudo systemctl stop snowowl.service

These commands provide no feedback as to whether Snow Owl was started successfully or not. Instead, this information will be written in the log files located in /var/log/snowowl/.

Debian packages (Coming Soon)

Docker images (Coming Soon)

Scheduler

# noop I/O scheduler, should be set in eg. /etc/rc.local for solid state disks:
echo noop > /sys/block/sdX/queue/scheduler

Snow Owl uses a mmapfs directory by default to store its data. The default operating system limits on mmap counts is likely to be too low, which may result in out of memory exceptions.

On Linux, you can increase the limits by running the following command as root:

sysctl -w vm.max_map_count=262144

To set this value permanently, update the vm.max_map_count setting in /etc/sysctl.conf. To verify after rebooting, run sysctl vm.max_map_count.

The RPM and Debian packages will configure this setting automatically. No further configuration is required.

Coming soon!

Snow Owl is provided as a .zip and as a .tar.gz package. These packages can be used to install Snow Owl on any system and are the easiest package format to use when trying out Snow Owl.

The latest stable version of Snow Owl can be found on the Snow Owl Releases page.

Download and install the zip package

The .zip archive for Snow Owl can be downloaded and installed as follows:

wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.zip
wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.zip.sha512
shasum -a 512 -c snowowl-oss-<version>.zip.sha512 # compares the SHA of the downloaded archive, should output: `snowowl-oss-<version>.zip: OK.`
unzip snowowl-oss-<version>.zip
cd snowowl-oss-<version>/ # This directory is known as `$SO_HOME`

Download and install the .tar.gz package

The .tar.gz archive for Snow Owl can be downloaded and installed as follows:

wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.tar.gz
wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.tar.gz.sha512
shasum -a 512 -c snowowl-oss-<version>.tar.gz.sha512 # compares the SHA of the downloaded archive, should output: `snowowl-oss-<version>.tar.gz: OK.` 
tar -xzf snowowl-oss-<version>.tar.gz
cd snowowl-oss-<version>/ # This directory is known as `$SO_HOME`

Running Snow Owl from the command line

Snow Owl can be started from the command line as follows:

./bin/startup

By default, Snow Owl runs in the foreground, prints its logs to the standard output (stdout), and can be stopped by pressing Ctrl-C.

Checking that Snow Owl is running

You can test that your instance is running by sending an HTTP request to Snow Owl's status endpoint:

curl http://localhost:8080/snowowl/admin/info

which should give you a response like this:

{
  "version": "7.0.0",
  "description": "You Know, for Terminologies",
  "repositories": {
    "items": [
      {
        "id": "snomedStore",
        "health": "GREEN"
      }
    ]
  }
}

Running in the background

You can send the Snow Owl process to the background using the combination of nohup and the & character:

nohup ./bin/startup > /dev/null &

Log messages can be found in the $SO_HOME/serviceability/logs/ directory.

To shut down Snow Owl, you can kill the process ID directly:

kill <pid>

or using the provided shutdown script:

./bin/shutdown

Directory layout of .zip and .tar.gz archives:

The .zip and .tar.gz packages are entirely self-contained. All files and directories are, by default, contained within $SO_HOME — the directory created when unpacking the archive.

This is very convenient because you don’t have to create any directories to start using Snow Owl, and uninstalling Snow Owl is as easy as removing the $SO_HOME directory. However, it is advisable to change the default locations of the config directory, the data directory, and the logs directory so that you do not delete important data later on.

Next steps

You now have a test Snow Owl environment set up. Before you start serious development or go into production with Snow Owl, you must do some additional setup:

• Learn how to configure Snow Owl.

• Configure important Snow Owl settings.

• Configure important system settings.

The RPM for Snow Owl can be downloaded from the Downloads section. It can be used to install Snow Owl on any RPM-based system such as OpenSuSE, SLES, Centos, Red Hat, and Oracle Enterprise.

Download and install

wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.rpm
wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.rpm.sha512
shasum -a 512 -c snow-owl-oss-<version>.rpm.sha512 # Compares the SHA of the downloaded RPM and the published checksum, which should output `snow-owl-oss-<version>.rpm: OK`.
sudo rpm --install snow-owl-oss-<version>.rpm

Running Snow Owl with SysV init

Use the chkconfig command to configure Snow Owl to start automatically when the system boots up:

sudo chkconfig --add snowowl

Snow Owl can be started and stopped using the service command:

sudo -i service snowowl start
sudo -i service snowowl stop

If Snow Owl fails to start for any reason, it will print the reason for failure to STDOUT. Log files can be found in /var/log/snowowl/.

Running Snow Owl with systemd

To configure Snow Owl to start automatically when the system boots up, run the following commands:

sudo /bin/systemctl daemon-reload
sudo /bin/systemctl enable snowowl.service

Snow Owl can be started and stopped as follows:

sudo systemctl start snowowl.service
sudo systemctl stop snowowl.service

These commands provide no feedback as to whether Snow Owl was started successfully or not. Instead, this information will be written in the log files located in /var/log/snowowl/.

