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INSTALL.md

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Installing a production ready server

On a Ubuntu server

copy the installation script on a ubuntu server 18.04 (could work with another deb)

curl -o chemotion_ELN_install.sh -L https://git.scc.kit.edu/complat/chemotion_ELN_server/raw/development/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: it 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: eln-admin@kit.edu, pw: PleaseChangeYourPassword)

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

curl -o chemotion_ELN_update.sh -L https://git.scc.kit.edu/complat/chemotion_ELN_server/raw/development/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 Docker

This is a setup for a 'pseudo' production stage using passenger and aimed for user testing. (For the development environment, change 'RAILS_ENV' to 'development' in docker-compose.yml) Make sure you have finished the BASIC SETUP FIRST

  1. Build the image from Dockerfile docker-compose build or pull the image: docker-compose pull
  2. Initialize database FIRST:
  • docker-compose run app bundle exec rake db:create
  • docker-compose run app bundle exec rake db:migrate
  • docker-compose run app bundle exec rake db:seed (optional). A "seed" user will be inserted into the db with the information as below: template.moderator@eln.edu - password: "@eln.edu"
  • docker-compose run app rake ketcherails:import:common_templates (optional)
  1. Precompile assets: docker-compose run app bundle exec rake assets:precompile
  2. To start the server: docker-compose up or start server and detach: docker-compose up -d

  • Start interactive shell with docker: docker-compose run app /bin/bash

  • NOTE: In this Docker image, we disabled the email verification progress

  • To enable email confirmation, uncomment ":confirmable" at line 5 of app/models/user.rb, stop the docker-compose by docker-compose stop and start docker-compose.

Basic Development Setup

  • Copy config/database.yml.example to config/database.yml and enter your database connection information.
  • Copy config/storage.yml.example to config/storage.yml and enter your database connection information.
  • Copy .ruby-gemset.example to .ruby-gemset.
  • Copy .ruby-version.example to .ruby-version. (Skip this step if you want to use Docker)
  • Reload directory to create rvm gemset.

Application Setup

  • Execute bundle install.
  • Execute rake db:reset (this creates and seeds the database).

Environment variables

Production

  • cp .env.production{.example,} # optionally enter SFTP credentials

Configure Data Collection

  • copy the config example file and edit the entries

  • create device entries and configure their profiles

cp db/datacollectors.yml.example db/datacollectors.yml

Deployment notes

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/0.34.0/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 npm@6.11.3
  • 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