Configuring the FAIR DO Lab

As the Lab is a set of components, configuring it means to configure these components and its composition.

Configure the component structure

The docker-compose.yml file defines ports and local hostnames of the services. It can be used to exclude services or include new ones.

Configure the services

Each service has its own folder in the repository, containing configuration files like Dockerfiles, application.properties files, or more. They will be included either when building the image or when starting the container. While the docker-compose.yml sets for example hostnames and ports for each service, the communication between the services is being configured in the appliation.properties file of each service.

Typed PID Maker

Configuration sub-folder: pit-service

Currently, there is no pre-built image of the Typed PID Maker. The configuration is included at build time of the image. This means to apply new configuration, you need to:

docker compose rm pit-service  # remove Typed PID Maker
docker compose build pit-service  # build new image
docker compose create pit-service  # create new container

Read more about how to configure the Typed PID Maker (application.properties). If you want to include your key and certificate files for configuration of a real PID prefix, you can put it into the config folder and refer to it in the application.properties via a relative path. Example: If you put the key in config/key/keyfile.bin, then use key/keyfile.bin to refer to it from the configuration file. If your file is password-protected, you can set the passphrase using the environment variable described in the Typed PID Maker configuration description within the docker-compose.yml.

Indexer

Configuration sub-folder: indexer

Applying the configuration currently works the same as with the Typed PID Maker, described above. The following is a list of the most important properties in the application.properties file.

• indexer.pit.resolvingURL: http://pit-service:8080/api/v1/pit/pid/%s
  • A url to resolve a PID with a HTTP GET from a PIT service. This is because the messages the indexer receives contain PIDs, but it is the indexers choice how to resolve it.
  • Use %s as a placeholder for the PID to resolve.
• indexer.recordMapping.mappingFiles: mytemplate
  • A list of filenames, stored in the classpath (i.e. java/main/resources) which will be used to map the records into elastic-compatible json.
  • Example: indexer.recordMapping.mappingFiles: mytemplate,yourtemplate (Assuming your files are in the classpaths root and named mytemplate.hbs and yourtemplate.hbs)
• indexer.elastic.folder: /elastic_json
  • The subfolder where the json files, which are ingested into elasticsearch are stored locally. This might be useful as a backup.
• indexer.elastic.baseUrl: http://elasticsearch:9200
  • The base URL of the elasticsearch service, including port.
• indexer.elastic.index: /record
  • The elastic index (“database”) where the records will be stored into.

The following properties define the communication with RabbitMQ.

• repo.messaging.enabled: true
  • Enables the messaging feature. The indexer will not work, if this is set to false.
• repo.messaging.hostname: messagebroker
  • Hostname of RabbitMQ.
• repo.messaging.port: 5672
  • Port of RabbitMQ
• repo.messaging.receiver.exchange: record_events
  • The exchange to listen to. This is the exchange where the Typed PID Maker puts its messages into.
• repo.messaging.receiver.queue: indexerQueue
  • The queue that will be registered for the indexer. Should be unique, except the plan is to have multiple indexers for parallelization.
• repo.messaging.receiver.routingKeys: pidrecord.#
  • The “routingKeys” or “topics” of the messages which should be indexed. The # is similar to * in regular expressions in this example. pidrecord is the topic prefix that the Typed PID Maker uses (e.g. pidrecord.create).

Fairris

Configuration sub-folder: fairris

Fairris is a small user interface for purely DEMO purposes. It allows you to create and update minimalistic FAIR DOs using the Typed PID Maker. The current version has no configuration options.