sciNote is an open source electronic lab notebook ([ELN](https://en.wikipedia.org/wiki/Electronic_lab_notebook)) 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.
sciNote is developed in [Ruby on Rails](http://rubyonrails.org/). It also makes use of [Docker](https://www.docker.com/) 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](#user-content-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](http://localhost:3000/). Use the seeded administrator account from [seeds.rb](db/seeds.rb) to login, or sign up for a new account.
1. Install command line developer tools (there are many resources online, like [this](http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/)).
2. Install Docker Toolbox as described [here](https://docs.docker.com/mac/step_one/).
3. Inside CLI, run `git clone https://github.com/biosistemika/scinote-web.git`.
4. Run Docker Quickstart Terminal (also described [here](https://docs.docker.com/mac/step_one/)).
5. Inside this terminal, navigate to cloned Git folder.
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`).
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.
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.
| 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. |
sciNote uses [delayed jobs](https://github.com/tobi/delayed_job) 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](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](#user-content-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.
