Add calibration controls to support clinical confidence in variant interpretation #754

Summary

Introduce a lightweight calibration controls data model that stores the variant → clinical status pairs used as empirical ground truth when deriving a calibration's score thresholds. Surfacing these controls gives clinicians the evidence they need to assess whether a calibration is appropriate for their specific interpretation context.

Background

MaveDB calibrations define how functional scores map to clinical interpretations (e.g., scores above threshold X are pathogenic). These thresholds are derived from a set of variants with independently known clinical significance — the "controls." Today, this empirical basis is not stored in MaveDB, making it impossible for clinicians to audit or gain confidence in a calibration before using it for variant interpretation.

Design Decisions

Out of Scope

• Controls cannot reference variants outside the calibration's score set
• No per-control phenotype or metadata beyond variant + status
• Inline editing for class-based calibration class assignments is tracked separately (mavedb-ui Configure database connection pool and Uvicorn workers for concurrent request handling #680)
• PHI legal strategy writeup (handled offline)

Architecture

Data model (mavedb-api)

• New calibration_controls table: calibration_id (FK, cascade delete), variant_id (FK), clinical_status enum (pathogenic | benign), audit fields; UNIQUE on (calibration_id, variant_id)
• CalibrationControl ORM model at src/mavedb/models/calibration_control.py
• CalibrationControlStatus enum at src/mavedb/models/enums/calibration_control_status.py
• New columns on score_calibrations: disease VARCHAR NULL, controls_not_phi BOOLEAN NULL

API (mavedb-api)

• Pydantic models: CalibrationControlBase, CalibrationControlCreate, SavedCalibrationControl
• ScoreCalibration response extended with controls: list[SavedCalibrationControl], disease, controls_not_phi
• Validation: controls must reference variants in the calibration's score set
• Publishing gate: calibrations with controls require controls_not_phi = True
• Create/update endpoints accept controls via inline JSON array or controls_file CSV (replace semantics); providing both returns 422

UI (mavedb-ui)

• New CalibrationVariantAssignmentTable component: reusable inline table with CSV upload, parameterized by assignment options
• Controls section in CalibrationFields.vue wired to draft.controls
• PHI acknowledgment checkbox shown when controls are present
• Controls table in calibration viewer (read-only mode of CalibrationVariantAssignmentTable)

Child Issues

Backend (mavedb-api)

• Define CalibrationControlStatus enum (pathogenic, benign) #748 Define CalibrationControlStatus enum (pathogenic, benign)
• Add calibration controls to schema (ORM model, migration, disease/controls_not_phi on ScoreCalibration) #749 Add calibration controls to schema (ORM model, migration, disease/controls_not_phi on ScoreCalibration)
• Pydantic view models for CalibrationControl #750 Pydantic view models for CalibrationControl
• Validate calibration controls belong to the calibration's score set #751 Validate calibration controls belong to the calibration's score set
• Gate calibration publishing on PHI acknowledgment when controls are present #752 Gate calibration publishing on PHI acknowledgment when controls are present
• Wire calibration controls into create/update/read endpoints (inline JSON + controls_file CSV) #753 Wire calibration controls into create/update/read endpoints (inline JSON + controls_file CSV)

Frontend (mavedb-ui)

• Build reusable CalibrationVariantAssignmentTable component (inline editing + CSV upload) mavedb-ui#679 Build reusable CalibrationVariantAssignmentTable component (inline editing + CSV upload)
• Wire CalibrationVariantAssignmentTable into calibration controls editor mavedb-ui#681 Wire CalibrationVariantAssignmentTable into calibration controls editor
• Calibration editor: PHI acknowledgment checkbox for controls mavedb-ui#677 Calibration editor: PHI acknowledgment checkbox for controls
• Calibration viewer: display controls table for authorized users mavedb-ui#678 Calibration viewer: display controls table for authorized users

Follow-up

• Extend class-based calibration editing to use CalibrationVariantAssignmentTable (inline variant → class assignment) mavedb-ui#680 Extend class-based calibration editing to use CalibrationVariantAssignmentTable (inline variant → class assignment, currently CSV-only)

Dependency Graph

#748 (enum)
  └─→ #749 (schema + migration)
        └─→ #750 (view models)
              └─→ #751 (validation)
              └─→ #752 (PHI gate)
              └─→ #753 (router wiring)
                    └─→ mavedb-ui#679 (reusable component)
                          └─→ mavedb-ui#681 (controls editor wiring)
                                └─→ mavedb-ui#677 (PHI checkbox)
                          └─→ mavedb-ui#678 (controls viewer)