snpseq-metadata-service

A (aiohttp) REST service that coordinates the extraction and export of metadata information for projects and sequencing runs.

This service will in turn call the snpseq-data REST API to extract project metadata from a Clarity LIMS instance and use the snpseq_metadata Python package to extract sequencing run metadata from a runfolder, as well as combine project and sequencing run metadata and export to relevant formats.

Installation

Pre-requisites

• You will need python >=3.8

• The service will expect the snpseq_metadata (>= v2.2.0) Python package to be available in the environment (refer to the README for installation instructions).

• Unless data extracted from Clarity LIMS will be supplied in a separate json file, the service needs the url of an accessible snpseq-data service.

Deploy

Clone this repository from GitHub

git clone https://github.com/Molmed/snpseq-metadata-service
cd snpseq-metadata-service

It is recommended to set up the service in a virtual environment. In the example below, venv is used.

python3 -m venv --upgrade-deps .venv
source .venv/bin/activate
pip install .

Configuration

See the config folder for example configs.

Running the service

usage: metadata-service [-h] [-c CONFIGROOT]

optional arguments:
  -h, --help            show this help message and exit
  -c CONFIGROOT, --configroot CONFIGROOT
                        Path to config root dir

Start the service and pass the path to the config directory on the command line:

metadata-service -c config/

Using the service

Assuming the service has been configured to listen on port 8345, an overview of the API endpoints can be obtained by accessing the api endpoint:

curl http://snpseq-metadata-service.url:8345/api

To gather and export metadata for a runfolder named 210415_A00001_0123_BXYZ321XY and sequenced on the host biotank-host, make a call to the export endpoint:

curl http://snpseq-metadata-service.url:8345/api/1.0/export/biotank-host/210415_A00001_0123_BXYZ321XY

This will create a directory named metadata in the runfolder and the metadata information will be exported to this directory. The service will issue a json dictionary response with a list of paths to the exported metadata files under the key metadata.

Testing the service

The unit test suite can be run by first installing the optional test dependencies:

source .venv/bin/activate
pip install .[test]

Then run the test suite:

pytest --asyncio-mode auto tests/