scinote-web/README.md

sciNote

About

sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders.

Build & run

sciNote is developed in Ruby on Rails. It also makes use of Docker technology, so the easiest way to run it is inside Docker containers.

Quick start

The following are minimal steps needed to start sciNote in development environment:

1. Clone this Git repository onto your development machine.
2. Create a file config/application.yml. Populate it with mandatory environmental variables (see environmental variables).
3. In sciNote folder, run the following command: make docker. This can take a while, since Docker must first pull an image from the Internet, and then also install all neccesary Gems required by sciNote.
4. Once the Docker image is created, run make cli command. Once inside the running Docker container, run the following command: rake db:reset. This should initialize the database and fill it with (very minimal) seed data.
5. Exit the Docker container by typing exit.
6. To start the server, run command make run. Wait until the server starts listening on port 3000.
7. Open your favourite browser and navigate to http://localhost:3000. Use the seeded administrator account from seeds.rb to login, or sign up for a new account.

OS-specific Install Instructions

Debian

1. Install Docker and add user 1000 to the docker group as described here.
2. Install Docker Compose as described here.
3. Follow Quick Start Guide above as user 1000.

Mac OS X

1. Install command line developer tools (there are many resources online, like this).
2. Install Docker Toolbox as described here.
3. Inside CLI, run git clone https://github.com/biosistemika/scinote-web.git.
4. Run Docker Quickstart Terminal (also described here).
5. Inside this terminal, navigate to cloned Git folder.
6. Follow the Quick Start Guide above.
7. When opening sciNote in browser, instead of navigating to localhost:3000, navigate to <docker-machine-ip>:3000 (you can get the docker machine IP by running command docker-machine ip default).

Docker structure

The main sciNote application runs in a Docker container called web. The database runs in a separate container, called db. This database container makes use of a special, persistent container called dbdata.

Commands

Call make commands to build Docker images and build Rails environment, including database.

Following commands are available:

Command	Description
make docker	Downloads the Docker image and build Gems. This should be called whenever Gemfile is changed.
make db-cli	Runs a /bin/bash inside the db container.
make run	Runs the db container & starts the Rails server in web container.
make start	Runs the db container & starts the Rails server in web container in background.
make stop	Stops the db & web containers.
make cli	Runs a /bin/bash inside the web container.
make tests	Execute all Rails tests.
make console	Enters the Rails console in web container.
make export	Zips the head of this Git repository into a .tar.gz file.

Environmental variables

sciNote reads configuration parameters from system environment parameters. On production servers, this can be simply be system environmental variables, while for development, a file config/application.yml can be created to specify those variables.

The following table describes all available environmental variables for sciNote server.

Variable	Mandatory	Description
SECRET_KEY_BASE	Yes	Random hash for Rails encryption. Can be generated by running rake secret.
PAPERCLIP_STORAGE	Yes	Set to 's3' to store files on Amazon S3, or 'filesystem' to store files on local server. If storing on S3, additional parameters need to be specified.
AWS_SECRET_ACCESS_KEY	No*	If storing files on Amazon S3, this must contain access key for accessing AWS S3 API.
AWS_ACCESS_KEY_ID	No*	If storing files on Amazon S3, this must contain access key ID for AWS S3.
S3_BUCKET	No*	If storing files on Amazon S3, this must contain S3 bucket on which files are stored.
AWS_REGION	No*	If storing files on Amazon S3, this must contain the AWS region.
PAPERCLIP_DIRECT_UPLOAD	No*	If storing files on Amazon S3, this must be set either to 1 (to upload files directly from client-side to S3, without passing through sciNote server) or to 0 (to upload files to S3 through sciNote server).
MAIL_FROM	Yes	The from address for emails sent from sciNote.
MAIL_REPLYTO	Yes	The reply to address for emails sent from sciNote.
SMTP_ADDRESS	Yes	The server address of the SMTP mailer used for delivering emails generated in sciNote.
SMTP_PORT	Yes	The port of the SMTP server. Defaults to 587.
SMTP_DOMAIN	Yes	The server domain of the SMTP mailer used for delivering emails generated in sciNote.
SMTP_USERNAME	Yes	The username for SMTP mailer used for delivering emails generated in sciNote.
SMTP_PASSWORD	Yes	The password for SMTP mailer used for delivering emails generated in sciNote.
MAIL_SERVER_URL	Yes	The root URL address of the actual sciNote server. This is used in sent emails to redirect user to the correct sciNote server URL. Defaults to localhost.
PAPERCLIP_HASH_SECRET	Yes	Random key for generating Paperclip hash key for URLs. Can be generated via following Ruby function: SecureRandom.base64(128).
ENABLE_TUTORIAL	Yes	Whether to display tutorial (and auto-generate demo project) to first-time users. Defaults to false on development, and to true on production.

