NUcore Open

Open source version of Northwestern University Core Facility Management Software

NUCore Open Environment

Staging: https://nucore.stage.tablexi.com

Note for School-specific Repos

As you pull in new features/bug fixes from open, please keep up with the CHANGELOG to see changes that may break your school-specific repo and optional/required rake tasks you may want to run.

See coding_standards.md for more information on recommended strategies for customizing NUCore for a specific school.

See HOWTO_related_repos.md for more information on merging changes from the open source repo and deployment processes.

Quickstart

Welcome to NUcore! This guide will help you get a development environment up and running.

Development within Docker Environment

We recommend running within a docker environment. Benefits:

• All daemons, processes are running at all times (easier to develop features)

To do this:

1. Install Docker and Docker Compose
2. Run ./docker-setup.sh. This sets up your database.yml and secrets.yml files. It also does an intial bundle install.
3. The output of the previous set is a randomly generated secret. Copy and paste it into your secrets.yml file as the secret_key_base.
4. This will also finish setting up the database
5. Seed the database with demo data (optional) docker-compose run app bundle exec rake demo:seed
6. Run docker-compose up
7. Open http://localhost:3000

If you seeded the demo data, you can log in with [email protected]/P@ssw0rd!!

Email

We use mailcatcher as an SMTP server and web client. Visit http://localhost:1080.

Useful Commands

• Rails Console: docker-compose exec app bundle exec rails c
• Command line in the container: docker-compose exec app bash
• Running tests: Get a command line in the container and bundle exec rspec

Development locally

It makes a few assumptions:

1. You write code on a Mac.
2. You have a running Oracle or MySQL instance with two brand new databases. (Oracle setup instructions here.)
3. You have the following installed:
   • Ruby
   • NodeJS
   • Bundler
   • Git
   • PhantomJS

Spin it up

1. Download the project code from Github

   git clone [email protected]:tablexi/nucore-open.git nucore
   

2. Install dependencies

   cd nucore
   bundle install
   

3. Configure your databases

   # For oracle, use config/database.yml.oracle.template
   cp config/database.yml.mysql.template config/database.yml
   

   Edit the adapter, database, username, and password settings for both the development and test DBs to match your database instance

4. Configure your secrets

cp config/secrets.yml.template config/secrets.yml
rake secret

• Paste the output from rake secret into config/secrets.yml for both development/secret_key_base and test/secret_key_base

5. Set up databases

   rake db:create
   rake db:schema:load
   rake db:seed
   

Known issue: if you run db:setup or all three in one rake command, the next time you run db:migrate, you will receive a Table 'splits' already exists error. Use the separate commands instead.

6. Seed your development database

   rake demo:seed
   

7. Configure your file storage

   By default, files are stored on the local filesystem. If you wish to use Amazon's S3 or Microsoft's Azure Blob Storage instead, see below.

   Amazon S3 (via Paperclip)

   Enable S3 in your environment by updating the local settings override file such as config/settings/development.local.yml or config/settings/production.local.yml. Uncomment the section under paperclip:

   paperclip:
     aws_access_key_id: <%= ENV.fetch("AWS_ACCESS_KEY", "Your-Key-Here") %>
     aws_secret_access_key: <ENV.fetch("AWS_SECRET_ACCESS_KEY", "Your-Key-Here") %>
     ...
   

   Then add your credentials to the ENV or secrets.yml.

   See migrating_to_s3.md for more info.

   Microsoft Azure Blob Storage (via Active Storage)

   Enable Active Storage in your environment by updating the settings.yml file with:

   features:
     active_storage: true
   

   In your gemfile, uncomment: gem "azure-storage-blob", "~> 2.0", require: false

   Environment files need to be updated as well (development.rb, production.rb): config.active_storage.service = :azure

   In storage.yml, uncomment the azure section:

   azure:
     service: AzureStorage
     storage_account_name: <%= Rails.application.secrets.dig(:active_storage, :azure, :storage_account_name) %>
     storage_access_key: <%= Rails.application.secrets.dig(:active_storage, :azure, :storage_access_key) %>
     container: <%= Rails.application.secrets.dig(:active_storage, :azure, :container) %>
   

   Then add your credentials to the ENV or secrets.yml.