Checking that Snow Owl is running

You can test that your Snow Owl instance is running by sending an HTTP request to:

curl http://localhost:8080/snowowl/admin/info

which should give you a response something like this:

{
  "version": "7.2.0",
  "description": "You Know, for Terminologies",
  "repositories": {
    "items": [
      {
        "id": "snomedStore",
        "health": "GREEN"
      }
    ]
  }
}

Configuring Snow Owl

Snow Owl defaults to using /etc/snowowl for runtime configuration. The ownership of this directory and all files in this directory are set to root:snowowl on package installation and the directory has the setgid flag set so that any files and subdirectories created under /etc/snowowl are created with this ownership as well (e.g., if a keystore is created using the keystore tool). It is expected that this be maintained so that the Snow Owl process can read the files under this directory via the group permissions.

Snow Owl loads its configuration from the /etc/snowowl/snowowl.yml file by default. The format of this config file is explained in Configuring Snow Owl.

Directory layout of RPM

The RPM places config files, logs, and the data directory in the appropriate locations for an RPM-based system:

Next steps

You now have a test Snow Owl environment set up. Before you start serious development or go into production with Snow Owl, you must do some additional setup:

• Learn how to configure Snow Owl.

• Configure important Snow Owl settings.

• Configure important system settings.

Ideally, Snow Owl should run alone on a server and use all of the resources available to it. In order to do so, you need to configure your operating system to allow the user running Snow Owl to access more resources than allowed by default.

The following settings must be considered before going to production:

• Disable swapping

• Increase file descriptors

• Ensure sufficient virtual memory

• Ensure sufficient threads

• Tweaking for performance

Configuring system settings

Where to configure systems settings depends on which package you have used to install Snow Owl, and which operating system you are using.

When using the .zip or .tar.gz packages, system settings can be configured:

• temporarily with ulimit, or

• permanently in /etc/security/limits.conf.

When using the RPM or Debian packages, most system settings are set in the system configuration file. However, systems which use systemd require that system limits are specified in a systemd configuration file.

ulimit

On Linux systems, ulimit can be used to change resource limits on a temporary basis. Limits usually need to be set as root before switching to the user that will run Snow Owl. For example, to set the number of open file handles (ulimit -n) to 65,536, you can do the following:

sudo su # Become `root`
ulimit -n 65536 # Change the max number of open files
su snowowl # Become the `snowowl` user in order to start Snow Owl

The new limit is only applied during the current session.

You can consult all currently applied limits with ulimit -a.

/etc/security/limits.conf

On Linux systems, persistent limits can be set for a particular user by editing the /etc/security/limits.conf file. To set the maximum number of open files for the snowowl user to 65,536, add the following line to the limits.conf file:

snowowl  -  nofile  65536

This change will only take effect the next time the snowowl user opens a new session.

# session    required   pam_limits.so

Sysconfig file

When using the RPM or Debian packages, system settings and environment variables can be specified in the system configuration file, which is located in:

However, for systems which uses systemd, system limits need to be specified via systemd.

Systemd configuration

When using the RPM or Debian packages on systems that use systemd, system limits must be specified via systemd.

The systemd service file (/usr/lib/systemd/system/snowowl.service) contains the limits that are applied by default.

To override them, add a file called /etc/systemd/system/snowowl.service.d/override.conf (alternatively, you may run sudo systemctl edit snowowl which opens the file automatically inside your default editor). Set any changes in this file, such as:

[Service]
LimitMEMLOCK=infinity

Once finished, run the following command to reload units:

sudo systemctl daemon-reload

The Debian package for Snow Owl can be downloaded from the Downloads section. It can be used to install Snow Owl on any Debian-based system such as Debian and Ubuntu.

Download and install

wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.deb
wget https://github.com/b2ihealthcare/snow-owl/releases/download/<version>/snow-owl-oss-<version>.deb.sha512
shasum -a 512 -c snow-owl-oss-<version>.deb.sha512 # Compares the SHA of the downloaded Debian package and the published checksum, which should output `snow-owl-oss-<version>.deb: OK`.
sudo dpkg -i snow-owl-oss-<version>.deb

Running Snow Owl with SysV init

Use the update-rc.d command to configure Snow Owl to start automatically when the system boots up:

sudo update-rc.d snowowl defaults 95 10

Snow Owl can be started and stopped using the service command:

sudo -i service snowowl start
sudo -i service snowowl stop

If Snow Owl fails to start for any reason, it will print the reason for failure to STDOUT. Log files can be found in /var/log/snowowl/.

Running Snow Owl with systemd

To configure Snow Owl to start automatically when the system boots up, run the following commands:

sudo /bin/systemctl daemon-reload
sudo /bin/systemctl enable snowowl.service

Snow Owl can be started and stopped as follows:

sudo systemctl start snowowl.service
sudo systemctl stop snowowl.service

These commands provide no feedback as to whether Snow Owl was started successfully or not. Instead, this information will be written in the log files located in /var/log/snowowl/.

