Fix bulk update encoding with defaults

[abnegate]

Summary by CodeRabbit

• Bug Fixes

  • Successive document updates no longer reset attributes with default values; updates now preserve defaults and previously set values for single and batch operations.

• Tests

  • Added end-to-end tests verifying defaults persist across successive batch and single-document updates.
  • Minor test cleanup to improve readability of assertions.

[coderabbitai]

Walkthrough

UpdateDocuments now suppresses default application during encoding by passing applyDefaults = false; encode is publicly exposed with a new third parameter to control defaults. Two e2e tests added to ensure successive updates do not reset defaulted attributes; two inline comments removed in relationship tests.

Changes

Cohort / File(s)	Summary
Core: encoding API src/Database/Database.php	Made encode public and added bool $applyDefaults = true param with docblock; behavior now allows skipping default application when false.
Core: update flow src/Database/Database.php	updateDocuments now calls encode(..., applyDefaults: false) during update paths so defaults are not applied/re-applied before validation/persistence.
E2E: defaults persistence tests tests/e2e/Adapter/Scopes/DocumentTests.php	Added two tests: testUpdateDocumentsSuccessiveCallsDoNotResetDefaults and testUpdateDocumentSuccessiveCallsDoNotResetDefaults to verify successive updates do not reset attributes with defaults.
Test cleanup tests/e2e/Adapter/Scopes/RelationshipTests.php	Removed two inline comments adjacent to assertEquals calls; no behavioral changes.

Sequence Diagram(s)

sequenceDiagram
autonumber
actor Client
participant DB as Database::updateDocuments
participant V as Validator
participant E as Encoder
participant A as Adapter
Client->>DB: updateDocuments(collection, ids, updates)
DB->>V: validate(updates) on raw input
alt validation fails
V-->>DB: validation error
DB-->>Client: error
else validation passes
loop for each document id
DB->>E: encode(document, updates, applyDefaults=false)
E-->>DB: encodedDocument (defaults not applied)
DB->>A: adapter.update(encodedDocument)
A-->>DB: result
end
DB-->>Client: aggregated result
end

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Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• Fix encode permissions #645 — Modifies Database::encode behavior; closely related to the encode signature/semantics changes.
• Fix update documents #646 — Also touches src/Database/Database.php update/encode logic; overlaps with update flow edits.
• Allow modifying createdAt and updatedAt #642 — Adjusts encode/updateDocument behavior and default handling; relevant to defaults suppression here.

Suggested reviewers

• ArnabChatterjee20k
• fogelito

Poem

I hop through code and nibble lines,
Defaults stay put, no fearful signs.
Encode I hold till just the right beat,
Successive updates — no retreat.
A carrot cheer for tests complete! 🥕🐇

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title succinctly captures the primary change, which is correcting how bulk updates handle encoding of default values during the update process. It is concise, clearly reflects the core update without extraneous detail, and aligns with the modifications to the updateDocuments method.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix-bulk-update-encode

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📥 Commits

Reviewing files that changed from the base of the PR and between 939c120 and b1f51f1.

📒 Files selected for processing (1)

• src/Database/Database.php (3 hunks)

🧰 Additional context used

🧬 Code graph analysis (1)

src/Database/Database.php (2)

src/Database/Document.php (1)

• Document (12-470)

src/Database/Validator/Queries/Document.php (1)

• Document (10-43)

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (11)

• GitHub Check: Adapter Tests (SharedTables/Postgres)
• GitHub Check: Adapter Tests (Pool)
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• GitHub Check: Adapter Tests (SharedTables/SQLite)
• GitHub Check: Adapter Tests (MySQL)
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🔇 Additional comments (1)

src/Database/Database.php (1)

7065-7119: encode() signature change safe: no subclasses override encode(), so the updated method signature is compatible.

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