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transcriptomics_data_service

WORK IN PROGRESS.

The Transcriptomics Data Service (TDS) is intended to ingest, organize and query data from transcriptomics experiments through an API.

Starting a standalone TDS

Start the TDS server with a database for testing by running the following command.

# start
docker compose up --build -d

# stop
docker compose down

The --build argument forces the image to be rebuilt. Be sure to use it if you want code changes to be present.

You can now interact with the API by querying localhost:5000/{endpoint}

For the OpenAPI browser interface, go to localhost:5000/docs.

Local dev

For local development, you can use the docker-compose.dev.yaml file to start a TDS development container that mounts the local directory. The server starts in reload mode to quickly reflect local changes, and debugpy is listening on the container's internal port 9511.

# start
docker compose -f ./docker-compose.dev.yaml up --build -d

# stop
docker compose -f ./docker-compose.dev.yaml down

You can then attach VS Code to the tds container, and use the preconfigured Python Debugger (TDS) for interactive debugging.

Endpoints

  • /service-info
    • GA4GH service info
  • /ingest (TODO)