Add new Specify instance to Specify Cloud

Example for

  1. Create Database

    1. Review the SQL file before importing to the production server. Test the import locally before uploading to a production instance.

    2. Ensure the new database has the same name as the subdomain the user wishes to use, remembering that underscores (_) are replaced with dashes (-) for the URL.

    3. Create the database:

      mariadb -u<master> -p<master_password> -e "CREATE DATABASE <dbname>;"

    4. Upload and restore the existing database:

      mariadb -u<master> -p<master_password> <dbname> < <dbname>.sql

    5. Note: You may GRANT ALL PRIVILEGES ON <dbname>.* TO <master_password>@'%'; if master doesn’t have access FLUSH PRIVILEGES;

  2. DNS Registration:

    1. Login to Dreamhost, select Websites -> Manage Websites

    2. For specifycloud.org, select DNS (Direct link)

    3. Add CNAME record that has a name matching the database name and links to the appropraite regional domain value (i.e. na-specify7-1.specifycloud.org., eu-specify7-1.specifycloud.org., etc.). If the database name has underscores (_), replace these with dashes (-).

      • <dbname> points to <subdomain>.specifycloud.org. For example, database name herb_rbge would have the name herb-rbge.specifycloud.org.

    4. Wait at least 10 minutes for domain to circulate.

    5. For the ku servers, request the dns CNAME record to bitech@ku.edu

  3. Config

    1. Add to spcloudservers.json on the appropriate server in the /home/ubuntu/docker-compositions/specifycloud dir.

    2. Make sure to add https: false

    3. Run make as ubuntu

    4. Run docker compose up -d

    5. Run docker compose restart nginx (reload should be just fine here: docker exec -it specifycloud_nginx_1 nginx -s reload)

    6. Check url

  4. Add SSL

    1. Run the add_ssl.sh script and follow the prompts.

       sudo bash add_ssl.sh

      You will need to provide the <subdomain> for the new instance that you wish to add. After this, it will update the spcloudservers.json and set "https": false to "https": true for that instance, then restart all of the running containers.

    2. Check URL

    3. Note: After an SSL certificate renewal, you can reload nginx without restarting the whole container:

      docker exec -it specifycloud-nginx-1 nginx -s reload

      1. For automatic nginx reloading on certificate renewal create /etc/letsencrypt/renewal-hooks/post/reload-nginx.sh #!/bin/bash docker exec -it specifycloud-nginx-1 nginx -s reload

      2. crontab -e; and then add the line 0 3 * * 0,2,4,6 docker exec specifycloud_nginx_1 nginx -s reload

      3. crontab -l to list cronjobs

  5. Add Specify Admin user credentials to the Bitwarden Vault

  6. Setup attachments for the database

    1. SSH into the appropriate Web Asset Server

    2. Navigate to the web-asset-server directory

    3. Use the manage_collection_dirs.py utility to add the new database(s) to the server:

      python3 manage_collection_dirs.py add <database_name>

      This creates a new attachment directory and updates the settings.py file to add the collection directory.

  7. Updown

    1. Add url: <subdomain>.specifycloud.org/context/system_info.json

    2. Add alias: <subdomain>

Misc

  • Add ssh key:

nano .ssh/authorized_keys
sudo systemctl reload sshd

Troubleshooting

  • Handle mariadb failing to restart after restarting the Database droplet:

mysqld --tc-heuristic-recover=ROLLBACK
systemctl start mariadb.service

  • Fix an instance by restarting it:

sudo docker exec -it specifycloud-nginx-1 nginx -s reload;
sudo docker stop client client-worker;
sudo docker compose up -d;
sudo docker exec -it specifycloud-nginx-1 nginx -s reload;