Deploying

• Recurring deployments
  • Deploying id3c or id3c-customizations
    • Prerequisites
    • Steps for deployment:
      • Schema changes to the database
      • Code changes to id3c
      • Data uploads to the database
  • Deploying husky-musher
  • Deploying scan-switchboard
  • Deploying specimen-manifests

Recurring deployments

Deploying id3c or id3c-customizations

• id3c source code
• id3c-customizations source code

Prerequisites

Before you get started, you'll need the following:

• a personal admin account to the production ID3C database plus the login information for the postgres user account.
• a configured sqitch environment on your local machine.

  See Infrastructure → Databases (PostgreSQL) → sqitch configuration

• a public key shared with the ubuntu account on backoffice.seattleflu.org.

Steps for deployment:

1. Merge code changes in id3c or id3c-customizations to each master branch, respectively.
2. Run pipenv update in the id3c-production directory of your backoffice checkout. This will lock ID3C and our customizations at the latest state of their master branch on GitHub. Review, commit, and push the changes.

Schema changes to the database

If you have no schema changes to deploy, you may skip this section.

3. Deploy database schema changes via sqitch from your local machine. Run the following commands, replacing the curly-bracketed text with your specifications.

   First, check that the plan looks good.

    PGUSER={your-admin-username} sqitch status {database name}
   

   Tip: check ~/.pg_service.conf for your admin username and other connection details

   If everything looks good, run the following using the postgres user.

    PGUSER=postgres sqitch deploy {database name}
   

4. Grant any newly needed roles to the backoffice database automation user via

    PGUSER={your-admin-username} PGSERVICE={service name} psql
   

   Once inside of the psql prompt, run:

    grant "{role}" to "backoffice-etl";
   

Code changes to id3c

If you have no code changes to deploy, you may skip this section.

4. Log onto the backoffice server.
5. Navigate to the /opt/backoffice directory and run git pull.
6. Add any newly needed secret environment variables under id3c-production/env.d/…. (Non-secret environment variables should be committed and pulled in via git.)
7. Install the latest production environment with (cd id3c-production; pipenv sync).
8. Install the latest crontabs with sudo make -C crontabs.
9. If there are updates to the web API, restart the web API backend by running sudo systemctl reload uwsgi.

   See the uWSGI documentation under Infrastructure → Hosts → backoffice.seattleflu.org

10. If the API was restarted, check web API log file with sudo tail -f /var/log/uwsgi/app/api-production.log.

Data uploads to the database

If you have no data to upload, you may skip this section.

10. Upload data to the receiving area of the database from your local machine. Run the desired id3c command(s) with a prefix of PGSERVICE={service name}.

Deploying husky-musher

• husky-musher source code

1. Log onto the backoffice server.
2. Navigate to the /opt/husky-musher directory and run git pull.
3. Reload the uWSGI server by running sudo systemctl reload uwsgi.

   See the uWSGI documentation under Infrastructure → Hosts → backoffice.seattleflu.org

4. Check log file at /var/log/uwsgi/app/husky-musher.log for any errors or warnings.

Deploying scan-switchboard

• scan-switchboard source code

1. Log onto the backoffice server.
2. Navigate to the /opt/scan-switchboard directory and run git pull.
3. Add any newly needed secret environment variables under /opt/backoffice/id3c-production/env.d/…. (Non-secret environment variables should be committed and pulled in via git.)
4. Install the latest code with pipenv sync.
5. If you've changed the structure of the record_barcodes table in the SQLite database, delete the old database file under data/.
6. Restart scan-switchboard with sudo systemctl restart scan-switchboard

There is a crontab that syncs the switchboard. If you have changed something in scan-switchboard that needs accompanying changes to the crontab, make that change in the backoffice repository and deploy that too.

Deploying specimen-manifests

• specimen-manifests source code

1. Log onto the backoffice server.
2. Navigate to the /opt/specimen-manifests directory and run git pull.