Rake tasks

Delayed jobs

sciNote uses delayed jobs library to do background processing, mostly for the following tasks:

• Sending emails,
• Extracting text from uploaded files (full-text search).

Best option to run delayed jobs is inside a worker process. To start a background worker process that will execute delayed jobs, run the following command:

rake jobs:work

To clear all currently queued jobs, you can use the following command:

rake jobs:clear

Warning! This is not advised to do on production environments.

Adding users

To simplify adding of new users to the system, couple of special rake tasks have been created.

The first, rake db:add_user simply queries all the information for a specific user via STDIN, and then proceeds to create the user.

The second task, rake db:load_users[file_path,create_orgs] takes 2 parameters as an input:

• Path to .yml file containing list of users & organizations to be added. The YAML file needs to be structured properly - field names must match those in the database, users need to have a name user_<id>, and organizations name org_<id>. For an example load users file, see db/load_users_template.yml file.
• A boolean ('true' or 'false') whether to create individual organizations for each user or not.

Both of those rake actions include all database operations inside a transaction, so as long as any error happens during the process, database will be unaffected.

Generating fake data

For testing purposes, two special tasks that will populate the database with randomized, fake data, have been implemented.

The first, rake db:fake:generate, will add fake data to an existing database. Since the algorithm that generates randomized data relies heavily on querying existing entries in database, use of this task is not advisable.

It is much better to use rake db:fake task, that will drop the database first, recreate it, and populate it with fake data afterwards.

Web statistics

To check current login statistics of registered users, use rake web_stats:login task.

Clearing data

Execute rake data:clean_temp_files to remove all temporary files. Temporary files are used when importing samples. Execute rake data:clean_unconfirmed_users to remove all users that registered, but never confirmed their email. Calling rake data:clean will execute both above tasks.

Mailer

sciNote needs a configured SMTP mail server to work properly. See environmental variables for configuration of the mailer.

Deploy onto Heroku

Before deploying to Heroku, install heroku client as describe on offical website. To use existing heroku application, add new git remote repository.

git remote add heroku git@heroku.com:my-random-app-name.git

Or create new heroku application by executing following command.

heroku create

Add graphviz buildpack:

heroku buildpacks:add --index 2 https://github.com/weibeld/heroku-buildpack-graphviz.git

Before pushing to heroku master branch, some environmental variables should be set.

Heroku environmental variables

For deployment of sciNote onto Heroku, additional environmental variables need to be specified.

Variable	Mandatory	Description
SKYLIGHT_AUTHENTICATION	No	The API key for Skylight code profiler, if choosing to use it.
LANG	Yes	The default localization language (e.g. en_US.UTF-8).
RAILS_ENV	Yes	Rails environment: production, test or development.
RACK_ENV	Yes	Rack environment: production, test or development.
RAILS_SERVE_STATIC_FILES	Yes	Whether to serve static files. Must be set to enabled.
WEB_CONCURRENCY	Yes	The concurrency of the server. See Heroku specifications for details.
MAX_THREADS	Yes	The max. number of threads. See Heroku specifications for details.
PORT	Yes	The port on which the application should run. See Heroku specifications for details.
S3_HOST_NAME	No*	If storing files on Amazon S3, this must contain the S3 service host name.
RAILS_FORCE_SSL	Yes	If set to 1, enforce SSL communication on all levels of application.
DATABASE_URL	Yes	Full URL for connecting to PostgreSQL database.

Testing

In current version, only model tests are implemented for sciNote. To execute them, call rake test:models.

Contributing

For contributing, see CONTRIBUTING.md.

License

sciNote is developed and maintained by BioSistemika USA, LLC, under Mozilla Public License Version 2.0.

See LICENSE-3RD-PARTY.txt for licenses of included third-party libraries.