PreClinVar

A ClinVar API submission helper written in FastAPI.

Availability:

A running instance of the service is available at https://preclinvar.scilifelab.se/docs

Available endpoints:

tsv2json

Transforms tsv submission files from a germline submission (Variant.tsv and CaseData.tsv) into a json submission object, ready to be used to submit via the ClinVar API. This document is validated against the ClinVar API submission schema

csv2json

Transforms csv submission files from a germline submission (Variant.csv and CaseData.csv) into a json submission object, ready to be used to submit via the ClinVar API. This document is validated against the ClinVar API submission schema

dry_run

Proxy endpoint to the ClinVar submissions API (dry-run): https://submit.ncbi.nlm.nih.gov/api/v1/submissions/?dry-run=true. Requires a valid API key and a json file containing a submission object. If the request is valid (and the json submission object is validated) returns a response with code 200 and json body with the message value "success".

apitest

Proxy endpoint to the validation API endpoint: (apitest) "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions". Requires a valid API key and a json file containing a submission object. If the json submission document is valid returns a submission ID which can be used for a real submission. If the json submission document is not validated, the endpoint returns a list of errors which will help fixing the document.

Running the application using Docker-compose

An example containing a demo setup for the app is included in the docker-compose file. Start the docker-compose demo using this command: docker-compose up -d The server will be running and accepting requests sent from outside the container (another terminal or a web browser) on port 7000 (http://0.0.0.0:7000)

Installing the application on a local conda environment

Given a conda environment containing Python 3.9 and poetry, clone the repository from Github with the following command:

git clone https://github.com/Clinical-Genomics/preClinVar.git

The command will create a folder named preClinVar in your current working directory. Move inside this directory:

cd preClinVar

And install the software with poetry:

poetry install

You can run an instance of the server by typing:

uvicorn preClinVar.main:app --reload --log-level debug

The server will run on localhost and default port 8000 (http://127.0.0.1:8000)

Testing the endpoints

The endpoints will be available under the docs: http://127.0.0.1:8000/docs (http://127.0.0.1:7000/docs if you are running the dockerized version of the app). They can be tested with files provided in this repository, in the demo folder: https://github.com/Clinical-Genomics/preClinVar/tree/main/preClinVar/demo