Native Installation

This documentation describes an installation solution of the chemotion ELN system for development purposes with Rails 5 on Ubuntu 20.04.

Before Installation

The installation script installs ELN through a default user, which is created during the installation. If you want to use another user or use an existing user, download the installation script (see Get installation script) and change the varibale PROD at the top of the script.
For the default user a random password is generated when newly created. If you want to login to the user after installation you can change the password in the script. For that search for the command chpasswd in the script.

Get the installation script

Download the current development installation script (14.07.2021) from GitHub and make it executable:

curl -o install_development.sh -L https://raw.githubusercontent.com/ComPlat/chemotion_ELN/development-5/scripts/install_development.sh
chmod 700 install_development.sh
sudo ./install_development.sh

Or install the current script directly via curl:

sudo curl -o- https://raw.githubusercontent.com/ComPlat/chemotion_ELN/development-5/scripts/install_development.sh | bash

Errors during installation

You need to run "nvm install vxx.xx.x" to install it before using it.

nvm install vxx.xx.x

Run the installation script again:

sudo ./install_development.sh

Another solution could be to comment out PART_5 in the installation script, where nvm and Node will be installed and run again:

sudo ./install_development.sh

curl: (23) Failed writing body

Extended error message:

Warning: Failed to create the file /tmp/x.x.x: Permission 
Warning: denied
  0 13.6M    0  1369    0     0   8398      0  0:28:19 --:--:--  0:28:19  8398
curl: (23) Failed writing body (0 != 1369)
000:09 removing tmp files..
000:09 removing tmp repo..
000:09 An error has occured

This may occure if you install the chemotion ELN for multiple users on the same machine, because the global packages to be installed already exists, so either comment out the installation of the package which causes the problem or delete it.

After Installation

Git clone

After the installation of the desired libraries to use the chemotion ELN you need to clone the source code from GitHub.

Change configuration files

Before using the chemotion ELN you have to change some configurations. Change to the root folder of your ELN (e. g. cd ~/chemotion_ELN) and paste the following commands at once in your terminal:

cp Gemfile.plugin.example Gemfile.plugin ;
cp .ruby-gemset.example .ruby-gemset ;
cp .ruby-version.example .ruby-version ;
cp ./config/database.yml.example ./config/database.yml ;
cp ./config/datacollectors.yml.example ./config/datacollectors.yml ;
cp ./config/editors.yml.example ./config/editors.yml ;
cp ./config/inference.yml.example ./config/inference.yml ;
cp ./config/spectra.yml.example ./config/spectra.yml ;
cp ./config/storage.yml.example ./config/storage.yml ;
cp ./config/user_props.yml.example ./config/user_props.yml

Install Ruby libraries

Change to the root folder of your ELN (e. g. cd ~/chemotion_ELN) where the Gemfile is located and type:

source ~/.rvm/scripts/rvm && bundle install

Errors

You might have to install separate package for the ruby development environment, ruby-dev or ruby-devel for example:

sudo apt-get install ruby-full

Install node_modules

source ~/.nvm/nvm.sh && yarn install

Errors

ERROR: [Errno 2] No such file or directory: 'install'

sudo apt-get remove --purge cmdtest
source ~/.nvm/nvm.sh && nvm use 14.16.0 && npm install -g yarn && yarn install

Update database

sudo -u postgres psql
ALTER USER postgres PASSWORD '<your password>';

Open file ./config/databse.yml, change host in development to localhost and update your password that you set above.

Errors

FATAL: database "chemotion_dev" does not exist (ActiveRecord::NoDatabaseError)

Either the database settings in the yml configuration file needs to be changed or the database needs to be created in Postgres.

Migrate data

bundle exec rake db:create RAILS_ENV=development
bundle exec rake db:migrate RAILS_ENV=development

Run the app

You need to run two servers simultaneously in two different terminals: one for the rails app and one for webpack:

bundle exec rails s
bundle exec bin/webpack-dev-server

Potentially a restart of the Rails server is needed because changes in JavaScript files below app/ are monitored by the webpack server process.

Errors

Undefined method `new' for BigDecimal:Class (NoMethodError)

Open Gemfile and add:

gem 'bigdecimal', '1.3.5'

Run again:

bundle install

Restart the servers.

yarn run v1.22.10

error Command "webpack" not found.

info Visit https://yarnpkg.com/en/docs/cli/run for documentation about this command.

Unable to run node_modules/.bin/browserify. Ensure you have installed it with npm. (BrowserifyRails::BrowserifyError)

source ~/.nvm/nvm.sh && nvm use 14.16.0 && yarn install

Restart the servers.

Update test data

Open web browser, signup and login. Download and import data from here.
Run:

bundle exec bin/delayed_job start

For old installations: Upgrade from Rails 4 to Rails 5

If you have an existing installation with Rails 4 and want to upgrade to Rails 5 you need to "update" your Ruby gems and node modules with yarn after checking out the development-5 branch:

bundle install

source ~/.nvm/nvm.sh && nvm install 14.16.0
source ~/.nvm/nvm.sh && nvm use 14.16.0 && npm install -g npm && npm install -g yarn && yarn install

For a clean install it might be helpful - but not always required - to remove the previous packages that were installed by npm, only need to be done once:

rm -rf node_modules

source ~/.nvm/nvm.sh && nvm use 14.16.0 && yarn install

You need to run two servers simultaneously in two different terminals: one for the rails app and one for webpack:

bundle exec rails s
bundle exec bin/webpack-dev-server

Potentially a restart of the Rails server is needed because changes in the JavaScript files below app/ are monitored by the webpack server process.