Gene panel Overview

Development

Quick start

Requirements: docker, make, git

• git clone [this repo]... && cd ...
• build database:
  GPSTORE_DIR=example/genepanel-store/ make docker_dbcreate_dev
  Alternatively, download the already build database file:
  ( cd www/dev/db && wget https://genepanels.ousamg.uiocloud.no/db/gpdb_v1.sqlite )
• run web UI:
  make -C ui docker_dev
• in new tab, start server to host web UI:
  make docker_devsrv
• open http://localhost:3010
• open ui/ folder in VSCode to make live changes

Without docker (optional)

Requirements:

• nodejs
• npm
• npx
• make
• git
• r-base

Run steps above, but without any docker_ docker prefixes. You might need to clean the .r_libs/ folder when switchig between docker and non-docker environments.

Overview, status and future development

Rationale

This webservice was created with the assumption the underlying data does not change often and read-only access is sufficient.

The data contained in the genepanel repository get compiled to a single database file. This DB file is served together with the webinterface as static files by a webserver. On the client a DBMS provided with the UI reads the DB file runs local queries. A high-enough cache time (Cache-Control max-age) on the DB file is used to reduce loading times and traffic.

Over time, with increasing genepanels, the size of the DB file might need to be reduced. One way to accomplish a reduction is file size is to replace all RefSeq IDs (type TEXT) used as PK and FK with generated IDs of type INT and use a lookup table to map back to the original IDs. This can also be done for HGNC IDs.

TDB how to build the db file

Production

Build the UI

• run web UI:
  make -C ui docker_prod
• copy the www/prod folder to the server

Update the DB

• Get the genepanels from the genepanel-store repository.
• Run GPSTORE_DIR=... make dbcreate_dev while pointing it to the corrent directory

Server setup

server_name=replace.me

#------------------------------------------------------------------------------

# install packages

sudo apt-get update && DEBIAN_FRONTEND=noninteractive sudo apt-get install -y \
  bash-completion \
  git \
  netcat-traditional \
  locales \
  nodejs \
  npm \
  nginx \
  certbot \
  python3-certbot-nginx

#------------------------------------------------------------------------------


# configure webserver

sudo tee /etc/nginx/sites-available/default << EOI
server {
  root /home/debian/genepanel_overview/;
  server_name ${server_name};

  location / {
    try_files \$uri \$uri/index.html;
    expires 1h;
    add_header Cache-Control "public";
  }
}
EOI

sudo service nginx restart


#------------------------------------------------------------------------------


# configure SSL

sudo certbot --nginx -d ${server_name} -m flo.krull@gmail.com

#------------------------------------------------------------------------------