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DOI

data-catalogue-pseudonymisation

This is the repository for the pseudonymisation part of the BBMRI.cz data catalog.

Pseudonymisation

Pseudonymizes predictive numbers, collects clinical data and removes unnecessary files before moving the data to SensitiveCloud at ICS-MUNI.

Supported sequencing types

Miseq, New Miseq, MammaPrint

How to run the scripts

Locally - Development

Using main.py

  1. Install requirements
pip install -r requiremenents.txt
  1. Run main.py
python main.py -s /path/to/runs/for/pseudonymization -d /path/to/sensitive/cloud/destination 
               -t /path/to/pseudonymisation/tables/folder -l /path/to/libraries 
               -lsc /path/to/sensitive/cloud/libraries"

Using docker-compose

docker-compose up -f compose.dev.yml -d --build

In production

Using docker-compose

# connect to seq server
su export
cd /home/export/data-catalogue-pseudonymisation
docker-compose up -f compose.prod.yml -d

Deployment in cron

# connect to seq serve
su export
crontab -e
# setting cron to run every Monday, Wednesday, Friday at 22:00
0 22 * * 1,3,5 /usr/local/bin/docker-compose -f /home/export/data-catalogue-pseudonymisation/compose.prod.yml up -d &>> /home/export/logs/`date +\%Y\%m\%d\%H\%M\%S`.log

Deploying new version in production

su export
cd /home/export/data-catalogue-pseudonymization
git switch main
git pull

The new version shouldthe new version should automatically start in production once the cronjob is run automatically start in production once the cronjob is run.