loqusdbapi

Small REST api to use with loqusdb.

Currently only supports get requests for variant, structural_variant, case and cases.

Usage

Running local installation

For all of the use cases below, do

1. git clone https://github.com/Clinical-Genomics/loqusdbapi
2. cd loqusdbapi

For all these examples you need to make sure that mongodb is running. If mongod is listening to another port than 27017, if it is on another server than localhost, if it needs password etc, use the environmental variable URI. If only testing the app use the docker-compose-solution below. More information about setup should be fairly easy to understand by looking at docker-compose.yml.

poetry

Poetry is the friendliest and most intuitive package manager for python.

1. poetry install
2. uvicorn loqusdbapi.main:app --reload

pip

To use with pip the easy solution is to install micropipenv and generate a requirements file:

1. pip install micropipenv[toml]
2. micropipenv requirements --method poetry --no-hashes > requirements.txt
3. pip install -r requirements.txt
4. uvicorn loqusdbapi.main:app --reload

Go to http://127.0.0.1:8000/docs

docker

To run with Docker build the image with docker build -t loqusapi .

Then start a container called myapi listening on port 80 with docker run -d --name myloqusapi -p 8000:80 -e APP_MODULE="loqusdbapi.main" loqusapi

Head over to http://127.0.0.1:8000/docs

Setup a test case with some data using docker compose

1. docker-compose up
2. Port 8000 is mapped to 9000 in the docker compose file so go to http://127.0.0.1:9000/docs
3. Request example to fetch a single-nucleotide (SNV) variant: curl -X GET "http://127.0.0.1:9000/variants/1_880086_T_C"
4. Request example to fetch a structural variant (SV): curl -X GET "http://127.0.0.1:9000/svs/?chrom=1&end_chrom=1&pos=7889972&end=7890026&sv_type=DEL"
5. Request example to get the number of cases with either SNVs or SVs present in database: curl -X GET "http://127.0.0.1:9000/cases"
6. Request example to fetch info on a specific case: curl -X GET "http://127.0.0.1:9000/cases/recessive_trio"