dkfz-unite/unite-specimens-feed

Unite cell line data feed service.

Specimens Data Feed Service

General

Specimens data feed service provides the following functionality:

• Specimens data feed web API - REST API for uploading specimens data to the portal (including input data validation).
• Specimens data indexing service - background service responsible for specimen-centric data index creation.

Dependencies

• SQL - SQL server with domain data and user identity data.
• Elasticsearch - Elasticsearch server with indices of domain data.

Access

Environment	Address	Port
Host	http://localhost:5104	5104
Docker	http://feed.specimens.unite.net	80

Configuration

To configure the application, change environment variables in either docker or launchSettings.json file (if running locally):

• ASPNETCORE_ENVIRONMENT - ASP.NET environment (Release).
• UNITE_API_KEY - API key for decription of JWT token and user authorization.
• UNITE_ELASTIC_HOST - Elasticsearch service host (es.unite.net:9200).
• UNITE_ELASTIC_USER - Elasticsearch service user.
• UNITE_ELASTIC_PASSWORD - Elasticsearch service password.
• UNITE_SQL_HOST - SQL server host (sql.unite.net).
• UNITE_SQL_PORT - SQL server port (5432).
• UNITE_SQL_USER - SQL server user.
• UNITE_SQL_PASSWORD - SQL server password.
• UNITE_INDEXING_BUCKET_SIZE - Indexing bucket size (100).

Installation

Docker Compose

The easiest way to install the application is to use docker-compose:

• Environment configuration and installation scripts: https://github.com/dkfz-unite/unite-environment
• Specimens data feed service configuration and installation scripts: https://github.com/dkfz-unite/unite-environment/tree/main/applications/unite-specimens-feed

Docker

The image of the service is available in our registry for the following environments:

• linux/amd64

Dockerfile is used to build an image of the application. To build an image run the following command:

docker build -t unite.specimens.feed:latest .

All application components should run in the same docker network. To create common docker network if not yet available run the following command:

docker network create unite

To run application in docker run the following command:

docker run \
--name unite.specimens.feed \
--restart unless-stopped \
--net unite \
--net-alias feed.specimens.unite.net \
-p 127.0.0.1:5104:80 \
-e ASPNETCORE_ENVIRONMENT=Release \
-e UNITE_API_KEY=[unite_api_key] \
-e UNITE_ELASTIC_HOST=http://es.unite.net:9200 \
-e UNITE_ELASTIC_USER=[elasticsearch_user] \
-e UNITE_ELASTIC_PASSWORD=[elasticsearch_password] \
-e UNITE_SQL_HOST=sql.unite.net \
-e UNITE_SQL_PORT=5432 \
-e UNITE_SQL_USER=[sql_user] \
-e UNITE_SQL_PASSWORD=[sql_password] \
-e UNITE_INDEXING_BUCKET_SIZE=100 \
-d \
unite.specimens.feed:latest