feat: parse config files as yaml

[sbliven]

Description

Use yaml to parse all JSON files (fix #1120)

This change is backwards compatible. No changes to existing json files are needed (although yaml features like comments can be added if desired). YAML features like comments can be added in the existing JSON files without changing the filename. If you want editor support for yaml it might be desirable to change the config file suffixes to .yaml; this is not done by default but is supported through environmental variables (FUNCTIONAL_ACCOUNT_FILE and similar).

Motivation

Use of yaml for the jobConfig.yaml file has been convenient. This PR extends that out to other JSON config files.

Fixes

• Parse config files as YAML #1120

Tests included

• Included for each change/fix?
• Passing?

Documentation

• swagger documentation updated (required for API changes)
• official documentation updated

official documentation info

[nitrosx]

Can you clarify my questions?

[Junjiequan]

looks good to me

[nitrosx]

Looks good to me.

[bpedersen2]

This would also enable us to provide commented sample config files, making admin docs more usable and probably easier to maintain.

[Junjiequan]

Hi @sbliven can we merge this PR?

[totopoloco]

Looks good to me

[totopoloco]

The failing job is caused by tests trying to access properties like db or close on undefined objects.

Code suggestion:

get(key: string) {
  if (key === "mongodbUri") {
    const superUri = super.get(key) || "mongodb://localhost:27017/scicat-e2e-test-default";
    const uriParts = superUri.split("/");
    uriParts[3] = `scicat-e2e-test-${faker.number.int()}`;
    return uriParts.join("/");
  }
  return super.get(key);
}

[totopoloco]

Fix Connection and Resource Initialization: Update createTestingApp in utlis.ts to handle undefined or failing resource initialization gracefully:

export async function createTestingApp(moduleFixture: TestingModule) {
    const app = moduleFixture.createNestApplication();
    app.setGlobalPrefix("api");
    app.enableVersioning({
        type: VersioningType.URI,
        defaultVersion: "3",
    });
    await app.init();
    try {
        await app.get<Promise<Connection>>(getConnectionToken()); // Ensure Mongo connection is available.
    } catch (err) {
        console.error("Failed to get MongoDB connection:", err); // Add debug output.
    }
    return app;
}