[wangyinz]

Summary

• persist storage_mode="gridfs" in the waveform document when update_data migrates samples from file storage
• treat storage_mode="file" as authoritative even when an earlier failed migration left a stale gridfs_id
• stage new GridFS data without deleting any pre-existing object; if the waveform reference update fails or matches no document, remove only the new blob and restore the caller's exact storage keys
• preserve the original file-backed document and verify successful results through the public read_data path

Root cause

Database.update_data changed the in-memory object and wrote new samples to GridFS, but did not persist storage_mode. The first repair recognized only pristine file documents without a gridfs_id; it therefore could not recover the mixed storage_mode=file + stale gridfs_id state produced by the original bug. Using the normal overwrite path for that state would also delete the pre-existing GridFS object before the waveform reference became durable.

Validation

• MongoDB 8.0.29 contract suite: 12 passed across TimeSeries/Seismogram, pristine/stale file states, success/exception/unmatched-update paths
• contract suite plus neighboring TestDatabase::test_update_data: 13 passed
• exact baseline 61b06b9 against the final suite: 10 failed, 2 passed
• failure snapshots prove the waveform document, readable file samples, caller storage keys, and every pre-existing GridFS file/chunk remain unchanged while the newly staged blob is removed
• Black 26.5.1, Python 3.12/3.13 py_compile, and git diff --check: passed

This remains a draft pending the repository-wide scientific/API re-audit.

Fixes #813

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 74.55%. Comparing base (85eba33) to head (6a00a1f).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #953      +/-   ##
==========================================
+ Coverage   74.53%   74.55%   +0.01%     
==========================================
  Files         183      183              
  Lines       36535    36544       +9     
  Branches     2540     2540              
==========================================
+ Hits        27232    27246      +14     
+ Misses       8395     8390       -5     
  Partials      908      908              

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[wangyinz]

Independent compatibility audit complete on the current #955/#1002 commit/rollback path. File storage remains authoritative beside a stale gridfs_id; success persists the new GridFS mode/reference without deleting that unrelated stale blob, and failure removes only the staged blob and restores the caller storage keys. Python 3.10/3.13, MongoDB, formatting, and Docker CI are fully green.