Refactor storage to use GridFS for binary samples and add orphan cleanup #84
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This commit addresses issue #80 by refactoring the MongoDB storage backend to utilize GridFS for storing binary sample data. Storing binary data in GridFS is more efficient for large files and is the recommended approach with MongoDB. Key changes include: - Modified `MongoDbStorage.py` and `SampleEntry.py` to integrate GridFS. - When samples are added via `addSmdaReport`, their binary content (assumed to be in `smda_report.buffer`) is now stored in GridFS. A reference (GridFS file ID) is stored in the `SampleEntry`. - Sample retrieval methods (`getSampleById`, `getSampleBySha256`) now fetch binary data from GridFS if a `gridfs_id` is present. - Deleting a sample via `deleteSample` now also removes the corresponding binary file from GridFS. - Implemented a new utility method `cleanup_orphan_gridfs_objects` in `MongoDbStorage.py`. This method identifies and deletes GridFS files that are no longer referenced by any `SampleEntry` in the database, helping to reclaim storage space. - Added comprehensive integration tests in `tests/testStorage.py` to cover: - Storing and retrieving sample binary data via GridFS. - Deletion of samples and their corresponding GridFS files. - Correct identification and removal of orphan GridFS files by the cleanup utility under different scenarios. This refactoring improves the scalability and efficiency of handling binary samples within mcrit.
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This commit addresses issue #80 by refactoring the MongoDB storage backend to utilize GridFS for storing binary sample data. Storing binary data in GridFS is more efficient for large files and is the recommended approach with MongoDB.
Key changes include:
MongoDbStorage.pyandSampleEntry.pyto integrate GridFS.addSmdaReport, their binary content (assumed to be insmda_report.buffer) is now stored in GridFS. A reference (GridFS file ID) is stored in theSampleEntry.getSampleById,getSampleBySha256) now fetch binary data from GridFS if agridfs_idis present.deleteSamplenow also removes the corresponding binary file from GridFS.cleanup_orphan_gridfs_objectsinMongoDbStorage.py. This method identifies and deletes GridFS files that are no longer referenced by anySampleEntryin the database, helping to reclaim storage space.tests/testStorage.pyto cover:This refactoring improves the scalability and efficiency of handling binary samples within mcrit.