[mauripunzueta]

Closes #2145.

Problem

A transaction Bundle PUT Patient/<id> where <id> is soft-deleted failed the whole Bundle with 400 … resource already exists, while the same PUT outside a Bundle restores the resource as a new version (FHIR http.html#delete).

This was not MongoDB-only, as the issue suggested checking: SQLite and PostgreSQL had the same gap. Their transaction read returns None for a tombstone, so the entry fell through to create, which collides with the tombstone's row (SQLite's existence probe / PG's ON CONFLICT DO NOTHING). Before the fix, the new SQLite test failed with exactly the issue's message:

BundleError { index: 0, message: "Entry processing failed: resource already exists: Patient/restored" }

Fix

On every backend, the Bundle PUT's "no current representation" arm now looks for a tombstone first and restores it inside the transaction. The restore continues the version chain (create 1, delete 2, restore 3), keeps the FHIR version the resource was stored under, rebuilds its search rows, and answers 201. Only an id that was never stored creates.

• MongoDB: read_deleted_in_bundle_transaction + restore_resource_in_bundle_transaction. The Bundle update and the restore share write_next_version_in_bundle_transaction (CAS on the stored document, then the history row and search rows).
• SQLite: SqliteTransaction::restore.
• PostgreSQL: PostgresTransaction::restore. The update's single compare-and-swap CTE moved into write_next_version, which update and restore both call. The large diff in transaction.rs is mostly that move.

ifMatch behavior is unchanged: a supplied ifMatch still fails against a deleted resource, because there is no current representation.

Out of scope, unchanged: POST with a reused id (live or deleted) still fails with AlreadyExists (a_body_id_of_a_deleted_resource_fails_at_its_entry still passes). Conditional PUT (PUT Patient?…) that matches nothing still creates.

Tests

• New bundle_identity_suite::put_over_a_deleted_id_restores_it, wired into SQLite, PostgreSQL and MongoDB.
• MongoDB a_put_that_creates_over_a_deleted_id_fails_as_before (from perf(mongodb): stage transaction Bundle creates and send them in chunks #2144), which pinned the old answer, is replaced by a_put_over_a_deleted_id_restores_it. It runs in both the inline and deferred search-row modes and checks document and history counts plus searchability of the restored body.

Run locally:

• SQLite transactions_suite: 89 passed. The new scenario fails on the unfixed code with the message above.
• MongoDB bundle_create_chunks (live MongoDB via testcontainers): 14 passed.
• PostgreSQL: in progress, results to follow in a comment.

[mauripunzueta]

PostgreSQL results, run locally (testcontainers, postgres:16-alpine):

• postgres_integration_put_over_a_deleted_id_restores_it: passed.
• Wider filtered run over the bundle identity, restore, if_match, conditional_url, update and transaction tests: 49 passed, 0 failed.

[codecov]

Codecov Report

❌ Patch coverage is 90.90909% with 11 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
crates/persistence/src/backends/mongodb/storage.rs	89.71%	11 Missing ⚠️

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[claude]

Code review

No issues found. Checked for bugs and CLAUDE.md compliance.