ambit-docker

This repo helps you test AMBIT on your machine or deploy it inside your organization. For more information on AMBIT and the eNanoMapper database, please see http://ambit.sourceforge.net/ and https://search.data.enanomapper.net/.

Quick start

AMBIT with the freely available data from NANoREG, NANoREG II, caLIBRAte, and GRACIOUS in under 30 seconds:

1. Make sure your Docker instance supports Docker Compose.
2. git clone https://github.com/ideaconsult/ambit-docker.git
3. cd ambit-docker
4. docker compose pull
5. docker compose up
6. Open the following addresses in your browser:
   • http://127.0.0.1:8080/ambit for NANoREG
   • http://127.0.0.1:8081/ambit for NANoREG II
   • http://127.0.0.1:8082/ambit for caLIBRAte
   • http://127.0.0.1:8083/ambit for GRACIOUS
7. Press Ctrl+C in the console, where docker compose up is running, to stop it.

• NOTE: These instances do not contain the data from the eNanoMapper database.
• NOTE: If using older Docker versions, replace docker compose with docker-compose.
• NOTE: Running the Docker commands will likely require sudo or equivalent.

Customization

Need different datasets? An empty instance to populate with your own data?

Copy the docker-compose.yml and ambit-config.env files to a new directory and edit them to suit your needs.

Examples

Check the examples for some ready-made solutions or see below for more technical information.

Importing custom datasets

Some publicly available datasets are automatically downloaded, when their names are recognized in the configuration. Currently, these include calibrate, gracious, nanoreg1 and nanoreg2.

If you have another SQL dump that you want to be imported:

1. Create a data_import subdirectory in the directory with your custom docker-compose.yml and ambit-config.env files.
2. Place the .sql dump in data_import and compress it with xz.
3. Set AMBIT_DATABASES in ambit-config.env to the name of the .sql.xz file without the extensions, e.g. AMBIT_DATABASES="myData" if the file is named myData.sql.xz.

ambit-config.env reference

AMBIT_PROFILE

Possible values: enanomapper, lri.

Changes mostly how AMBIT looks. Does not change its behaviour or available features.

AMBIT_DATABASES

Space-separated list of database names.

For each name, there must be a corresponding xz-compressed SQL dump of the database placed in the data_import subdirectory, unless it's a publicly available database, as explained earlier. For example, if this is set to datasetA datasetB, in the data_import subdirectory there must be files datasetA.sql.xz and datasetB.sql.xz containing the respective dumps.

AMBIT_AA_ENABLE

Possble values: false, true.

Determines whether the web interface will require authentication. Note that unless you explicitly instruct Docker otherwise, the interface will be available only on your local system. So, authentication isn't strictly necessary if you are doing only testing and in these cases this setting can be left at false. If set to true, two default users are available in the web interface: admin and guest with their passwords the same as the username. This obviously is suitable only for testing and you should change the passwords if you plan to make the instance visible on the network or—even more so—on the internet. Note that these users and passwords are entirely different from the AMBIT_DB_USER and AMBIT_DB_PASS below. While the former are used by the users to access the web interface, the latter is an internal user that is used only by the system to connect to the database service.

AMBIT_DB_HOST

DNS name of the database service.

By default, it is set to the name of the database service from the docker-compose.yml file. You may provide the DNS name of an external RDBMS server, but please note that if you use such server, instead of the one run by Docker Compose, you will need to import all the databases and set all DB users manually (we may be able to provide custom support—for enquiries please write to [email protected]).

AMBIT_DB_USER

The name of the internal user that is used by the system to connect to the database service.

For testing the default should be fine. In production environments, it may be advisable to change this to something more secure.

AMBIT_DB_PASS

The password of the internal user that is used by the system to connect to the database service.

For testing the default should be fine. In production environments, it is strongly advisable to change this to something more secure.

AMBIT_USERS_DB

The name of the database holding the web interface users.

