/aebs-db

Primary LanguagePython

AEBS-DB

Analysing AEBS (Ættarbandsskráin), the Multi-Generation Registry of the Genetic Biobank of the Faroe Islands. Using aebs-db-utils to manage AEBS data and PedGraph to analyse the data.

Install

Install all requirements to a Python3 virtual environment using pip.

# Create Python virtual environment called "venv".
python3 -m venv venv
# Activate venv.
source venv/bin/activate
# Install requirements.
pip install -r requirements.txt

Neo4j DB

Deploy the neo4j database container:

rancher kubectl create -f db_setup/aebs-db-master.yaml

Then deploy the service, to expose the HTTP and Bolt ports to an IP:

rancher kubectl create -f db_setup/aebs-db-service.yaml

Now the database should be available through bolt://aebs-db:7687.

Alternatively, setup the Neo4j database as done here.

Setup DB

NOTE: paths and URIs are hardcoded into these scripts.

Convert the GEDCOM genealogy file to a CSV file.

./ged2csv.py

Build the Neo4j database.

./build_db.py

Notebooks

Start JupyterLab.

cd notebooks
jupyter lab

If you're running in a container you need to use the following arguments.

jupyter lab --ip=0.0.0.0 --port=80 --allow-root