feat(sage-monorepo): integrate SQL formatter and linter (ARCH-296)

[tschaffter]

Closes https://sagebionetworks.jira.com/browse/ARCH-296

Changelog

• Add and configure SQL plugin for Prettier to format SQL files
• Add and configure SQLFluff to lint SQL files
• Configure lint-staged to format and lint staged SQL files
• Add and configure SQLFluff VS Code extension to the dev container
• Configure SQLFluff to use the mysql dialect by default.
• Demonstrate how to specify a dialect to SQLFluff per file.

Notes

• SQLFluff configuration is defined in the root pyproject.toml since that's also where Black configuration is located. It is also possible to specify SQLFluff in other files, including .sqlfluff.
• SQLFluff configuration supports inheritance (see docs). If needed, projects could extend the root configuration defined in pyproject.toml.
• SQLFluff VS Code extension has a formatter and can format on save. I've disabled this feature because I'd prefer to use Prettier, which is more generalizable. A future task could be to evaluate how Prettier's plugin for SQL and SQLFluff format files.

References

• https://docs.sqlfluff.com/en/1.3.0/configuration.html
• https://marketplace.visualstudio.com/items?itemName=dorzey.vscode-sqlfluff

Preview

Format SQL files on Save with Prettier

Before:

CREATE USER keycloak
WITH ENCRYPTED PASSWORD 'changeme';
CREATE DATABASE keycloak;
GRANT all PRIVILEGES ON DATABASE keycloak TO keycloak;

Upon saving:

CREATE USER keycloak
WITH
  ENCRYPTED PASSWORD 'changeme';

CREATE DATABASE keycloak;

GRANT all PRIVILEGES ON DATABASE keycloak TO keycloak;

Lint SQL files with SQLFluff CLI

$ poetry run sqlfluff lint apps/openchallenges/user-service/session.sql
== [apps/openchallenges/user-service/session.sql] FAIL                                                           
L:   3 | P:   1 | AM04 | Query produces an unknown number of result columns.
                       | [ambiguous.column_count]
L:   3 | P:   1 | LT09 | Select targets should be on a new line unless there is
                       | only one select target. [layout.select_targets]
L:   4 | P:   1 | LT02 | Expected indent of 4 spaces. [layout.indent]
L:   6 | P:   1 | LT02 | Expected indent of 4 spaces. [layout.indent]
L:  11 | P:   1 | LT02 | Expected indent of 4 spaces. [layout.indent]

Lint SQL files with SQLFluff VS Code extension