There's probably little reason to change this from the default value, but it may be useful for custom RDBMS setups.

MYSQL_ROOT_PASSWORD

The password for the root user of the RDBMS server run by Docker Compose.

For testing the default should be fine. In production environments, it is strongly advisable to change this to something more secure. Use this password when connecting to the RDBMS server as root (see the section #Tips for more information). Note that the value of the option is irrelevant if using a custom RDBMS server.

docker-compose.yml reference

• For each database name in the AMBIT_DATABASES option above, add a new api-<something> section in the docker-compose.yml file. Use the existing sections of this type as an example. The api-<something> sections must be in sync with AMBIT_DATABASES. For example, if you have set the latter to nanoreg1 datasetA datasetB, docker-compose.yml must have and only have the api-<something> sections of api-nanoreg1, api-datasetA, and api-datasetB. You can actually use arbitrary names for these sections, but keeping the name of the dataset in the name keeps everything tidy. Note also that the db section must be present at all times, unless you opt to use a custom RDBMS server.
• In each api-<something> section set the AMBIT_DATABASE environment variable (note the singular, unlike in ambit-config.env, where it is plural!) to the corresponding database.
• In each api-<something> section set the ports option to a different host port (the one after 127.0.0.1). With three datasets you may use, for example, 127.0.0.1:8080:8080, 127.0.0.1:8081:8080, and 127.0.0.1:8082:8080. You may use any port numbers here (subject to OS permissions), just remember to open the same ports in your browser. For the service port (the last one), however, keep it at 8080.

Tips

• You can connect to the RDBMS server by using this command from the same directory where the relevant docker-compose.yml is located: docker compose exec db mysql -uroot -p. When asked for a password, enter the password defined by MYSQL_ROOT_PASSWORD in ambit-config.env. Note that db here is the name of the RDBMS service in docker-compose.yml. If you have changed this name, update the command accordingly.
• When you make changes to docker-compose.yml, Docker Compose automatically recreates the containers for you. However, if you make changes to ambit-config.env and other files, these changes might not be picked up. In such cases it is advisable to run docker compose down before running docker compose up again. Do note, however, that even this command will not affect the databases. If you want to have the datases recreated, for example, if you have changed AMBIT_DATABASES, you should run docker compose down -v. WARNING: The latter command will irreversibly destroy the existing databases! If you have entered custom data, make a dump before running the command! One way of doing this could be docker compose exec db mysqldump -uroot -p<value-of-MYSQL_ROOT_PASSWORD> --single-transaction --add-drop-database --databases --routines <database-name>; redirect the output as needed, e.g. to a file.
• You can run the setup in background by using docker compose up -d. To stop run docker compose stop from the same directory.
• Instead of running docker-compose in the same directory as the docker-compose.yml file, you can specify its location with the -f option, e.g. docker compose -f ~/my-docker-test/docker-compose.yml stop.

Supported tags

Container	Tags
ambit-api	ci/ambit-api/tags.txt
ambit-db	ci/ambit-db/tags.txt

Notes on specific versions

• Java 11 and 17 are supported, but for maximum stability we still recommend Java 8 as the most thoroughly tested platform.
• MySQL 8+ is not supported. We may add support for it in the future, but for the time being please use MariaDB instead.
• Tomcat 10 is not supported and most likely will never be supported. We plan to transition to Quarkus.

Troubleshooting

• If you hit the Docker Hub pull limits, use GitHub Container Registry. You'll need to edit the docker compose files and prepend the image settings with ghcr.io/, e.g. ideaconsult/ambit-db:latest becomes ghcr.io/ideaconsult/ambit-db:latest.
• If docker compose up refuses to start with errors like Bind for 127.0.0.1:8080 failed: port is already allocated, something is using the said ports on your system. Try changing the port in docker-compose.yml to some different value. On Linux you can use something like echo $(( ${RANDOM}/2 + 49152 )) to get a suitable random high port.