- Fix lab chart reference bands: parse DOB in DossierFromEntry, generate
deterministic ref_ids in import-caliper (was collapsing 4363 rows to 1)
- Consolidate DossierFromEntry into lib/dbcore.go (eliminate portal duplicate)
- Add Import field to entries for batch undo (NextImportID, all import paths)
- MyChart direct JSON parsing (skip Gemini for structured lab data)
- Multi-order extraction from markdown/text tables
- Normalize progress callback for UI feedback
- DICOM import, genome import, API, portal, MCP, translation updates
- Remove test DICOM data from repo
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reference data simplification (choke point pattern):
- Remove RefSave/RefDelete from lib (import-time only, not runtime)
- Remove LabTestSave*, LabRefSave* from lib/lab_reference.go
- Remove PopulateReferences (LLM-based ref generation)
- Keep only RefQuery() for runtime reads
- Import tools handle their own SQL inserts
Rate limiting removed:
- Delete new_signups table and all rate limit code
- Solved via different approach (not in codebase)
Database consolidation (on staging):
- Moved genotypes table (30K SNPs) to reference.db
- Deleted empty DBs: portal.db, rate_limit.db, snpedia.db, ratelimit.db
Net -293 lines. Runtime code now only reads reference data via RefQuery().
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Simplify access control from 500+ lines to ~50 lines of core logic:
- New permission bitmask (PermRead/Write/Delete/Manage)
- Hierarchical access (dossier → category → entry)
- Single choke points: CheckAccess(), EntryQuery(), DossierQuery()
- All data access now enforced through lib RBAC layer
- Removed complex role templates and permission caching
Also improved NewID() to use UUID v4 + SHA-256 hash for better
randomness distribution (was limited to 0-7 hex start).
Net -210 lines across 28 files. Ready for staging deployment.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Rename Query→dbQuery, Save→dbSave, Load→dbLoad, Delete→dbDelete,
Count→dbCount in lib/db_queries.go. Go compiler now prevents any code
outside lib/ from bypassing RBAC checks.
All external callers migrated to RBAC-checked functions:
- EntryCategoryCounts, EntryCount, EntryListByDossier (new)
- LabTestList, LabEntryListForIndex, LabRefLookupAll (new)
- GenomeQuery now requires AccessContext
- EntryDeleteByCategory/EntryDeleteTree now require AccessContext
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add /legal/terms with comprehensive ToS content
- Add terms link to footer navigation
- Add /legal/terms to defense.go whitelist for external access
- Update privacy policy and DPA templates with improved styling
- Refactor RBAC editor template formatting
- Add prompts AI setup documentation
- Include database migration scripts
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Removed the backward compatibility fallback that checked the old
dossier_access table from CanManageDossier/CanAccessDossier - it was
a security risk (hidden path that bypassed the new RBAC system).
Instead, added MigrateOldAccess() that converts existing dossier_access
entries to proper access grants on startup (idempotent - skips existing).
Migration rules:
- Self-references (accessor == target) skipped (owner access is automatic)
- can_edit = 1 → "rwdm" root grant
- can_edit = 0 → "r" root grant
- Role set to "Migrated" for tracking
Result: 12 grants migrated from old table.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Changed from empty accessorID bypassing checks to explicit SystemAccessorID
for better security and audit trail.
Before: accessorID == "" → bypass all checks (security risk)
After: accessorID == "system-internal" → bypass (explicit, auditable)
Changes:
- Added SystemAccessorID constant = "system-internal"
- Updated SystemContext to use SystemAccessorID
- Updated checkAccess() to check for specific ID
- Updated accessorIDFromContext() to return SystemAccessorID
- Updated all EntryList calls to use SystemAccessorID
- Updated auth.go helpers to use SystemAccessorID
Benefits:
- Explicit backdoor ID visible in audit logs
- No accidental bypass from empty strings
- Clear intent for system operations
- Can't collide with real hex dossier IDs (uses "system" prefix)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Complete refactor from AccessContext struct to simple accessorID string
parameter for RBAC enforcement, as requested. All access control remains
in lib layer - API/Portal just pass accessor + dossier to lib functions.
Changes:
- Added accessorIDFromContext() helper in lib/v2.go
- Updated all checkAccess() calls to extract accessorID from context
- Updated all EntryList() calls (nil → "" for system context)
- Fixed auth.go helper functions to extract accessorID
- Updated categories API to pass accessor through to lib
All RBAC enforcement stays in lib - no API-level access checks.
Empty accessorID bypasses checks (system/internal operations).
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- Updated all genome functions to accept AccessContext parameter
- GenomeGetExtraction, GenomeGetTiers, GenomeGetTierByCategory,
GenomeGetVariants, GenomeGetVariantsByTier now pass context to EntryList
- API genome handler uses system context after dossier access check
- Categories endpoint uses system context for counting operations
- Fixes MCP query_genome returning 403/no data errors
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
- New dossier_sections.go with DossierSection struct and BuildDossierSections()
- Single section_block template replaces 12+ copy-pasted HTML blocks
- All 26 categories supported with default handler for unknown ones
- /dossier/{id} now uses v2, /dossier/{id}/v1 keeps legacy
- Added missing translation keys for all section types
- CSS: added .section-children and .hidden-row classes
James
Johan Jongsma