invitae-lab-platform-exercise - Variant Service

A Variant is broadly defined as an alteration in a DNA nucleotide sequence. The Variant Service is intended to serve as the source repository for billions of variants across the globe.

Some of a Variant's attributes include:

- Gene	
- Nucleotide Change	
- Protein Change	
- Last Evaluated

A json representation of a sample variant:

{
  "gene": "PGAM4",
  "nucleotideChange": "NG_013224.2:g.(?_4960)_(103567_105489)dup,NC_000023.11:g.(?_77910656)_(78009263_78011185)dup",
  "proteinChange": "NG_013224.2,NC_000023.11",
  "lastEvaluated": "2017-09-14"
}

Tech Stack

This project is bootstrapped using the Spring-Boot and Kotlin stack. Please attempt to incorporate language/framework idioms and best practices.

Tasks:

1. Build a REST endpoint that enables creation of a variant. The variant is saved in the service's persistence store - a Postgres database. What choices would you make for the database connectivity (JDBC, JPA, etc.)? Why? What does the schema of the Variant table look like? What would be the "type" of the primary key (Variant id)? Also store a Variant creation timestamp. How would you manage db migrations (flyway, Liquidbase, etc.)? Why?

2. Broadcast a VariantEvent to a Kafka topic after a Variant record is saved, for interested downstream consumers. For this contrived example, the event shape consists of all Variant attributes from the DB table. What library would you choose for the integration with Kafka (spring-cloud-stream, spring-kafka, etc.)? Why? What is your strategy for broadcasting events? What are some considerations? What serialization format would you choose - plaintext (json, etc.) vs binary (protobuf, avro, thrift, etc.)?

Please treat these tasks as production-grade software (unit tests, etc.).

Prerequisites

This application requires Git and Rancher Desktop to be locally installed.

Docker Environment

A fully dockerized environment is provided with all the batteries:

$ nerdctl compose up -d

For faster development cycles, consider running the lab-platform-exercise locally instead of in docker

$ nerdctl compose -f docker-compose-without-app.yml up -d

$ ./gradlew bootRun

Kafka UI

The Kafka UI can be accessed at http://localhost:3030/. Of particular interest will be the Topics UI, which lists the topics and the messages on each. It can be accessed at http://localhost:3030/kafka-topics-ui/#/.