fix(bundles): stop optimistic tag rows duplicating GraphQL tags

[arielmelendez]

Problem

A GraphQL transactions(ids: [...]) query for a recently uploaded data item
returns every tag twice:

"tags": [
  { "name": "ArFS", "value": "0.15" },
  { "name": "ArFS", "value": "0.15" },
  { "name": "Entity-Type", "value": "drive-state" },
  { "name": "Entity-Type", "value": "drive-state" },
  ...
]

The data item itself is fine — its ANS-104 header carries each tag once.

Cause

new_data_item_tags has

PRIMARY KEY (tag_name_hash, tag_value_hash, root_transaction_id,
             data_item_id, data_item_tag_index)

and root_transaction_id became nullable in
2024.06.13T13.52.01.bundles.nullable-parent-and-root.sql while staying in the
key. The optimistic indexing path writes NULL there
(NormalizedOptimisticDataItem.root_tx_id), and SQLite treats every NULL in a
unique index as distinct. So upsertNewDataItemTag can never conflict with an
optimistic row.

A data item that is indexed optimistically at upload time and then unbundled a
few minutes later ends up with two complete tag sets: one NULL-rooted, one
rooted. selectNewDataItemTags filters on data_item_id alone and orders by
data_item_tag_index, so both sets come back interleaved.

Observed on a canary gateway's indexer for one affected item:

root_transaction_id	rows	height	indexed_at
NULL	15	NULL	upload + 23 s
the bundle	15	1993536	upload + 4 min

398 of 400 sampled optimistically-indexed items from the preceding hour already
carried a second tag set.

The same NULL-distinctness makes a repeated optimistic POST stack another copy
of its own tags, and makes an optimistic POST that arrives after the unbundle
add a NULL-rooted set alongside the rooted one. Both are covered here.

Scope

The duplication is confined to the unstable window. flushStableDataItems
drops the NULL-rooted rows because they fail both ndit.height < @end_height
and the join on stable_block_transactions.transaction_id, so stable SQLite,
the Parquet export and ClickHouse are unaffected. The ClickHouse streamer
already skips items with a null root_tx_id. Confirmed by walking one owner's
history: only the newest, still-unstable item is doubled.

Fix

Both writer paths go through one writeNewDataItemTags helper, inside the
transactions that already wrapped the tag upserts. No new transaction. It holds
two invariants:

• The unrooted tag set is cleared before every write, so a repeated write
  replaces its own rows instead of stacking a second copy.
• An unrooted write is skipped once a rooted set exists, because tags are
  immutable per data item id and the two sets would each be returned.

The root is applied to the rows from an explicit argument rather than read off
the rows, so the optimistic path cannot write a rooted set even if a caller
binds one — the same contract insertOptimisticDataItem already enforces for
the row-level root atom.

Cost

deleteStaleNewDataItemTags already deletes exactly these rows once
indexed_at passes the threshold, so this reschedules the deletion rather than
adding one. The genuinely new work is one index seek per data item on
new_data_item_tags_data_item_id_idx, plus one seek on the optimistic path.
Measured on a canary indexer: ~2.3 optimistic items/s, ~16.5 tag rows/s, ~7
tags per item, and ~64k NULL-height rows resident — about one hour's worth.

Testing

Six regression tests in src/database/standalone-sqlite.test.ts cover: the tag
rows after an optimistic-then-unbundle sequence, the GraphQL result for the
same sequence, a repeated optimistic write, an optimistic write that follows
the unbundle, a repeated unrooted full-claim write, and an optimistic write
carrying a root. yarn build and yarn lint:check are clean and the full
standalone-sqlite.test.ts suite passes (82/82).

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---

📝 Walkthrough

Walkthrough

This change fixes duplicate GraphQL tags after optimistic data-item writes. SQLite statements remove unrooted tag rows and detect rooted rows. Shared write logic applies these rules, with regression tests for replacement and idempotency.

Changes

Optimistic tag replacement

Layer / File(s)	Summary
Tag cleanup and rooted-row queries src/database/sql/bundles/import.sql	Adds SQL statements to delete unrooted tag rows and detect existing rooted tag rows.
Data-item write behavior and regression coverage src/database/standalone-sqlite.ts, src/database/standalone-sqlite.test.ts, CHANGELOG.md	Full-claim and optimistic writes use shared cleanup logic. The tests cover replacement, repeated writes, rooted optimistic writes, and GraphQL tag uniqueness. The changelog records the fix.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Merge Risk: ⚪ Minimal · up to 831e7

This change replaces optimistic tag rows with rooted rows to prevent duplicate GraphQL tags after unbundling. No current merge-readiness risk remains.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 2…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly and concisely describes the main fix: preventing optimistic tag rows from duplicating GraphQL tags.
Description check	✅ Passed	The description directly explains the duplicate-tag problem, its SQLite cause, the centralized fix, and the regression tests.

Full details: Docstring Coverage

Explanation

No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 2 files.

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Inline comments:
In `@src/database/standalone-sqlite.ts`:
- Around line 677-678: Add TSDoc at the declarations of insertDataItemFn and
insertOptimisticDataItemFn, documenting the root-state invariant and required
tag cleanup order for their writer contracts. Keep the documentation focused on
the new tag lifecycle rules and place it directly with each function declaration
rather than relying on constructor comments.
- Around line 631-635: Ensure both tag-writing paths preserve consistent NULL
root state: in standalone-sqlite.ts lines 631-635, make the
deleteOptimisticNewDataItemTags cleanup unconditional before full-path tag
writes; in lines 704-710, force root_transaction_id to null for rows inserted by
insertOptimisticDataItem. Add regression coverage in standalone-sqlite.test.ts
lines 2820-2843 for repeated root-null full writes and optimistic writes with
populated root_tx_id.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.04%. Comparing base (2bedbb1) to head (831e7a6).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #883      +/-   ##
===========================================
+ Coverage    80.83%   82.04%   +1.21%     
===========================================
  Files          144      144              
  Lines        57947    58021      +74     
  Branches      4515     4558      +43     
===========================================
+ Hits         46843    47605     +762     
+ Misses       11048    10360     -688     
  Partials        56       56              

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