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Installing a production ready server

On a Ubuntu server

Server requirement: the installation can fail if not enough memory is available. A minimum of 3GB memory is recommended.

copy the installation script on a ubuntu server 18.04 or 20.04 (also works with debian buster)

curl -o chemotion_ELN_install.sh -L https://github.com/ComPlat/chemotion_ELN/raw/development-5/scripts/install_production.sh

Check the variables at the beginning of the file, but also check the whole script to see what it is doing.

TLDR: the script will ...

  • install OS package dependencies
  • install passenger
  • create a new user
  • install ruby and nodejs for the user
  • create a postgresql DB
  • copy the chemotion_ELN code and prepare basic config files
  • do a capistrano app deploy
  • config nginx (NB: no ssl set) and UFW

When ready, make the script executable and run it as a non-root user (but in the sudo group):

chmod 700 chemotion_ELN_install.sh

sudo ./chemotion_ELN_install.sh

After reboot the application should be up and running at the ip of the machine (http://...) An admin account should have been created (email: [email protected], pw: PleaseChangeYourPassword)

To update the application code for such an installation, use the update script:

curl -o chemotion_ELN_update.sh -L https://github.com/ComPlat/chemotion_ELN/raw/development-5/scripts/update_production.sh

If needed, edit the file (change the variables or comments out parts to disable), then

chmod 700 chemotion_ELN_update.sh

sudo ./chemotion_ELN_update.sh

Using Windows Subsytem for Linux 2

The instalation script works with Ubuntu 20 under WSL2.

NB:

  • openssh-server should be reinstalled.
  • services (postgres, nginx) needs to be started manually.
  • UFW should not be used and disabled.

Using Docker

see online docs

Basic Development Setup

Ubuntu native or under WSL-2

See the scripts/install_development.sh for guidance or run it. Application should be all set up and ready to run.

When using WLS-2:

  • postgres service needs to be started (sudo service postgresql start )
  • you may want to move the application code somewhere to /mnt/...
  • bind the WSL ip address when starting the rails s (rails s -b ip.ad.dr.ess)

Using Docker

see https://github.com/ptrxyz/chemotion/tree/main/client-chemotion-dev

Application Setup Notes

  • config/database.yml and config/storage.yml are needed to start the application.
  • Copy .ruby-version.example to .ruby-version. (Skip this step if you want to use Docker)
  • Environment variables: see the corresponding .env files

Resetting the db:

If you like to reset the database, you have to execute the following commands (under the assumption your production database is called chemotion)

sudo -u postgres psql -d chemotion -c 'DROP SCHEMA public CASCADE;CREATE SCHEMA public; GRANT ALL ON SCHEMA public TO postgres; GRANT ALL ON SCHEMA public TO public;'

or alternatively, drop and recreate DB using rake task:

RAILS_ENV=production bundle exec rake db:drop db:create

then, create DB extensions:

sudo -u postgres psql -d chemotion -c 'CREATE EXTENSION IF NOT EXISTS "pg_trgm"; CREATE EXTENSION IF NOT EXISTS "hstore";  CREATE EXTENSION IF NOT EXISTS "uuid-ossp";'

and run DB migrations:

RAILS_ENV=production bundle exec rake db:migrate db:seed

JS Setup & Testing

  • Install nvm: curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/0.35.0/install.sh | bash (see https://github.com/nvm-sh/nvm#installation) or for OSX: brew install nvm && echo "source $(brew --prefix nvm)/nvm.sh" >> ~/.profile
  • Execute nvm install 10.15.3
  • Execute npm install -g [email protected]
  • Execute npm install.

Mailing in Development Environment

Run rake jobs:work for asynchronous handling of email notifications. Run mailcatcher in your console and go to localhost:1080 to see all sent mails.

Icon Font

  • put new icons as SVG files (e.g. '<ICON_NAME>.svg') in app/assets/images/svg_icons
  • run rake icons:compile

Icons are now available as css classes: '.icon-<ICON_NAME'

OS Dependencies

nokogiri

if there are errors with nokogiri compilation with new xcode7: gem install nokogiri -- --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 --use-system-libraries

openbabel

  • Require

    1. CMake (the cmake package in Ubuntu)
    2. Eigen (the libeigen2-dev or libeigen3-dev package in Ubuntu)
    3. Swig (the swigpackage in Ubuntu)
    4. libxml2 (the libxml2-dev package in Ubuntu)

  • openbabel will be automatically installed through bundle install

rmagick

  • brew install imagemagick gs for OSX
  • apt-get install libmagickcore-dev libmagickwand-dev for linux
  • if installing the rmagick gem fails you may try: IM_PREFIX=$(brew list imagemagick 2>&1 | grep -E 'identify$' | sed 's/bin\/identify$//g') PKG_CONFIG_PATH=${IM_PREFIX}lib/pkgconfig/ C_INCLUDE_PATH=${IM_PREFIX}include/ImageMagick*/ gem install rmagick (OSX only)

inkscape

  • sudo apt-get install inkscape for Linux
  • For Mac OSX, you need to install XQuartz before inkscape: brew install Caskroom/cask/xquartz, and brew install homebrew/gui/inkscape.

Dataset previews

  • brew install imagemagick mplayer for OSX
  • sudo apt-get -y install imagemagick mplayer for Linux

FontCustom Dependencies

  • brew install fontforge --with-python
  • brew install eot-utils