Checking that Snow Owl is running

You can test that your Snow Owl instance is running by sending an HTTP request to:

curl http://localhost:8080/snowowl/admin/info

which should give you a response something like this:

{
  "version": "7.2.0",
  "description": "You Know, for Terminologies",
  "repositories": {
    "items": [
      {
        "id": "snomedStore",
        "health": "GREEN"
      }
    ]
  }
}

Configuring Snow Owl

Snow Owl defaults to using /etc/snowowl for runtime configuration. The ownership of this directory and all files in this directory are set to root:snowowl on package installation and the directory has the setgid flag set so that any files and subdirectories created under /etc/snowowl are created with this ownership as well (e.g., if a keystore is created using the keystore tool). It is expected that this be maintained so that the Snow Owl process can read the files under this directory via the group permissions.

Snow Owl loads its configuration from the /etc/snowowl/snowowl.yml file by default. The format of this config file is explained in Configuring Snow Owl.

Directory layout of Debian package

The Debian package places config files, logs, and the data directory in the appropriate locations for a Debian-based system:

Next steps

You now have a test Snow Owl environment set up. Before you start serious development or go into production with Snow Owl, you must do some additional setup:

• Learn how to configure Snow Owl.

• Configure important Snow Owl settings.

• Configure important system settings.

You can configure security to communicate with a Lightweight Directory Access Protocol (LDAP) server to authenticate and authorize users.

To integrate with LDAP, you configure an ldap realm in the snowowl.yml configuration file.

identity:
  providers:
    - ldap:
        uri: <ldap_uri>
        bindDn: cn=admin,dc=snowowl,dc=b2international,dc=com
        bindDnPassword: <adminpwd>
        baseDn: dc=snowowl,dc=b2international,dc=com
        roleBaseDn: {baseDn}
        userFilter: (objectClass={userObjectClass})
        roleFilter: (objectClass={roleObjectClass})
        userObjectClass: inetOrgPerson
        roleObjectClass: groupOfUniqueNames
        userIdProperty: uid
        permissionProperty: description
        memberProperty: uniqueMember
        usePool: false

Configuration

The following configuration settings are supported:

The default configuration values are selected to support both OpenLDAP and Active Directory without needing to customize the default schema that comes with their default installation.

Configure Authentication

When users send their username and password with their request in the Authorization header, the LDAP security realm performs the following steps to authenticate the user: 1. Searches for a user entry in the configured baseDn to get the DN 2. Authenticates with the LDAP instance using the received DN and the provided password

If any of the above-mentioned steps fails for any reason, the user is not allowed to access the terminology server's content and the server will respond with HTTP 401 Unauthorized.

To configure authentication, you need to configure the uri, baseDn, bindDn, bindDnPassword, userObjectClass and userIdProperty configuration settings.

Adding a user

To add a user in the LDAP realm, create an entry under the specified baseDn using the configured userObjectClass as class and the userIdProperty as the property where the user's username/e-mail address is configured.

Example user entry:

dn: cn=John Doe+sn=Doe+uid=johndoe@b2international.com,dc=snowowl,dc=b2international,dc=com
objectClass: inetOrgPerson
objectClass: organizationalPerson
objectClass: person
objectClass: top
cn: John Doe
sn: Doe
uid: johndoe@b2international.com
userPassword: <encrypted_password>

Configure Authorization

On top of the authentication part, the LDAP realm provides configuration values to support full role-based access control and authorization.

When a user's request is successfully authenticated with the LDAP realm, Snow Owl authorizes the request using the user's currently set roles and permissions in the configured LDAP instance.

Adding a role

To add a role in the LDAP realm, create an entry under the specified baseDn using the configured roleObjectClass as class and the configured permissionProperty and memberProperty properties for permission and user mappings, respectively.

Example read-only role:

dn: cn=Browser,dc=snowowl,dc=b2international,dc=com
objectClass: top
objectClass: groupOfUniqueNames
cn: Browser
description: browse:*
description: export:*
uniqueMember: cn=John Doe+sn=Doe+uid=johndoe@b2international.com,dc=snowowl,dc=b2international,dc=com

Snow Owl is provided in the following package formats:

By default, Snow Owl is starting and connecting to an embedded Elasticsearch cluster available on http://localhost:9200. This cluster has only a single node and its discovery method is set to single-node, which means it is not able to connect to other Elasticsearch clusters and will be used exclusively by Snow Owl.

This single node Elasticsearch cluster can easily serve Snow Owl in testing, evaluation and small authoring environments, but it is recommended to customize how Snow Owl connects to an Elasticsearch cluster in larger environments (especially when planning to scale with user demand).

You have two options to configure Elasticsearch used by Snow Owl.

Configure the embedded instance

The first option is to configure the underlying Elasticsearch instance by editing the configuration file elasticsearch.yml, which depending on your installation is available in the configuration directory (you can create the file, if it is not available, Snow Owl will pick it up during the next startup).

Connect to a remote cluster

The second option is to configure Snow Owl to use a remote Elasticsearch cluster without the embedded instance. In order to use this feature you need to set the repository.index.clusterUrl configuration parameter to the remote address of your Elasticsearch cluster. When Snow Owl is configured to connect to a remote Elasticsearch cluster, it won't boot up the embedded instance, which reduces the memory requirements of Snow Owl slightly.

You can connect to self-hosted clusters or hosted solutions provided by AWS and Elastic.co for example.