feat: add MONGO_URI environment variable support (#253)#256
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minhpham1810 wants to merge 4 commits intoelixir-cloud-aai:devfrom
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feat: add MONGO_URI environment variable support (#253)#256minhpham1810 wants to merge 4 commits intoelixir-cloud-aai:devfrom
minhpham1810 wants to merge 4 commits intoelixir-cloud-aai:devfrom
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Add support for a MONGO_URI environment variable that, when set, is used as the complete MongoDB connection string, taking precedence over individual component variables (MONGO_HOST, MONGO_PORT, MONGO_USERNAME, MONGO_PASSWORD, MONGO_DBNAME). This enables advanced connection features such as replica sets, SRV records, TLS options, and URIs from external secret managers. A warning is logged when MONGO_URI is set alongside individual variables to help users avoid configuration confusion. Full backward compatibility is maintained.
Reviewer's GuideAdds support for a MONGO_URI environment variable that, when set and non-empty, is used as the complete MongoDB connection string with precedence over individual MongoDB env vars and config, along with tests, logging, and documentation/template updates describing this behavior. Sequence diagram for Flask app initialization with MONGO_URI supportsequenceDiagram
participant Env as Environment
participant App as FlaskApp
participant Reg as register_mongodb
participant Mongo as PyMongo
App->>Reg: _create_mongo_client(app, host, port, db)
Reg->>Env: get MONGO_URI
Env-->>Reg: MONGO_URI value or null
alt MONGO_URI set and non-empty
Reg->>Env: get MONGO_HOST, MONGO_PORT,
Env-->>Reg: individual env values
Reg->>Reg: build list of set individual vars
alt any individual vars set
Reg->>App: logger.warning(MONGO_URI overrides individual vars)
end
Reg->>App: set app.config[MONGO_URI]
Reg->>Mongo: create PyMongo(app)
Mongo-->>Reg: PyMongo client
Reg->>App: logger.info(registered via MONGO_URI)
Reg-->>App: PyMongo client
else MONGO_URI not set or empty
Reg->>Env: get MONGO_USERNAME, MONGO_PASSWORD,
Env-->>Reg: individual env values
Reg->>Reg: build connection URI from env or config
Reg->>Mongo: create PyMongo(app)
Mongo-->>Reg: PyMongo client
Reg-->>App: PyMongo client
end
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Hey - I've left some high level feedback:
- In
_create_mongo_client, consider normalizingMONGO_URIand the individual env vars (e.g., using.strip()and treating empty strings as unset) so that whitespace/empty-string values don’t unintentionally trigger URI usage or get included in the "ignored" warning list.
Prompt for AI Agents
Please address the comments from this code review:
## Overall Comments
- In `_create_mongo_client`, consider normalizing `MONGO_URI` and the individual env vars (e.g., using `.strip()` and treating empty strings as unset) so that whitespace/empty-string values don’t unintentionally trigger URI usage or get included in the "ignored" warning list.Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.
- add INFO log after casbin enforcer registration in register_access_control.py - add INFO log after permission spec registration in register_access_control.py - add INFO log after access-control registration in foca.py - add focused log-flow unit test in test_register_access_control.py - update access-control tests to assert emitted logs via stderr capture in test_foca.py - replace deprecated importlib.resources path usage with files/as_file in config.py and register_access_control.py - suppress known third-party deprecation noise in pytest config in setup.cfg Suggested PR title Add readable access-control setup logs and clean up deprecation/test noise Suggested PR description Summary This PR implements issue elixir-cloud-aai#250 by adding readable confirmation logs for the access-control setup flow, then updates tests and warning handling so CI output is reliable and low-noise. What changed 1. Access-control setup logging - Added log confirming enforcer registration in register_access_control.py. - Added log confirming permission spec registration in register_access_control.py. - Added top-level log confirming access-control registration completion in foca.py. 2. Test updates - Added a focused unit test to validate setup-step logs in test_register_access_control.py. - Updated access-control assertions in test_foca.py to use stderr capture, matching current project logging behavior. 3. Deprecation cleanup - Replaced deprecated importlib.resources path usage with files/as_file in: - config.py - register_access_control.py - Added pytest warning filters for known external deprecations in setup.cfg. Why - Improves operator visibility during bootstrap by clearly signaling successful access-control setup steps. - Prevents flaky/false-negative log assertions caused by logger capture differences. - Reduces warning noise from dependency internals so real regressions are easier to spot. Validation - Ran: pytest -q test_foca.py - Result: 15 passed Issue - Closes elixir-cloud-aai#250
…d-aai#253)" This reverts commit 6e19fe8.
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Description
Add support for a MONGO_URI environment variable that, when set, is used as the complete MongoDB connection string, taking precedence over individual component variables (MONGO_HOST, MONGO_PORT, MONGO_USERNAME, MONGO_PASSWORD, MONGO_DBNAME). This enables advanced connection features such as replica sets, SRV records, TLS options, and URIs from external secret managers.
A warning is logged when MONGO_URI is set alongside individual variables to help users avoid configuration confusion. Full backward compatibility is maintained.
Fixes #253
Type of change
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Summary by Sourcery
Add support for configuring the MongoDB client via a single MONGO_URI environment variable that takes precedence over individual MongoDB settings while preserving existing behavior as a fallback.
New Features:
Enhancements:
Documentation:
Tests: