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SQLAlchemy data models and configuration tools used in the CIDC API

Project description

CIDC API

Environment Branch Status Maintainability Test Coverage
production production Continuous Integration
staging master Continuous Integration Maintainability Test Coverage

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.

Development

Install Python dependencies

Install both the production and development dependencies.

pip install -r requirements.dev.txt

Install and configure pre-commit hooks.

pre-commit install

Database Management

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:

psql cidc

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

In your .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 cloud_sql_proxy):

# 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 .env config:

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

Serving Locally

Once you have a development database set up and running, run the API server:

ENV=dev gunicorn cidc_api.app:app

Testing

This project uses pytest for testing.

To run the tests, simply run:

pytest

Code Formatting

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.

Deployment

CI/CD

This project uses GitHub Actions for continuous integration and deployment. To deploy an update to this application, follow these steps:

  1. Create a new branch locally, commit updates to it, then push that branch to this repository.
  2. 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.
  3. 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.
  4. Try out your deployed changes in the staging environment once the build completes.
  5. If you're satisfied that staging should be deployed into production, make a PR from master into production.
  6. Once the PR build passes, merge master into 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 .github/workflows/ci.yml.

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

Currently, the staging API is hosted at https://staging-api.cimac-network.org and the production instance is hosted at https://api.cimac-network.org.

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 PROVISION.md.

JIRA Integration

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 .githooks to .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.

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