The documentation website at dsri.maastrichtuniversity.nl is automatically updated by a GitHub Action at each push to this master branch.

📝 Contribute

Contributions are welcome! See the guidelines to contribute to the website.

Edit documentation pages

Editing a documentation file is as easy as going to https://github.com/MaastrichtU-IDS/dsri-documentation/edit/master/website/docs/introduction.md.

• Edit a page by login with an account that has edit permissions.

• Otherwise fork the repository and modify the files you want. Pull requests are welcome!

Browse all documentation pages here.

We recommend using Typora to edit markdown files on your computer.

Files locations

• All documentation pages are in website/docs
• Add new docs pages links to the sidebar: website/sidebars.json.
• Main parameters of the website can be found in website/docusaurus.config.js.
• Static content (any resource to download, images, css, js) can be provided in website/static
• Pages other than docs are in website/src/pages (e.g. help.md or index.tsx)

Add an announcement

You can easily add a general announcement bar on the website if you want to pass some information to your users, like dates of maintenance

Open the file website/docusaurus.config.js and update the announcementBar variable.

You can comment the announcementBar code block when you want to remove the announcement bar.

🧑‍💻 Run for development

Just run the website

To check changes in the documentation, go to the /website directory and start the website on http://localhost:19006 using the production API for user statistics:

cd website
yarn install
yarn start

Run the full stack

To run the full stack including the database and API, we use docker-compose

1. Define the .env file to change the default configuration (user credential to enable/disable GPU on the cluster, Slack config):

   DB_PASSWORD=password
   API_PASSWORD=password
   CLUSTER_API_KEY=token
   SLACK_BOT_TOKEN=xoxb-0000000000-0000000000-0000000000
   SLACK_CHANNEL=C03B48CQ3QW

2. Run the stack:

   • API on http://localhost:8000, automatically reloaded on change to the code, with CRON job enabled
   • The GPU calendar on http://localhost:8001
   • Database accessible through phpMyAdmin on http://localhost:8002

   docker-compose up

   ⚠️ The first time you start the stack you might need to stop and restart the stack once the SQL database has been initialized for the API to properly connect to the database

3. In another terminal, run the website on http://localhost:3000, it will use the local API to display stats:

   cd website
   yarn install
   yarn dev

Update dependencies

Dependabot will automatically create pull requests to update libraries containing a known vulnerability that have been fixed in newer version.

You can also use yarn to automatically upgrade packages that can:

yarn upgrade

Alternatively you can also change the packages versions requirements in the package.json and run yarn

🚀 Deploy in production

Deploy the frontend to GitHub pages

The documentation website at dsri.maastrichtuniversity.nl is automatically updated by a GitHub Action at each push to the master branch of this repository.

The GitHub Action will automatically compile the website to HTML in the gh-page branch which is served by GitHub Page.

Deploy the backend on a server

Define the .env file to change the default configuration (user credential to enable/disable GPU on the cluster, Slack config):

DB_PASSWORD=password
API_PASSWORD=password
CLUSTER_USER=dsri.username
CLUSTER_PASSWORD=password
SLACK_BOT_TOKEN=xoxb-0000000000-0000000000-0000000000
SLACK_CHANNEL=C03B48CQ3QW

Start the docker-compose in production using nginx-proxy.

docker-compose -f docker-compose.yml -f docker-compose.prod.yml up -d

Database setup

Import CSV

To import a CSV of users in the database: remove the header, set created_at and use_dsri_dateas a VARCHAR(255), import the CSV file via phpMyAdmin, then set back created_at and use_dsri_date as DATETIME

UPDATE user SET created_at = STR_TO_DATE(created_at, '%d-%m-%Y %H:%i:%s');
UPDATE user SET use_dsri_date = STR_TO_DATE(use_dsri_date, '%d-%m-%Y');

Create new database users

Login with the root user, and click on the SQL tab

Replace username by the username, and password by the password (thanks captain obvious):

Commands to create a read-only user:

DROP USER IF EXISTS 'username'@'%';
CREATE USER 'username'@'%' IDENTIFIED BY 'password';
GRANT USAGE ON *.* TO 'username'@'%' IDENTIFIED BY 'password';
GRANT SELECT ON `dsri-db`.* TO 'username'@'%';
FLUSH PRIVILEGES;

Or give full access:

GRANT ALL PRIVILEGES ON `dsri-db`.* TO 'username'@'%';

Change your user password

To change the password of your database user, click on the SQL tab, and execute:

SET PASSWORD FOR 'username'@'%' = PASSWORD('newpassword');

Backup

Export as CSV

1. Go to phpMyAdmin > click on the dsri-db database > go to the Export tab
2. Change the Export method to Custom
3. Change the Format to CSV or CSV for MS Excel
4. Check Export tables as separate files
5. Click Go

Complete database backup

A CSV backup of the database is generated every week by a CRON job (cf. https://github.com/MaastrichtU-IDS/dsri-documentation/blob/master/server/api/main.py#L52) and stored locally on the server where the service is deployed.

For reliability reason we choose to export as CSV: open, lightweight, hard to corrupt, and contains all information we need to backup (otherwise we would need to fight with weird backup tools poorly built by lost sysadmins that fails most of the time just to save some useless indexes, which just leads to increased chances of corrupting the data we backup...)

💡 Markdown tips

:::note
Grey box
:::
:::tip You can specify an optional title
Green box
:::
:::info
Blue box
:::
:::caution
Orange bpx
:::
:::danger
Red box
:::

Embed a Google docs presentation (size does not change dynamically). You can check the "documentation" by gitlab but it does not work (how can they expect to get a responsive website by providing hardcoded pixel size?):

<figure class="video_container">
  <iframe src="https://docs.google.com/presentation/d/e/2PACX-1vRAfZdOfGt761tIAj2e35OYrOL4uIKWiAQB15MXvsqso3XJ5Mr3-W4dOa9KjDTZpi1LE_D2CU1F5Thy/embed?start=false&loop=false&delayms=15000" frameborder="0" width="960" height="569" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>
</figure>

# With CSS:
<script>
.video-container{
  position: absolute;
  top: 0%;
  left: 0%;
  height: 100%;
  width: 100%;
  /* overflow: hidden; */
}
</script>

Convert a mkv video to webm (better for direct embedding):

ffmpeg -i video_dsri_introduction.mkv -c:v libvpx -crf 10 -c:a libvorbis video_dsri_introduction.webm

🧜‍♀️ Mermaid sourcecodes

Request access to UM internal servers

sequenceDiagram
    Researcher->>+DSRI-team: Request DSRI access to UM system
    DSRI-team->>+UM-SOC: Request DSRI access to UM system
    UM-SOC-->>+DSRI-team: Go ahead
    DSRI-team-->>+System admin:



    sequenceDiagram
     Researcher->>+DSRI-team: Request DSRI access to UM system
    DSRI-team->>+UM-SOC: Request DSRI access to UM system
    UM-SOC-->>+DSRI-team: Go ahead
    DSRI-team->>+UM System admin: Request access from DSRI
    UM System admin-->>+ICTS: Request change in firewall
    DSRI-team-->>+ICTS: Request change in firewall
    DSRI-team->>+Researcher: UM system accessible from DSRI

🙏 Acknowledgments

Documentation website generated using Docusaurus.