SMILE Message Publisher

Spring Boot LIMS SampleMetadata publisher framework

SMILE Publisher 📘

The SMILE Publisher is one of several components that comprise the SMILE distributed microservices system. It runs as a standalone tool that may publish directly to specific SMILE topics given the appropriate consumer permissions are provided.

The SMILE Publisher runs in 2 modes:

1. LIMS Request IDs mode

• Option 1: Provide comma-separated list of request ids directly
• Option 2: Provide a start date and (optionally) an end date to fetch LIMS requests delivered within the specified date range

2. File reading (or message recovery) mode This mode can be run to publish messages to a stream directly from a file with tab-separated values. The file must follow the same structure that the publishing logger file uses.

File structure:

• Column 1: Date message was received (YYYY/MM/DD)
• Column 2: Message topic
• Column 2: Message contents

Run

Custom properties

Make an application.properties based on application.properties.EXAMPLE.

All properties are required with the exception of some NATS connection-specific properties. The following are only required if nats.tls_channel is set to true:

• nats.keystore_path : path to client keystore
• nats.truststore_path : path to client truststore
• nats.key_password : keystore password
• nats.store_password : truststore password

Configure your log4j.properties based on log4j.properties.EXAMPLE. The default configuration writes to std.out which is standard for container environments.

Locally

Requirements:

• maven 3.6.1
• java 8

Add application.properties and log4j.properties to the local application resources: src/main/resources

Build with

mvn clean install

Run with

java -jar target/smile_publisher.jar

With Docker

Requirements

• docker

Build image with Docker

docker build -t <repo>/<tag>:<version> .

Push image to DockerHub

docker push <repo>/<tag>:<version>

If the Docker image is built with the properties baked in then simply run with:

docker run --name sample-publisher <repo>/<tag>:<version> -jar /publisher/smile_publisher.jar

Otherwise use a bind mount to make the local files available to the Docker image and add --spring.config.location to the java arg

docker run --mount type=bind,source=<local path to properties files>,target=/publisher/src/main/resources --name sample-publisher <repo>/<tag>:<version> -jar /publisher/smile_publisher.jar --spring.config.location=/publisher/src/main/resources/application.properties