The next generation of the CIDC API, reworked to use Google Cloud-managed services. This API is built with the Eve REST API framework backed by Google Cloud SQL, running on Google App Engine.
- Install Python dependencies
- Database Management
- Serving Locally
- Code Formatting
- Connecting to the API
- Provisioning the system from scratch
Install Python dependencies
Install both the production and development dependencies.
pip install -r requirements.dev.txt
Install and configure pre-commit hooks.
Setting up a local development database
In production, the CIDC API connects to a PostgreSQL instance hosted by Google Cloud SQL, but for local development, you should generally use a local PostgreSQL instance.
To do so, first install and start PostgreSQL:
brew install postgresql brew services start postgresql # launches the postgres service whenever your computer launches
or for Ubuntu/Debian
sudo apt install postgresql service postgresql start sudo update-rc.d postgres defaults # launches the postgres service whenever your computer launches sudo -i -u postgres # used to access postgresql user
By default, the postgres service listens on port 5432. Next, create the
cidcdev user, your local
cidc development database, and a local
cidctest database that the unit/integration tests will use:
psql -c "create user cidcdev with password '1234'" # Database to use for local development psql -c "create database cidc" psql -c "grant all privileges on database cidc to cidcdev" psql cidc -c "create extension citext" psql cidc -c "create extension pgcrypto" # Database to use for automated testing psql -c "create database cidctest" psql -c "grant all privileges on database cidctest to cidcdev" psql cidctest -c "create extension citext" psql cidctest -c "create extension pgcrypto"
Now, you should be able to connect to your development database with the URI
postgresql://cidcdev:1234@localhost:5432/cidc. Or, in the postgres REPL:
Next, you'll need to set up the appropriate tables, indexes, etc. in your local database. To do so,
cd into the
cidc_api directory (as your local user), then run:
FLASK_APP=cidc_api.app:app flask db upgrade
You will also need to set the
GOOGLE_APPLICATION_CREDENTIALS environment variable to the local path of the credentials file for the staging environment's App Engine service account.
Connecting to a Cloud SQL database instance
Install the Cloud SQL Proxy:
curl -o /usr/local/bin/cloud_sql_proxy https://dl.google.com/cloudsql/cloud_sql_proxy.darwin.amd64 chmod +x /usr/local/bin/cloud_sql_proxy mkdir ~/.cloudsql
Proxy to the staging Cloud SQL instance:
cloud_sql_proxy -instances cidc-dfci-staging:us-central1:cidc-postgresql-staging -dir ~/.cloudsql
.env file, comment out
POSTGRES_URI and uncomment all environment variables prefixed with
CLOUD_SQL_. Restart your local API instance, and it will connect to the staging Cloud SQL instance via the local proxy.
If you wish to connect to the staging Cloud SQL instance via the postgres REPL, download and run the CIDC sql proxy tool (a wrapper for
# Download the proxy curl https://raw.githubusercontent.com/CIMAC-CIDC/cidc-devops/master/scripts/cidc_sql_proxy.sh -o /usr/local/bin/cidc_sql_proxy chmod +x /usr/local/bin/cidc_sql_proxy # Run the proxy cidc_sql_proxy staging # or cidc_sql_proxy prod
Running database migrations
This project uses
Flask Migrate for managing database migrations. To create a new migration and upgrade the database specified in your
export FLASK_APP=cidc_api/app.py # Generate the migration script flask db migrate -m "<a message describing the changes in this migration>" # Apply changes to the database flask db upgrade
To revert an applied migration, run:
flask db downgrade
If you're updating
models.py, you should create a migration and commit the resulting
Once you have a development database set up and running, run the API server:
ENV=dev gunicorn cidc_api.app:app
This project uses
pytest for testing.
To run the tests, simply run:
This project uses
black for code styling.
We recommend setting up autoformatting-on-save in your IDE of choice so that you don't have to worry about running
black on your code.
This project uses GitHub Actions for continuous integration and deployment. To deploy an update to this application, follow these steps:
- Create a new branch locally, commit updates to it, then push that branch to this repository.
- Make a pull request from your branch into
master. This will trigger GitHub Actions to run various tests and report back success or failure. You can't merge your PR until it passes the build, so if the build fails, you'll probably need to fix your code.
- Once the build passes (and pending approval from collaborators reviewing the PR), merge your changes into
master. This will trigger GitHub Actions to re-run tests on the code then deploy changes to the staging project.
- Try out your deployed changes in the staging environment once the build completes.
- If you're satisfied that staging should be deployed into production, make a PR from
- Once the PR build passes, merge
production. This will trigger GitHub Actions to deploy the changes on staging to the production project.
For more information or to update the CI workflow, check out the configuration in
Deploying by hand
Should you ever need to deploy the application to Google App Engine by hand, you can do so by running the following:
gcloud app deploy <app.staging.yaml or app.prod.yaml> --project <gcloud project id>
That being said, avoid doing this! Deploying this way circumvents the safety checks built into the CI/CD pipeline and can lead to inconsistencies between the code running on GAE and the code present in this repository. Luckily, though, GAE's built-in versioning system makes it hard to do anything catastrophic :-)
Connecting to the API
To connect to the staging API with
curl or a REST API client like Insomnia, get an id token from stagingportal.cimac-network.org, and include the header
Authorization: Bearer YOUR_ID_TOKEN in requests you make to the staging API. If your token expires, generate a new one following this same procedure.
To connect to the production API locally, follow the same procedure, but instead get your token from portal.cimac-network.org.
Provisioning the system from scratch
For an overview of how to set up the CIDC API service from scratch, see the step-by-step guide in
To set-up the git hook for JIRA integration, run:
ln -s ../../.githooks/commit-msg .git/hooks/commit-msg chmod +x .git/hooks/commit-msg rm .git/hooks/commit-msg.sample
This symbolic link is necessary to correctly link files in
.git/hooks. Note that setting the
core.hooksPath configuration variable would lead to pre-commit failing. The
commit-msg hook runs after the
pre-commit hook, hence the two are de-coupled in this workflow.
To associate a commit with an issue, you will need to reference the JIRA Issue key (For eg 'CIDC-1111') in the corresponding commit message.