8. Start your server

   bin/rails s
   

9. Log in

   Visit http://localhost:3000

   demo:seed creates several users with various permissions. All users have the default password of "P@ssw0rd!!"

   Email/username	Role
   [email protected]	Admin
   [email protected]	PI
   [email protected]	Normal User
   [email protected]	Facility Staff
   [email protected]	Facility Director

10. Play around! You're running NUcore!

11. Run delayed_job to support in-browser email previews.

    Run delayed jobs indefinitely in the background:

    ./script/delayed_job start
    

    Or run delayed jobs once for one-off jobs:

    ./script/delayed_job run
    

Test it

NUcore uses Rspec to run tests. Try any of the following from NUcore's root directory.

• To run all tests (this will take awhile!)

  rake spec
  

• To run just the model tests

  rake spec:models
  

• To run just the controller tests

  rake spec:controllers
  

Github Actions

To use Github Actions for CI testing you may need to maintain a testing image with specific versions of dependencies set. To do this:

# Set your desired version of node and bundler
export NODE_VERSION=setup_16.x
export BUNDLER_VERSION=2.3.11

# Build the image
docker build . -f Dockerfile.github-actions --build-arg NODE_VERSION=$NODE_VERSION --build-arg BUNDLER_VERSION

# Check the IMAGE ID
docker image ls

# Tag the image with the appropriate ruby version
docker tag {IMAGE ID} nucoretxi/ruby-node-chrome-pack:2.7.5

# Check the image was tagged correctly
docker image ls

# login and push the new tag
docker login -u nucoretxi
docker push nucoretxi/ruby-node-chrome-pack:2.7.5

Parallel Tests

You can run specs in parallel during local development using the parallel_tests gem.

• Create additional databases:

  rake parallel:create
  

• Run migrations (only needed if building from scratch):

  rake parallel:create
  

  OR

  rake parallel:load_schema
  

• Copy development schema (repeat after migrations):

   rake parallel:prepare
  

• Run tests:

  rake parallel:spec
  

• Example RegEx patterns:

   rake parallel:spec[^spec/requests] # every spec file in spec/requests folder
   rake parallel:spec[user]  # run users_controller + user_helper + user specs
   rake parallel:spec['user|instrument']  # run user and product related specs
   rake parallel:spec['spec\/(?!features)'] # run RSpec tests except the tests in spec/features
  

• ZSH users may need to run it with the brackets escaped, like this:

    bundle exec rake parallel:spec\['spec\/(?!features)'\]
  

Optional Modules

The following modules are provided as optional features via Rails engines. These are enabled by adding the appropriate engine to your Gemfile (all are on by default). They exist in the vendor/engines directory.

• Accept Credit Cards & Purchase Orders (c2po)
• Connect to Dataprobe Power Relays (dataprobe)
• Link orders together as a Project (projects)
• Sanger Sequencing order form and well plate management
• Split charges between different accounts
• Authenticate against an LDAP server
• Authenticate with SSO via SAML

Engine-specific migrations should live in the engine's db/migrate directory and use an engine initializer to add that path to the list of paths Rails checks. If you need to disable an engine, you can undo all of the engine's migrations with the rake engines:db:migrate_down[ENGINE_NAME] task.

Learn more

There are valuable resources in the NUcore's doc directory.

• Want to conform to the project's established coding standards? See coding_standards.md

• Want to know more about the instrument pricing model? See instrument_pricing.md

• Need to move changes between nucore-open and your school-specific repo? See HOWTO_related_repos.md

• Need help getting Oracle running on your Mac? See HOWTO_oracle.md

• Want to authenticate users against your institution's LDAP server? See the ldap_authentication engine

• Need to use a 3rd party service with your NUcore? See HOWTO_external_services.txt

• Need to asynchronously monitor some aspect of NUcore? See HOWTO_daemons.txt

• Want to integrate with Form.io? See form.io_tips_and_tricks