inou/docs/update-2026-01-19-portal-cleanup.md

Portal Cleanup Update - January 19, 2026

Summary

Completed consolidation of portal's database access through lib functions. Removed all direct SQL calls and the duplicate database connection.

Changes Made

1. New File: portal/upload.go (359 lines)

Extracted all upload-related code from main.go into a dedicated file:

• Upload struct - display model for uploads
• UploadData struct - JSON structure for Entry.Data
• formatBytes() - human-readable file sizes
• getUploads() - list uploads using lib.EntryList()
• getUploadEntry() - get single upload using lib.EntryGet()
• findUploadByFilename() - find existing uploads using lib.EntryList()
• handleUploadPage() - upload page handler
• handleUploadPost() - upload POST handler
• handleDeleteFile() - file deletion handler
• handleUpdateFile() - file update handler

Key improvements:

• All SQL replaced with lib.Entry* functions
• uuid.New().String() replaced with lib.NewID() (Hex16 format)
• Proper JSON marshaling for upload metadata

2. Modified: portal/main.go

Removed:

• db *sql.DB variable declaration (line 29)
• db, err = sql.Open(...) from initDB() (line 125)
• import "github.com/google/uuid"
• import "encoding/json" (unused after extraction)
• import "io" (unused after extraction)
• func generateUUID() (dead code)
• type Upload struct (moved to upload.go)
• func formatBytes() (moved to upload.go)
• func getUploads() (moved to upload.go)
• func getUploadEntry() (moved to upload.go)
• func handleUploadPage() (moved to upload.go)
• func handleUploadPost() (moved to upload.go)
• func handleDeleteFile() (moved to upload.go)
• func handleUpdateFile() (moved to upload.go)

Changed:

• hasGenome check: Direct SQL → lib.EntryList() with filter
• Language update: lib.DB().Exec() → lib.DossierWrite()

Result: main.go reduced from ~1540 lines to ~1290 lines

3. Modified: portal/genome.go

Removed:

• Buggy cleanup code that queried integer category column as string
• Direct db.Query() and db.Exec() calls

Changed:

• db.Begin() → lib.DB().Begin() (transactions for batch inserts)

Note: Genome import still uses transactions for bulk inserts (performance). This is acceptable as it goes through lib.DB().

Database Connection Architecture

Before:

portal/main.go:  db *sql.DB  ──┐
                               ├──► same database file
lib/db.go:       db *sql.DB  ──┘

After:

lib/db.go:       db *sql.DB  ──► single connection
portal/*:        lib.DB()    ──► uses lib's connection
portal/main.go:  rateDB      ──► separate rate-limit database (unchanged)

Remaining lib.DB() Usage

Only 2 locations in portal still use lib.DB() directly:

File	Line	Purpose
genome.go	263	tx.Begin() for batch insert
genome.go	292	tx.Begin() for batch insert (continuation)

These are performance-critical bulk operations using transactions. Acceptable.

File Naming Change

Before: Uploaded files stored with UUID names like:

uploads/a1b2c3d4e5f67890/550e8400-e29b-41d4-a716-446655440000

After: Uploaded files stored with Hex16 names like:

uploads/a1b2c3d4e5f67890/f1e2d3c4b5a69078

Existing files with UUID names will continue to work (paths stored in entry data).

Verification

• ✅ go build ./portal - passes
• ✅ go build ./api - passes
• ✅ No direct db.Query/Exec/QueryRow in portal/*.go
• ✅ All entry operations use lib.Entry* functions
• ✅ Single database connection via lib.DB()

Next Steps

Per the store consolidation plan (docs/store-consolidation-plan.md):

1. Phase 2: Consolidate remaining direct SQL in api/ (21 operations in 4 files)
2. Phase 4: Add RBAC layer to lib/store.go

The portal is now clean and ready for RBAC enforcement.