Implement API endpoints related to fetching BERtron data#54
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: eecavanna <134325062+eecavanna@users.noreply.github.com>
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Pull Request Overview
Adds initial API endpoints to serve and query the MongoDB entities collection, including generic and geospatial search functionality.
- Introduces endpoints:
/bertron(list all),/bertron/find(dynamic queries),/bertron/geo/nearby,/bertron/geo/bbox, and/bertron/{id}. - Defines
MongoDBQueryPydantic model for flexible query parameters. docker-compose.ymlshows unresolved merge conflict markers that must be cleaned up.
Reviewed Changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| src/server.py | Implements new FastAPI routes for entity retrieval and querying (generic & geo). |
| docker-compose.yml | Contains merge conflict markers that prevent a valid YAML configuration. |
Comments suppressed due to low confidence (4)
src/server.py:239
- [nitpick] Using 'id' shadows the built-in function
idand is ambiguous; consider renaming to 'entity_id' for clarity.
def get_entity_by_id(id: str):
src/server.py:56
- This new endpoint lacks associated tests; consider adding unit tests to cover the query functionality and edge cases.
@app.post("/bertron/find")
docker-compose.yml:53
- Unresolved merge conflict marker '<<<<<<< HEAD' in docker-compose.yml; resolve the conflict and remove these markers.
<<<<<<< HEAD
docker-compose.yml:65
- Unresolved merge conflict marker '>>>>>>> main' in docker-compose.yml; resolve the conflict and remove these markers.
>>>>>>> main
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| import json | ||
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The 'json' import is not used and can be removed to clean up unused imports.
Suggested change
| import json |
jeff-cohere
reviewed
Jun 12, 2025
| - mongo | ||
| # Run ingest with data dir mounted to /data | ||
| command: ["uv", "run", "python", "/app/mongodb/ingest_data.py", "--mongo-uri", "mongodb://admin:root@mongo:27017", "--input", "/data"] | ||
| <<<<<<< HEAD |
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This looks like an unresolved conflict.
jeff-cohere
requested changes
Jun 12, 2025
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jeff-cohere
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jeff-cohere
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Looks good, aside from some unresolved conflict kibble and formatting changes. I'll approve after these are fixed.
eecavanna
changed the title
eecavanna
approved these changes
Jun 12, 2025
jeff-cohere
approved these changes
Jun 12, 2025
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Initial support for API endpoints.
Note that we aren't using the Pydantic LinkML model for BERTron yet because the DB expects things to be in GeoJSON. This is converted on ingest, but once the schema supports GeoJSON it should simplify things.