# First, follow this link, if you want to install docker-compose: 
# https://docs.docker.com/compose/install/

#  Clone this repository and change into the created directory
git clone https://github.com/daisybio/DIGGER.git && cd DIGGER

# Download a copy of all the data files into domain/data/
# If you have more organisms, add the files into respective foldes, e.g. domain/data/Mus musculus[mouse]/
wget https://zenodo.org/records/12517244/files/data.zip

# unzip this data to the appropriate directory
unzip data.zip -d container/domain/

# repeat this with the nease data:
wget https://zenodo.org/records/12517244/files/nease_data.zip
unzip nease_data.zip -d container/domain/nease/


# Create a copy of the .env.sample file and edit the .env file
cp .env.sample .env   # now edit the .env file 

# Deploy and build the containers
docker-compose up -d --build

# Apply migrations (make sure the containers are up an running, else you will get an error)
docker-compose exec web python manage.py migrate --noinput 

# Import all the datasets into the database
docker-compose exec web python manage.py import_datasets

# Collect all the static files
docker-compose exec web python manage.py collectstatic --no-input

# Create the superuser for the admin page
# This can be found under https://WEBSITE/admin and is used to manage the django models
sudo docker compose exec web python manage.py createsuperuser

# Enjoy your instance of DIGGER

# First, create a conda environment to ensure you have all dependencies installed
conda env create -f DIGGER_env.yml

# Activate the environment
conda activate DIGGER

# Make sure you have the necessary files in the sourcedata folder
# more info about what these files should look like can be found in the sourcedata README.md

# copy the example database_sources to have a backup and list of all options. 
# Edit the database_sources.yml file to your needs
cp preprocess/sourcedata/example.database_sources.yml preprocess/sourcedata/database_sources.yml

# Run the prediction script
cd preprocess
python main_ddi_extend.py

# Once this has run, depending on your settings, restarting the DIGGER container will show the new data
cd ..
docker-compose up -d --force-recreate