Readme

Quickstart

git clone https://github.com/Ozbek-Lab/RareIndex
cd RareIndex
virtualenv venv
source venv/bin/activate
pip install -r requirements.txt
python manage.py makemigrations
python manage.py migrate --run-syncdb
python manage.py generate_sample_data (will also create superuser admin)
#python manage.py createsuperuser
python manage.py clear_database (will remove class objects of lab app)
python manage.py import_ozbek_lab path/to/file --admin-user admin
python manage.py import_analiz_takip path/to/file --admin-user admin

sync ontologies

python manage.py sync_ontology --ontology HP

import from excel

python manage.py import_ids '..\..\RareIndex_Real_Sample_Data\OZBEK_Lab. Örnek Takip Çizelgesi - OZBEK LAB.tsv' --admin-username emre
python manage.py import_biobank '..\..\RareIndex_Real_Sample_Data\OZBEK_Lab. Örnek Takip Çizelgesi - Biyobankada kayıtlı RB örnekler.tsv' --admin-username emre
python manage.py import_ozbek_lab '..\..\RareIndex_Real_Sample_Data\OZBEK_Lab. Örnek Takip Çizelgesi - OZBEK LAB.tsv' --admin-user emre
python manage.py import_analiz_takip '..\..\RareIndex_Real_Sample_Data\OZBEK_Lab. Örnek Takip Çizelgesi - Analiz Takip.tsv' --admin-user emre